bioRxiv Channel: Cold Spring Harbor Laboratory https://biorxiv.org This feed contains articles for bioRxiv Channel "Cold Spring Harbor Laboratory" bioRxiv bioRxiv https://biorxiv.org <![CDATA[ Comment on “TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions” by Kim et al. ]]> https://biorxiv.org/content/10.1101/000851v1?rss=1 3) number of mismatches, low sensitivity and high false discovery rate for splice junction detection, loss of precision for the realignment algorithm, and large number of false chimeric alignments. ... ]]> Alexander Dobin Thomas R Gingeras 2013-11-22 doi:10.1101/000851 Cold Spring Harbor Laboratory Press 2013-11-22 <![CDATA[ Accurate detection of de novo and transmitted INDELs within exome-capture data using micro-assembly ]]> https://biorxiv.org/content/10.1101/001370v1?rss=1 10000 simulated and >1000 experimentally validated INDELs between 1 and 100bp against two recent algorithms for INDEL discovery: GATK HaplotypeCaller and SOAPindel. We report anomalies for these tools in their ability to detect INDELs, especially in regions containing near-perfect repeats which contribute to high false positive rates. In contrast, Scalpel demonstrates superior specificity while maintaining high sensitivity. We also present a large-scale application of Scalpel for detecting de novo and transmitted INDELs in 593 families with autistic children from the Simons Simplex Collection. Scalpel demonstrates enhanced power to detect long ([≥]20bp) transmitted events, and strengthens previous reports of enrichment for de novo likely gene-disrupting INDEL mutations in children with autism with many new candidate genes. The source code and documentation for the algorithm is available at http://scalpel.sourceforge.net. ]]> Giuseppe Narzisi Jason A O'Rawe Ivan Iossifov Han Fang Yoon-ha Lee Zihua Wang Yiyang Wu Gholson J Lyon Michael Wigler Michael C Schatz 2013-12-13 doi:10.1101/001370 Cold Spring Harbor Laboratory Press 2013-12-13 <![CDATA[ Parametric inference in the large data limit using maximally informative models ]]> https://biorxiv.org/content/10.1101/001396v1?rss=1 Justin B. Kinney Gurinder S. Atwal 2013-12-13 doi:10.1101/001396 Cold Spring Harbor Laboratory Press 2013-12-13 <![CDATA[ Significantly distinct branches of hierarchical trees: A framework for statistical analysis and applications to biological data ]]> https://biorxiv.org/content/10.1101/002188v1?rss=1 Guoli Sun Alexander Krasnitz 2014-01-29 doi:10.1101/002188 Cold Spring Harbor Laboratory Press 2014-01-29 <![CDATA[ Broadly tuned and respiration-independent inhibition in the olfactory bulb of awake mice ]]> https://biorxiv.org/content/10.1101/002410v1?rss=1 Brittany N Cazakoff Billy Y B Lau Kerensa L Crump Heike Demmer Stephen David Shea 2014-02-06 doi:10.1101/002410 Cold Spring Harbor Laboratory Press 2014-02-06 <![CDATA[ Noradrenergic plasticity of olfactory sensory neuron inputs to the main olfactory bulb ]]> https://biorxiv.org/content/10.1101/002550v1?rss=1 Dennis Eckmeier Stephen David Shea 2014-02-09 doi:10.1101/002550 Cold Spring Harbor Laboratory Press 2014-02-09 <![CDATA[ A GWAS platform built on iPlant cyber-infrastructure ]]> https://biorxiv.org/content/10.1101/002881v1?rss=1 Liya Wang Doreen Ware Carol Lushbough Nirav Merchant Lincoln Stein 2014-02-20 doi:10.1101/002881 Cold Spring Harbor Laboratory Press 2014-02-20 <![CDATA[ New whole genome de novo assemblies of three divergent strains of rice (O. sativa) documents novel gene space of aus and indica ]]> https://biorxiv.org/content/10.1101/003764v1?rss=1 Michael C Schatz Lyza G Maron Joshua C Stein Alejandro Hernandez Wences James Gurtowski Eric Biggers Hayan Lee Melissa Kramer Eric Antonio Elena Ghiban Mark H Wright Jer-ming Chia Doreen Ware Susan R McCouch William Richard McCombie 2014-04-02 doi:10.1101/003764 Cold Spring Harbor Laboratory Press 2014-04-02 <![CDATA[ Comparison of the theoretical and real-world evolutionary potential of a genetic circuit. ]]> https://biorxiv.org/content/10.1101/003772v1?rss=1 Manuel Razo-Mejia James Boedicker Daniel Jones Alexander de Luna Justin Block Kinney Rob Phillips 2014-04-02 doi:10.1101/003772 Cold Spring Harbor Laboratory Press 2014-04-02 <![CDATA[ SplitMEM: Graphical pan-genome analysis with suffix skips ]]> https://biorxiv.org/content/10.1101/003954v1?rss=1 Shoshana Marcus Hayan Lee Michael Schatz 2014-04-06 doi:10.1101/003954 Cold Spring Harbor Laboratory Press 2014-04-06 <![CDATA[ In vivo generation of DNA sequence diversity for cellular barcoding ]]> https://biorxiv.org/content/10.1101/004499v1?rss=1 Ian Peikon Diana Gizatullina Anthony Zador 2014-04-24 doi:10.1101/004499 Cold Spring Harbor Laboratory Press 2014-04-24 <![CDATA[ Reducing INDEL calling errors in whole-genome and exome sequencing data ]]> https://biorxiv.org/content/10.1101/006148v1?rss=1 5 bp) than alignment based callers, consistent with published data. The concordance of INDEL detection between WGS and WES is low (52%), and WGS data uniquely identifies 10.8-fold more high-quality INDELs. The validation rate for WGS-specific INDELs is also much higher than that for WES-specific INDELs (85% vs. 54%), and WES misses many large INDELs. In addition, the concordance for INDEL detection between standard WGS and PCR-free sequencing is 71%, and standard WGS data uniquely identifies 6.3-fold more low-quality INDELs. Furthermore, accurate detection with Scalpel of heterozygous INDELs requires 1.2-fold higher coverage than that for homozygous INDELs. Lastly, homopolymer A/T INDELs are a major source of low-quality INDEL calls, and they are highly enriched in the WES data.nnConclusionsOverall, we show that accuracy of INDEL detection with WGS is much greater than WES even in the targeted region. We calculated that 60X WGS depth of coverage from the HiSeq platform is needed to recover 95% of INDELs detected by Scalpel. While this is higher than current sequencing practice, the deeper coverage may save total project costs because of the greater accuracy and sensitivity. Finally, we investigate sources of INDEL errors (e.g. capture deficiency, PCR amplification, homopolymers) with various data that will serve as a guideline to effectively reduce INDEL errors in genome sequencing. ]]> Han Fang Yiyang Wu Giuseppe Narzisi Jason A. O'Rawe Laura T. Jimenez Barrón Julie Rosenbaum Michael Ronemus Ivan Iossifov Michael C. Schatz Gholson J. Lyon 2014-06-10 doi:10.1101/006148 Cold Spring Harbor Laboratory Press 2014-06-10 <![CDATA[ Error correction and assembly complexity of single molecule sequencing reads. ]]> https://biorxiv.org/content/10.1101/006395v1?rss=1 Hayan Lee James Gurtowski Shinjae Yoo Shoshana Marcus W. Richard McCombie Michael Schatz 2014-06-18 doi:10.1101/006395 Cold Spring Harbor Laboratory Press 2014-06-18 <![CDATA[ Redefining Genomic Privacy: Trust and Empowerment ]]> https://biorxiv.org/content/10.1101/006601v1?rss=1 Arvind Narayanan Kenneth Yocum David Glazer Nita Farahany Maynard Olson Lincoln D. Stein James B. Williams Jan A. Witkowski Robert C. Kain Yaniv Erlich 2014-06-25 doi:10.1101/006601 Cold Spring Harbor Laboratory Press 2014-06-25 <![CDATA[ Sources of PCR-induced distortions in high-throughput sequencing datasets ]]> https://biorxiv.org/content/10.1101/008375v1?rss=1 Justus M Kebschull Anthony M Zador 2014-08-23 doi:10.1101/008375 Cold Spring Harbor Laboratory Press 2014-08-23 <![CDATA[ Automated placement of stereotactic injections using a laser scan of the skull ]]> https://biorxiv.org/content/10.1101/010603v1?rss=1 Margaret Henderson Vadim Pinskiy Alexander Tolpygo Stephen Savoia Pascal Grange Partha Mitra 2014-10-22 doi:10.1101/010603 Cold Spring Harbor Laboratory Press 2014-10-22 <![CDATA[ Enhanced Transcriptome Maps from Multiple Mouse Tissues Reveal Evolutionary Constraint in Gene Expression for Thousands of Genes ]]> https://biorxiv.org/content/10.1101/010884v1?rss=1 Dmitri Pervouchine Sarah Djebali Alessandra Breschi Carrie A Davis Pablo Prieto Barja Alex Dobin Andrea Tanzer Julien Lagarde Chris Zaleski Lei-Hoon See Meagan Fastuca Jorg Drenkow Huaien Wang Giovanni Bussotti Baikang Pei Suganthi Balasubramanian Jean Monlong Arif Harmanci Mark Gerstein Michael A Beer Cedric Notredame Roderic Guigo Thomas R Gingeras 2014-10-30 doi:10.1101/010884 Cold Spring Harbor Laboratory Press 2014-10-30 <![CDATA[ Interactive analysis and quality assessment of single-cell copy-number variations ]]> https://biorxiv.org/content/10.1101/011346v1?rss=1 Tyler Garvin Robert Aboukhalil Jude Kendall Timour Baslan Gurinder S Atwal James Hicks Michael Wigler Michael Schatz 2014-11-12 doi:10.1101/011346 Cold Spring Harbor Laboratory Press 2014-11-12 <![CDATA[ Oxford Nanopore Sequencing, Hybrid Error Correction, and de novo Assembly of a Eukaryotic Genome ]]> https://biorxiv.org/content/10.1101/013490v1?rss=1 Sara Goodwin James Gurtowski Scott Ethe-Sayers Panchajanya Deshpande Michael Schatz W Richard McCombie 2015-01-06 doi:10.1101/013490 Cold Spring Harbor Laboratory Press 2015-01-06 <![CDATA[ A variant in TAF1 is associated with a new syndrome with severe intellectual disability and characteristic dysmorphic features ]]> https://biorxiv.org/content/10.1101/014050v1?rss=1 Jason O'Rawe Yiyang Wu Alan Rope Laura T. Jimenez Barrón Jeffrey Swensen Han Fang David Mittelman Gareth Highnam Reid Robison Edward Yang Kai Wang Gholson Lyon 2015-01-21 doi:10.1101/014050 Cold Spring Harbor Laboratory Press 2015-01-21 <![CDATA[ The biological functions of Naa10—from amino-terminal acetylation to human disease ]]> https://biorxiv.org/content/10.1101/014324v1?rss=1 Max Doerfel Gholson Lyon 2015-01-29 doi:10.1101/014324 Cold Spring Harbor Laboratory Press 2015-01-29 <![CDATA[ Metassembler: Merging and optimizing de novo genome assemblies ]]> https://biorxiv.org/content/10.1101/016352v1?rss=1 Alejandro Hernandez Wences Michael Schatz 2015-03-10 doi:10.1101/016352 Cold Spring Harbor Laboratory Press 2015-03-10 <![CDATA[ Simple genetic models for autism spectrum disorder ]]> https://biorxiv.org/content/10.1101/017301v1?rss=1 Swagatam Mukhopadhyay Michael Wigler Dan Levy 2015-03-30 doi:10.1101/017301 Cold Spring Harbor Laboratory Press 2015-03-30 <![CDATA[ A mathematical framework for statistical decision confidence ]]> https://biorxiv.org/content/10.1101/017400v1?rss=1 Balázs Hangya Joshua I. Sanders Adam Kepecs 2015-04-01 doi:10.1101/017400 Cold Spring Harbor Laboratory Press 2015-04-01 <![CDATA[ Building Genomic Analysis Pipelines in a Hackathon Setting with Bioinformatician Teams: DNA-seq, Epigenomics, Metagenomics and RNA-seq ]]> https://biorxiv.org/content/10.1101/018085v1?rss=1 Ben Busby Allissa Dillman Claire L. Simpson Ian Fingerman Sijung Yun David M. Kristensen Lisa Federer Naisha Shah Matthew C. LaFave Laura Jimenez-Barron Manusha Pande Wen Luo Brendan Miller Cem Mayden Dhruva Chandramohan Kipper Fletez-Brant Paul W. Bible Sergej Nowoshilow Alfred Chan Eric JC Galvez Jeremy Chignell Joseph N. Paulson Manoj Kandpal Suhyeon Yoon Esther Asaki Abhinav Nellore Adam Stine Robert Sanders Jesse Becker Matt Lesko Mordechai Abzug Eugene Yaschenko 2015-04-16 doi:10.1101/018085 Cold Spring Harbor Laboratory Press 2015-04-16 <![CDATA[ SCT promoter methylation is a highly discriminative biomarker for lung and many other cancers ]]> https://biorxiv.org/content/10.1101/018515v1?rss=1 10 cancer types profiled by ENCODE. We found that SCT promoter is hyper-methylated in primary tumors from TCGA lung cancer cohort. Additionally, we found that SCT promoter is methylated at high frequencies in fifteen malignancies and is not methylated in [~]1000 non-cancerous tissues across >30 organ types. Our study indicates that SCT promoter methylation is a highly discriminative biomarker for lung and many other cancers. ]]> Adwait Sathe Xiaotu Ma Michael Zhang 2015-04-24 doi:10.1101/018515 Cold Spring Harbor Laboratory Press 2015-04-24 <![CDATA[ Whole genome analysis of an extended pedigree with Prader–Willi Syndrome, hereditary hemochromatosis, and dysautonomia-like symptoms ]]> https://biorxiv.org/content/10.1101/019182v1?rss=1 Han Fang Yiyang Wu Margaret Yoon Laura T. Jiménez-Barrón Jason A. O'Rawe Gareth Highnam David Mittelman Gholson Lyon 2015-05-11 doi:10.1101/019182 Cold Spring Harbor Laboratory Press 2015-05-11 <![CDATA[ Genome Wide Variant Analysis of Simplex Autism Families with an Integrative Clinical-Bioinformatics Pipeline ]]> https://biorxiv.org/content/10.1101/019208v1?rss=1 Laura T Jiménez-Barrón Jason A O'Rawe Yiyang Wu Margaret Yoon Han Fang Ivan Iossifov Gholson Lyon 2015-05-11 doi:10.1101/019208 Cold Spring Harbor Laboratory Press 2015-05-11 <![CDATA[ Learning quantitative sequence-function relationships from high-throughput biological data ]]> https://biorxiv.org/content/10.1101/020172v1?rss=1 Gurinder S Atwal Justin B Kinney 2015-05-31 doi:10.1101/020172 Cold Spring Harbor Laboratory Press 2015-05-31 <![CDATA[ The next 20 years of genome research ]]> https://biorxiv.org/content/10.1101/020289v1?rss=1 Michael Schatz 2015-06-02 doi:10.1101/020289 Cold Spring Harbor Laboratory Press 2015-06-02 <![CDATA[ Concerted activities of Mcm4, Sld3 and Dbf4 in control of origin activation and DNA replication fork progression ]]> https://biorxiv.org/content/10.1101/021832v1?rss=1 Yi-Jun Sheu Justin B Kinney Bruce Stillman 2015-07-01 doi:10.1101/021832 Cold Spring Harbor Laboratory Press 2015-07-01 <![CDATA[ Ancient trans-acting siRNAs Confer Robustness and Sensitivity onto the Auxin Response ]]> https://biorxiv.org/content/10.1101/024307v1?rss=1 Yevgeniy Plavskin Akitomo Nagashima Pierre-François Perroud Mitsuyasu Hasebe Ralph S Quatrano Gurinder S Atwal Marja CP Timmermans 2015-08-10 doi:10.1101/024307 Cold Spring Harbor Laboratory Press 2015-08-10 <![CDATA[ Teaser: Individualized benchmarking and optimization of read mapping results for NGS data ]]> https://biorxiv.org/content/10.1101/025858v1?rss=1 Moritz Smolka Philipp Rescheneder Michael C Schatz Arndt von Haeseler Fritz J Sedlazeck 2015-09-01 doi:10.1101/025858 Cold Spring Harbor Laboratory Press 2015-09-01 <![CDATA[ Construction of the third generation Zea mays haplotype map ]]> https://biorxiv.org/content/10.1101/026963v1?rss=1 Robert Bukowski Xiaosen Guo Yanli Lu Cheng Zou Bing He Zhengqin Rong Bo Wang Dawen Xu Bicheng Yang Chuanxiao Xie Longjiang Fan Shibin Gao Xun Xu Gengyun Zhang Yingrui Li Yinping Jiao John Doebley Jeffrey Ross-Ibarra Vince Buffalo Cinta M Romay Edward S Buckler Yunbi Xu Jinsheng Lai Doreen Ware Qi Sun 2015-09-16 doi:10.1101/026963 Cold Spring Harbor Laboratory Press 2015-09-16 <![CDATA[ Indel variant analysis of short-read sequencing data with Scalpel ]]> https://biorxiv.org/content/10.1101/028050v1?rss=1 Han Fang Ewa A. Grabowska Kanika Arora Vladimir Vacic Michael C. Zody Ivan Iossifov Jason A. ORawe Yiyang Wu Laura T Jimenez Barron Julie Rosenbaum Michael Ronemus Yoon-ha Lee Zihua Wang Gholson J. Lyon Michael Wigler Michael C. Schatz Giuseppe Narzisi 2015-10-01 doi:10.1101/028050 Cold Spring Harbor Laboratory Press 2015-10-01 <![CDATA[ Shared generative rules of locomotor behavior in arthropods and vertebrates ]]> https://biorxiv.org/content/10.1101/031716v1?rss=1 Alex Gomez-Marin Efrat Oron Anna Gakamsky Dan Valente Yoav Benjamini Ilan Golani 2015-11-14 doi:10.1101/031716 Cold Spring Harbor Laboratory Press 2015-11-14 <![CDATA[ Architecting a distributed bioinformatics platform with iRODS and iPlant Agave API ]]> https://biorxiv.org/content/10.1101/034488v1?rss=1 Liya Wang Peter Van Buren Doreen Ware 2015-12-15 doi:10.1101/034488 Cold Spring Harbor Laboratory Press 2015-12-15 <![CDATA[ Measuring the sequence-affinity landscape of antibodies with massively parallel titration curves ]]> https://biorxiv.org/content/10.1101/036335v1?rss=1 Rhys M Adams Justin B Kinney Thierry Mora Aleksandra M Walczak 2016-01-10 doi:10.1101/036335 Cold Spring Harbor Laboratory Press 2016-01-10 <![CDATA[ Identification and characterization of long non-coding RNAs as targets of mammary tumor cell proliferation and migration ]]> https://biorxiv.org/content/10.1101/036418v1?rss=1 Sarah D Diermeier Kung-Chi Chang Susan M Freier Junyan Song Alexander Krasnitz Frank Rigo C. Frank Bennett David Spector 2016-01-11 doi:10.1101/036418 Cold Spring Harbor Laboratory Press 2016-01-11 <![CDATA[ Single-chromosome aneuploidy commonly functions as a tumor suppressor ]]> https://biorxiv.org/content/10.1101/040162v1?rss=1 Jason Meyer Sheltzer Julie H. Ko Nicole C. Habibe Burgos Erica S. Chung Colleen M. Meehl Verena Passerini Zuzana Storchova Angelika Amon 2016-02-19 doi:10.1101/040162 Cold Spring Harbor Laboratory Press 2016-02-19 <![CDATA[ MECP2 regulates cortical plasticity underlying a learned behavior in adult female mice ]]> https://biorxiv.org/content/10.1101/041707v1?rss=1 Keerthi Krishnan Billy Lau Gabrielle Ewall Z. Josh Huang Stephen David Shea 2016-02-28 doi:10.1101/041707 Cold Spring Harbor Laboratory Press 2016-02-28 <![CDATA[ Assessment of functional convergence across study designs in autism ]]> https://biorxiv.org/content/10.1101/043422v1?rss=1 Sara Ballouz Jesse Gillis 2016-03-12 doi:10.1101/043422 Cold Spring Harbor Laboratory Press 2016-03-12 <![CDATA[ AuPairWise: a method to estimate RNA-seq replicability through co-expression ]]> https://biorxiv.org/content/10.1101/044669v1?rss=1 Sara Ballouz Jesse Gillis 2016-03-21 doi:10.1101/044669 Cold Spring Harbor Laboratory Press 2016-03-21 <![CDATA[ Assemblytics: a web analytics tool for the detection of assembly-based variants ]]> https://biorxiv.org/content/10.1101/044925v1?rss=1 Maria Nattestad Michael C Schatz 2016-03-20 doi:10.1101/044925 Cold Spring Harbor Laboratory Press 2016-03-20 <![CDATA[ Modeling multi-particle complexes in stochastic chemical systems ]]> https://biorxiv.org/content/10.1101/045435v1?rss=1 Muir J Morrison Justin B Kinney 2016-03-23 doi:10.1101/045435 Cold Spring Harbor Laboratory Press 2016-03-23 <![CDATA[ The mutational landscape of EGFR-, MYC-, and Kras- driven genetically-engineered mouse models of lung adenocarcinoma ]]> https://biorxiv.org/content/10.1101/048058v1?rss=1 David McFadden Katerina Politi Arjun Bhutkar Frances K Chen Xiaoling Song Mono Pirun Philip M Santiago Caroline Kim James T Platt Emily Lee Emily Hodges Adam P Rosebrock Roderick Bronson Nicholas D Socci Gregory Hannon Tyler Jacks Harold Varmus 2016-04-11 doi:10.1101/048058 Cold Spring Harbor Laboratory Press 2016-04-11 <![CDATA[ Third-generation sequencing and the future of genomics ]]> https://biorxiv.org/content/10.1101/048603v1?rss=1 Hayan Lee James Gurtowski Shinjae Yoo Maria Nattestad Shoshana Marcus Sara Goodwin W. Richard McCombie Michael Schatz 2016-04-13 doi:10.1101/048603 Cold Spring Harbor Laboratory Press 2016-04-13 <![CDATA[ C. elegans PVD Neurons: A Platform for Functionally Validating and Characterizing Neuropsychiatric Risk Genes ]]> https://biorxiv.org/content/10.1101/053900v1?rss=1 14-fold as compared to unbiased RNAi screening10. Furthermore, we find that RNAi phenotypes associated with the depletion of NRG orthologs is recapitulated in genetic mutant animals, and, via genetic interaction studies, we show that the NRG ortholog of ANK2, unc-44, is required for SAX-7/MNR-1/DMA-1 signaling. Collectively, our studies demonstrate that C. elegans PVD neurons are a tractable model in which to discover and dissect the fundamental molecular mechanisms underlying neuropsychiatric disease pathogenesis. ]]> Cristina Aguirre-Chen Nuri Kim Olivia Mendivil Ramos Melissa Kramer W. Richard McCombie Christopher M. Hammell 2016-05-17 doi:10.1101/053900 Cold Spring Harbor Laboratory Press 2016-05-17 <![CDATA[ High-throughput mapping of single neuron projections by sequencing of barcoded RNA ]]> https://biorxiv.org/content/10.1101/054312v1?rss=1 Justus M Kebschull Pedro Garcia da Silva Ashlan P Reid Ian D Peikon Dinu F Albeanu Anthony M Zador 2016-05-20 doi:10.1101/054312 Cold Spring Harbor Laboratory Press 2016-05-20 <![CDATA[ MPAthic: quantitative modeling of sequence-function relationships for massively parallel assays ]]> https://biorxiv.org/content/10.1101/054676v1?rss=1 William T. Ireland Justin B. Kinney 2016-05-21 doi:10.1101/054676 Cold Spring Harbor Laboratory Press 2016-05-21 <![CDATA[ Parvalbumin interneuron dysfunction in a thalamus - prefrontal cortex circuit in Disc1 deficiency mice ]]> https://biorxiv.org/content/10.1101/054759v1?rss=1 Kristen Delevich Hanna Jaaro-Peled Mario Penzo Akira Sawa Bo Li 2016-05-21 doi:10.1101/054759 Cold Spring Harbor Laboratory Press 2016-05-21 <![CDATA[ Phased Diploid Genome Assembly with Single Molecule Real-Time Sequencing ]]> https://biorxiv.org/content/10.1101/056887v1?rss=1 Chen-Shan Chin Paul Peluso Fritz J. Sedlazeck Maria Nattestad Gregory T. Concepcion Alicia Clum Christopher Dunn Ronan O'Malley Rosa Figueroa-Balderas Abraham Morales-Cruz Grant R. Cramer Massimo Delledonne Chongyuan Luo Joseph R. Ecker Dario Cantu David R. Rank Michael C. Schatz 2016-06-03 doi:10.1101/056887 Cold Spring Harbor Laboratory Press 2016-06-03 <![CDATA[ Rare copy number variants in NRXN1 and CNTN6 increase risk for Tourette syndrome ]]> https://biorxiv.org/content/10.1101/062471v1?rss=1 Alden Y Huang Dongmei Yu Lea K Davis Jae-Hoon Sul Fotis Tsetsos Vasily Ramensky Ivette Zelaya Eliana Marisa Ramos Lisa Osiecki Jason A Chen Lauren M McGrath Cornelia Illmann Paul Sandor Cathy L Barr Marco Grados Harvey S Singer Markus M Noethen Johannes Hebebrand Robert A King Yves Dion Guy Rouleau Cathy L Budman Christel Depienne Yulia Worbe Andreas Hartmann Kirsten R Muller-Vahl Manfred Stuhrmann Harald Aschauer Mara Stamenkovic Monika Schloegelhofer Anastasios Konstantinidis Gholson L Lyon William M McMahon Csaba Barta Zsanett Tarnok Peter Nagy James R Batterson Renata Rizzo Danielle C Cath 2016-07-08 doi:10.1101/062471 Cold Spring Harbor Laboratory Press 2016-07-08 <![CDATA[ Posterior parietal cortex guides visual decisions in rats ]]> https://biorxiv.org/content/10.1101/066639v1?rss=1 Angela M. Licata Matthew T. Kaufman David Raposo Michael B. Ryan John P. Sheppard Anne K. Churchland 2016-07-29 doi:10.1101/066639 Cold Spring Harbor Laboratory Press 2016-07-29 <![CDATA[ Fast, scalable prediction of deleterious noncoding variants from functional and population genomic data ]]> https://biorxiv.org/content/10.1101/069682v1?rss=1 Yi-Fei Huang Brad Gulko Adam Siepel 2016-08-15 doi:10.1101/069682 Cold Spring Harbor Laboratory Press 2016-08-15 <![CDATA[ GenomeScope: Fast reference-free genome profiling from short reads ]]> https://biorxiv.org/content/10.1101/075978v1?rss=1 Gregory W Vurture Fritz J Sedlazeck Maria Nattestad Charles J. Underwood Han Fang James Gurtowski Michael Schatz 2016-09-19 doi:10.1101/075978 Cold Spring Harbor Laboratory Press 2016-09-19 <![CDATA[ SiLiCO: A Simulator of Long Read Sequencing in PacBio and Oxford Nanopore ]]> https://biorxiv.org/content/10.1101/076901v1?rss=1 nnSupplementary informationSupplementary data are available at Bioinformatics online. ]]> Ethan Alexander Garcia Baker Sara Goodwin W. Richard McCombie Olivia Mendivil Ramos 2016-09-22 doi:10.1101/076901 Cold Spring Harbor Laboratory Press 2016-09-22 <![CDATA[ An odor delivery system for arbitrary time-varying patterns of odors, mixtures and concentrations ]]> https://biorxiv.org/content/10.1101/077875v1?rss=1 Priyanka Gupta Dinu F Albeanu Upinder S Bhalla 2016-09-29 doi:10.1101/077875 Cold Spring Harbor Laboratory Press 2016-09-29 <![CDATA[ MUMdex: MUM-based structural variation detection ]]> https://biorxiv.org/content/10.1101/078261v1?rss=1 Peter A Andrews Ivan Iossifov Jude Kendall Steven Marks Lakshmi Muthuswamy Zihua Wang Dan Levy Michael Wigler 2016-09-30 doi:10.1101/078261 Cold Spring Harbor Laboratory Press 2016-09-30 <![CDATA[ The complex sequence landscape of maize revealed by single molecule technologies ]]> https://biorxiv.org/content/10.1101/079004v1?rss=1 Jiao, Y. Peluso, P. Shi, J. Liang, T. Stitzer, M. C. Wang, B. Campbell, M. Stein, J. C. Wei, X. Chin, C.-S. Guill, K. Regulski, M. Kumari, S. Olson, A. Gent, J. Schneider, K. L. Wolfgruber, T. K. May, M. Springer, N. Antoniou, E. McCombie, R. Presting, G. G. McMullen, M. Ross-Ibarra, J. Dawe, R. K. Hastie, A. Rank, D. R. Ware, D. 2016-12-19 doi:10.1101/079004 Cold Spring Harbor Laboratory Press 2016-12-19 <![CDATA[ Using predictive specificity to determine when gene set analysis is biologically meaningful ]]> https://biorxiv.org/content/10.1101/080127v1?rss=1 Sara Ballouz Paul Pavlidis Jesse Gillis 2016-10-10 doi:10.1101/080127 Cold Spring Harbor Laboratory Press 2016-10-10 <![CDATA[ Ribbon: Visualizing complex genome alignments and structural variation ]]> https://biorxiv.org/content/10.1101/082123v1?rss=1 Nattestad, M. Chin, C.-S. Schatz, M. C. 2016-10-20 doi:10.1101/082123 Cold Spring Harbor Laboratory Press 2016-10-20 <![CDATA[ Natural Selection has Shaped Coding and Non-coding Transcription in Primate CD4+ T-cells ]]> https://biorxiv.org/content/10.1101/083212v1?rss=1 Danko, C. G. Wang, Z. Rice, E. J. Chu, T. Martins, A. L. Tait Wojno, E. Lis, J. T. Kraus, L. W. Siepel, A. 2016-10-25 doi:10.1101/083212 Cold Spring Harbor Laboratory Press 2016-10-25 <![CDATA[ Rare disruptive variants in the DISC1 Interactome and Regulome: association with cognitive ability and schizophrenia ]]> https://biorxiv.org/content/10.1101/083816v1?rss=1 Teng, S. Thomson, P. McCarthy, S. Kramer, M. Muller, S. Lihm, J. Morris, S. Soares, D. Hennah, W. Harris, S. Camargo, L. M. Malkov, V. McIntosh, A. Millar, J. K. Blackwood, D. Evans, K. Deary, I. Porteous, D. McCombie, W. R. 2016-10-27 doi:10.1101/083816 Cold Spring Harbor Laboratory Press 2016-10-27 <![CDATA[ Metrics for comparing Neuronal Tree Shapes based on Persistent Homology ]]> https://biorxiv.org/content/10.1101/087551v1?rss=1 Li, Y. Ascoli, G. Mitra, P. P. Wang, Y. 2016-11-14 doi:10.1101/087551 Cold Spring Harbor Laboratory Press 2016-11-14 <![CDATA[ SplitThreader: Exploration and analysis of rearrangements in cancer genomes ]]> https://biorxiv.org/content/10.1101/087981v1?rss=1 Nattestad, M. Alford, M. C. Sedlazeck, F. J. Schatz, M. C. 2016-11-15 doi:10.1101/087981 Cold Spring Harbor Laboratory Press 2016-11-15 <![CDATA[ The DOE Systems Biology Knowledgebase (KBase) ]]> https://biorxiv.org/content/10.1101/096354v1?rss=1 Arkin, A. P. Stevens, R. L. Cottingham, R. W. Maslov, S. Henry, C. S. Dehal, P. Ware, D. Perez, F. Harris, N. L. Canon, S. Sneddon, M. W. Henderson, M. L. Riehl, W. J. Gunter, D. Murphy-Olson, D. Chan, S. Kamimura, R. T. Brettin, T. S. Meyer, F. Chivian, D. Weston, D. J. Glass, E. M. Davison, B. H. Kumari, S. Allen, B. H. Baumohl, J. Best, A. A. Bowen, B. Brenner, S. E. Bun, C. C. Chandonia, J.-M. Chia, J.-M. Colasanti, R. Conrad, N. Davis, J. J. DeJongh, M. Devoid, S. Dietrich, E. Drake, M. M. Dubchak, I. Edirisinghe, J. N. Fang, G. Faria, J. P. Fryb 2016-12-22 doi:10.1101/096354 Cold Spring Harbor Laboratory Press 2016-12-22 <![CDATA[ Network cloning using DNA barcodes ]]> https://biorxiv.org/content/10.1101/098343v1?rss=1 Shuvaev, S. A. Başerdem, B. Zador, A. Koulakov, A. A. 2017-01-04 doi:10.1101/098343 Cold Spring Harbor Laboratory Press 2017-01-04 <![CDATA[ LRSim: a Linked Reads Simulator generating insights for better genome partitioning ]]> https://biorxiv.org/content/10.1101/103549v1?rss=1 Luo, R. Sedlazeck, F. J. Darby, C. A. Kelly, S. M. Schatz, M. C. 2017-01-26 doi:10.1101/103549 Cold Spring Harbor Laboratory Press 2017-01-26 <![CDATA[ High-throughput annotation of full-length long noncoding RNAs with Capture Long-Read Sequencing (CLS) ]]> https://biorxiv.org/content/10.1101/105064v1?rss=1 Lagarde, J. Uszczynska-Ratajczak, B. Carbonell, S. Davis, C. Gingeras, T. R. Frankish, A. Harrow, J. Guigo, R. Johnson, R. 2017-02-01 doi:10.1101/105064 Cold Spring Harbor Laboratory Press 2017-02-01 <![CDATA[ Unmet Needs for Analyzing Biological Big Data: A Survey of 704 NSF Principal Investigators ]]> https://biorxiv.org/content/10.1101/108555v1?rss=1 Barone, L. Williams, J. Micklos, D. 2017-02-14 doi:10.1101/108555 Cold Spring Harbor Laboratory Press 2017-02-14 <![CDATA[ 16GT: a fast and sensitive variant caller using a 16-genotype probabilistic model ]]> https://biorxiv.org/content/10.1101/111393v1?rss=1 Luo, R. Schatz, M. C. Salzberg, S. 2017-02-24 doi:10.1101/111393 Cold Spring Harbor Laboratory Press 2017-02-24 <![CDATA[ Discovery and reporting of clinically-relevant germline variants in advanced cancer patients assessed using whole-exome sequencing ]]> https://biorxiv.org/content/10.1101/112672v1?rss=1 Zhang, T. Romanel, A. Eng, K. W. Rennert, H. Tan, A. Y. Xue, Y. Cyrta, J. Mosquera, J. M. Sboner, A. Iossifov, I. Lipkin, S. M. Xiang, J. Feng, X. Nelson, P. Beltran, H. Pritchard, C. C. Rubin, M. A. Demichelis, F. Elemento, O. 2017-03-01 doi:10.1101/112672 Cold Spring Harbor Laboratory Press 2017-03-01 <![CDATA[ Estrogen receptor alpha is required in GABAergic, but not glutamatergic, neurons to masculinize the brain ]]> https://biorxiv.org/content/10.1101/114835v1?rss=1 Wu, M. V. Tollkuhn, J. 2017-03-07 doi:10.1101/114835 Cold Spring Harbor Laboratory Press 2017-03-07 <![CDATA[ STAR-Fusion: Fast and Accurate Fusion Transcript Detection from RNA-Seq ]]> https://biorxiv.org/content/10.1101/120295v1?rss=1 Haas, B. Dobin, A. Stransky, N. Li, B. Yang, X. Tickle, T. Bankapur, A. Ganote, C. Doak, T. Pochet, N. Sun, J. Wu, C. Gingeras, T. Regev, A. 2017-03-24 doi:10.1101/120295 Cold Spring Harbor Laboratory Press 2017-03-24 <![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[ Concentration invariant odor coding ]]> https://biorxiv.org/content/10.1101/125039v1?rss=1 Wilson, C. D. Serrano, G. O. Koulakov, A. A. Rinberg, D. 2017-04-06 doi:10.1101/125039 Cold Spring Harbor Laboratory Press 2017-04-06 <![CDATA[ Deep experimental profiling of microRNA diversity, deployment, and evolution across the <ital>Drosophila</ital> genus ]]> https://biorxiv.org/content/10.1101/125997v1?rss=1 Flynt, A. S. Panzarino, A. Mondal, M. M. H. Siepel, A. Mohammed, J. Lai, E. 2017-04-11 doi:10.1101/125997 Drosophila genus]]> Cold Spring Harbor Laboratory Press 2017-04-11 <![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[ Not by systems alone: identifying functional outliers in rare disease pedigrees ]]> https://biorxiv.org/content/10.1101/128439v1?rss=1 Ballouz, S. Doerfel, M. Crain, J. Crow, M. Faivre, L. Keegan, C. E. Kitsiou-Tzeli, S. Tzetis, M. Lyon, G. J. Gillis, J. 2017-04-18 doi:10.1101/128439 Cold Spring Harbor Laboratory Press 2017-04-18 <![CDATA[ A lncRNA/Lin28/Let7 Axis Coupled To DNA Methylation Fine Tunes The Dynamics Of A Cell State Transition ]]> https://biorxiv.org/content/10.1101/131110v1?rss=1 Li, M. A. Amaral, P. P. Cheung, P. Bergmann, J. H. Kinoshita, M. Kalkan, T. Ralser, M. Robson, S. von Meyenn, F. Paramor, M. Yang, F. Chen, C. Nichols, J. Spector, D. L. Kouzarides, T. He, L. Smith, A. 2017-04-26 doi:10.1101/131110 Cold Spring Harbor Laboratory Press 2017-04-26 <![CDATA[ A High Resolution Whole Brain Imaging Using Oblique Light Sheet Tomography ]]> https://biorxiv.org/content/10.1101/132423v1?rss=1 Narasimhan, A. Mizrachi, J. Umadevi Venkatraju, K. Albeanu, D. F. Osten, P. 2017-04-30 doi:10.1101/132423 Cold Spring Harbor Laboratory Press 2017-04-30 <![CDATA[ FastNet: Fast and accurate inference of phylogenetic networks using large-scale genomic sequence data ]]> https://biorxiv.org/content/10.1101/132795v1?rss=1 Hejase, H. VandePol, N. Bonito, G. A. Liu, K. J. 2017-05-01 doi:10.1101/132795 Cold Spring Harbor Laboratory Press 2017-05-01 <![CDATA[ Categorical Representations Of Decision-Variables In Orbitofrontal Cortex ]]> https://biorxiv.org/content/10.1101/135707v1?rss=1 Hirokawa, J. Vaughan, A. Kepecs, A. 2017-05-09 doi:10.1101/135707 Cold Spring Harbor Laboratory Press 2017-05-09 <![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[ Damaging Mutations are Associated with Diminished Motor Skills and IQ in Children on the Autism Spectrum ]]> https://biorxiv.org/content/10.1101/141200v1?rss=1 Buja, A. Volfovsky, N. Krieger, A. Lord, C. Lash, A. Wigler, M. Iossifov, I. 2017-05-23 doi:10.1101/141200 Cold Spring Harbor Laboratory Press 2017-05-23 <![CDATA[ Mutational sequencing for accurate count and long-range assembly ]]> https://biorxiv.org/content/10.1101/149740v1?rss=1 Kumar, V. Rosenbaum, J. Wang, Z. Forcier, T. Ronemus, M. Wigler, M. Levy, D. 2017-06-13 doi:10.1101/149740 Cold Spring Harbor Laboratory Press 2017-06-13 <![CDATA[ Addressing the looming identity crisis in single cell RNA-seq ]]> https://biorxiv.org/content/10.1101/150524v1?rss=1 Crow, M. Paul, A. Ballouz, S. Huang, Z. J. Gillis, J. 2017-06-16 doi:10.1101/150524 Cold Spring Harbor Laboratory Press 2017-06-16 <![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[ An insula-central amygdala circuit for behavioral inhibition ]]> https://biorxiv.org/content/10.1101/156216v1?rss=1 Schiff, H. C. Bouhuis, A. L. Yu, K. Penzo, M. A. Li, H. He, M. Li, B. 2017-06-26 doi:10.1101/156216 Cold Spring Harbor Laboratory Press 2017-06-26 <![CDATA[ Scikit-ribo: Accurate estimation and robust modeling of translation dynamics at codon resolution ]]> https://biorxiv.org/content/10.1101/156588v1?rss=1 Fang, H. Huang, Y.-F. Radhakrishnan, A. Siepel, A. Lyon, G. J. Schatz, M. C. 2017-06-27 doi:10.1101/156588 Cold Spring Harbor Laboratory Press 2017-06-27 <![CDATA[ Conserved noncoding transcription and core promoter regulatory code in early Drosophila development ]]> https://biorxiv.org/content/10.1101/156596v1?rss=1 Batut, P. J. Gingeras, T. R. 2017-06-27 doi:10.1101/156596 Cold Spring Harbor Laboratory Press 2017-06-27 <![CDATA[ Nucleosomes and DNA methylation shape meiotic DSB frequency in Arabidopsis transposons and gene regulatory regions ]]> https://biorxiv.org/content/10.1101/160911v1?rss=1 Choi, K. Zhao, X. Lambing, C. Underwood, C. J. Hardcastle, T. J. Serra, H. Tock, A. J. Ziolkowski, P. A. Yelina, N. E. Martienssen, R. A. Henderson, I. R. 2017-07-08 doi:10.1101/160911 Cold Spring Harbor Laboratory Press 2017-07-08 <![CDATA[ Epigenetic activation of meiotic recombination in Arabidopsis centromeres via loss of H3K9me2 and non-CG DNA methylation ]]> https://biorxiv.org/content/10.1101/160929v1?rss=1 Underwood, C. J. Choi, K. Lambing, C. Zhao, X. Serra, H. Borges, F. Simorowski, J. Ernst, E. Jacob, Y. Henderson, I. R. Martienssen, R. A. 2017-07-08 doi:10.1101/160929 Cold Spring Harbor Laboratory Press 2017-07-08 <![CDATA[ A human-specific switch of alternatively spliced AFMID isoforms contributes to TP53 mutations and tumor recurrence in hepatocellular carcinoma ]]> https://biorxiv.org/content/10.1101/169029v1?rss=1 Lin, K.-T. Ma, W.-K. Scharner, J. Liu, Y.-R. Krainer, A. R. 2017-07-26 doi:10.1101/169029 Cold Spring Harbor Laboratory Press 2017-07-26 <![CDATA[ Accurate detection of complex structural variations using single molecule sequencing ]]> https://biorxiv.org/content/10.1101/169557v1?rss=1 Sedlazeck, F. J. Rescheneder, P. Smolka, M. Fang, H. Nattestad, M. von Haeseler, A. Schatz, M. 2017-07-28 doi:10.1101/169557 Cold Spring Harbor Laboratory Press 2017-07-28 <![CDATA[ Bioinformatics Core Competencies for Undergraduate Life Sciences Education ]]> https://biorxiv.org/content/10.1101/170993v1?rss=1 Wilson Sayres, M. A. Hauser, C. Sierk, M. Robic, S. Rosenwald, A. G. Smith, T. M. Triplett, E. W. Williams, J. J. Dinsdale, E. Morgan, W. Burnette, J. M. Donovan, S. S. Drew, J. C. Elgin, S. C. R. Fowlks, E. R. Galindo-Gonzalez, S. Goodman, A. L. Grandgenett, N. F. Goller, C. C. Jungck, J. Newman, J. D. Pearson, W. R. Ryder, E. Tosado-Acevedo, R. Tapprich, W. Tobin, T. C. Toro-Martinez, A. Welch, L. R. Wright, R. Ebenbach, D. Olney, K. C. McWilliams, M. Pauley, M. A. 2017-08-03 doi:10.1101/170993 Cold Spring Harbor Laboratory Press 2017-08-03 <![CDATA[ Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line ]]> https://biorxiv.org/content/10.1101/174938v1?rss=1 Nattestad, M. Goodwin, S. Ng, K. Baslan, T. Sedlazeck, F. J. Rescheneder, P. Garvin, T. Fang, H. Gurtowski, J. Hutton, E. Tseng, E. Chin, C.-S. Beck, T. Sundaravadanam, Y. Kramer, M. Antoniou, E. McPherson, J. D. Hicks, J. McCombie, W. R. Schatz, M. C. 2017-08-10 doi:10.1101/174938 Cold Spring Harbor Laboratory Press 2017-08-10 <![CDATA[ Transcriptional Architecture of Synaptic Communication Delineates Cortical GABAergic Neuron Identity ]]> https://biorxiv.org/content/10.1101/180034v1?rss=1 Paul, A. Crow, M. Raudales, R. Gillis, J. Huang, Z. J. 2017-08-30 doi:10.1101/180034 Cold Spring Harbor Laboratory Press 2017-08-30 <![CDATA[ Efficient in situ barcode sequencing using padlock probe-based BaristaSeq ]]> https://biorxiv.org/content/10.1101/180323v1?rss=1 Chen, X. Sun, Y.-C. Church, G. M. Lee, J. H. Zador, A. M. 2017-08-24 doi:10.1101/180323 Cold Spring Harbor Laboratory Press 2017-08-24 <![CDATA[ An integrated analysis of the epigenetic, genetic, and transcriptional patterns associated with outcome across cancer types ]]> https://biorxiv.org/content/10.1101/186528v1?rss=1 Smith, J. C. Sheltzer, J. M. 2017-09-08 doi:10.1101/186528 Cold Spring Harbor Laboratory Press 2017-09-08 <![CDATA[ Endoplasmic reticulum stress engenders immune-resistant, latent pancreatic cancer metastases ]]> https://biorxiv.org/content/10.1101/187484v1?rss=1 Pommier, A. Anaparthy, N. Memos, N. Larkin Kelley, Z. Gouronnec, A. Albrengues, J. Egeblad, M. Iacobuzio-Donahue, C. A. Lyons, S. K. Fearon, D. T. 2017-09-11 doi:10.1101/187484 Cold Spring Harbor Laboratory Press 2017-09-11 <![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[ The CLAVATA receptor FASCIATED EAR2 responds to different CLE peptides by signaling through different downstream effectors. ]]> https://biorxiv.org/content/10.1101/194951v1?rss=1 Je, B. I. Xu, F. Wu, Q. Liu, L. Meeley, R. Jackson, D. 2017-09-27 doi:10.1101/194951 Cold Spring Harbor Laboratory Press 2017-09-27 <![CDATA[ Visual evidence accumulation behavior in unrestrained mice ]]> https://biorxiv.org/content/10.1101/195792v1?rss=1 Odoemene, O. Nguyen, H. Churchland, A. K. 2017-09-29 doi:10.1101/195792 Cold Spring Harbor Laboratory Press 2017-09-29 <![CDATA[ The transcriptional legacy of developmental stochasticity ]]> https://biorxiv.org/content/10.1101/2019.12.11.873265v1?rss=1 Ballouz, S. Pena, M. Knight, F. M. Adams, L. Gillis, J. 2019-12-12 doi:10.1101/2019.12.11.873265 Cold Spring Harbor Laboratory Press 2019-12-12 <![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. 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Janowitz, T. Martins, C. P. Welsh, S. P. Shields, J. D. 2020-01-11 doi:10.1101/2020.01.10.901686 Cold Spring Harbor Laboratory Press 2020-01-11 <![CDATA[ Gapless assembly of maize chromosomes using long read technologies ]]> https://biorxiv.org/content/10.1101/2020.01.14.906230v1?rss=1 Dawe, K. Liu, J. Seetharam, A. S. Chougule, K. Ou, S. Swentowsky, K. W. Gent, J. I. Llaca, V. Woodhouse, M. Manchanda, N. Presting, G. G. Kudrna, D. Alabady, M. Hirsch, C. Fengler, K. Ware, D. Michael, T. Hufford, M. 2020-01-15 doi:10.1101/2020.01.14.906230 Cold Spring Harbor Laboratory Press 2020-01-15 <![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[ Deciphering the regulatory genome of Escherichiacoli, one hundred promoters at a time ]]> https://biorxiv.org/content/10.1101/2020.01.18.910323v1?rss=1 Ireland, W. T. T. Beeler, S. M. Flores-Bautista, E. Belliveau, N. M. Sweredoski, M. J. Moradian, A. Kinney, J. B. Phillips, R. 2020-01-18 doi:10.1101/2020.01.18.910323 Cold Spring Harbor Laboratory Press 2020-01-18 <![CDATA[ Comparing DNA replication programs reveals large timing shifts at centromeres of endocycling cells in maize roots ]]> https://biorxiv.org/content/10.1101/2020.01.24.917914v1?rss=1 Wear, E. E. Song, J. Zynda, G. J. Mickelson-Young, L. LeBlanc, C. Lee, T.-J. Deppong, D. O. Allen, G. C. Martienssen, R. A. Vaughn, M. W. Hanley-Bowdoin, L. Thompson, W. F. 2020-01-24 doi:10.1101/2020.01.24.917914 Cold Spring Harbor Laboratory Press 2020-01-24 <![CDATA[ The Arabidopsis "retrovirome" and its regulation by epigenetically activated small RNA ]]> https://biorxiv.org/content/10.1101/2020.01.24.919167v1?rss=1 Lee, S. C. Ernst, E. Berube, B. Borges, F. Schorn, A. Parent, J.-S. Ledon, P. Martienssen, R. A. 2020-01-25 doi:10.1101/2020.01.24.919167 Cold Spring Harbor Laboratory Press 2020-01-25 <![CDATA[ MaTAR25 LncRNA Regulates the Tensin1 Gene to Impact Breast Cancer Progression ]]> https://biorxiv.org/content/10.1101/2020.02.03.931881v1?rss=1 Chang, K.-C. Diermeier, S. D. Yu, A. T. Brine, L. D. Russo, S. Bhatia, S. Alsudani, H. Kostroff, K. Bhuiya, T. Brogi, E. Bennett, C. F. Rigo, F. Spector, D. L. 2020-02-03 doi:10.1101/2020.02.03.931881 Cold Spring Harbor Laboratory Press 2020-02-03 <![CDATA[ iGenomics: Comprehensive DNA Sequence Analysis on your Smartphone ]]> https://biorxiv.org/content/10.1101/2020.02.11.944132v1?rss=1 Palatnick, A. Zhou, B. Ghedin, E. Schatz, M. C. 2020-02-12 doi:10.1101/2020.02.11.944132 Cold Spring Harbor Laboratory Press 2020-02-12 <![CDATA[ Basal forebrain-derived acetylcholine encodes valence-free reinforcement prediction error. ]]> https://biorxiv.org/content/10.1101/2020.02.17.953141v1?rss=1 Sturgill, J. F. Hegedüs, P. Li, S. Chevy, Q. Siebels, A. Jing, M. Li, Y. Hangya, B. Kepecs, A. 2020-02-18 doi:10.1101/2020.02.17.953141 Cold Spring Harbor Laboratory Press 2020-02-18 <![CDATA[ Semantic segmentation of microscopic neuroanatomical data by combining topological priors with encoder-decoder deep networks ]]> https://biorxiv.org/content/10.1101/2020.02.18.955237v1?rss=1 Banerjee, S. Magee, L. Wang, D. Li, X. Huo, B.-X. Jayakumar, J. Matho, K. Lin, M.-K. Ram, K. Sivaprakasam, M. Huang, Z. J. Wang, Y. Mitra, P. P. 2020-02-19 doi:10.1101/2020.02.18.955237 Cold Spring Harbor Laboratory Press 2020-02-19 <![CDATA[ Interpreting Deep Neural Networks Beyond Attribution Methods: Quantifying Global Importance of Genomic Features ]]> https://biorxiv.org/content/10.1101/2020.02.19.956896v1?rss=1 Koo, P. K. Ploenzke, M. 2020-02-20 doi:10.1101/2020.02.19.956896 Cold Spring Harbor Laboratory Press 2020-02-20 <![CDATA[ Methods for Running a Successful Women-in-STEM Organization on an Academic Campus ]]> https://biorxiv.org/content/10.1101/2020.02.20.958629v1?rss=1 Rupert, D. Nowlan, A. C. Tam, O. H. Gale Hammell, M. 2020-02-23 doi:10.1101/2020.02.20.958629 Cold Spring Harbor Laboratory Press 2020-02-23 <![CDATA[ An integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell types ]]> https://biorxiv.org/content/10.1101/2020.02.29.970558v1?rss=1 Yao, Z. Liu, H. Xie, F. Fischer, S. Adkins, R. S. Aldrige, A. I. Ament, S. A. Bartlett, A. Behrens, M. M. Van den Berge, K. Bertagnolli, D. Biancalani, T. Booeshaghi, A. S. Corrada Bravo, H. Casper, T. Colantuoni, C. Crabtree, J. Creasy, H. Crichton, K. Crow, M. Dee, N. Dougherty, E. L. Doyle, W. I. Dudoit, S. Fang, R. Felix, V. Fong, O. Giglio, M. Goldy, J. Hawrylycz, M. Bezieux, H. R. d. Herb, B. R. Hertzano, R. Hou, X. Hu, Q. Huang, Z. J. Kancherla, J. Kroll, M. Lathia, K. Li, Y. E. Lucero, J. D. Luo, C. Mahurkar, A. McMillen, D. Nadaf, N. M. Ner 2020-03-02 doi:10.1101/2020.02.29.970558 Cold Spring Harbor Laboratory Press 2020-03-02 <![CDATA[ Citric Acid water as an alternative to water scheduling in behaving mice ]]> https://biorxiv.org/content/10.1101/2020.03.02.973016v1?rss=1 Urai, A. E. Aguillon-Rodriguez, V. Laranjeira, I. Cazettes, F. The International Brain Laboratory, Mainen, Z. F. Churchland, A. K. 2020-03-02 doi:10.1101/2020.03.02.973016 Cold Spring Harbor Laboratory Press 2020-03-02 <![CDATA[ Improving replicability in single-cell RNA-Seq cell type discovery with Dune ]]> https://biorxiv.org/content/10.1101/2020.03.03.974220v1?rss=1 Roux de Bezieux, H. Street, K. Fischer, S. Van den Berge, K. Chance, R. Risso, D. Gillis, J. Ngai, J. Purdom, E. Dudoit, S. 2020-03-04 doi:10.1101/2020.03.03.974220 Cold Spring Harbor Laboratory Press 2020-03-04 <![CDATA[ Parallel organization of cerebellar pathways to sensorimotor, associative, and modulatory forebrain ]]> https://biorxiv.org/content/10.1101/2020.03.06.979153v1?rss=1 View larger version (45K): org.highwire.dtl.DTLVardef@1bead0corg.highwire.dtl.DTLVardef@1531de2org.highwire.dtl.DTLVardef@1cf02f6org.highwire.dtl.DTLVardef@1cb6774_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Pisano, T. J. Dhanerawala, Z. M. Kislin, M. Bakshinskaya, D. Engel, E. A. Lee, J. de Oude, N. L. Umadevi Venkataraju, K. Verpeut, J. L. Boele, H.-J. Wang, S. S.- H. 2020-03-08 doi:10.1101/2020.03.06.979153 Cold Spring Harbor Laboratory Press 2020-03-08 <![CDATA[ Choices Change the Temporal Weighting of Decision Evidence ]]> https://biorxiv.org/content/10.1101/2020.03.06.979690v1?rss=1 Talluri, B. C. Urai, A. E. Bronfman, Z. Z. Brezis, N. Tsetsos, K. Usher, M. Donner, T. H. 2020-03-06 doi:10.1101/2020.03.06.979690 Cold Spring Harbor Laboratory Press 2020-03-06 <![CDATA[ Genomic islands of differentiation in a rapid avian radiation have been driven by recent selective sweeps ]]> https://biorxiv.org/content/10.1101/2020.03.07.977694v1?rss=1 Hejase, H. A. Salman-Minkov, A. Campagna, L. Hubisz, M. J. Lovette, I. J. Gronau, I. Siepel, A. 2020-03-08 doi:10.1101/2020.03.07.977694 Cold Spring Harbor Laboratory Press 2020-03-08 <![CDATA[ Detection and skeletonization of single neurons and tracer injections using topological methods ]]> https://biorxiv.org/content/10.1101/2020.03.21.000323v1?rss=1 Wang, D. Magee, L. Huo, B.-X. Banerjee, S. Li, X. Jayakumar, J. Lin, M. K. Ram, K. Wang, S. Wang, Y. Mitra, P. P. 2020-03-22 doi:10.1101/2020.03.21.000323 Cold Spring Harbor Laboratory Press 2020-03-22 <![CDATA[ Solving the where problem in neuroanatomy: a generative framework with learned mappings to register multimodal, incomplete data into a reference brain ]]> https://biorxiv.org/content/10.1101/2020.03.22.002618v1?rss=1 Tward, D. J. Li, X. Huo, B. Lee, B. C. Miller, M. Mitra, P. P. 2020-03-23 doi:10.1101/2020.03.22.002618 Cold Spring Harbor Laboratory Press 2020-03-23 <![CDATA[ Top-down coordination of local cortical state during selective attention ]]> https://biorxiv.org/content/10.1101/2020.03.26.009365v1?rss=1 van Kempen, J. Gieselmann, M. A. Boyd, M. Steinmetz, N. A. Moore, T. Engel, T. Thiele, A. 2020-03-26 doi:10.1101/2020.03.26.009365 Cold Spring Harbor Laboratory Press 2020-03-26 <![CDATA[ Cigarette smoke triggers the expansion of a subpopulation of respiratory epithelial cells that express the SARS-CoV-2 receptor ACE2 ]]> https://biorxiv.org/content/10.1101/2020.03.28.013672v1?rss=1 Smith, J. C. Sheltzer, J. M. 2020-03-31 doi:10.1101/2020.03.28.013672 Cold Spring Harbor Laboratory Press 2020-03-31 <![CDATA[ Evolution of cellular diversity in primary motor cortex of human, marmoset monkey, and mouse ]]> https://biorxiv.org/content/10.1101/2020.03.31.016972v1?rss=1 Bakken, T. E. Jorstad, N. L. Hu, Q. Lake, B. B. Tian, W. Kalmbach, B. E. Crow, M. Hodge, R. D. Krienen, F. M. Sorensen, S. A. Eggermont, J. Yao, Z. Aevermann, B. D. Aldridge, A. I. Bartlett, A. Bertagnolli, D. Casper, T. Castanon, R. G. Crichton, K. Daigle, T. L. Dalley, R. Dee, N. Dembrow, N. Diep, D. Ding, S.-L. Dong, W. Fang, R. Fischer, S. Goldman, M. Goldy, J. Graybuck, L. T. Herb, B. R. Hou, X. Kancherla, J. Kroll, M. Lathia, K. Lew, B. v. Li, Y. E. Liu, C. S. Liu, H. Mahurkar, A. McMillen, D. Miller, J. A. Moussa, M. Nery, J. R. Orvis, J. Ow 2020-04-01 doi:10.1101/2020.03.31.016972 Cold Spring Harbor Laboratory Press 2020-04-01 <![CDATA[ Genome and time-of-day transcriptome of Wolffia australiana link morphological extreme minimization with un-gated plant growth ]]> https://biorxiv.org/content/10.1101/2020.03.31.018291v1?rss=1 Michael, T. P. Ernst, E. Hartwick, N. Chu, P. Bryant, D. Gilbert, S. Ortleb, S. Baggs, E. L. Sree, K. S. Appenroth, K. J. Fuchs, J. Jupe, F. Sandoval, J. P. Krasileva, K. V. Borisjuk, L. Mockler, T. C. Ecker, J. R. Martienssen, R. A. Lam, E. 2020-04-01 doi:10.1101/2020.03.31.018291 Cold Spring Harbor Laboratory Press 2020-04-01 <![CDATA[ Multiscale Co-expression in the Brain ]]> https://biorxiv.org/content/10.1101/2020.03.31.018630v1?rss=1 Harris, B. D. Crow, M. Fisher, S. Gillis, J. 2020-04-01 doi:10.1101/2020.03.31.018630 Cold Spring Harbor Laboratory Press 2020-04-01 <![CDATA[ BSAseq: an interactive and integrated web-based workflow for identification of causal mutations in bulked F2 populations ]]> https://biorxiv.org/content/10.1101/2020.04.08.029801v1?rss=1 Wang, L. 2020-04-09 doi:10.1101/2020.04.08.029801 Cold Spring Harbor Laboratory Press 2020-04-09 <![CDATA[ The Microbes Found in the Honey of New York City Beehives ]]> https://biorxiv.org/content/10.1101/2020.04.16.042762v1?rss=1 Weiss, T. Mayle, A. Nash, B. 2020-04-17 doi:10.1101/2020.04.16.042762 Cold Spring Harbor Laboratory Press 2020-04-17 <![CDATA[ Corticostriatal Plasticity Established by Initial Learning Persists After Behavioral Reversal ]]> https://biorxiv.org/content/10.1101/2020.04.16.045625v1?rss=1 Ghosh, S. Zador, A. M. 2020-04-18 doi:10.1101/2020.04.16.045625 Cold Spring Harbor Laboratory Press 2020-04-18 <![CDATA[ CoCoCoNet: Conserved and Comparative Co-expression Across a Diverse Set of Species ]]> https://biorxiv.org/content/10.1101/2020.04.21.053900v1?rss=1 Lee, J. Shah, M. Ballouz, S. Crow, M. Gillis, J. 2020-04-23 doi:10.1101/2020.04.21.053900 Cold Spring Harbor Laboratory Press 2020-04-23 <![CDATA[ Genetic dissection of glutamatergic neuron subpopulations and developmental trajectories in the cerebral cortex ]]> https://biorxiv.org/content/10.1101/2020.04.22.054064v1?rss=1 Matho, K. S. H. Huilgol, D. Galbavy, W. Kim, G. He, M. An, X. Lu, J. Wu, P. Di Bella, D. J. Shetty, A. S. Palaniswamy, R. Hatfield, J. Raudales, R. Narasimhan, A. Gamache, E. Levine, J. M. Tucciarone, J. Mitra, P. P. Osten, P. Arlotta, P. Huang, Z. J. 2020-04-24 doi:10.1101/2020.04.22.054064 Cold Spring Harbor Laboratory Press 2020-04-24 <![CDATA[ Causal integration of multi-omics data with prior knowledge to generate mechanistic hypotheses ]]> https://biorxiv.org/content/10.1101/2020.04.23.057893v1?rss=1 View larger version (28K): org.highwire.dtl.DTLVardef@37d2d7org.highwire.dtl.DTLVardef@f333d4org.highwire.dtl.DTLVardef@cfcac3org.highwire.dtl.DTLVardef@90318_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> dugourd, A. Kuppe, C. Sciacovelli, M. Gjerga, E. Emdal, K. B. Bekker-Jensen, D. B. Kranz, J. Bindels, E. J. M. Costa, S. Olsen, J. V. Frezza, C. Kramann, R. Saez-Rodriguez, J. 2020-04-25 doi:10.1101/2020.04.23.057893 Cold Spring Harbor Laboratory Press 2020-04-25 <![CDATA[ A central amygdala-globus pallidus circuit conveys unconditioned stimulus information and controls fear learning ]]> https://biorxiv.org/content/10.1101/2020.04.28.066753v1?rss=1 Giovanniello, J. R. Yu, K. Furlan, A. Nachtrab, G. T. Sharma, R. Chen, X. Li, B. 2020-04-30 doi:10.1101/2020.04.28.066753 Cold Spring Harbor Laboratory Press 2020-04-30 <![CDATA[ Hypothalamic circuitry underlying stress-induced insomnia and peripheral immunosuppression ]]> https://biorxiv.org/content/10.1101/2020.04.29.069393v1?rss=1 Li, S.-B. Borniger, J. C. Yamaguchi, H. Hédou, J. Gaudillière, B. de Lecea, L. 2020-05-01 doi:10.1101/2020.04.29.069393 Cold Spring Harbor Laboratory Press 2020-05-01 <![CDATA[ Highly accurate long-read HiFi sequencing data for five complex genomes ]]> https://biorxiv.org/content/10.1101/2020.05.04.077180v1?rss=1 Hon, T. Mars, K. Young, G. Tsai, Y.-C. Karalius, J. W. Landolin, J. M. Maurer, N. Kudrna, D. Hardigan, M. A. Steiner, C. C. Knapp, S. J. Ware, D. Shapiro, B. Peluso, P. Rank, D. R. 2020-05-05 doi:10.1101/2020.05.04.077180 Cold Spring Harbor Laboratory Press 2020-05-05 <![CDATA[ A scale-space approach for 3D neuronal traces analysis ]]> https://biorxiv.org/content/10.1101/2020.06.01.127035v1?rss=1 Phan, M.-S. Matho, K. S. Livet, J. Beaurepaire, E. Chessel, A. 2020-06-01 doi:10.1101/2020.06.01.127035 Cold Spring Harbor Laboratory Press 2020-06-01 <![CDATA[ Detection of Chemotherapy-Resistant Pancreatic Cancer Using a Glycan Biomarker ]]> https://biorxiv.org/content/10.1101/2020.06.01.128082v1?rss=1 Gao, C. Wisniewski, L. Liu, Y. Staal, B. Beddows, I. Plenker, D. Aldakkak, M. Hall, J. Barnett, D. Kheir Gouda, M. Allen, P. Drake, R. Zureikat, A. Huang, Y. Evans, D. Singhi, A. Brand, R. E. Tuveson, D. A. Tsai, S. Haab, B. 2020-06-02 doi:10.1101/2020.06.01.128082 Cold Spring Harbor Laboratory Press 2020-06-02 <![CDATA[ Improving representations of genomic sequence motifs in convolutional networks with exponential activations ]]> https://biorxiv.org/content/10.1101/2020.06.14.150706v1?rss=1 Koo, P. K. Ploenzke, M. 2020-06-15 doi:10.1101/2020.06.14.150706 Cold Spring Harbor Laboratory Press 2020-06-15 <![CDATA[ The role of CLV signalling in the negative regulation of mycorrhizal colonisation and nitrogen response of tomato ]]> https://biorxiv.org/content/10.1101/2020.07.03.185991v1?rss=1 Wang, C. Velandia, K. Kwon, C.-T. Wulf, K. E. Nichols, D. S. Reid, J. B. Foo, E. 2020-07-04 doi:10.1101/2020.07.03.185991 Cold Spring Harbor Laboratory Press 2020-07-04 <![CDATA[ Evolution of DNA Replication Origin Specification and Gene Silencing Mechanisms ]]> https://biorxiv.org/content/10.1101/2020.07.04.187286v1?rss=1 Hu, Y. Tareen, A. Sheu, Y.-J. Ireland, W. T. T. Speck, C. Li, H. Joshua-Tor, L. Kinney, J. B. Stillman, B. 2020-07-04 doi:10.1101/2020.07.04.187286 Cold Spring Harbor Laboratory Press 2020-07-04 <![CDATA[ Activating a collaborative innate-adaptive immune response to control breast and ovarian cancer metastasis ]]> https://biorxiv.org/content/10.1101/2020.07.13.200477v1?rss=1 Sun, L. Kees, T. Almeida, A. S. Liu, B. He, X.-Y. Ng, D. Spector, D. McNeish, I. M. Gimotty, P. Adams, S. EGEBLAD, M. 2020-07-14 doi:10.1101/2020.07.13.200477 Cold Spring Harbor Laboratory Press 2020-07-14 <![CDATA[ MAVE-NN: Quantitative Modeling of Genotype-Phenotype Maps as Information Bottlenecks ]]> https://biorxiv.org/content/10.1101/2020.07.14.201475v1?rss=1 Tareen, A. Ireland, W. T. Posfai, A. McCandlish, D. M. Kinney, J. B. 2020-07-14 doi:10.1101/2020.07.14.201475 Cold Spring Harbor Laboratory Press 2020-07-14 <![CDATA[ A correspondence between normalization strategies in artificial and biological neural networks ]]> https://biorxiv.org/content/10.1101/2020.07.17.197640v1?rss=1 Shen, Y. Wang, J. Navlakha, S. 2020-07-17 doi:10.1101/2020.07.17.197640 Cold Spring Harbor Laboratory Press 2020-07-17 <![CDATA[ Camostat mesylate inhibits SARS-CoV-2 activation by TMPRSS2-related proteases and its metabolite GBPA exerts antiviral activity ]]> https://biorxiv.org/content/10.1101/2020.08.05.237651v1?rss=1 Hoffmann, M. Hofmann-Winkler, H. Smith, J. C. Krueger, N. Sorensen, L. K. Sogaard, O. S. Hasselstrom, J. B. Winkler, M. Hempel, T. Raich, L. Olsson, S. Yamazoe, T. Yamatsuta, K. Mizuno, H. Ludwig, S. Noe, F. Sheltzer, J. M. Kjolby, M. Poehlmann, S. 2020-08-05 doi:10.1101/2020.08.05.237651 Cold Spring Harbor Laboratory Press 2020-08-05 <![CDATA[ The human Origin Recognition Complex is essential for pre-RC assembly, mitosis and maintenance of nuclear structure. ]]> https://biorxiv.org/content/10.1101/2020.08.06.240358v1?rss=1 Chou, H.-C. Bhalla, K. Demerdesh, O. E. Klingbeil, O. Hanington, K. Aganezov, S. Andrews, P. Alsudani, H. Chang, K. Vakoc, C. R. Schatz, M. C. McCombie, W. R. Stillman, B. 2020-08-06 doi:10.1101/2020.08.06.240358 Cold Spring Harbor Laboratory Press 2020-08-06 <![CDATA[ SVCollector: Optimized sample selection for cost-efficient long-read population sequencing ]]> https://biorxiv.org/content/10.1101/2020.08.06.240390v1?rss=1 Ranallo-Benavidez, T. R. Lemmon, Z. H. Soyk, S. Aganezov, S. Salerno, W. J. McCoy, R. C. Lippman, Z. B. Schatz, M. C. Sedlazeck, F. J. 2020-08-06 doi:10.1101/2020.08.06.240390 Cold Spring Harbor Laboratory Press 2020-08-06 <![CDATA[ Estimation of autocorrelation timescales with Approximate Bayesian Computations ]]> https://biorxiv.org/content/10.1101/2020.08.11.245944v1?rss=1 Zeraati, R. Engel, T. A. Levina, A. 2020-08-12 doi:10.1101/2020.08.11.245944 Cold Spring Harbor Laboratory Press 2020-08-12 <![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[ The dynamic nature of the human Origin Recognition Complex revealed through five cryoEM structures ]]> https://biorxiv.org/content/10.1101/2020.08.13.250019v1?rss=1 Jaremko, M. J. On, K. F. Thomas, D. R. Stillman, B. Joshua-Tor, L. 2020-08-14 doi:10.1101/2020.08.13.250019 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[ Super-resolution light-sheet fluorescence microscopy by SOFI. ]]> https://biorxiv.org/content/10.1101/2020.08.17.254797v1?rss=1 Mizrachi, J. Narasimhan, A. Qi, X. Drewes, R. Palaniswamy, R. Wu, Z. Osten, P. 2020-08-18 doi:10.1101/2020.08.17.254797 Cold Spring Harbor Laboratory Press 2020-08-18 <![CDATA[ Integrating barcoded neuroanatomy with spatial transcriptional profiling reveals cadherin correlates of projections shared across the cortex ]]> https://biorxiv.org/content/10.1101/2020.08.25.266460v1?rss=1 Sun, Y.-C. Chen, X. Fischer, S. Lu, S. Gillis, J. Zador, A. M. 2020-08-26 doi:10.1101/2020.08.25.266460 Cold Spring Harbor Laboratory Press 2020-08-26 <![CDATA[ Gene disruption by structural mutations drives selection in US rice breeding over the last century ]]> https://biorxiv.org/content/10.1101/2020.08.26.268342v1?rss=1 50 bp) and orient them with respect to their ancestral state using the outgroup, Oryza glaberrima. Supporting prior work, we find substantial genome expansion is the sativa branch. While transposable elements (TEs) account for the largest share of size variation, the majority of events are not directly TE-mediated. Tandem duplications are the most common source of insertions and are highly enriched among 50-200bp mutations. To explore the relative impact of various mutational classes on crop fitness, we then track these structural events over the last century of US rice improvement using 101 resequenced varieties. Within this material, a pattern of temporary hybridization between medium and long-grain varieties was followed by recent divergence. During this long-term selection, structural mutations that impact gene exons have been removed at a greater rate than intronic indels and single-nucleotide mutations. These results support the use of ab initio estimates of mutational burden, based on structural data, as an orthogonal predictor in genomic selection. Significance StatementSome crop varieties have superior performance across years and environments. In hybrids, harmful mutations in one parent are masked by the ancestral alleles in the other parent, resulting in increased vigor. Unfortunately, these mutations are very difficult to identify precisely because, individually, they only have a small effect. In this study, we use long-read sequencing to characterize the entire mutational spectrum between two rice varieties. We then track these mutations through the last century of rice breeding. We show that large structural mutations in exons are selected against at a greater rate than any other mutational class. These findings illuminate the nature of deleterious alleles and will guide attempts to predict variety vigor based solely on genomic information. ]]> Vaughn, J. N. Korani, W. Stein, J. C. Edwards, J. D. Peterson, D. G. Simpson, S. A. Youngblood, R. C. Grimwood, J. Ware, D. H. McClung, A. M. Scheffler, B. E. 2020-08-27 doi:10.1101/2020.08.26.268342 Cold Spring Harbor Laboratory Press 2020-08-27 <![CDATA[ An Epigenetic Priming Mechanism Mediated by Nutrient Sensing Regulates Transcriptional Output ]]> https://biorxiv.org/content/10.1101/2020.09.01.278127v1?rss=1 Stec, N. Doerfel, K. Hills-Muckey, K. Ettorre, V. Ercan, S. Keil, W. Hammell, C. 2020-09-03 doi:10.1101/2020.09.01.278127 Cold Spring Harbor Laboratory Press 2020-09-03 <![CDATA[ ASO-based PKM Splice-switching Therapy Inhibits Hepatocellular Carcinoma Cell Growth ]]> https://biorxiv.org/content/10.1101/2020.09.01.278580v1?rss=1 Ma, W. K. Scharner, J. Costa, A. S. H. Jeong, H. Y. Jackson, M. Rigo, F. Bennett, F. C. Krainer, A. 2020-09-02 doi:10.1101/2020.09.01.278580 Cold Spring Harbor Laboratory Press 2020-09-02 <![CDATA[ Influence of On-Off dynamics and selective attention on the spatial pattern of correlated variability in neocortex ]]> https://biorxiv.org/content/10.1101/2020.09.02.279893v1?rss=1 Shi, Y.-L. Steinmetz, N. A. Moore, T. Boahen, K. Engel, T. A. 2020-09-03 doi:10.1101/2020.09.02.279893 Cold Spring Harbor Laboratory Press 2020-09-03 <![CDATA[ Combining Natural Language Processing and Metabarcoding to Reveal Pathogen-Environment Associations ]]> https://biorxiv.org/content/10.1101/2020.09.02.280578v1?rss=1 View larger version (66K): org.highwire.dtl.DTLVardef@135ce50org.highwire.dtl.DTLVardef@17bf52borg.highwire.dtl.DTLVardef@11cf682org.highwire.dtl.DTLVardef@7be6ea_HPS_FORMAT_FIGEXP M_FIG C_FIG Cryptococcus neoformans cells budding. Image Provided Courtesy of Felipe H. Santiago-Tirado, colored by Kristina Davis, CC-BY 4.0 ]]> Molik, D. C. Tomlinson, D. Davitt, S. Morgan, E. L. Roche, B. Meyers, N. Pfrender, M. E. 2020-09-03 doi:10.1101/2020.09.02.280578 Cold Spring Harbor Laboratory Press 2020-09-03 <![CDATA[ Dietary suppression of MHC-II expression in intestinal stem cells enhances intestinal tumorigenesis ]]> https://biorxiv.org/content/10.1101/2020.09.05.284174v1?rss=1 Beyaz, S. Roper, J. Xifaras, M. E. Bauer-Rowe, K. E. Ergin, I. Dohnalova, L. Biton, M. Shekar, K. Mou, H. Eskiocak, O. Ozata, D. M. Chung, C. Papciak, K. Almeqdadi, M. Fein, M. Erdemir, A. Valle-Encinas, E. Dogum, K. Garipcan, A. Meyer, H. Fox, J. G. Elinav, E. Kucukural, A. Kumar, P. McAleer, J. Thaiss, C. A. Regev, A. Orkin, S. H. Yilmaz, O. H. 2020-09-08 doi:10.1101/2020.09.05.284174 Cold Spring Harbor Laboratory Press 2020-09-08 <![CDATA[ Global Importance Analysis: A Method to QuantifyImportance of Genomic Features in Deep NeuralNetworks ]]> https://biorxiv.org/content/10.1101/2020.09.08.288068v1?rss=1 Koo, P. K. Ploenzke, M. Anand, P. Paul, S. Majdandzic, A. 2020-09-09 doi:10.1101/2020.09.08.288068 Cold Spring Harbor Laboratory Press 2020-09-09 <![CDATA[ Chromosome-level Genome Assembly of a Regenerable Maize Inbred Line A188 ]]> https://biorxiv.org/content/10.1101/2020.09.09.289611v1?rss=1 Lin, G. He, C. Zheng, J. Koo, D.-H. Le, H. Zheng, H. Tamang, T. M. Lin, J. Liu, Y. Zhao, M. Hao, Y. McFarland, F. Wang, B. Qin, Y. Tang, H. McCarty, D. R. Wei, H. Cho, M.-J. Park, S. Kaeppler, H. Kaeppler, S. Liu, Y. Springer, N. M. Schnable, P. S. Wang, G. White, F. F. Liu, S. 2020-09-10 doi:10.1101/2020.09.09.289611 Cold Spring Harbor Laboratory Press 2020-09-10 <![CDATA[ Unraveling molecular mechanisms of immunity and cancer-resistance using the genomes of the Neotropical bats Artibeus jamaicensis and Pteronotus mesoamericanus ]]> https://biorxiv.org/content/10.1101/2020.09.09.290502v1?rss=1 Scheben, A. Mendivil Ramos, O. Kramer, M. Goodwin, S. Oppenheim, S. J. Becker, D. J. Schatz, M. C. Simmons, N. B. Siepel, A. McCombie, W. R. 2020-09-09 doi:10.1101/2020.09.09.290502 Cold Spring Harbor Laboratory Press 2020-09-09 <![CDATA[ DETECTION OF INCIPIENT PANCREATIC CANCER WITH NOVEL TUMOR-SPECIFIC ANTIBODIES IN MOUSE MODELS ]]> https://biorxiv.org/content/10.1101/2020.09.10.292193v1?rss=1 Oni, T. E. Bautista, C. Merrill, J. R. Goos, J. A. C. M. Rivera, K. D. Miyabayashi, K. Biffi, G. Garcia, L. Plenker, D. Patel, H. Elyada, E. Samaritano, M. Yu, K. H. Pappin, D. J. Goggins, M. G. Hruban, R. H. Lewis, J. S. Yeh, J. T. Tuveson, D. A. 2020-09-10 doi:10.1101/2020.09.10.292193 Cold Spring Harbor Laboratory Press 2020-09-10 <![CDATA[ Oncogenic KRAS engages an RSK1/NF1 complex in pancreatic cancer ]]> https://biorxiv.org/content/10.1101/2020.09.14.295394v1?rss=1 90% of PDAC patients, targeting KRAS mutants directly has been challenging in PDAC. Similarly, strategies targeting known KRAS downstream effectors have had limited clinical success due to feedback mechanisms, alternate pathways and toxicity due to the targeting of normal tissues. Therefore, identifying additional functionally relevant KRAS interactions in PDAC may allow for a better understanding of feedback mechanisms and unveil new potential therapeutic targets. Here, we used proximity labelling to identify protein interactors of active KRAS in PDAC cells. Fusions of wildtype (BirA-KRAS4B), mutant (BirA-KRAS4BG12D) and non-transforming and cytosolic double mutant (BirA-KRAS4BG12D/C185S) KRAS with the BirA biotin ligase were expressed in murine PDAC cells. Mass spectrometry analysis revealed that RSK1 was enriched among proteins that selectively interacted with membrane-bound KRASG12D. RSK1 required the NF1 and SPRED proteins to interact with KRAS-GTP at the membrane. In both murine and human PDAC lines, membrane-targeted RSK1 was tolerated but inhibited cell proliferation following oncogenic KRAS abrogation to reveal a negative feedback role for membrane-localized RSK1 on wild-type KRAS. Inhibition of the wild-type KRAS, which has been previously proposed to suppress KRAS oncogenesis, may partially explain how RSK1 has been identified as a dependency in some KRAS mutant cells and may provide an additional function for NF1 in tumorigenesis. Significance StatementFor decades, KRAS interactors have been sought after as potential therapeutic targets in KRAS mutant cancers, especially pancreatic adenocarcinoma (PDAC). Our proximity labeling screen with KRAS in PDAC cells highlight RSK1 as a notable mutant-specific interactor. Functionally, we show that RSK1 mediates negative feedback on wild-type KRAS in PDAC cells. ]]> Cheng, D. K. Oni, T. E. Park, Y. Thalappillil, J. S. Ting, H.-c. Prasad, N. Alagesan, B. Rivera, K. D. Pappin, D. J. Van Aelst, L. Tuveson, D. A. 2020-09-14 doi:10.1101/2020.09.14.295394 Cold Spring Harbor Laboratory Press 2020-09-14 <![CDATA[ Chromosomal instability accelerates the evolution of resistance to anti-cancer therapies ]]> https://biorxiv.org/content/10.1101/2020.09.25.314229v1?rss=1 Lukow, D. A. Sausville, E. L. Suri, P. Chunduri, N. K. Leu, J. Kendall, J. Wang, Z. Storchova, Z. Sheltzer, J. M. 2020-09-26 doi:10.1101/2020.09.25.314229 Cold Spring Harbor Laboratory Press 2020-09-26 <![CDATA[ A non-canonical feedforward pathway for computing odor identity ]]> https://biorxiv.org/content/10.1101/2020.09.28.317248v1?rss=1 Chae, H. Banerjee, A. Albeanu, D. F. 2020-09-30 doi:10.1101/2020.09.28.317248 Cold Spring Harbor Laboratory Press 2020-09-30 <![CDATA[ Two independent approaches converge to the cloning of a new Leptosphaeria maculans avirulence effector gene, AvrLmS-Lep2 ]]> https://biorxiv.org/content/10.1101/2020.10.02.322479v1?rss=1 Neik, T. X. Ghanbarnia, K. Ollivier, B. Scheben, A. Severn-Ellis, A. Larkan, N. J. Haddadi, P. Fernando, D. G. Rouxel, T. Batley, J. Borhan, H. M. Balesdent, M.-H. 2020-10-03 doi:10.1101/2020.10.02.322479 Cold Spring Harbor Laboratory Press 2020-10-03 <![CDATA[ Cellular Anatomy of the Mouse Primary Motor Cortex ]]> https://biorxiv.org/content/10.1101/2020.10.02.323154v1?rss=1 Munoz-Castaneda, R. Zingg, B. Matho, K. S. Wang, Q. Chen, X. Foster, N. N. Narasimhan, A. Li, A. Hirokawa, K. E. Huo, B. Banerjee, S. Korobkova, L. Park, C. S. Park, Y.-G. Bienkowski, M. S. Chon, U. Wheeler, D. W. Li, X. Wang, Y. Kelly, K. An, X. Attili, S. M. Bowman, I. Bludova, A. Cetin, A. Ding, L. Drewes, R. D'Orazi, F. Elowsky, C. Fischer, S. Galbavy, W. Gao, L. Gillis, J. Groblewski, P. A. Gou, L. Hahn, J. D. Hatfield, J. T. Hintiryan, H. Huang, J. Kondo, H. Kuang, X. Lesnar, P. Li, X. Li, Y. Lin, M. Liu, L. Lo, D. Mizrachi, J. Mok, S. Nae 2020-10-02 doi:10.1101/2020.10.02.323154 Cold Spring Harbor Laboratory Press 2020-10-02 <![CDATA[ A fluorescent sensor for spatiotemporally resolved endocannabinoid dynamics in vitro and in vivo ]]> https://biorxiv.org/content/10.1101/2020.10.08.329169v1?rss=1 Dong, A. He, K. Dudok, B. Farrell, J. S. Guan, W. Liput, D. J. Puhl, H. L. Cai, R. Duan, J. Albarran, E. Ding, J. Lovinger, D. M. Li, B. Soltesz, I. Li, Y. 2020-10-08 doi:10.1101/2020.10.08.329169 Cold Spring Harbor Laboratory Press 2020-10-08 <![CDATA[ Empirical variance component regression for sequence-function relationships ]]> https://biorxiv.org/content/10.1101/2020.10.14.339804v1?rss=1 Zhou, J. Wong, M. S. Chen, W.-C. Krainer, A. R. Kinney, J. B. McCandlish, D. M. 2020-10-15 doi:10.1101/2020.10.14.339804 Cold Spring Harbor Laboratory Press 2020-10-15 <![CDATA[ Replicability of spatial gene expression atlas data from the adult mouse brain ]]> https://biorxiv.org/content/10.1101/2020.10.16.343210v1?rss=1 Lu, S. Ortiz, C. Furth, D. Fischer, S. Meletis, K. Zador, A. Gillis, J. 2020-10-17 doi:10.1101/2020.10.16.343210 Cold Spring Harbor Laboratory Press 2020-10-17 <![CDATA[ A multimodal cell census and atlas of the mammalian primary motor cortex ]]> https://biorxiv.org/content/10.1101/2020.10.19.343129v1?rss=1 BRAIN Initiative Cell Census Network (BICCN), Adkins, R. S. Aldridge, A. I. Allen, S. Ament, S. A. An, X. Armand, E. Ascoli, G. A. Bakken, T. E. Bandrowski, A. Banerjee, S. Barkas, N. Bartlett, A. Bateup, H. S. Behrens, M. M. Berens, P. Berg, J. Bernabucci, M. Bernaerts, Y. Bertagnolli, D. Biancalani, T. Boggeman, L. Booeshaghi, A. S. Bowman, I. Bravo, H. C. Cadwell, C. R. Callaway, E. M. Carlin, B. O'Connor, C. Carter, R. Casper, T. Castanon, R. G. Castro, J. R. Chance, R. K. Chatterjee, A. Chen, H. Chun, J. Colantuoni, C. Crabtree, J. Creasy, H. Cric 2020-10-21 doi:10.1101/2020.10.19.343129 Cold Spring Harbor Laboratory Press 2020-10-21 <![CDATA[ Regulation of neural gene expression by estrogen receptor alpha ]]> https://biorxiv.org/content/10.1101/2020.10.21.349290v1?rss=1 Gegenhuber, B. Wu, M. V. Bronstein, R. Tollkuhn, J. 2020-10-21 doi:10.1101/2020.10.21.349290 Cold Spring Harbor Laboratory Press 2020-10-21 <![CDATA[ Transcriptional silencing of ALDH2 in acute myeloid leukemia confers a dependency on Fanconi anemia proteins ]]> https://biorxiv.org/content/10.1101/2020.10.23.352070v1?rss=1 Yang, Z. Wei, Y. Wu, X. S. Iyer, S. V. Jung, M. Adelman, E. R. Klingbeil, O. Kramer, M. Demerdash, O. E. Chang, K. Goodwin, S. Hodges, E. McCombie, W. R. Figueroa, M. E. Smogorzewska, A. Vakoc, C. R. 2020-10-23 doi:10.1101/2020.10.23.352070 Cold Spring Harbor Laboratory Press 2020-10-23 <![CDATA[ Quantitative genetic basis of floral design in a natural plant population ]]> https://biorxiv.org/content/10.1101/2020.11.06.371831v1?rss=1 Zhou, J. Fenster, C. B. Reynolds, R. J. 2020-11-08 doi:10.1101/2020.11.06.371831 Cold Spring Harbor Laboratory Press 2020-11-08 <![CDATA[ Darwinian dynamics over recurrent neural computations for combinatorial problem solving ]]> https://biorxiv.org/content/10.1101/2020.11.06.372284v1?rss=1 Czegel, D. Giaffar, H. Csillag, M. Futo, B. Szathmary, E. 2020-11-06 doi:10.1101/2020.11.06.372284 Cold Spring Harbor Laboratory Press 2020-11-06 <![CDATA[ Coexpression reveals conserved mechanisms of transcriptional cell identity ]]> https://biorxiv.org/content/10.1101/2020.11.10.375758v1?rss=1 Crow, M. Suresh, H. Lee, J. Gillis, J. 2020-11-10 doi:10.1101/2020.11.10.375758 Cold Spring Harbor Laboratory Press 2020-11-10 <![CDATA[ Sex-specific stress-related behavioral phenotypes and central amygdala dysfunction in a mouse model of 16p11.2 microdeletion ]]> https://biorxiv.org/content/10.1101/2020.11.12.380501v1?rss=1 Giovanniello, J. R. Ahrens, S. Yu, K. Li, B. 2020-11-15 doi:10.1101/2020.11.12.380501 Cold Spring Harbor Laboratory Press 2020-11-15 <![CDATA[ Non-parametric Bayesian density estimation for biological sequence space with applications to pre-mRNA splicing and the karyotypic diversity of human cancer ]]> https://biorxiv.org/content/10.1101/2020.11.25.399253v1?rss=1 Chen, W.-C. Zhou, J. Sheltzer, J. M. Kinney, J. B. McCandlish, D. M. 2020-11-27 doi:10.1101/2020.11.25.399253 Cold Spring Harbor Laboratory Press 2020-11-27 <![CDATA[ The structure-fitness landscape of pairwise relations in generative sequence models ]]> https://biorxiv.org/content/10.1101/2020.11.29.402875v1?rss=1 Marshall, D. Wang, H. Stiffler, M. Dauparas, J. Koo, P. Ovchinnikov, S. 2020-11-30 doi:10.1101/2020.11.29.402875 Cold Spring Harbor Laboratory Press 2020-11-30 <![CDATA[ Acute systemic loss of Mad2 leads to intestinal atrophy in adult mice ]]> https://biorxiv.org/content/10.1101/2020.12.03.404186v1?rss=1 Schukken, K. M. Zhu, Y. Bakker, P. L. Harkema, L. Youssef, S. A. de Bruin, A. Foijer, F. 2020-12-03 doi:10.1101/2020.12.03.404186 Cold Spring Harbor Laboratory Press 2020-12-03 <![CDATA[ Ranked Choice Voting for Representative Transcripts with TRaCE ]]> https://biorxiv.org/content/10.1101/2020.12.15.422742v1?rss=1 Olson, A. J. Ware, D. 2020-12-16 doi:10.1101/2020.12.15.422742 Cold Spring Harbor Laboratory Press 2020-12-16 <![CDATA[ Naa12 rescues embryonic lethality in Naa10-Deficient Mice in the amino-terminal acetylation pathway ]]> https://biorxiv.org/content/10.1101/2020.12.19.422860v1?rss=1 Kweon, H. Y. Lee, M. Dorfel, M. Seo, S. Gottlieb, L. PaPazyan, T. McTiernan, N. Ree, R. Garcia, A. Flory, M. Crain, J. Sebold, A. Lyons, S. Ismail, A. Marchi, E. Sonn, S.-k. Jeong, S.-J. Jeon, S. Ju, S. Conway, S. J. Kim, T. Kim, H.-S. Lee, C. Roh, T.-Y. Arnesen, T. Marmorstein, R. Lyon, G. J. Oh, G. 2020-12-20 doi:10.1101/2020.12.19.422860 Cold Spring Harbor Laboratory Press 2020-12-20 <![CDATA[ Single Layers of Attention Suffice to Predict Protein Contacts ]]> https://biorxiv.org/content/10.1101/2020.12.21.423882v1?rss=1 Bhattacharya, N. Thomas, N. Rao, R. Daupras, J. Koo, P. Baker, D. Song, Y. S. Ovchinnikov, S. 2020-12-22 doi:10.1101/2020.12.21.423882 Cold Spring Harbor Laboratory Press 2020-12-22 <![CDATA[ Virtue as the mean: Pan-human consensus genome significantly improves the accuracy of RNA-seq analyses ]]> https://biorxiv.org/content/10.1101/2020.12.22.423111v1?rss=1 Kaminow, B. Ballouz, S. Gillis, J. Dobin, A. 2020-12-22 doi:10.1101/2020.12.22.423111 Cold Spring Harbor Laboratory Press 2020-12-22 <![CDATA[ In vivo genetic screen identifies a SLC5A3-dependent myo-inositol auxotrophy in acute myeloid leukemia ]]> https://biorxiv.org/content/10.1101/2020.12.22.424018v1?rss=1 Wei, Y. Iyer, S. Costa, S. Yang, Z. Kramer, M. Adelman, E. Klingbeil, O. Demerdash, O. Polyanskaya, S. Chang, K. Goodwin, S. Hodges, E. McCombie, W. R. Figueroa, M. Vakoc, C. 2020-12-22 doi:10.1101/2020.12.22.424018 Cold Spring Harbor Laboratory Press 2020-12-22 <![CDATA[ High resolution copy number inference in cancer using short-molecule nanopore sequencing ]]> https://biorxiv.org/content/10.1101/2020.12.28.424602v1?rss=1 Baslan, T. Kovaka, S. Sedlazeck, F. J. Zhang, Y. Wappel, R. Lowe, S. J. Goodwin, S. Schatz, M. C. 2020-12-29 doi:10.1101/2020.12.28.424602 Cold Spring Harbor Laboratory Press 2020-12-29 <![CDATA[ Rapid expression of COVID-19 proteins by transient expression in tobacco. ]]> https://biorxiv.org/content/10.1101/2020.12.29.424712v1?rss=1 Lindsay, P. L. Ackerman, A. Jian, Y. Artz, O. Rosado, D. Skopelitis, T. Kitagawa, M. Pedmale, U. V. Jackson, D. 2020-12-29 doi:10.1101/2020.12.29.424712 Cold Spring Harbor Laboratory Press 2020-12-29 <![CDATA[ Pan-genome Analysis in Sorghum Highlights the Extent of Genomic Variation and Sugarcane Aphid Resistance Genes ]]> https://biorxiv.org/content/10.1101/2021.01.03.424980v1?rss=1 Wang, B. Jiao, Y. Chougule, K. Olson, A. Huang, J. Llaca, V. Fengler, K. Wei, X. Wang, L. Wang, X. Regulski, M. Drenkow, J. Gingeras, T. R. Hayes, C. Armstrong, J. S. Huang, Y. Xin, Z. Ware, D. 2021-01-04 doi:10.1101/2021.01.03.424980 Cold Spring Harbor Laboratory Press 2021-01-04 <![CDATA[ The H3K36me2 writer-reader dependency in H3K27M-DIPG ]]> https://biorxiv.org/content/10.1101/2021.01.06.425580v1?rss=1 Reinberg, D. Yu, J.-R. LeRoy, G. Bready, D. Frenster, J. D. Saldana-Meyer, R. Jin, Y. Descostes, N. Stafford, J. M. Placantonakis, D. G. 2021-01-06 doi:10.1101/2021.01.06.425580 Cold Spring Harbor Laboratory Press 2021-01-06 <![CDATA[ An epigenetic switch regulates the ontogeny of AXL positive/EGFR-TKI resistant cells by modulating miR-335 expression ]]> https://biorxiv.org/content/10.1101/2021.01.06.425631v1?rss=1 Sordella, R. Pal, D. Safaric Tepes, P. Lindsted, T. Ibarra, I. Lujambio, A. Jimenez Sabinina, V. Senturk, S. Miller, M. Korimerla, N. Huang, J. Glassman, L. Lee, P. Zeltsman, D. Hyman, K. Esposito, M. Hannon, G. 2021-01-07 doi:10.1101/2021.01.06.425631 Cold Spring Harbor Laboratory Press 2021-01-07 <![CDATA[ Clr4SUV39H1 and Bdf2BRD4 ubiquitination mediate transcriptional silencing via heterochromatic phase transitions ]]> https://biorxiv.org/content/10.1101/2021.01.08.425919v1?rss=1 Kim, H.-S. Roche, B. Bhattacharjee, S. Todeschini, L. Chang, A.-Y. Hammell, C. Verdel, A. Martienssen, R. A. 2021-01-08 doi:10.1101/2021.01.08.425919 Cold Spring Harbor Laboratory Press 2021-01-08 <![CDATA[ Dicer promotes genome stability via the bromodomain transcriptional co-activator Brd4. ]]> https://biorxiv.org/content/10.1101/2021.01.08.425946v1?rss=1 Gutbrod, M. Roche, B. Steinberg, J. Lakhani, A. Chang, K. Schorn, A. Martienssen, R. A. 2021-01-08 doi:10.1101/2021.01.08.425946 Cold Spring Harbor Laboratory Press 2021-01-08 <![CDATA[ A Unified Probabilistic Modeling Framework for Eukaryotic Transcription Based on Nascent RNA Sequencing Data ]]> https://biorxiv.org/content/10.1101/2021.01.12.426408v1?rss=1 Siepel, A. 2021-01-14 doi:10.1101/2021.01.12.426408 Cold Spring Harbor Laboratory Press 2021-01-14 <![CDATA[ De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes ]]> https://biorxiv.org/content/10.1101/2021.01.14.426684v1?rss=1 Hufford, M. B. Seetharam, A. S. Woodhouse, M. R. Chougule, K. M. Ou, S. LIU, J. Ricci, W. A. Guo, T. Olson, A. Qiu, Y. Della Coletta, R. Tittes, S. Hudson, A. I. Marand, A. P. Wei, S. Lu, Z. Wang, B. Tello-Ruiz, M. K. Piri, R. D. Wang, N. Kim, D. w. Zeng, Y. O'Connor, C. H. Li, X. Gilbert, A. M. Baggs, E. Krasileva, K. V. Portwood, J. L. Cannon, E. K. Andorf, C. M. MANCHANDA, N. Snodgrass, S. J. Hufnagel, D. E. Jiang, Q. Pedersen, S. Syring, M. L. Kudrna, D. A. Llaca, V. Fengler, K. Schmitz, R. J. Ross-Ibarra, J. Yu, J. Gent, J. I. Hirsch, C. N. Ware 2021-01-16 doi:10.1101/2021.01.14.426684 Cold Spring Harbor Laboratory Press 2021-01-16 <![CDATA[ Teosinte introgression modulates phosphatidylcholine levels and induces early maize flowering time ]]> https://biorxiv.org/content/10.1101/2021.01.25.426574v1?rss=1 Rodriguez-Zapata, F. Barnes, A. C. Blocher-Juarez, K. A. Gates, D. J. Kur, A. Wang, L. Jensen, S. E. Estevez-Palmas, J. M. M. Janzen, G. M. Crow, T. M. Aguilar-Rangel, R. Demesa-Arevalo, E. Skopelitis, T. Perez-Limon, S. Stutts, W. L. Thomson, P. M. Chiu, Y.-C. Jackson, D. Fiehn, O. Runcie, D. Buckler, E. S. Ross-Ibarra, J. Hufford, M. Sawers, R. J. Rellan-Alvarez, R. 2021-01-26 doi:10.1101/2021.01.25.426574 Cold Spring Harbor Laboratory Press 2021-01-26 <![CDATA[ Deconvolution of Expression for Nascent RNA Sequencing Data (DENR) Highlights Pre-RNA Isoform Diversity in Human Cells ]]> https://biorxiv.org/content/10.1101/2021.03.16.435537v1?rss=1 200 genes whose dominant isoforms make use of different TSSs in these two cell types. Finally, we apply DENR and StringTie to newly generated PRO-seq and RNA-seq data, respectively, for human CD4+ T cells and CD14+ monocytes, and show that entropy at the pre-RNA level makes a disproportionate contribution to overall isoform diversity, especially across cell types. Altogether, DENR is the first computational tool to enable abundance quantification of pre-RNA isoforms based on nascent RNA sequencing data, and it reveals high levels of pre-RNA isoform diversity in human cells. ]]> Zhao, Y. Dukler, N. E. Barshad, G. Toneyan, S. Danko, C. G. Siepel, A. 2021-03-17 doi:10.1101/2021.03.16.435537 Cold Spring Harbor Laboratory Press 2021-03-17 <![CDATA[ PHAROH lncRNA regulates c-Myc translation in hepatocellular carcinoma via sequestering TIAR ]]> https://biorxiv.org/content/10.1101/2021.03.23.436634v1?rss=1 Yu, A. T. Berasain, C. Bhatia, S. Rivera, K. Liu, B. Rigo, F. Pappin, D. J. Spector, D. L. 2021-03-23 doi:10.1101/2021.03.23.436634 Cold Spring Harbor Laboratory Press 2021-03-23 <![CDATA[ The long non-coding RNA MaTAR20 promotes mammary tumor growth by regulating angiogenesis pathways ]]> https://biorxiv.org/content/10.1101/2021.03.30.437774v1?rss=1 Diermeier, S. D. Chang, K.-C. Frewen, A. Benz, B. A. Russo, S. Nowak, D. Hearn, S. Yu, A. Wilkinson, J. E. Rigo, F. Spector, D. 2021-03-31 doi:10.1101/2021.03.30.437774 Cold Spring Harbor Laboratory Press 2021-03-31 <![CDATA[ Precise and pervasive phasic bursting in locus coeruleus during maternal behavior ]]> https://biorxiv.org/content/10.1101/2021.03.31.437751v1?rss=1 Dvorkin, R. Shea, S. D. 2021-04-01 doi:10.1101/2021.03.31.437751 Cold Spring Harbor Laboratory Press 2021-04-01 <![CDATA[ Exploiting marker genes for robust classification and characterization of single-cell chromatin accessibility ]]> https://biorxiv.org/content/10.1101/2021.04.01.438068v1?rss=1 Kawaguchi, R. K. Tang, Z. Fischer, S. Tripathy, R. Koo, P. K. Gillis, J. 2021-04-03 doi:10.1101/2021.04.01.438068 Cold Spring Harbor Laboratory Press 2021-04-03 <![CDATA[ Promoter-sequence determinants and structural basis of primer-dependent transcription initiation in Escherichia coli ]]> https://biorxiv.org/content/10.1101/2021.04.06.438613v1?rss=1 Skalenko, K. S. Li, L. Zhang, Y. Vvedenskaya, I. O. Winkelman, J. T. Cope, A. Taylor, D. M. Shah, P. Ebright, R. H. Kinney, J. B. Zhang, Y. Nickels, B. E. 2021-04-07 doi:10.1101/2021.04.06.438613 Cold Spring Harbor Laboratory Press 2021-04-07 <![CDATA[ Maize RAMOSA3 accumulates in nuclear condensates enriched in RNA POLYMERASE II isoforms during the establishment of axillary meristem determinacy. ]]> https://biorxiv.org/content/10.1101/2021.04.06.438639v1?rss=1 Demesa-Arevalo, E. Abraham-Juarez, M. J. Xu, X. Bartlett, M. Jackson, D. 2021-04-06 doi:10.1101/2021.04.06.438639 Cold Spring Harbor Laboratory Press 2021-04-06 <![CDATA[ Mutation bias shapes the spectrum of adaptive substitutions ]]> https://biorxiv.org/content/10.1101/2021.04.14.438663v1?rss=1 V Cano, A. Rozhonova, H. Stoltzfus, A. McCandlish, D. M. Payne, J. L. 2021-04-15 doi:10.1101/2021.04.14.438663 Cold Spring Harbor Laboratory Press 2021-04-15 <![CDATA[ Meta-analytic markers reveal a generalizable description of cortical cell types ]]> https://biorxiv.org/content/10.1101/2021.04.16.439807v1?rss=1 Fischer, S. Gillis, J. 2021-04-16 doi:10.1101/2021.04.16.439807 Cold Spring Harbor Laboratory Press 2021-04-16 <![CDATA[ The UBAP2L ortholog PQN-59 contributes to stress granule assembly and development in C. elegans ]]> https://biorxiv.org/content/10.1101/2021.04.16.440123v1?rss=1 Abbatemarco, S. Bondaz, A. Schwager, F. Wang, J. Hammell, C. M. Gotta, M. 2021-04-16 doi:10.1101/2021.04.16.440123 Cold Spring Harbor Laboratory Press 2021-04-16 <![CDATA[ AGO104 is an RdDM effector of paramutation at the maize b1 locus ]]> https://biorxiv.org/content/10.1101/2021.04.21.440773v1?rss=1 AUBERT, J. BELLEGARDE, F. OLTEHUA-LOPEZ, O. LEBLANC, O. ARTEAGA-VAZQUEZ, M. A. MARTIENSSEN, R. A. GRIMANELLI, D. 2021-04-22 doi:10.1101/2021.04.21.440773 Cold Spring Harbor Laboratory Press 2021-04-22 <![CDATA[ Ground tissue circuitry regulates organ complexity in cereal roots ]]> https://biorxiv.org/content/10.1101/2021.04.28.441892v1?rss=1 Ortiz-Ramirez, C. H. Dias Araujo, P. C. Zhang, S. Demesa-Arevalo, E. Yan, Z. Xu, X. Rahni, R. Gingeras, T. R. Jackson, D. Gallagher, K. L. Birnbaum, K. D. 2021-04-29 doi:10.1101/2021.04.28.441892 Cold Spring Harbor Laboratory Press 2021-04-29 <![CDATA[ UBP12 and UBP13 deubiquitinases destabilize the CRY2 blue-light receptor to regulate growth ]]> https://biorxiv.org/content/10.1101/2021.04.29.441934v1?rss=1 Noren Lindback, L. Artz, O. Ackermann, A. Pedmale, U. V. 2021-04-29 doi:10.1101/2021.04.29.441934 Cold Spring Harbor Laboratory Press 2021-04-29 <![CDATA[ STARsolo: accurate, fast and versatile mapping/quantification of single-cell and single-nucleus RNA-seq data ]]> https://biorxiv.org/content/10.1101/2021.05.05.442755v1?rss=1 Kaminow, B. Yunusov, D. Dobin, A. 2021-05-05 doi:10.1101/2021.05.05.442755 Cold Spring Harbor Laboratory Press 2021-05-05 <![CDATA[ The SCP4-STK35/PDIK1L complex is a dual phospho-catalytic signaling dependency in acute myeloid leukemia ]]> https://biorxiv.org/content/10.1101/2021.05.09.443327v1?rss=1 Polyanskaya, S. A. Moreno, R. Y. Lu, B. Feng, R. Yao, Y. Irani, S. Klingbeil, O. Yang, Z. Wei, Y. Demerdash, O. E. Benjamin, L. A. Weiss, M. J. Zhang, Y. Vakoc, C. R. 2021-05-10 doi:10.1101/2021.05.09.443327 Cold Spring Harbor Laboratory Press 2021-05-10 <![CDATA[ Spatiotemporal 3D image registration for mesoscale studies of brain development. ]]> https://biorxiv.org/content/10.1101/2021.05.12.443839v1?rss=1 Shuvaev, S. Lazutkin, A. Kiryanov, R. Anokhin, K. Enikolopov, G. Koulakov, A. A. 2021-05-13 doi:10.1101/2021.05.12.443839 Cold Spring Harbor Laboratory Press 2021-05-13 <![CDATA[ Wiring logic of the early rodent olfactory system revealed by high-throughput sequencing of single neuron projections ]]> https://biorxiv.org/content/10.1101/2021.05.12.443929v1?rss=1 Chen, Y. Chen, X. Baserdem, B. Zhan, H. Li, Y. Davis, M. B. Kebschull, J. M. Zador, A. M. Koulakov, A. A. Albeanu, D. 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Steinmetz, N. A. Gieselmann, M. A. Thiele, A. Moore, T. Levina, A. Engel, T. A. 2021-05-18 doi:10.1101/2021.05.17.444537 Cold Spring Harbor Laboratory Press 2021-05-18 <![CDATA[ The cellular architecture of microvessels, pericytes and neuronal cell types in organizing regional brain energy homeostasis in mice ]]> https://biorxiv.org/content/10.1101/2021.05.19.444854v1?rss=1 Wu, Y.-t. Bennett, H. C. Chon, U. Vanselow, D. J. Zhang, Q. Munoz-Castaneda, R. Cheng, K. C. Osten, P. Drew, P. J. Kim, Y. 2021-05-21 doi:10.1101/2021.05.19.444854 Cold Spring Harbor Laboratory Press 2021-05-21 <![CDATA[ Prevalent and Dynamic Binding of the Cell Cycle Checkpoint Kinase Rad53 to Gene Promoters ]]> https://biorxiv.org/content/10.1101/2021.05.23.445333v1?rss=1 Sheu, Y.-J. Kawaguchi, R. K. Gillis, J. Stillman, B. 2021-05-23 doi:10.1101/2021.05.23.445333 Cold Spring Harbor Laboratory Press 2021-05-23 <![CDATA[ Sorghum Root Epigenetic Landscape During Limiting Phosphorus Conditions ]]> https://biorxiv.org/content/10.1101/2021.05.25.445633v1?rss=1 Gladman, N. P. Hufnagel, B. Regulski, M. Liu, Z. Wang, X. Chougule, K. Kochian, L. V. Magalhaes, J. Ware, D. 2021-05-25 doi:10.1101/2021.05.25.445633 Cold Spring Harbor Laboratory Press 2021-05-25 <![CDATA[ The genetic and epigenetic landscape of the Arabidopsis centromeres ]]> https://biorxiv.org/content/10.1101/2021.05.30.446350v1?rss=1 Naish, M. R. Alonge, M. Wlodzimierz, P. Tock, A. J. Abramson, B. W. Lambing, C. A. Kuo, P. Yelina, N. Hartwick, N. Colt, K. Kakutani, T. Martienssen, R. A. Bousios, A. Michael, T. P. Schatz, M. C. Henderson, I. 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Scheben, A. 2021-06-02 doi:10.1101/2021.06.01.446647 Cold Spring Harbor Laboratory Press 2021-06-02 <![CDATA[ Shade-induced WRKY transcription factors restrict root growth during the shade avoidance response ]]> https://biorxiv.org/content/10.1101/2021.06.01.446656v1?rss=1 Rosado, D. Ackermann, A. Spassibojko, O. Rossi, M. Pedmale, U. V. 2021-06-01 doi:10.1101/2021.06.01.446656 Cold Spring Harbor Laboratory Press 2021-06-01 <![CDATA[ Combustible and electronic cigarette exposures increase ACE2 activity and SARS-CoV-2 Spike binding ]]> https://biorxiv.org/content/10.1101/2021.06.04.447156v1?rss=1 Ghosh, A. Girish, V. Yuan, M. L. Coakley, R. D. Alexis, N. E. Sausville, E. L. Vasudevan, A. Chait, A. R. Sheltzer, J. M. Tarran, R. 2021-06-06 doi:10.1101/2021.06.04.447156 Cold Spring Harbor Laboratory Press 2021-06-06 <![CDATA[ Comparative Analysis of Sorghum EMS Mutants and Natural Populations ]]> https://biorxiv.org/content/10.1101/2021.06.06.447271v1?rss=1 Wang, L. 2021-06-07 doi:10.1101/2021.06.06.447271 Cold Spring Harbor Laboratory Press 2021-06-07 <![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[ Extensive protein dosage compensation in aneuploid human cancers ]]> https://biorxiv.org/content/10.1101/2021.06.18.449005v1?rss=1 Schukken, K. M. Sheltzer, J. M. 2021-06-18 doi:10.1101/2021.06.18.449005 Cold Spring Harbor Laboratory Press 2021-06-18 <![CDATA[ SIA: Selection Inference Using the Ancestral Recombination Graph ]]> https://biorxiv.org/content/10.1101/2021.06.22.449427v1?rss=1 Hejase, H. A. Mo, Z. Campagna, L. Siepel, A. 2021-06-23 doi:10.1101/2021.06.22.449427 Cold Spring Harbor Laboratory Press 2021-06-23 <![CDATA[ Gene-Specific Nonsense-Mediated mRNA Decay Targeting for Cystic Fibrosis Therapy ]]> https://biorxiv.org/content/10.1101/2021.07.13.452144v1?rss=1 Kim, Y. J. Nomakuchi, T. Papaleonidopoulou, F. Krainer, A. R. 2021-07-13 doi:10.1101/2021.07.13.452144 Cold Spring Harbor Laboratory Press 2021-07-13 <![CDATA[ Designing Interpretable Convolution-Based Hybrid Networks for Genomics ]]> https://biorxiv.org/content/10.1101/2021.07.13.452181v1?rss=1 Ghotra, R. S. Lee, N. K. Tripathy, R. Koo, P. 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Parent, J.-S. van Ex, F. Wolff, P. Martinez, G. Kohler, C. Martienssen, R. A. 2017-10-15 doi:10.1101/203612 Cold Spring Harbor Laboratory Press 2017-10-15 <![CDATA[ Combining CRISPR/Cas9 mutagenesis and a small-molecule inhibitor to probe the function of MELK in cancer ]]> https://biorxiv.org/content/10.1101/203984v1?rss=1 Giuliano, C. J. Lin, A. Smith, J. C. Palladino, A. C. Sheltzer, J. M. 2017-10-16 doi:10.1101/203984 Cold Spring Harbor Laboratory Press 2017-10-16 <![CDATA[ Barriers to Integration of Bioinformatics into Undergraduate Life Sciences Education ]]> https://biorxiv.org/content/10.1101/204420v1?rss=1 Williams, J. Drew, J. Galindo-Gonzalez, S. Robic, S. Dinsdale, E. Morgan, W. Triplett, E. Burnette, J. Donovan, S. Elgin, S. Fowlks, E. Goodman, A. Grandgenett, N. Goller, C. Hauser, C. Jungck, J. R. Newman, J. Pearson, W. Ryder, E. Wilson Sayres, M. Sierk, M. Smith, T. Tosado-Acevedo, R. Tapprich, W. Tobin, T. Toro-Martinez, A. Welch, L. Wright, R. Ebenbach, D. McWilliams, M. Rosenwald, A. Pauley, M. 2017-10-19 doi:10.1101/204420 Cold Spring Harbor Laboratory Press 2017-10-19 <![CDATA[ Allosteric activation dictates PRC2 activity independent of its recruitment to chromatin ]]> https://biorxiv.org/content/10.1101/206383v1?rss=1 Lee, C.-H. Yu, J.-R. Kumar, S. Jin, Y. Kaneko, S. Hamilton, A. D. Reinberg, D. 2017-10-20 doi:10.1101/206383 Cold Spring Harbor Laboratory Press 2017-10-20 <![CDATA[ Single-cell sequencing reveals αβ chain pairing shapes the T cell repertoire ]]> https://biorxiv.org/content/10.1101/213462v1?rss=1 Grigaityte, K. Carter, J. A. Goldfless, S. J. Jeffery, E. W. Hause, R. J. Jiang, Y. Koppstein, D. Briggs, A. W. Church, G. M. Vigneault, F. Atwal, G. S. 2017-11-02 doi:10.1101/213462 Cold Spring Harbor Laboratory Press 2017-11-02 <![CDATA[ Genetic Single Neuron Anatomy reveals fine granularity of cortical interneuron subtypes ]]> https://biorxiv.org/content/10.1101/219485v1?rss=1 Wang, X. Tucciarone, J. Jiang, S. Yin, F. 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Mora, T. 2017-12-11 doi:10.1101/232645 Cold Spring Harbor Laboratory Press 2017-12-11 <![CDATA[ Macrophage-derived granulin drives resistance to immune checkpoint inhibition in metastatic pancreatic cancer ]]> https://biorxiv.org/content/10.1101/234906v1?rss=1 Quaranta, V. Rainer, C. Nielsen, S. R. Raymant, M. Ahmed, M. S. Engle, D. Taylor, A. Murray, T. Campbell, F. Palmer, D. Tuveson, D. Mielgo, A. Schmid, M. 2017-12-15 doi:10.1101/234906 Cold Spring Harbor Laboratory Press 2017-12-15 <![CDATA[ A systematic approach for dissecting the molecular mechanisms of transcriptional regulation in bacteria ]]> https://biorxiv.org/content/10.1101/239335v1?rss=1 Belliveau, N. M. Barnes, S. L. Ireland, W. T. Jones, D. L. Sweredoski, M. Moradian, A. Hess, S. Kinney, J. B. Phillips, R. 2017-12-23 doi:10.1101/239335 Cold Spring Harbor Laboratory Press 2017-12-23 <![CDATA[ A computational framework for converting high-throughput DNA sequencing data into neural circuit connectivity. ]]> https://biorxiv.org/content/10.1101/244079v1?rss=1 Oyibo, H. Cao, C. Ferrante, D. D. Zhan, H. Koulakov, A. A. Enquist, L. Dubnau, J. Zador, A. 2018-01-07 doi:10.1101/244079 Cold Spring Harbor Laboratory Press 2018-01-07 <![CDATA[ Radial glial lineage progression and differential intermediate progenitor amplification underlie striatal compartments and circuit organization ]]> https://biorxiv.org/content/10.1101/244327v1?rss=1 Kelly, S. M. He, M. Lee, J. Kim, Y. Gibb, L. G. Wu, P. Matho, K. Osten, P. Graybiel, A. M. Huang, Z. J. 2018-01-08 doi:10.1101/244327 Cold Spring Harbor Laboratory Press 2018-01-08 <![CDATA[ Choice history biases subsequent evidence accumulation ]]> https://biorxiv.org/content/10.1101/251595v1?rss=1 Urai, A. E. de Gee, J. W. Donner, T. H. 2018-01-16 doi:10.1101/251595 Cold Spring Harbor Laboratory Press 2018-01-16 <![CDATA[ High precision automated detection of labelednuclei in terabyte-scale whole-brain volumetricimage data of mouse ]]> https://biorxiv.org/content/10.1101/252247v1?rss=1 Pahariya, G. Das, S. Jayakumar, J. Bannerjee, S. Vangala, V. Ram, K. Mitra, P. P. 2018-01-23 doi:10.1101/252247 Cold Spring Harbor Laboratory Press 2018-01-23 <![CDATA[ Primacy model and the evolution of the olfactory receptor repertoire ]]> https://biorxiv.org/content/10.1101/255661v1?rss=1 Giaffar, H. Rinberg, D. Koulakov, A. A. 2018-01-29 doi:10.1101/255661 Cold Spring Harbor Laboratory Press 2018-01-29 <![CDATA[ Mosaic representations of odors in the input and output layers of the mouse olfactory bulb ]]> https://biorxiv.org/content/10.1101/259945v1?rss=1 Chae, H. Kepple, D. Bast, W. G. Murthy, V. N. Koulakov, A. Albeanu, D. F. 2018-02-05 doi:10.1101/259945 Cold Spring Harbor Laboratory Press 2018-02-05 <![CDATA[ YAP1 Oncogene is a Context-specific Driver for Pancreatic Ductal Adenocarcinoma ]]> https://biorxiv.org/content/10.1101/270314v1?rss=1 Tu, B. Yao, W. Yao, J. Ferri-Borgogno, S. Chen, S. Wang, Q. Yan, L. Zhu, C. Bang, S. Chang, Q. Bristow, C. A. Kang, Y. Zheng, H. Wang, H. Fleming, J. B. Kim, M. Draetta, G. F. Pan, D. Maitra, A. Gupta, S. Ying, H. 2018-02-23 doi:10.1101/270314 Cold Spring Harbor Laboratory Press 2018-02-23 <![CDATA[ On variational solutions for whole brain serial-section histology using the computational anatomy random orbit model ]]> https://biorxiv.org/content/10.1101/271692v1?rss=1 Lee, B. C. Tward, D. J. Mitra, P. P. Miller, M. 2018-02-25 doi:10.1101/271692 Cold Spring Harbor Laboratory Press 2018-02-25 <![CDATA[ Inferring the shape of global epistasis ]]> https://biorxiv.org/content/10.1101/278630v1?rss=1 Otwinowski, J. McCandlish, D. M. Plotkin, J. 2018-03-08 doi:10.1101/278630 Cold Spring Harbor Laboratory Press 2018-03-08 <![CDATA[ T-cell receptor αβ chain pairing is associated with CD4+ and CD8+ lineage specification ]]> https://biorxiv.org/content/10.1101/293852v1?rss=1 Carter, J. A. Preall, J. B. Grigaityte, K. Goldfless, S. J. Briggs, A. W. Vigneault, F. Atwal, G. S. 2018-04-03 doi:10.1101/293852 Cold Spring Harbor Laboratory Press 2018-04-03 <![CDATA[ Spatial organization of projection neurons in the mouse auditory cortex identified by in situ barcode sequencing ]]> https://biorxiv.org/content/10.1101/294637v1?rss=1 Chen, X. Kebschull, J. M. Zhan, H. Sun, Y.-C. Zador, A. M. 2018-04-03 doi:10.1101/294637 Cold Spring Harbor Laboratory Press 2018-04-03 <![CDATA[ An optimized toolkit for precision base editing ]]> https://biorxiv.org/content/10.1101/303131v1?rss=1 Zafra, M. P. Schatoff, E. M. Katti, A. Foronda, M. Breinig, M. Schweitzer, A. Y. Simon, A. Han, T. Goswami, S. Montgomery, E. Thibado, J. Sanchez-Rivera, F. J. Shi, J. Vakoc, C. R. Lowe, S. W. Tschaharganeh, D. F. Dow, L. E. 2018-04-17 doi:10.1101/303131 Cold Spring Harbor Laboratory Press 2018-04-17 <![CDATA[ Movement-related activity dominates cortex during sensory-guided decision making ]]> https://biorxiv.org/content/10.1101/308288v1?rss=1 Musall, S. Kaufman, M. T. Gluf, S. Churchland, A. 2018-04-25 doi:10.1101/308288 Cold Spring Harbor Laboratory Press 2018-04-25 <![CDATA[ Olfactory marker protein regulates refinement of the glomerular map ]]> https://biorxiv.org/content/10.1101/309401v1?rss=1 Albeanu, D. F. Provost, A. C. Agarwal, P. Soucy, E. Murthy, V. N. 2018-05-01 doi:10.1101/309401 Cold Spring Harbor Laboratory Press 2018-05-01 <![CDATA[ Continuity between koniocellular layers of dorsal lateral geniculate and inferior pulvinar nuclei in common marmosets ]]> https://biorxiv.org/content/10.1101/315598v1?rss=1 Huo, B.-X. Zeater, N. Lin, M. K. Takahashi, Y. S. Hanada, M. Nagashima, J. Lee, B. C. Grunert, U. Miller, M. I. Rosa, M. Okano, H. Martin, P. R. Mitra, P. P. 2018-05-07 doi:10.1101/315598 Cold Spring Harbor Laboratory Press 2018-05-07 <![CDATA[ A High-throughput Neurohistological Pipeline for Brain-Wide Mesoscale Connectivity Mapping of the Common Marmoset ]]> https://biorxiv.org/content/10.1101/315804v1?rss=1 Lin, M. K. Takahashi, Y. S. Huo, B.-X. Hanada, M. Nagashima, J. Hata, J. Tolpygo, A. S. Ram, K. Lee, B. C. Miller, M. I. Rosa, M. G. P. Sasaki, E. Iriki, A. Okano, H. Mitra, P. P. 2018-05-08 doi:10.1101/315804 Cold Spring Harbor Laboratory Press 2018-05-08 <![CDATA[ How Much Information is Provided by Human Epigenomic Data? An Evolutionary View ]]> https://biorxiv.org/content/10.1101/317719v1?rss=1 Gulko, B. Siepel, A. 2018-05-09 doi:10.1101/317719 Cold Spring Harbor Laboratory Press 2018-05-09 <![CDATA[ Population coding of valence in the basolateral amygdala ]]> https://biorxiv.org/content/10.1101/321232v1?rss=1 Zhang, X. Li, B. 2018-05-13 doi:10.1101/321232 Cold Spring Harbor Laboratory Press 2018-05-13 <![CDATA[ Topological Skeletonization and Tree-Summarization of Neurons Using Discrete Morse Theory ]]> https://biorxiv.org/content/10.1101/321489v1?rss=1 Wang, S. Li, X. Mitra, P. Wang, Y. 2018-05-13 doi:10.1101/321489 Cold Spring Harbor Laboratory Press 2018-05-13 <![CDATA[ NECorr, a Tool to Rank Gene Importance in Biological Processes using Molecular Networks and Transcriptome Data ]]> https://biorxiv.org/content/10.1101/326868v1?rss=1 Liseron-Monfils, C. V. Olson, A. Ware, D. 2018-05-21 doi:10.1101/326868 Cold Spring Harbor Laboratory Press 2018-05-21 <![CDATA[ phastWeb: a web interface for evolutionary conservation scoring of multiple sequence alignments using phastCons and phyloP ]]> https://biorxiv.org/content/10.1101/327569v1?rss=1 Ramani, R. Krumholz, K. Huang, Y. Siepel, A. 2018-05-21 doi:10.1101/327569 Cold Spring Harbor Laboratory Press 2018-05-21 <![CDATA[ Mapping DNA sequence to transcription factor binding energy in vivo ]]> https://biorxiv.org/content/10.1101/331124v1?rss=1 Barnes, S. L. Belliveau, N. M. Ireland, W. T. Kinney, J. B. Phillips, R. 2018-05-25 doi:10.1101/331124 Cold Spring Harbor Laboratory Press 2018-05-25 <![CDATA[ Endoplasmic Reticulum Retention Motif Fused to Recombinant Anti-cancer Monoclonal Antibody (mAb) CO17-1A Affects mAb Expression and Plant Stress Response ]]> https://biorxiv.org/content/10.1101/335646v1?rss=1 Song, I. Kang, Y. J. Lee, Y. K. Myung, S.-c. Ko, K. 2018-05-31 doi:10.1101/335646 Cold Spring Harbor Laboratory Press 2018-05-31 <![CDATA[ Selection for protein stability enriches for epistatic interactions ]]> https://biorxiv.org/content/10.1101/338004v1?rss=1 Posfai, A. Zhou, J. Plotkin, J. B. Kinney, J. B. McCandlish, D. M. 2018-06-03 doi:10.1101/338004 Cold Spring Harbor Laboratory Press 2018-06-03 <![CDATA[ Computational algorithms and neural circuitry for compressed sensing in the mammalian main olfactory bulb ]]> https://biorxiv.org/content/10.1101/339689v1?rss=1 Kepple, D. Cazakoff, B. N. Demmer, H. S. Eckmeier, D. Shea, S. D. Koulakov, A. A. 2018-06-05 doi:10.1101/339689 Cold Spring Harbor Laboratory Press 2018-06-05 <![CDATA[ SVCollector: Optimized sample selection for validating and long-read resequencing of structural variants ]]> https://biorxiv.org/content/10.1101/342386v1?rss=1 Sedlazeck, F. J. Lemmon, Z. Soyk, S. Salerno, W. J. Lippman, Z. Schatz, M. C. 2018-06-08 doi:10.1101/342386 Cold Spring Harbor Laboratory Press 2018-06-08 <![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[ TEsmall identifies small RNAs associated with targeted inhibitor resistance in melanoma ]]> https://biorxiv.org/content/10.1101/359471v1?rss=1 O'Neill, K. Liao, W.-W. Patel, A. Gale Hammell, M. 2018-06-29 doi:10.1101/359471 Cold Spring Harbor Laboratory Press 2018-06-29 <![CDATA[ Loss of CG methylation in Marchantia polymorpha causes disorganization of cell division and reveals unique DNA methylation regulatory mechanisms of non-CG methylation. ]]> https://biorxiv.org/content/10.1101/363937v1?rss=1 Ikeda, Y. Nishihama, R. Yamaoka, S. Arteaga-Vazquez, M. A. Aguilar-Cruz, A. Grimanelli, D. Pogorelcnik, R. Martienssen, R. A. Yamato, K. T. Kohchi, T. Hirayama, T. Mathieu, O. 2018-07-09 doi:10.1101/363937 Cold Spring Harbor Laboratory Press 2018-07-09 <![CDATA[ Long term impact of intensive post graduate laboratory training at the Cold Spring Harbor Neurobiology of Drosophila summer course ]]> https://biorxiv.org/content/10.1101/369892v1?rss=1 Ly, S. Kaun, K. Li, C.-h. Stewart, D. Pulver, S. R. Keene, A. C. 2018-07-16 doi:10.1101/369892 Cold Spring Harbor Laboratory Press 2018-07-16 <![CDATA[ Distinct Cortical-Thalamic-Striatal Circuits Through the Parafascicular Nucleus ]]> https://biorxiv.org/content/10.1101/370734v1?rss=1 Mandelbaum, G. Taranda, J. Haynes, T. Hochbaum, D. Huang, K. W. Hyun, M. Venkataraju, K. U. Straub, C. Wang, W. Robertson, K. Osten, P. Sabatini, B. 2018-07-16 doi:10.1101/370734 Cold Spring Harbor Laboratory Press 2018-07-16 <![CDATA[ Unidirectional monosynaptic connections from auditory areas to the primary visual cortex in the marmoset monkey ]]> https://biorxiv.org/content/10.1101/373779v1?rss=1 Rosa, M. G. P. Majka, P. Bai, S. Chan, J. M. Huo, B.-X. Jermakow, N. Lin, M. K. Takahashi, Y. S. Wolkowicz, I. H. Worthy, K. H. Rajan, R. Reser, D. H. Wojcik, D. K. Okano, H. Mitra, P. P. 2018-07-20 doi:10.1101/373779 Cold Spring Harbor Laboratory Press 2018-07-20 <![CDATA[ Single-cell molecular connectomics of intracortically-projecting neurons ]]> https://biorxiv.org/content/10.1101/378760v1?rss=1 Klingler, E. Prados, J. Kebschull, J. M. Dayer, A. Zador, A. M. Jabaudon, D. 2018-07-27 doi:10.1101/378760 Cold Spring Harbor Laboratory Press 2018-07-27 <![CDATA[ Precision measurement of cis-regulatory energetics in living cells ]]> https://biorxiv.org/content/10.1101/380972v1?rss=1 Forcier, T. Ayaz, A. Gill, M. S. Jones, D. Phillips, R. Kinney, J. B. 2018-07-31 doi:10.1101/380972 Cold Spring Harbor Laboratory Press 2018-07-31 <![CDATA[ Delivery of GalNAc-conjugated splice-switching ASOs to non-hepatic cells through ectopic expression of asialoglycoprotein receptor ]]> https://biorxiv.org/content/10.1101/382606v1?rss=1 Scharner, J. Qi, S. Rigo, F. Bennett, C. F. Krainer, A. R. 2018-08-02 doi:10.1101/382606 Cold Spring Harbor Laboratory Press 2018-08-02 <![CDATA[ Cancer cell CCR2 orchestrates suppression of the adaptive immune response ]]> https://biorxiv.org/content/10.1101/390187v1?rss=1 Fein, M. R. He, X. Y. R. Almeida, A. S. Bruzas, E. S. Pommier, A. Eberhardt, A. Fearon, D. T. Wilkinson, J. E. dos Santos, C. O. Egeblad, M. 2018-08-13 doi:10.1101/390187 Cold Spring Harbor Laboratory Press 2018-08-13 <![CDATA[ Chronically-implanted Neuropixels probes enable high yield recordings in freely moving mice ]]> https://biorxiv.org/content/10.1101/406074v1?rss=1 Juavinett, A. L. Bekheet, G. Churchland, A. K. 2018-09-05 doi:10.1101/406074 Cold Spring Harbor Laboratory Press 2018-09-05 <![CDATA[ Dopaminergic and frontal signals for decisions guided by sensory evidence and reward value ]]> https://biorxiv.org/content/10.1101/411413v1?rss=1 Lak, A. Okun, M. Moss, M. Gurnani, H. Wells, M. J. Reddy, C. B. Harris, K. D. Carandini, M. 2018-09-07 doi:10.1101/411413 Cold Spring Harbor Laboratory Press 2018-09-07 <![CDATA[ Nuclear transcriptomes of the seven neuronal cell types that constitute the Drosophila mushroom bodies. ]]> https://biorxiv.org/content/10.1101/412569v1?rss=1 Shih, M.-F. M. Davis, F. P. Henry, G. L. Dubnau, J. 2018-09-10 doi:10.1101/412569 Cold Spring Harbor Laboratory Press 2018-09-10 <![CDATA[ High-throughput mapping of mesoscale connectomes in individual mice ]]> https://biorxiv.org/content/10.1101/422477v1?rss=1 Huang, L. Kebschull, J. Furth, D. Musall, S. Kaufman, M. T. Churchland, A. K. Zador, A. 2018-09-20 doi:10.1101/422477 Cold Spring Harbor Laboratory Press 2018-09-20 <![CDATA[ RegTools: Integrated analysis of genomic and transcriptomic data for discovery of splicing variants in cancer ]]> https://biorxiv.org/content/10.1101/436634v1?rss=1 Feng, Y.-Y. Ramu, A. Cotto, K. C. Skidmore, Z. L. Kunisaki, J. Conrad, D. F. Lin, Y. Chapman, W. Uppaulri, R. Govindan, R. Griffith, O. L. Griffith, M. 2018-10-05 doi:10.1101/436634 Cold Spring Harbor Laboratory Press 2018-10-05 <![CDATA[ Estimation of allele-specific fitness effects across human protein-coding sequences and implications for disease ]]> https://biorxiv.org/content/10.1101/441337v1?rss=1 Huang, Y.-F. Siepel, A. 2018-10-13 doi:10.1101/441337 Cold Spring Harbor Laboratory Press 2018-10-13 <![CDATA[ A brain network basis of Fragile X syndrome behavioral penetrance determined by X chromosome inactivation in female mice ]]> https://biorxiv.org/content/10.1101/458992v1?rss=1 Szelenyi, E. Fisenne, D. Knox, J. E. Harris, J. A. Gornet, J. A. Palaniswamy, R. Kim, Y. Venkataraju, K. U. Osten, P. 2018-11-02 doi:10.1101/458992 Cold Spring Harbor Laboratory Press 2018-11-02 <![CDATA[ DeepNose: Using artificial neural networks to represent the space of odorants ]]> https://biorxiv.org/content/10.1101/464735v1?rss=1 Tran, N. Kepple, D. Shuvaev, S. A. Koulakov, A. A. 2018-11-07 doi:10.1101/464735 Cold Spring Harbor Laboratory Press 2018-11-07 <![CDATA[ Detection of rare disease-related genetic variants using the birthday model ]]> https://biorxiv.org/content/10.1101/464842v1?rss=1 10,000) may improve statistical power to associate more variants, while the aggregation of distinct rare variants associated with a given disease can make the identification of causal genes statistically challenging. Therefore, new methods for rare variant association are imperative to identify causative genes of complex disorders.nnResultsHere we propose a method to predict causative rare variants using a popular probabilistic problem: The Birthday Model, which estimates the probability that multiple individuals in a group share the same birthday. We consider the probability and coincidence of samples sharing a variant akin to the chance of individuals sharing the same birthday. We investigated the parameter effects of our model, providing guidelines for its use and interpretation of the results. Using published data on autism spectrum disorder, hypertriglyceridemia in addition to a current case-control study on bipolar disorder, we evaluated this probabilistic method to identify potential causative variants. Several genes in the top results of the case-control study were associated with autism spectrum and bipolar disorder. Given that the core probability based on the birthday model is very sensitive to low recurrence, the method successfully tests the association of rare variants, which generally do not provide enough signal in commonly used statistical tests. Importantly, the simplicity of the model allows quick interpretation of genomic data, enabling users to select gene candidates for further biological validation of specific mutations and downstream functional or other studies.nnAvailabilityhttps://github.com/yberstein/Birthday-Alqorithm http://labshare.cshl.edu/shares/mccombielab/www-data/Birthday-Algorithm/Birthday-Alqorithm.htmlnnContactyberstei@cshl.edu (or yaelberstein@gmail.com)nnSupplementary informationSupplementary data are available online. ]]> Berstein, Y. McCarthy, S. E. Kramer, M. McCombie, W. R. 2018-11-07 doi:10.1101/464842 Cold Spring Harbor Laboratory Press 2018-11-07 <![CDATA[ SYNPLA: A synapse-specific method for identifying learning-induced synaptic plasticity loci ]]> https://biorxiv.org/content/10.1101/473314v1?rss=1 Dore, K. Pao, Y. Soria Lopez, J. Aronson, S. Zhan, H. Ghosh, S. Merrill, S. Zador, A. M. Malinow, R. Kebschull, J. M. 2018-11-19 doi:10.1101/473314 Cold Spring Harbor Laboratory Press 2018-11-19 <![CDATA[ Overly strong priors for socially meaningful visual signals in psychosis proneness ]]> https://biorxiv.org/content/10.1101/473421v1?rss=1 Stuke, H. Kress, E. Weilnhammer, V. A. Sterzer, P. Schmack, K. 2018-11-19 doi:10.1101/473421 Cold Spring Harbor Laboratory Press 2018-11-19 <![CDATA[ Diversity of GABAergic interneurons and diversification of communication modules in cortical networks ]]> https://biorxiv.org/content/10.1101/490797v1?rss=1 Huang, Z. J. Paul, A. 2018-12-08 doi:10.1101/490797 Cold Spring Harbor Laboratory Press 2018-12-08 <![CDATA[ Dynamics of microRNA expression during mouse prenatal development ]]> https://biorxiv.org/content/10.1101/492918v1?rss=1 Murad, R. Rahmanian, S. Breschi, A. Zeng, W. Williams, B. A. Mackiewicz, M. Roberts, B. Meadows, S. Moore, D. Davis, C. Trout, D. Zaleski, C. Dobin, A. Sei, L.-H. Drenkow, J. Scavelli, A. Gingeras, T. R. Wold, B. Myers, R. M. Guigo, R. Mortazavi, A. 2018-12-10 doi:10.1101/492918 Cold Spring Harbor Laboratory Press 2018-12-10 <![CDATA[ Fast and accurate reference-guided scaffolding of draft genomes ]]> https://biorxiv.org/content/10.1101/519637v1?rss=1 Alonge, M. Soyk, S. Ramakrishnan, S. Wang, X. Goodwin, S. Sedlazeck, F. J. Lippman, Z. B. Schatz, M. C. 2019-01-13 doi:10.1101/519637 Cold Spring Harbor Laboratory Press 2019-01-13 <![CDATA[ Is it time to change the reference genome? ]]> https://biorxiv.org/content/10.1101/533166v1?rss=1 Ballouz, S. Dobin, A. Gillis, J. 2019-01-29 doi:10.1101/533166 Cold Spring Harbor Laboratory Press 2019-01-29 <![CDATA[ Cell non-autonomous interactions during non-immune stromal progression in the breast tumor microenvironment ]]> https://biorxiv.org/content/10.1101/540112v1?rss=1 Utama, R. Bastian, A. Sadagopan, N. Jin, Y. Antoniou, E. Gao, Q. Huang, Y. J. Pillai, S. Lee, P. P. Atwal, G. S. 2019-02-04 doi:10.1101/540112 Cold Spring Harbor Laboratory Press 2019-02-04 <![CDATA[ Control of Shoot Meristem Size by an Aminoacyl tRNA Synthetase, OKI1, in Arabidopsis ]]> https://biorxiv.org/content/10.1101/548164v1?rss=1 Kitagawa, M. Balkunde, R. S. Bui, H. T. Jackson, D. S. 2019-02-13 doi:10.1101/548164 Cold Spring Harbor Laboratory Press 2019-02-13 <![CDATA[ Samovar: Single-sample mosaic SNV calling with linked reads ]]> https://biorxiv.org/content/10.1101/560532v1?rss=1 Darby, C. A. Fitch, J. R. Brennan, P. J. Kelly, B. J. Bir, N. Magrini, V. Leonard, J. Cottrell, C. E. Gastier-Foster, J. M. Wilson, R. K. Mardis, E. R. White, P. Langmead, B. Schatz, M. C. 2019-02-25 doi:10.1101/560532 Cold Spring Harbor Laboratory Press 2019-02-25 <![CDATA[ GCNA interacts with Spartan and Topoisomerase II to regulate genome stability. ]]> https://biorxiv.org/content/10.1101/570200v1?rss=1 Davis, G. M. Dokshin, G. Sawle, A. D. Eldridge, M. D. Romer, K. A. Gourley, T. E. Molesworth, L. W. Tatnell, H. R. Ozturk, A. R. de Rooij, D. G. Hannon, G. J. Page, D. C. Mello, C. C. Carmell, M. A. 2019-03-07 doi:10.1101/570200 Cold Spring Harbor Laboratory Press 2019-03-07 <![CDATA[ Postmortem Cortex Samples Identify Distinct Molecular Subtypes of ALS: Retrotransposon Activation, Oxidative Stress, and Activated Glia ]]> https://biorxiv.org/content/10.1101/574509v1?rss=1 Tam, O. Rozhkov, N. V. Shaw, R. Kim, D. Hubbard, I. Fennessey, S. Propp, N. The NYGC ALS Consortium, Fagegaltier, D. Ostrow, L. W. Phatnani, H. Ravits, J. Dubnau, J. Gale Hammell, M. 2019-03-11 doi:10.1101/574509 Cold Spring Harbor Laboratory Press 2019-03-11 <![CDATA[ High-resolution cryo-EM structures of outbreak strain human norovirus shells reveal size variations ]]> https://biorxiv.org/content/10.1101/580167v1?rss=1 Jung, J. Grant, T. Thomas, D. R. Diehnelt, C. W. Grigorieff, N. Joshua-Tor, L. 2019-03-16 doi:10.1101/580167 Cold Spring Harbor Laboratory Press 2019-03-16 <![CDATA[ The role of mutation bias in adaptive molecular evolution: insights from convergent changes in protein function ]]> https://biorxiv.org/content/10.1101/580175v1?rss=1 Storz, J. F. Natarajan, C. Signore, A. V. Witt, C. C. McCandlish, D. M. Stoltzfus, A. 2019-03-17 doi:10.1101/580175 Cold Spring Harbor Laboratory Press 2019-03-17 <![CDATA[ Discovery of ongoing selective sweeps within Anopheles mosquito populations using deep learning ]]> https://biorxiv.org/content/10.1101/589069v1?rss=1 Xue, A. T. Schrider, D. R. Kern, A. D. Ag1000G Consortium, 2019-03-28 doi:10.1101/589069 Cold Spring Harbor Laboratory Press 2019-03-28 <![CDATA[ Single chromosome gains can function as metastasis suppressors and metastasis promoters ]]> https://biorxiv.org/content/10.1101/590547v1?rss=1 Vasudevan, A. Baruah, P. S. Smith, J. C. Wang, Z. Sayles, N. M. Andrews, P. Kendall, J. Chunduri, N. K. Levy, D. Wigler, M. Storchova, Z. Sheltzer, J. M. 2019-03-27 doi:10.1101/590547 Cold Spring Harbor Laboratory Press 2019-03-27 <![CDATA[ Opposing contributions of GABAergic and glutamatergic ventral pallidal neurons to motivational behaviours ]]> https://biorxiv.org/content/10.1101/594887v1?rss=1 Stephenson-Jones, M. Bravo-Rivera, C. Ahrens, S. Furlan, A. Fernandes-Henriques, C. Li, B. 2019-03-31 doi:10.1101/594887 Cold Spring Harbor Laboratory Press 2019-03-31 <![CDATA[ Retinal and callosal activity-dependent chandelier cell elimination shapes binocularity in primary visual cortex ]]> https://biorxiv.org/content/10.1101/612358v1?rss=1 Wang, B.-S. Bernardez Sarria, M. S. He, M. Crair, M. C. Huang, Z. J. 2019-04-18 doi:10.1101/612358 Cold Spring Harbor Laboratory Press 2019-04-18 <![CDATA[ Lapses in perceptual judgments reflect exploration ]]> https://biorxiv.org/content/10.1101/613828v1?rss=1 Pisupati, S. Chartarifsky-Lynn, L. Khanal, A. Churchland, A. K. 2019-04-19 doi:10.1101/613828 Cold Spring Harbor Laboratory Press 2019-04-19 <![CDATA[ Tissue-specific Genome Editing in vivo by MicroRNA-repressible Anti-CRISPR Proteins ]]> https://biorxiv.org/content/10.1101/631689v1?rss=1 Lee, J. Mou, H. Ibraheim, R. Liang, S.-Q. Xue, W. Sontheimer, E. J. 2019-05-08 doi:10.1101/631689 Cold Spring Harbor Laboratory Press 2019-05-08 <![CDATA[ HYPER-sol: flash-frozen results from archival FFPE tissue for clinical proteomics ]]> https://biorxiv.org/content/10.1101/632315v1?rss=1 Marchione, D. M. Ilieva, I. Garcia, B. A. Pappin, D. J. Wilson, J. P. Wojcik, J. B. 2019-05-09 doi:10.1101/632315 Cold Spring Harbor Laboratory Press 2019-05-09 <![CDATA[ Differential functions of splicing factors in breast-cancer initiation and metastasis ]]> https://biorxiv.org/content/10.1101/634154v1?rss=1 Das, S. Akerman, M. Park, S. Brugioli, M. Geier, A. Kesarwani, A. K. Fan, M. Leclair, N. Urbanski, L. Lin, K.-T. Hu, C. Hua, X. George, J. Muthuswamy, S. K. Krainer, A. R. Anczukow, O. 2019-05-10 doi:10.1101/634154 Cold Spring Harbor Laboratory Press 2019-05-10 <![CDATA[ Logomaker: beautiful sequence logos in Python ]]> https://biorxiv.org/content/10.1101/635029v1?rss=1 Tareen, A. Kinney, J. B. 2019-05-13 doi:10.1101/635029 Cold Spring Harbor Laboratory Press 2019-05-13 <![CDATA[ The Salt-Inducible Kinase inhibitor YKL-05-099 suppresses MEF2C function and acute myeloid leukemia progression in vivo ]]> https://biorxiv.org/content/10.1101/636969v1?rss=1 Tarumoto, Y. Lin, S. Wang, J. Milazzo, J. Xu, Y. Gray, N. Stegmaier, K. Vakoc, C. 2019-05-14 doi:10.1101/636969 Cold Spring Harbor Laboratory Press 2019-05-14 <![CDATA[ Methods Matter -- Standard Production Platforms For Recombinant AAV Can Produce Chemically And Functionally Distinct Vectors ]]> https://biorxiv.org/content/10.1101/640169v1?rss=1 Rumachik, N. G. Malaker, S. A. Poweleit, N. Maynard, L. H. Adams, C. M. Leib, R. D. Cirolia, G. Thomas, D. Stamnes, S. Holt, K. Sinn, P. May, A. P. Paulk, N. K. 2019-05-17 doi:10.1101/640169 Cold Spring Harbor Laboratory Press 2019-05-17 <![CDATA[ In the presence of population structure: From genomics to candidate genes underlying local adaptation ]]> https://biorxiv.org/content/10.1101/642306v1?rss=1 Price, N. Lopez, L. Platts, A. E. E. Lasky, J. R. McKay, J. K. 2019-05-19 doi:10.1101/642306 Cold Spring Harbor Laboratory Press 2019-05-19 <![CDATA[ Pregnancy reprograms the enhancer landscape of mammary epithelial cells and alters the response to cMYC-driven oncogenesis ]]> https://biorxiv.org/content/10.1101/642330v1?rss=1 Feigman, M. J. Moss, M. A. Chen, C. Cyrill, S. L. Ciccone, M. Frey, W. D. Yang, S. T. Wilkinson, J. E. dos Santos, C. O. 2019-05-20 doi:10.1101/642330 Cold Spring Harbor Laboratory Press 2019-05-20 <![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[ Variant Phasing and Haplotypic Expression from Single-molecule Long-read Sequencing in Maize ]]> https://biorxiv.org/content/10.1101/654533v1?rss=1 Wang, B. Tseng, E. Baybayan, P. Eng, K. Regulski, M. Jiao, Y. Wang, L. Olson, A. Chougule, K. Van Buren, P. Ware, D. 2019-05-31 doi:10.1101/654533 Cold Spring Harbor Laboratory Press 2019-05-31 <![CDATA[ Double triage to identify poorly annotated genes in Maize: The missing link in community curation ]]> https://biorxiv.org/content/10.1101/654848v1?rss=1 Tello-Ruiz, M. K. Marco, C. F. Hsu, F.-M. Khangura, R. S. Qiao, P. Sapkota, S. Stitzer, M. C. Wasikowski, R. Wu, H. Zhan, J. Chougule, K. Barone, L. C. Ghiban, C. Muna, D. Olson, A. C. Wang, L. C. Ware, D. Micklos, D. A. 2019-06-05 doi:10.1101/654848 Cold Spring Harbor Laboratory Press 2019-06-05 <![CDATA[ Maternal experience-dependent cortical plasticity in mice is circuit- and stimulus-specific and requires Mecp2 ]]> https://biorxiv.org/content/10.1101/655035v1?rss=1 Lau, B. Y. B. Krishnan, K. Huang, Z. J. Shea, S. D. 2019-05-30 doi:10.1101/655035 Cold Spring Harbor Laboratory Press 2019-05-30 <![CDATA[ FAIRshake: toolkit to evaluate the findability, accessibility, interoperability, and reusability of research digital resources ]]> https://biorxiv.org/content/10.1101/657676v1?rss=1 Clark, D. J. B. Wang, L. Jones, A. Wojciechowicz, M. L. Torre, D. Jagodnik, K. M. Jenkins, S. L. McQuilton, P. Flamholz, Z. Silverstein, M. C. Schilder, B. M. Robasky, K. Castillo, C. Idaszak, R. Ahalt, S. C. Williams, J. J. Schurer, S. Cooper, D. J. de Miranda Azevedo, R. Klenk, J. A. Haendel, M. A. Nedzel, J. Avillach, P. Shimoyama, M. Harris, R. M. Gamble, M. Poten, R. Charbonneau, A. L. Larkin, J. Brown, C. T. Bonazzi, V. R. Dumontier, M. J. Assunta-Sansone, S. Ma'ayan, A. 2019-06-03 doi:10.1101/657676 Cold Spring Harbor Laboratory Press 2019-06-03 <![CDATA[ Minimum epistasis interpolation for sequence-function relationships ]]> https://biorxiv.org/content/10.1101/657841v1?rss=1 Zhou, J. McCandlish, D. M. 2019-06-02 doi:10.1101/657841 Cold Spring Harbor Laboratory Press 2019-06-02 <![CDATA[ Benchmarking Transposable Element Annotation Methods for Creation of a Streamlined, Comprehensive Pipeline ]]> https://biorxiv.org/content/10.1101/657890v1?rss=1 Ou, S. Su, W. Liao, Y. Chougule, K. Ware, D. Peterson, T. Jiang, N. Hirsch, C. N. Hufford, M. B. 2019-06-03 doi:10.1101/657890 Cold Spring Harbor Laboratory Press 2019-06-03 <![CDATA[ Bayesian inference of power law distributions ]]> https://biorxiv.org/content/10.1101/664243v1?rss=1 Atwal, G. S. Grigaityte, K. 2019-06-18 doi:10.1101/664243 Cold Spring Harbor Laboratory Press 2019-06-18 <![CDATA[ Complete single neuron reconstruction reveals morphological diversity in molecularly defined claustral and cortical neuron types ]]> https://biorxiv.org/content/10.1101/675280v1?rss=1 Wang, Y. Xie, P. Gong, H. Zhou, Z. Kuang, X. Wang, Y. Li, A.-a. Li, Y. Liu, L. Veldman, M. B. Daigle, T. L. Hirokawa, K. E. Qu, L. Lesnar, P. Jiang, S. Yu, Y. Wakeman, W. Zeng, S. Li, X. Yuan, J. Nguyen, T. N. Larsen, R. Kedebe, S. Song, Y. Yin, L. Zhao, S. Feiner, A. Shen, E. Hill, C. Wang, Q. Mok, S. Sunkin, S. M. Huang, Z. J. Esposito, L. Yao, Z. Hawrylycz, M. J. Tasic, B. Ng, L. Sorensen, S. A. Yang, X. W. Harris, J. A. Koch, C. Luo, Q. Peng, H. Zeng, H. 2019-06-20 doi:10.1101/675280 Cold Spring Harbor Laboratory Press 2019-06-20 <![CDATA[ Tankyrase inhibition sensitizes cells to CDK4 blockade ]]> https://biorxiv.org/content/10.1101/677823v1?rss=1 Foronda, M. Tarumoto, Y. Schatoff, E. M. Leach, B. I. Diaz, B. J. Goswami, S. Shusterman, M. Vakoc, C. R. Dow, L. 2019-06-21 doi:10.1101/677823 Cold Spring Harbor Laboratory Press 2019-06-21 <![CDATA[ Fractal dimension, occupancy and hotspot analyses of B cell spatial distribution predict clinical outcome in breast cancer ]]> https://biorxiv.org/content/10.1101/678607v1?rss=1 Wortman, J. C. He, T.-F. Solomon, S. Zhang, R. Z. Rosario, A. Wang, R. Tu, T. Y. Schmolze, D. Yuan, Y. Yost, S. E. Li, X. Levine, H. Atwal, G. Lee, P. P. Yu, C. C. 2019-06-21 doi:10.1101/678607 Cold Spring Harbor Laboratory Press 2019-06-21 <![CDATA[ Cyclin binding Cy motifs have multiple activities in the initiation of DNA replication ]]> https://biorxiv.org/content/10.1101/681668v1?rss=1 Hossain, M. Bhalla, K. Stillman, B. 2019-06-24 doi:10.1101/681668 Cold Spring Harbor Laboratory Press 2019-06-24 <![CDATA[ Evolutionary implementation of Bayesian computations ]]> https://biorxiv.org/content/10.1101/685842v1?rss=1 Czegel, D. Giaffar, H. Zachar, I. Szathmary, E. 2019-06-28 doi:10.1101/685842 Cold Spring Harbor Laboratory Press 2019-06-28 <![CDATA[ Mapping gene flow between ancient hominins through demography-aware inference of the ancestral recombination graph ]]> https://biorxiv.org/content/10.1101/687368v1?rss=1 Hubisz, M. J. Williams, A. L. Siepel, A. 2019-06-30 doi:10.1101/687368 Cold Spring Harbor Laboratory Press 2019-06-30 <![CDATA[ Characterizing RNA stability genome-wide through combined analysis of PRO-seq and RNA-seq data ]]> https://biorxiv.org/content/10.1101/690644v1?rss=1 Blumberg, A. Zhao, Y. Huang, Y.-F. Dukler, N. Rice, E. J. Krumholz, K. Danko, C. G. Siepel, A. 2019-07-02 doi:10.1101/690644 Cold Spring Harbor Laboratory Press 2019-07-02 <![CDATA[ Spatial Ecology of Territorial Populations ]]> https://biorxiv.org/content/10.1101/694257v1?rss=1 Weiner, B. G. Posfai, A. Wingreen, N. S. 2019-07-05 doi:10.1101/694257 Cold Spring Harbor Laboratory Press 2019-07-05 <![CDATA[ Pairwise tests for conditional selection use evolutionary logic to predict intrinsic drug resistance in ALK alterations ]]> https://biorxiv.org/content/10.1101/696294v1?rss=1 Inam, H. Pritchard, J. R. 2019-07-09 doi:10.1101/696294 Cold Spring Harbor Laboratory Press 2019-07-09 <![CDATA[ Distinct synchronization, cortical coupling and behavioural function of basal forebrain cholinergic neuron types ]]> https://biorxiv.org/content/10.1101/703090v1?rss=1 Laszlovszky, T. Schlingloff, D. Tamas, F. F. Gulyas, A. Kepecs, A. Hangya, B. 2019-07-17 doi:10.1101/703090 Cold Spring Harbor Laboratory Press 2019-07-17 <![CDATA[ Better tired than lost: turtle ant trail networks favor coherence over shortest paths ]]> https://biorxiv.org/content/10.1101/714410v1?rss=1 Chandrasekhar, A. Marshall, J. A. R. Austin, C. Navlakha, S. Gordon, D. M. 2019-07-26 doi:10.1101/714410 Cold Spring Harbor Laboratory Press 2019-07-26 <![CDATA[ Specialization of the Drosophila nuclear export family protein, Nxf3, for piRNA precursor export ]]> https://biorxiv.org/content/10.1101/716258v1?rss=1 Kneuss, E. Munafo, M. Eastwood, E. L. Deumer, U.-S. Preall, J. B. Hannon, G. J. Czech, B. 2019-07-26 doi:10.1101/716258 Cold Spring Harbor Laboratory Press 2019-07-26 <![CDATA[ A water-soluble, synthetic auxin analog for rapid degradation of target proteins during C. elegans development ]]> https://biorxiv.org/content/10.1101/716837v1?rss=1 Martinez, M. A. Kinney, B. A. Ashley, G. Ragle, J. M. Hammell, C. M. Ward, J. D. Matus, D. Q. 2019-07-27 doi:10.1101/716837 Cold Spring Harbor Laboratory Press 2019-07-27 <![CDATA[ In Situ Transcriptome Accessibility Sequencing (INSTA-seq) ]]> https://biorxiv.org/content/10.1101/722819v1?rss=1 Furth, D. Hatini, V. Lee, J. H. 2019-08-05 doi:10.1101/722819 Cold Spring Harbor Laboratory Press 2019-08-05 <![CDATA[ Multipotent radial glia progenitors and fate-restricted intermediate progenitors sequentially generate diverse cortical interneuron types ]]> https://biorxiv.org/content/10.1101/735019v1?rss=1 Kelly, S. M. Raudales, R. Moissidis, M. Kim, G. Huang, Z. J. 2019-08-15 doi:10.1101/735019 Cold Spring Harbor Laboratory Press 2019-08-15 <![CDATA[ Hingepoints and neural folds reveal conserved features of primary neurulation in the zebrafish forebrain ]]> https://biorxiv.org/content/10.1101/738161v1?rss=1 Werner, J. M. Negesse, M. Y. Brooks, D. L. Caldwell, A. R. Johnson, J. M. Brewster, R. 2019-08-16 doi:10.1101/738161 Cold Spring Harbor Laboratory Press 2019-08-16 <![CDATA[ Miswired enhancer logic drives translocation positive rhabdomyosarcoma ]]> https://biorxiv.org/content/10.1101/757369v1?rss=1 Gryder, B. E. Wachtel, M. Chang, K. Demerdash, O. E. Aboreden, N. G. Ewert, W. Pomella, S. Mohammed, W. Rota, R. Wei, J. S. Song, Y. Schaefer, B. Vakoc, C. R. Khan, J. 2019-09-04 doi:10.1101/757369 Cold Spring Harbor Laboratory Press 2019-09-04 <![CDATA[ Adeno-Associated Virus Technologies and Methods for Targeted Neuronal Manipulation ]]> https://biorxiv.org/content/10.1101/759936v1?rss=1 Haery, L. Deverman, B. E. Matho, K. Cetin, A. H. Woodard, K. Cepko, C. Guerin, K. I. Rego, M. A. Ersing, I. Bachle, S. M. Kamens, J. Fan, M. 2019-09-12 doi:10.1101/759936 Cold Spring Harbor Laboratory Press 2019-09-12 <![CDATA[ Fertility of Pedicellate Spikelets in Sorghum is Controlled by a Jasmonic Acid Regulatory Module ]]> https://biorxiv.org/content/10.1101/773564v1?rss=1 Gladman, N. P. Jiao, Y. Lee, Y. K. Zhang, L. Chopra, R. Regulski, M. Burow, G. Hayes, C. Christensen, S. A. Dampanaboina, L. Chen, J. Burke, J. Ware, D. Xin, Z. 2019-09-19 doi:10.1101/773564 Cold Spring Harbor Laboratory Press 2019-09-19 <![CDATA[ Phylogenetic modeling of regulatory element turnover based on epigenomic data ]]> https://biorxiv.org/content/10.1101/773614v1?rss=1 Dukler, N. E. Huang, Y.-F. Siepel, A. 2019-09-18 doi:10.1101/773614 Cold Spring Harbor Laboratory Press 2019-09-18 <![CDATA[ Transglutaminase-2 of pancreatic cancer cells assembles a CXCL12-keratin 19-coat that mediates the resistance to immunotherapy ]]> https://biorxiv.org/content/10.1101/776419v1?rss=1 Wang, Z. Li, J. Gao, Y. Janowitz, T. Fearon, D. 2019-09-19 doi:10.1101/776419 Cold Spring Harbor Laboratory Press 2019-09-19 <![CDATA[ Estrogen Drives Melanocortin Neurons To Reduce Sedentary Behavior ]]> https://biorxiv.org/content/10.1101/794792v1?rss=1 Krause, W. C. Rodriguez, R. Gegenhuber, J. B. Matharu, N. Rodriguez, A. N. Padilla, A. Herber, C. B. Correa, S. M. Ahituv, N. M. Tollkuhn, J. Ingraham, H. A. 2019-10-08 doi:10.1101/794792 Cold Spring Harbor Laboratory Press 2019-10-08 <![CDATA[ The maize heterotrimeric G-protein β subunit controls shoot meristem development and immune responses. ]]> https://biorxiv.org/content/10.1101/797985v1?rss=1 Wu, Q. Xu, F. Liu, L. Char, S. N. Ding, Y. Schmelz, E. A. Yang, B. Jackson, D. 2019-10-08 doi:10.1101/797985 Cold Spring Harbor Laboratory Press 2019-10-08 <![CDATA[ Social isolation uncovers a brain-wide circuit underlying context-dependent territory-covering micturition behavior ]]> https://biorxiv.org/content/10.1101/798132v1?rss=1 Hyun, M. Radeljic, G. Miner, L. Wang, W. Ochandarena, N. Huang, K. W. Osten, P. Sabatini, B. 2019-10-08 doi:10.1101/798132 Cold Spring Harbor Laboratory Press 2019-10-08 <![CDATA[ G-Graph: An interactive genomic graph viewer ]]> https://biorxiv.org/content/10.1101/803015v1?rss=1 Andrews, P. A. Alexander, J. Kendall, J. Wigler, M. 2019-11-18 doi:10.1101/803015 Cold Spring Harbor Laboratory Press 2019-11-18 <![CDATA[ Beyond generalization: Enhancing accurate interpretation of flexible models ]]> https://biorxiv.org/content/10.1101/808261v1?rss=1 Genkin, M. Engel, T. A. 2019-10-17 doi:10.1101/808261 Cold Spring Harbor Laboratory Press 2019-10-17 <![CDATA[ Data architecture and visualization for a large-scale neuroscience collaboration ]]> https://biorxiv.org/content/10.1101/827873v1?rss=1 The International Brain Laboratory, Bonacchi, N. Chapuis, G. Churchland, A. K. Harris, K. D. Rossant, C. Sasaki, M. Shen, S. Steinmetz, N. A. Walker, E. Y. Winter, O. Wells, M. 2019-11-02 doi:10.1101/827873 Cold Spring Harbor Laboratory Press 2019-11-02 <![CDATA[ Squamous trans-differentiation of pancreatic cancer cells promotes stromal inflammation ]]> https://biorxiv.org/content/10.1101/833046v1?rss=1 Somerville, T. Biffi, G. Dassler-Plenker, J. Miyabayashi, K. Xu, Y. Maia-Silva, D. Klingbeil, O. Demerdash, O. Egeblad, M. Tuveson, D. Vakoc, C. 2019-11-06 doi:10.1101/833046 Cold Spring Harbor Laboratory Press 2019-11-06 <![CDATA[ bioRxiv: the preprint server for biology ]]> https://biorxiv.org/content/10.1101/833400v1?rss=1 Sever, R. Roeder, T. Hindle, S. Sussman, L. Black, K.-J. Argentine, J. Manos, W. Inglis, J. R. 2019-11-06 doi:10.1101/833400 Cold Spring Harbor Laboratory Press 2019-11-06 <![CDATA[ Biophysical models of cis-regulation as interpretable neural networks ]]> https://biorxiv.org/content/10.1101/835942v1?rss=1 Tareen, A. Kinney, J. B. 2019-11-08 doi:10.1101/835942 Cold Spring Harbor Laboratory Press 2019-11-08 <![CDATA[ Promotion of hyperthermic-induced rDNA hypercondensation in Saccharomyces cerevisiae ]]> https://biorxiv.org/content/10.1101/838821v1?rss=1 Shen, D. Skibbens, R. V. 2019-11-12 doi:10.1101/838821 Cold Spring Harbor Laboratory Press 2019-11-12 <![CDATA[ qKW9 encodes a pentatricopeptide repeat protein affecting photosynthesis and grain filling in maize ]]> https://biorxiv.org/content/10.1101/847145v1?rss=1 Yan, J. Huang, J. Lu, G. Liu, L. Raihan, M. S. Xu, J. Jian, L. Zhao, L. Tran, T. M. Zhang, Q. Liu, J. Li, W. Wei, C. Braun, D. M. Li, Q. Fernie, A. R. Jackson, D. 2019-11-20 doi:10.1101/847145 Cold Spring Harbor Laboratory Press 2019-11-20 <![CDATA[ Comprehensive analysis of structural variants in breast cancer genomes using single molecule sequencing ]]> https://biorxiv.org/content/10.1101/847855v1?rss=1 Aganezov, S. Goodwin, S. Sherman, R. Sedlazeck, F. J. Arun, G. Bhatia, S. Lee, I. Kirsche, M. Wappel, R. Kramer, M. Kostroff, K. Spector, D. L. Timp, W. McCombie, W. R. Schatz, M. C. 2019-11-19 doi:10.1101/847855 Cold Spring Harbor Laboratory Press 2019-11-19 <![CDATA[ SciApps: A Cloud-Based Platform for Analyses and Distribution of the MaizeCODE data ]]> https://biorxiv.org/content/10.1101/852269v1?rss=1 Wang, L. 2019-11-23 doi:10.1101/852269 Cold Spring Harbor Laboratory Press 2019-11-23 <![CDATA[ A limited set of transcriptional programs define major histological types and provide the molecular basis for a cellular taxonomy of the human body ]]> https://biorxiv.org/content/10.1101/857169v1?rss=1 Breschi, A. Munoz-Aguirre, M. Wucher, V. Davis, C. A. Garrido-Martin, D. Djebali, S. Gillis, J. Pervouchine, D. D. Vlasova, A. Dobin, A. Zaleski, C. Drenkow, J. Danyko, C. Scavelli, A. Reverter, F. Snyder, M. P. Gingeras, T. R. Guigo, R. 2019-11-27 doi:10.1101/857169 Cold Spring Harbor Laboratory Press 2019-11-27 <![CDATA[ Structure and assembly of calcium homeostasis modulator proteins ]]> https://biorxiv.org/content/10.1101/857698v1?rss=1 Syrjanen, J. L. Michalski, K. Chou, T.-H. Grant, T. Rao, S. Simorowski, N. Tucker, S. J. Grigorieff, N. Furukawa, H. 2019-11-27 doi:10.1101/857698 Cold Spring Harbor Laboratory Press 2019-11-27 <![CDATA[ Effect of Sequence Depth and Length in Long-read Assembly of the Maize Inbred NC358 ]]> https://biorxiv.org/content/10.1101/858365v1?rss=1 Ou, S. LIU, J. Chougule, K. M. Fungtammasan, A. Seetharam, A. Stein, J. Llaca, V. MANCHANDA, N. Gilbert, A. M. Wei, X. Chin, C.-S. Hufnagel, D. E. Pedersen, S. Snodgrass, S. Fengler, K. Woodhouse, M. Walenz, B. P. Koren, S. Phillippy, A. M. Hannigan, B. T. Dawe, R. K. Hirsch, C. Hufford, M. Ware, D. 2019-11-29 doi:10.1101/858365 Cold Spring Harbor Laboratory Press 2019-11-29 <![CDATA[ Functional role of Polymerase IV during pollen development in Capsella ]]> https://biorxiv.org/content/10.1101/863522v1?rss=1 Wang, Z. Butel, N. Santos-Gonzalez, J. Borges, F. Yi, J. Martienssen, R. A. Martinez, G. Kohler, C. 2019-12-03 doi:10.1101/863522 Cold Spring Harbor Laboratory Press 2019-12-03 <![CDATA[ ZBED2 is an antagonist of Interferon Regulatory Factor 1 and modulates cell identity in pancreatic cancer ]]> https://biorxiv.org/content/10.1101/868141v1?rss=1 Somerville, T. Xu, Y. Wu, X. Vakoc, C. 2019-12-06 doi:10.1101/868141 Cold Spring Harbor Laboratory Press 2019-12-06 <![CDATA[ ACE: A Probabilistic Model for Characterizing Gene-Level Essentiality in CRISPR Screens ]]> https://biorxiv.org/content/10.1101/868919v1?rss=1 Hutton, E. Siepel, A. 2019-12-08 doi:10.1101/868919 Cold Spring Harbor Laboratory Press 2019-12-08 <![CDATA[ Human genetics and clinical aspects of neurodevelopmental disorders ]]> https://biorxiv.org/content/10.1101/000687v1?rss=1 Gholson J Lyon Jason O'Rawe 2013-11-18 doi:10.1101/000687 Cold Spring Harbor Laboratory Press 2013-11-18 <![CDATA[ Selective corticostriatal plasticity during acquisition of an auditory discrimination task ]]> https://biorxiv.org/content/10.1101/010066v1?rss=1 Qiaojie Xiong Petr Znamenskiy Anthony Zador 2014-10-06 doi:10.1101/010066 Cold Spring Harbor Laboratory Press 2014-10-06 <![CDATA[ A rapid and tunable method to temporally control Cas9 expression enables the identification of essential genes and the interrogation of functional gene interactions in vitro and in vivo. ]]> https://biorxiv.org/content/10.1101/023366v1?rss=1 Serif Senturk Nitin H Shirole Dawid D. Nowak Vincenzo Corbo Alexander Vaughan David A. Tuveson Lloyd C. Trotman Adam Kepecs Frank Stegmeier Raffaella Sordella 2015-07-28 doi:10.1101/023366 Cold Spring Harbor Laboratory Press 2015-07-28 <![CDATA[ A new Defective Helper RNA to produce Sindbis virus that infects neurons but does not propagate ]]> https://biorxiv.org/content/10.1101/033738v1?rss=1 Justus M Kebschull Pedro Garcia da Silva Anthony M Zador 2015-12-06 doi:10.1101/033738 Cold Spring Harbor Laboratory Press 2015-12-06 <![CDATA[ Effectors and potential targets selectively upregulated in human KRAS mutant lung adenocarcinomas ]]> https://biorxiv.org/content/10.1101/041137v1?rss=1 Jinyu Li Raffaella Sordella Scott Powers 2016-02-23 doi:10.1101/041137 Cold Spring Harbor Laboratory Press 2016-02-23 <![CDATA[ Proteomic and genomic characterization of a yeast model for Ogden syndrome ]]> https://biorxiv.org/content/10.1101/045047v1?rss=1 C (p.Ser37Pro) variant in NAA10. In the present study we performed in-depth characterization of a yeast model of Ogden syndrome. Stress tests and proteomic analyses suggest that the S37P mutation disrupts Naa10 function thereby reducing cellular fitness, possibly due to an impaired functionality of molecular chaperones, Hsp104, Hsp40 and the Hsp70 family. Microarray and RNA-seq revealed a pseudo-diploid gene expression profile in {Delta}Naa10 cells, likely responsible for a mating defect. In conclusion, the data presented here further support the disruptive nature of the S37P/Ogden mutation and identify affected cellular processes potentially contributing to the severe phenotype seen in Ogden syndrome. ]]> Max Doerfel Han Fang Jonathan Crain Michael E Klingener Jake Weiser Gholson J Lyon 2016-03-21 doi:10.1101/045047 Cold Spring Harbor Laboratory Press 2016-03-21 <![CDATA[ EGAD: Ultra-fast functional analysis of gene networks ]]> https://biorxiv.org/content/10.1101/053868v1?rss=1 Sara Ballouz Melanie Weber Paul Pavlidis Jesse Gillis 2016-05-17 doi:10.1101/053868 Cold Spring Harbor Laboratory Press 2016-05-17 <![CDATA[ A self-initiated two-alternative forced choice paradigm for head-fixed mice ]]> https://biorxiv.org/content/10.1101/073783v1?rss=1 Fred Marbach Anthony M Zador 2016-09-08 doi:10.1101/073783 Cold Spring Harbor Laboratory Press 2016-09-08 <![CDATA[ Using high-throughput barcode sequencing to efficiently map connectomes ]]> https://biorxiv.org/content/10.1101/099093v1?rss=1 Peikon, I. D. Kebschull, J. M. Vagin, V. V. Ravens, D. I. Brouzes, E. Correa, I. R. Bressan, D. Zador, A. 2017-01-09 doi:10.1101/099093 Cold Spring Harbor Laboratory Press 2017-01-09 <![CDATA[ Nascent RNA sequencing reveals a dynamic global transcriptional response at genes and enhancers to the natural medicinal compound celastrol ]]> https://biorxiv.org/content/10.1101/117689v1?rss=1 Dukler, N. Booth, G. T. Huang, Y.-F. Tippens, N. Danko, C. G. Lis, J. Siepel, A. 2017-03-16 doi:10.1101/117689 Cold Spring Harbor Laboratory Press 2017-03-16 <![CDATA[ De novo indels within introns contribute to ASD incidence ]]> https://biorxiv.org/content/10.1101/137471v1?rss=1 Munoz, A. Yamrom, B. Lee, Y.-h. Andrews, P. Marks, S. Lin, K.-T. Wang, Z. Krainer, A. R. Darnell, R. B. Wigler, M. Iossifov, I. 2017-05-24 doi:10.1101/137471 Cold Spring Harbor Laboratory Press 2017-05-24 <![CDATA[ A single-cell anatomical blueprint for intracortical information transfer from primary visual cortex ]]> https://biorxiv.org/content/10.1101/148031v1?rss=1 Han, Y. Kebschull, J. M. Campbell, R. A. A. Cowan, D. Imhof, F. Zador, A. M. Mrsic-Flogel, T. D. 2017-06-09 doi:10.1101/148031 Cold Spring Harbor Laboratory Press 2017-06-09 <![CDATA[ Regulation of HDAC2-PDX1 by RNF125 defines pancreatic cancer development ]]> https://biorxiv.org/content/10.1101/2020.01.06.896555v1?rss=1 Hasnis, E. Kim, H. Verma, S. Feng, Y. Almog, R. Matsliah, S. Vavinskaya, V. Alelbaum, R. Ben-Ishay, O. Tuveson, D. Sears, R. Ronai, Z. A. 2020-01-07 doi:10.1101/2020.01.06.896555 Cold Spring Harbor Laboratory Press 2020-01-07 <![CDATA[ Dissecting cell type-specific metabolism in pancreatic ductal adenocarcinoma ]]> https://biorxiv.org/content/10.1101/2020.03.09.984237v1?rss=1 Lau, A. N. Li, Z. Danai, L. V. Westermark, A. M. Darnell, A. M. Ferreira, R. Gocheva, V. Sivanand, S. Lien, E. C. Sapp, K. M. Mayers, J. R. Biffi, G. Chin, C. R. Davidson, S. M. Tuveson, D. A. Jacks, T. Matheson, N. J. Yilmaz, O. H. Vander Heiden, M. 2020-03-10 doi:10.1101/2020.03.09.984237 Cold Spring Harbor Laboratory Press 2020-03-10 <![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[ 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[ Encoding innate ability through a genomic bottleneck ]]> https://biorxiv.org/content/10.1101/2021.03.16.435261v1?rss=1 Koulakov, A. Shuvaev, S. Zador, A. 2021-03-16 doi:10.1101/2021.03.16.435261 Cold Spring Harbor Laboratory Press 2021-03-16 <![CDATA[ Multi-tissue integrative analysis of personal epigenomes ]]> https://biorxiv.org/content/10.1101/2021.04.26.441442v1?rss=1 10 assays in four donors (>1500 open-access functional genomic and proteomic datasets, in total). Each dataset is mapped to a matched, diploid personal genome, which has long-read phasing and structural variants. The mappings enable us to identify >1 million loci with allele-specific behavior. These loci exhibit coordinated epigenetic activity along haplotypes and less conservation than matched, non-allele-specific loci, in a fashion broadly paralleling tissue-specificity. Surprisingly, they can be accurately modelled just based on local nucleotide-sequence context. Combining EN-TEx with existing genome annotations reveals strong associations between allele-specific and GWAS loci and enables models for transferring known eQTLs to difficult-to-profile tissues. Overall, EN-TEx provides rich data and generalizable models for more accurate personal functional genomics. ]]> Rozowsky, J. Drenkow, J. Yang, Y. Gursoy, G. Galeev, T. Borsari, B. Epstein, C. Xiong, K. Xu, J. Gao, J. Yu, K. Berthel, A. Chen, Z. Navarro, F. Liu, J. Sun, M. Wright, J. Chang, J. Cameron, C. Shoresh, N. Gaskell, E. Adrian, J. Aganezov, S. Balderrama-Gutierrez, G. Banskota, S. Corona, G. Chee, S. Chhetri, S. Martins, G. Danyko, C. Davis, C. Farid, D. Farrell, N. Gabdank, I. Gofin, Y. Gorkin, D. Gu, M. Hecht, V. Hitz, B. Issner, R. Kirsche, M. Kong, X. Lam, B. Li, S. Li, B. Li, T. Li, X. Lin, K. Luo, R. Mackiewicz, M. Moore, J. Mudge, J. Nel 2021-04-26 doi:10.1101/2021.04.26.441442 Cold Spring Harbor Laboratory Press 2021-04-26 <![CDATA[ SAKE (Single-cell RNA-Seq Analysis and Klustering Evaluation) Identifies Markers of Resistance to Targeted BRAF Inhibitors in Melanoma Cell Populations ]]> https://biorxiv.org/content/10.1101/239319v1?rss=1 Ho, Y.-J. Anaparthy, N. Molik, D. Aicher, T. Patel, A. Hicks, J. Gale Hammell, M. 2017-12-24 doi:10.1101/239319 Cold Spring Harbor Laboratory Press 2017-12-24 <![CDATA[ A genetic, genomic, and computational resource for exploring neural circuit function ]]> https://biorxiv.org/content/10.1101/385476v1?rss=1 Davis, F. P. Nern, A. Picard, S. Reiser, M. B. Rubin, G. M. Eddy, S. R. Henry, G. L. 2018-08-05 doi:10.1101/385476 Cold Spring Harbor Laboratory Press 2018-08-05 <![CDATA[ PP2A inhibitor PME-1 suppresses anoikis, and is associated with therapy relapse of PTEN-deficient prostate cancers ]]> https://biorxiv.org/content/10.1101/581660v1?rss=1 Rupp, C. Aakula, A. Isomursu, A. Erickson, A. Kauko, O. Shah, P. Padzik, A. Kaur, A. Li, S.-P. Pokharel, Y. R. Trottman, L. Rannikko, A. Taimen, P. Lammerding, J. Paatero, I. Mirtti, T. Ivaska, J. Westermarck, J. 2019-03-18 doi:10.1101/581660 Cold Spring Harbor Laboratory Press 2019-03-18 <![CDATA[ A Critique of Pure Learning: What Artificial Neural Networks can Learn from Animal Brains ]]> https://biorxiv.org/content/10.1101/582643v1?rss=1 Zador, A. 2019-03-20 doi:10.1101/582643 Cold Spring Harbor Laboratory Press 2019-03-20 <![CDATA[ An engineered, orthogonal auxin analog/AtTIR1(F79G) pairing improves both specificity and efficacy of the auxin degradation system in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2021.08.06.455414v1?rss=1 Hiils-Muckey, K. Martinez, M. A. Q. Stec, N. Hebbar, S. Saldanha, J. Medwig-Kinney, T. N. Moore, F. E. Q. Ivanova, M. Moraro, A. Ward, J. D. Moss, E. G. Ercan, S. Zinovyeva, A. Matus, D. Q. Hammell, C. 2021-08-06 doi:10.1101/2021.08.06.455414 Cold Spring Harbor Laboratory Press 2021-08-06 <![CDATA[ Patient-derived triple negative breast cancer organoids provide robust model systems that recapitulate tumor intrinsic characteristics ]]> https://biorxiv.org/content/10.1101/2021.08.09.455691v1?rss=1 Bhatia, S. Kramer, M. Russo, S. Naik, P. Arun, G. Brophy, K. Andrews, P. A. Fan, C. Perou, C. M. Preall, J. Ha, T. Rishi, A. Wilkinson, J. E. McCombie, W. R. Kostroff, K. Spector, D. L. 2021-08-10 doi:10.1101/2021.08.09.455691 Cold Spring Harbor Laboratory Press 2021-08-10 <![CDATA[ Early neutrophilia marked by aerobic glycolysis sustains host metabolism and delays cancer cachexia ]]> https://biorxiv.org/content/10.1101/2021.08.11.455851v1?rss=1 Petruzzelli, M. Ferrer, M. Schuijs, M. Hall, Z. Perera, D. Raghunathan, S. Vacca, M. Gaude, E. Lukey, M. J. Jodrell, D. I. Frezza, C. Wagner, E. F. Janowitz, T. Halim, T. Y. F. Venkitaraman, A. R. 2021-08-11 doi:10.1101/2021.08.11.455851 Cold Spring Harbor Laboratory Press 2021-08-11 <![CDATA[ Exon-Skipping Antisense Oligonucleotides for Cystic Fibrosis Therapy ]]> https://biorxiv.org/content/10.1101/2021.08.11.455936v1?rss=1 Kim, Y. J. Sivetz, N. Layne, J. Voss, D. M. Yang, L. Zhang, Q. Krainer, A. R. 2021-08-11 doi:10.1101/2021.08.11.455936 Cold Spring Harbor Laboratory Press 2021-08-11 <![CDATA[ A Meta-Analytic Single-Cell Atlas of Mouse Bone Marrow Hematopoietic Development ]]> https://biorxiv.org/content/10.1101/2021.08.12.456098v1?rss=1 Harris, B. D. Lee, J. Gillis, J. 2021-08-12 doi:10.1101/2021.08.12.456098 Cold Spring Harbor Laboratory Press 2021-08-12 <![CDATA[ The cytokine receptor Fn14 regulates neuronal transcription during development and brain function in the adult ]]> https://biorxiv.org/content/10.1101/2021.08.16.456505v1?rss=1 Ferro, A. Vrudhula, U. Auguste, Y. S. S. Cheadle, L. 2021-08-16 doi:10.1101/2021.08.16.456505 Cold Spring Harbor Laboratory Press 2021-08-16 <![CDATA[ Excess dietary sugar impairs colonic epithelial regeneration in response to damage. ]]> https://biorxiv.org/content/10.1101/2021.08.18.456840v1?rss=1 Burr, A. Ji, J. Ozler, K. Eskiocak, O. Yueh, B. Menk, A. V. Costa, A. S. H. Rittenhouse, N. Marshall, C. W. Chiaranunt, P. Mullinax, L. Overacre-Delgoffe, A. Cooper, V. S. Poholek, A. C. Delgoffe, G. M. Beyaz, S. Hand, T. 2021-08-19 doi:10.1101/2021.08.18.456840 Cold Spring Harbor Laboratory Press 2021-08-19 <![CDATA[ Extreme purifying selection against point mutations in the human genome ]]> https://biorxiv.org/content/10.1101/2021.08.23.457339v1?rss=1 Dukler, N. Mughal, M. R. Ramani, R. Huang, Y.-F. Siepel, A. 2021-08-23 doi:10.1101/2021.08.23.457339 Cold Spring Harbor Laboratory Press 2021-08-23 <![CDATA[ Parity-induced changes to mammary epithelial cells control NKT cell expansion and mammary oncogenesis ]]> https://biorxiv.org/content/10.1101/2021.08.23.457350v1?rss=1 Hanasoge Somasundara, A. V. Moss, M. A. Feigman, M. J. Chen, C. Cyrill, S. L. Ciccone, M. F. Trousdell, M. C. Vollbrecht, M. Li, S. Kendall, J. Beyaz, S. Wilkinson, J. E. Dos Santos, C. O. 2021-08-24 doi:10.1101/2021.08.23.457350 Cold Spring Harbor Laboratory Press 2021-08-24 <![CDATA[ BRCA mutational status shapes the stromal microenvironment of pancreatic cancer linking CLU+ CAF expression with HSF1 signaling ]]> https://biorxiv.org/content/10.1101/2021.08.18.456576v1?rss=1 Shaashua, L. Pevsner-Fischer, M. Friedman, G. Levi-Galibov, O. Nandakumar, S. Nevo, R. Brown, L. E. Zhang, W. Stein, Y. Kim, H. S. Bojmar, L. Jarnagin, W. R. Lecomte, N. Stok, R. Bishara, H. Hamodi, R. Levy-Lahad, E. Golan, T. Porco, J. A. Iacobuzio-Donahue, C. A. Schultz, N. Lyden, D. Tuveson, D. Kelsen, D. Scherz-Shouval, R. 2021-08-19 doi:10.1101/2021.08.18.456576 Cold Spring Harbor Laboratory Press 2021-08-19 <![CDATA[ FoxA1 and FoxA2 regulate growth and cellular identity in NKX2-1-positive lung adenocarcinoma ]]> https://biorxiv.org/content/10.1101/2021.06.29.450247v1?rss=1 Orstad, G. Jones, A. Lohman, B. Gillis, K. L. Snyder, E. L. 2021-06-29 doi:10.1101/2021.06.29.450247 Cold Spring Harbor Laboratory Press 2021-06-29 <![CDATA[ Contiguously-hydrophobic sequences are functionally significant throughout the human exome ]]> https://biorxiv.org/content/10.1101/2021.09.02.458776v1?rss=1 Lohia, R. Hansen, M. E. Brannigan, G. H. 2021-09-04 doi:10.1101/2021.09.02.458776 Cold Spring Harbor Laboratory Press 2021-09-04 <![CDATA[ Defining the extent of gene function using ROC curvature ]]> https://biorxiv.org/content/10.1101/2021.09.03.458825v1?rss=1 Fischer, S. Gillis, J. 2021-09-05 doi:10.1101/2021.09.03.458825 Cold Spring Harbor Laboratory Press 2021-09-05 <![CDATA[ Recruitment of an ancient branching program to suppress carpel development in maize flowers ]]> https://biorxiv.org/content/10.1101/2021.09.03.458935v1?rss=1 Klein, H. Gallagher, J. P. Demesa-Arevalo, E. Abraham-Juarez, M. J. Heeney, M. Feil, R. Lunn, J. E. Xiao, Y. Chuck, G. S. Whipple, C. J. Jackson, D. Bartlett, M. E. 2021-09-04 doi:10.1101/2021.09.03.458935 Cold Spring Harbor Laboratory Press 2021-09-04 <![CDATA[ tascCODA: Bayesian tree-aggregated analysis of compositional amplicon and single-cell data ]]> https://biorxiv.org/content/10.1101/2021.09.06.459120v1?rss=1 Ostner, J. Carcy, S. Müller, C. L. 2021-09-06 doi:10.1101/2021.09.06.459120 Cold Spring Harbor Laboratory Press 2021-09-06 <![CDATA[ Cross-tissue analysis of allelic X-chromosome inactivation ratios resolves features of human development ]]> https://biorxiv.org/content/10.1101/2021.09.13.460075v1?rss=1 Werner, J. M. Ballouz, S. Hover, J. Gillis, J. 2021-09-14 doi:10.1101/2021.09.13.460075 Cold Spring Harbor Laboratory Press 2021-09-14 <![CDATA[ Nitrogen partitioning between branched-chain amino acids and urea cycle enzymes sustains renal cancer progression ]]> https://biorxiv.org/content/10.1101/2021.09.17.460635v1?rss=1 Sciacovelli, M. Dugourd, A. Valcarcel Jimenez, L. Yang, M. Nikitopoulou, E. Costa, A. S. Tronci, L. Caraffini, V. Rodrigues, P. Schmidt, C. Ryan, D. G. Young, T. Zecchini, V. Rossi, S. H. Massie, C. Lohoff, C. Masid, M. Hatzimanikatis, V. Kuppe, C. Von Kriegsheim, A. Kramann, R. Gnanapragasam, V. Warren, A. Y. Stewart, G. D. Erez, A. Vanharanta, S. Saez-Rodriguez, J. Frezza, C. 2021-09-18 doi:10.1101/2021.09.17.460635 Cold Spring Harbor Laboratory Press 2021-09-18 <![CDATA[ Towards a combined therapy for spinal muscular atrophy based on opposing effects of an antisense oligonucleotide on chromatin and splicing ]]> https://biorxiv.org/content/10.1101/2021.09.24.461646v1?rss=1 Marasco, L. E. Dujardin, G. Sousa-Luis, R. Hsiu Liu, Y. Stigliano, J. Nomakuchi, T. Proudfoot, N. R. Krainer, A. Kornblihtt, A. R. 2021-09-24 doi:10.1101/2021.09.24.461646 Cold Spring Harbor Laboratory Press 2021-09-24 <![CDATA[ Pyramidal cell types drive functionally distinct cortical activity patterns during decision-making ]]> https://biorxiv.org/content/10.1101/2021.09.27.461599v1?rss=1 Musall, S. Sun, X. R. Mohan, H. An, X. Gluf, S. Churchland, A. K. 2021-09-27 doi:10.1101/2021.09.27.461599 Cold Spring Harbor Laboratory Press 2021-09-27 <![CDATA[ Loss of KRASG12D feedback regulation involving splicing factor SRSF1 accelerates pancreatic cancer ]]> https://biorxiv.org/content/10.1101/2021.10.13.464210v1?rss=1 Wan, L. Lin, K.-T. Rahman, M. A. Wang, Z. Jensen, M. A. Park, Y. Tuveson, D. A. Krainer, A. R. 2021-10-13 doi:10.1101/2021.10.13.464210 Cold Spring Harbor Laboratory Press 2021-10-13 <![CDATA[ End-to-end learning of multiple sequence alignments with differentiable Smith-Waterman ]]> https://biorxiv.org/content/10.1101/2021.10.23.465204v1?rss=1 Petti, S. Bhattacharya, N. Rao, R. Dauparas, J. Thomas, N. Zhou, J. Rush, A. M. Koo, P. K. Ovchinnikov, S. 2021-10-24 doi:10.1101/2021.10.23.465204 Cold Spring Harbor Laboratory Press 2021-10-24 <![CDATA[ Balancing memory fidelity and representational stability in the female mouse accessory olfactory bulb ]]> https://biorxiv.org/content/10.1101/2021.10.27.466073v1?rss=1 Yoles-Frenkel, M. Shea, S. D. Davison, I. G. Ben-Shaul, Y. 2021-10-28 doi:10.1101/2021.10.27.466073 Cold Spring Harbor Laboratory Press 2021-10-28 <![CDATA[ Prostate tumor-induced stromal reprogramming generates Tenascin C that promotes prostate cancer metastasis through YAP/TAZ inhibition ]]> https://biorxiv.org/content/10.1101/2021.11.08.467778v1?rss=1 Lin, S.-H. Lee, Y.-C. Lin, S.-C. Yu, G. Zhu, M. Song, J. H. Rivera, K. Pappin, D. J. Logothetis, C. J. Panaretakis, T. Wang, G. Yu-Lee, L.-y. 2021-11-08 doi:10.1101/2021.11.08.467778 Cold Spring Harbor Laboratory Press 2021-11-08 <![CDATA[ PTP1B is an intracellular checkpoint that limits T cell and CAR T cell anti-tumor immunity ]]> https://biorxiv.org/content/10.1101/2021.11.11.468140v1?rss=1 Wiede, F. Lu, K.-H. Du, X. Zessig, M. Xu, R. Goh, P. K. Xirouchaki, C. Hogarth, S. Greatorex, S. Sek, K. Daly, R. Beavis, P. Darcy, P. Tonks, N. Tiganis, T. 2021-11-12 doi:10.1101/2021.11.11.468140 Cold Spring Harbor Laboratory Press 2021-11-12 <![CDATA[ Automated assembly scaffolding elevates a new tomato system for high-throughput genome editing ]]> https://biorxiv.org/content/10.1101/2021.11.18.469135v1?rss=1 Alonge, M. Lebeigle, L. Kirsche, M. Aganezov, S. Wang, X. Lippman, Z. B. Schatz, M. C. Soyk, S. 2021-11-19 doi:10.1101/2021.11.18.469135 Cold Spring Harbor Laboratory Press 2021-11-19 <![CDATA[ Particle-associated and free-living microbial assemblages are distinct in a permanently redox-stratified freshwater lake ]]> https://biorxiv.org/content/10.1101/2021.11.24.469905v1?rss=1 2.7 {micro}m and 0.2 - 2.7 {micro}m) were surveyed at the peak (July) and end (October) of concurrent cyanobacteria, purple and green sulfur bacteria blooms that result in substantial vertical fluxes of particulate organic carbon. Assemblage compositions varied significantly among redox conditions and size fractions (PA or FL). Temporal differences were only apparent among samples from the mixolimnion and oxycline, coinciding with seasonal hydrographic changes. PA assemblages of the mixolimnion and oxycline shifted from aerobic heterotrophs in July to fermenters, iron-reducers, and denitrifiers in October, likely reflecting seasonal variability in photoautotroph biomass and inorganic nitrogen. Within a light-scattering layer spanning the lower oxycline and upper monimolimnion, photoautotrophs were more abundant in July than in October, when Desulfocapsa, a sulfate-reducing and sulfur-disproportionating bacterium, and Chlorophyte chloroplasts were abundant in PA assemblages. In this layer, microbial activity and cell concentrations were also highest. Below, the most abundant resident taxa were sulfate-reducing bacteria and anaerobic respirers. Results suggest PA and FL assemblage niche partitioning interconnects multiple elemental cycles that involve particulate and dissolved phases. ]]> Cohen, A. B. Klepac-Ceraj, V. Butler, K. Weber, F. Garber, A. I. Christensen, L. N. Cram, J. A. McCormick, M. L. Taylor, G. T. 2021-11-25 doi:10.1101/2021.11.24.469905 Cold Spring Harbor Laboratory Press 2021-11-25 <![CDATA[ Asking the Wrong Questions About American Science Education: Insights from a Longitudinal Study of High School Biotechnology Lab Instruction ]]> https://biorxiv.org/content/10.1101/2021.11.29.470152v1?rss=1 Micklos, D. Barone, L. 2021-11-29 doi:10.1101/2021.11.29.470152 Cold Spring Harbor Laboratory Press 2021-11-29 <![CDATA[ A shape-shifting nuclease unravels structured RNA ]]> https://biorxiv.org/content/10.1101/2021.11.30.470623v1?rss=1 Meze, K. Axhemi, A. Thomas, D. R. Doymaz, A. Joshua-Tor, L. 2021-11-30 doi:10.1101/2021.11.30.470623 Cold Spring Harbor Laboratory Press 2021-11-30 <![CDATA[ Accurate measurement of microsatellite length by disrupting its tandem repeat structure ]]> https://biorxiv.org/content/10.1101/2021.12.09.471828v1?rss=1 Levy, D. Wang, Z. Moffitt, A. Wigler, M. H. 2021-12-10 doi:10.1101/2021.12.09.471828 Cold Spring Harbor Laboratory Press 2021-12-10 <![CDATA[ Prefrontal top-down projections control context-dependent strategy selection ]]> https://biorxiv.org/content/10.1101/2021.12.14.472559v1?rss=1 Gschwend, O. Yang, T. van de Lisdonk, D. Zhang, X. Sharma, R. Li, B. 2021-12-15 doi:10.1101/2021.12.14.472559 Cold Spring Harbor Laboratory Press 2021-12-15 <![CDATA[ Cortical glutamatergic projection neuron types contribute to distinct functional subnetworks ]]> https://biorxiv.org/content/10.1101/2021.12.30.474537v1?rss=1 Mohan, H. An, X. Kondo, H. Zhao, S. Musall, S. Mitra, P. P. Huang, J. Z. 2021-12-30 doi:10.1101/2021.12.30.474537 Cold Spring Harbor Laboratory Press 2021-12-30 <![CDATA[ Loss of p53 tumor suppression function drives invasion and genomic instability in models of murine pancreatic cancer ]]> https://biorxiv.org/content/10.1101/2021.12.31.472823v1?rss=1 Tonelli, C. Deschenes, A. Yao, M. A. Park, Y. Tuveson, D. A. 2022-01-01 doi:10.1101/2021.12.31.472823 Cold Spring Harbor Laboratory Press 2022-01-01 <![CDATA[ Dynamic evolution of small signaling peptide compensation in plant stem cell control ]]> https://biorxiv.org/content/10.1101/2022.01.03.474791v1?rss=1 Kwon, C.-T. Tang, L. Wang, X. Gentile, I. Hendelman, A. Robitaille, G. Van Eck, J. Xu, C. Lippman, Z. 2022-01-03 doi:10.1101/2022.01.03.474791 Cold Spring Harbor Laboratory Press 2022-01-03 <![CDATA[ Target binding triggers hierarchical phosphorylation of human Argonaute-2 to promote target release ]]> https://biorxiv.org/content/10.1101/2022.01.06.475261v1?rss=1 Bibel, B. Elkayam, E. Silletti, S. Komives, E. A. Joshua-Tor, L. 2022-01-06 doi:10.1101/2022.01.06.475261 Cold Spring Harbor Laboratory Press 2022-01-06 <![CDATA[ Systematic histone H4 replacement in Arabidopsis thaliana reveals a role for H4R17 in regulating flowering time ]]> https://biorxiv.org/content/10.1101/2022.01.17.476649v1?rss=1 Corcoran, E. T. LeBlanc, C. Arias Tsang, M. Sarkiss, A. Hu, Y. Pedmale, U. V. Jacob, Y. 2022-01-18 doi:10.1101/2022.01.17.476649 Cold Spring Harbor Laboratory Press 2022-01-18 <![CDATA[ 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[ Do place cells dream of deceptive moves in a signaling game? ]]> https://biorxiv.org/content/10.1101/2022.01.30.478398v1?rss=1 Fenton, A. A. Hurtado, J. R. Broek, J. A. C. PARK, E. H. Mishra, B. 2022-01-31 doi:10.1101/2022.01.30.478398 Cold Spring Harbor Laboratory Press 2022-01-31 <![CDATA[ Structural and mechanistic basis of σ-dependent transcriptional pausing ]]> https://biorxiv.org/content/10.1101/2022.01.24.477500v1?rss=1 Pukhrambam, C. Molodtsov, V. Kooshkbaghi, M. Tareen, A. Vu, H. Skalenko, K. S. Su, M. Zhou, Y. Winkelman, J. T. Kinney, J. B. Ebright, R. H. Nickels, B. E. 2022-01-25 doi:10.1101/2022.01.24.477500 Cold Spring Harbor Laboratory Press 2022-01-25 <![CDATA[ Two roles for choice selective inhibition in decision-making circuits ]]> https://biorxiv.org/content/10.1101/2022.01.24.477635v1?rss=1 Roach, J. P. Churchland, A. K. Engel, T. A. 2022-01-25 doi:10.1101/2022.01.24.477635 Cold Spring Harbor Laboratory Press 2022-01-25 <![CDATA[ Autosomal monoallelic genes are differentially regulated based on parental origin ]]> https://biorxiv.org/content/10.1101/2022.02.01.478691v1?rss=1 Balasooriya, G. I. Spector, D. L. 2022-02-02 doi:10.1101/2022.02.01.478691 Cold Spring Harbor Laboratory Press 2022-02-02 <![CDATA[ Accurate and robust inference of genetic ancestry from cancer-derived molecular data across genomic platforms ]]> https://biorxiv.org/content/10.1101/2022.02.01.478737v1?rss=1 Belleau, P. Deschenes, A. Tuveson, D. A. Krasnitz, A. 2022-02-04 doi:10.1101/2022.02.01.478737 Cold Spring Harbor Laboratory Press 2022-02-04 <![CDATA[ ACME: an Affinity-based Cas9 Mediated Enrichment method for targeted nanopore sequencing ]]> https://biorxiv.org/content/10.1101/2022.02.03.478550v1?rss=1 60-fold target enrichment, close to 70x coverage, and 3-20 reads spanning the entire 95kb target. We observed an increase in enrichment, depth, and number of whole gene spanning reads for other genes on the panel as well across both cell lines, with enrichment as high as 4000-fold for some genes. Furthermore, ACME identified all SVs previously called within our targets by ONT and PacBio whole genome sequencing and performed on par with these platforms for SNP detection when compared with Illumina short-read whole genome sequencing. ]]> Iyer, S. V. Kramer, M. Goodwin, S. McCombie, W. R. 2022-02-04 doi:10.1101/2022.02.03.478550 Cold Spring Harbor Laboratory Press 2022-02-04 <![CDATA[ Oligodendrocyte precursor cells engulf synaptic inputs in an experience- and microglia-dependent manner ]]> https://biorxiv.org/content/10.1101/2022.02.10.479887v1?rss=1 Auguste, Y. S. S. Ferro, A. Dixon, J. Vrudhula, U. Kahng, J. Nichitiu, A.-S. Cheadle, L. 2022-02-10 doi:10.1101/2022.02.10.479887 Cold Spring Harbor Laboratory Press 2022-02-10 <![CDATA[ Multisensory integration of social signals by a pathway from the basal amygdala to the auditory cortex in maternal mice ]]> https://biorxiv.org/content/10.1101/2022.02.17.480854v1?rss=1 Nowlan, A. C. Kelahan, C. Shea, S. D. 2022-02-17 doi:10.1101/2022.02.17.480854 Cold Spring Harbor Laboratory Press 2022-02-17 <![CDATA[ Excitatory and inhibitory D-serine binding to the NMDA receptor ]]> https://biorxiv.org/content/10.1101/2022.03.07.483247v1?rss=1 Yovanno, R. A. Chou, T. H. Brantley, S. J. Furukawa, H. Lau, A. Y. 2022-03-08 doi:10.1101/2022.03.07.483247 Cold Spring Harbor Laboratory Press 2022-03-08 <![CDATA[ Direct and indirect neurogenesis generate a mosaic of distinct glutamatergic projection neuron types and cortical subnetworks ]]> https://biorxiv.org/content/10.1101/2022.03.13.484161v1?rss=1 Huilgol, D. Levine, J. M. Galbavy, W. Wang, B.-S. He, M. Suryanarayana, S. M. Huang, Z. J. 2022-03-14 doi:10.1101/2022.03.13.484161 Cold Spring Harbor Laboratory Press 2022-03-14 <![CDATA[ SPDEF promotes the classical subtype of pancreatic ductal adenocarcinoma. ]]> https://biorxiv.org/content/10.1101/2022.03.18.484951v1?rss=1 Tonelli, C. Yordanov, G. N. Hao, Y. Deschenes, A. Klingbeil, O. Ting, H.-C. Brosnan, E. Doshi, A. Park, Y. Vakoc, C. R. Preall, J. Tuveson, D. 2022-03-19 doi:10.1101/2022.03.18.484951 Cold Spring Harbor Laboratory Press 2022-03-19 <![CDATA[ A reinforcement learning algorithm shapes maternal care in mice ]]> https://biorxiv.org/content/10.1101/2022.03.21.485130v1?rss=1 Xie, Y. Huang, L. Corona, A. Pagliaro, A. H. Shea, S. D. 2022-03-21 doi:10.1101/2022.03.21.485130 Cold Spring Harbor Laboratory Press 2022-03-21 <![CDATA[ A global high-density chromatin interaction network reveals functional long-range and trans-chromosomal relationships ]]> https://biorxiv.org/content/10.1101/2022.03.24.485503v1?rss=1 Lohia, R. Fox, N. Gillis, J. 2022-03-27 doi:10.1101/2022.03.24.485503 Cold Spring Harbor Laboratory Press 2022-03-27 <![CDATA[ CRISPR-induced exon skipping of β-catenin reveals tumorigenic mutants driving distinct subtypes of liver cancer ]]> https://biorxiv.org/content/10.1101/2022.03.27.485965v1?rss=1 Mou, H. Yue, J. Jin, Y. Wang, Z. Gao, Y. Janowitz, T. Meyer, H. V. Kucukural, A. Wilkinson, J. E. Ozata, D. M. Beyaz, S. 2022-03-27 doi:10.1101/2022.03.27.485965 Cold Spring Harbor Laboratory Press 2022-03-27 <![CDATA[ T cell-mediated development of stromal fibroblasts with an immune-enhancing chemokine profile ]]> https://biorxiv.org/content/10.1101/2022.04.03.486884v1?rss=1 Yan, R. Fearon, D. T. 2022-04-05 doi:10.1101/2022.04.03.486884 Cold Spring Harbor Laboratory Press 2022-04-05 <![CDATA[ Multilevel selection analysis reveals diversity in selfish mitochondrial genome dynamics ]]> https://biorxiv.org/content/10.1101/2022.04.08.487647v1?rss=1 Gitschlag, B. L. Patel, M. R. 2022-04-10 doi:10.1101/2022.04.08.487647 Cold Spring Harbor Laboratory Press 2022-04-10 <![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[ Quantitative Cell Proteomic Atlas: Pathway-scale targeted mass spectrometry for high-resolution functional profiling of cell signaling ]]> https://biorxiv.org/content/10.1101/2022.04.14.488331v1?rss=1 Cifani, P. Kentsis, A. 2022-04-14 doi:10.1101/2022.04.14.488331 Cold Spring Harbor Laboratory Press 2022-04-14 <![CDATA[ Newly discovered alleles of the tomato antiflorigen gene SELF PRUNING provide a range of plant compactness and yield ]]> https://biorxiv.org/content/10.1101/2022.04.17.488597v1?rss=1 Kang, M.-S. Kim, Y. J. Heo, J. Rajendran, S. Wang, X. Bae, J. H. Lippman, Z. Park, S. J. 2022-04-17 doi:10.1101/2022.04.17.488597 Cold Spring Harbor Laboratory Press 2022-04-17 <![CDATA[ RNA Pol II pausing facilitates phased pluripotency transitions by buffering transcription ]]> https://biorxiv.org/content/10.1101/2022.04.21.489065v1?rss=1 Abuhashem, A. Chivu, A. G. Zhao, Y. Rice, E. J. Siepel, A. Danko, C. G. Hadjantonakis, A.-K. 2022-04-21 doi:10.1101/2022.04.21.489065 Cold Spring Harbor Laboratory Press 2022-04-21 <![CDATA[ Cortex-wide fast activation of VIP-expressing inhibitory neurons by reward and punishment ]]> https://biorxiv.org/content/10.1101/2022.04.27.489695v1?rss=1 Szadai, Z. Pi, H.-J. Chevy, Q. Ocsai, K. Albeanu, F. Chiovini, B. Szalay, G. Katona, G. Kepecs, A. Rozsa, B. 2022-04-29 doi:10.1101/2022.04.27.489695 Cold Spring Harbor Laboratory Press 2022-04-29 <![CDATA[ Evaluating deep learning for predicting epigenomic profiles ]]> https://biorxiv.org/content/10.1101/2022.04.29.490059v1?rss=1 Toneyan, S. Tang, Z. Koo, P. 2022-05-01 doi:10.1101/2022.04.29.490059 Cold Spring Harbor Laboratory Press 2022-05-01 <![CDATA[ Statistical correction of input gradients for black box models trained with categorical input features ]]> https://biorxiv.org/content/10.1101/2022.04.29.490102v1?rss=1 Majdandzic, A. Koo, P. 2022-05-01 doi:10.1101/2022.04.29.490102 Cold Spring Harbor Laboratory Press 2022-05-01 <![CDATA[ Neurotransmitter content heterogeneity within an interneuron class shapes inhibitory transmission at a central synapse ]]> https://biorxiv.org/content/10.1101/2022.05.03.490471v1?rss=1 Dumontier, D. Mailhes-Hamon, C. Supplisson, S. Dieudonne, S. 2022-05-04 doi:10.1101/2022.05.03.490471 Cold Spring Harbor Laboratory Press 2022-05-04 <![CDATA[ Single-cell genomic analysis of triple-negative breast cancer fibroblasts uncovers evolutionarily conserved features and potential therapeutic targets ]]> https://biorxiv.org/content/10.1101/2022.05.05.490693v1?rss=1 Delgado, A. P. Nemajerova, A. Li, J. Marchenko, N. Preall, J. Moll, U. M. Egeblad, M. Powers, S. 2022-05-05 doi:10.1101/2022.05.05.490693 Cold Spring Harbor Laboratory Press 2022-05-05 <![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[ A neural theory for counting memories ]]> https://biorxiv.org/content/10.1101/2022.05.18.492502v1?rss=1 Dasgupta, S. Hattori, D. Navlakha, S. 2022-05-18 doi:10.1101/2022.05.18.492502 Cold Spring Harbor Laboratory Press 2022-05-18 <![CDATA[ Programmable RNA Sensing for Cell Monitoring and Manipulation ]]> https://biorxiv.org/content/10.1101/2022.05.25.493141v1?rss=1 Qian, Y. Li, J. Zhao, S. Matthews, E. A. Adoff, M. Zhong, W. An, X. Yeo, M. Park, C. Wang, B.-S. Southwell, D. G. Huang, Z. J. 2022-05-26 doi:10.1101/2022.05.25.493141 Cold Spring Harbor Laboratory Press 2022-05-26 <![CDATA[ Internally-controlled and dynamic optical measures of functional tumor biology ]]> https://biorxiv.org/content/10.1101/2022.05.30.493733v1?rss=1 Chung, T. Garcia, L. Swamynathan, M. M. Froeling, F. E. M. Trotman, L. C. Tuveson, D. A. Lyons, S. K. 2022-05-31 doi:10.1101/2022.05.30.493733 Cold Spring Harbor Laboratory Press 2022-05-31 <![CDATA[ Genetic or transcranial magnetic stimulation of B-RAF-MEK signaling promotes CST axon sprouting and functional regeneration ]]> https://biorxiv.org/content/10.1101/2022.06.01.494346v1?rss=1 Boato, F. Guan, X. Zhu, Y. Ryu, Y. Voutounou, M. Rynne, C. Freschlin, C. R. Zumbo, P. Betel, D. Matho, K. S. Makarov, S. N. Wu, Z. Son, Y.-J. Nummenmaa, A. Huang, J. Z. Edwards, D. J. Zhong, J. 2022-06-03 doi:10.1101/2022.06.01.494346 Cold Spring Harbor Laboratory Press 2022-06-03 <![CDATA[ Senescence rewires microenvironment sensing to facilitate anti-tumor immunity ]]> https://biorxiv.org/content/10.1101/2022.06.04.494739v1?rss=1 Chen, H.-A. Ho, Y.-J. Mezzadra, R. Adrover, J. M. Smolkin, R. M. Zhu, C. Wei, L. Wuest, A. Tian, S. Li, X. Hendrickson, R. C. Egeblad, M. Alonso-Curbelo, D. Lowe, S. W. 2022-06-05 doi:10.1101/2022.06.04.494739 Cold Spring Harbor Laboratory Press 2022-06-05 <![CDATA[ Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice (Oryza sativa) ]]> https://biorxiv.org/content/10.1101/2022.06.11.495682v1?rss=1 Zhou, Y. Yu, Z. Chebotarov, D. Chougule, K. Lu, Z. Rivera, L. Kathiresan, N. Al-Bader, N. Mohammed, N. Alsantely, A. Mussurova, S. Santos, J. Thimma, M. Troukhan, M. Fornasiero, A. Green, C. Copetti, D. Kudrna, D. Llaca, V. Lorieux, M. Zuccolo, A. Ware, D. McNally, K. Zhang, J. Wing, R. 2022-06-13 doi:10.1101/2022.06.11.495682 Cold Spring Harbor Laboratory Press 2022-06-13 <![CDATA[ Synaptic homeostasis transiently leverages Hebbian mechanisms for a multiphasic response to inactivity ]]> https://biorxiv.org/content/10.1101/2022.06.18.496642v1?rss=1 Sun, S. Levenstein, D. Li, B. Mandelberg, N. Chenouard, N. Suutari, B. S. Sanchez, S. Tian, G. Rinzel, J. Buzsaki, G. Tsien, R. W. 2022-06-19 doi:10.1101/2022.06.18.496642 Cold Spring Harbor Laboratory Press 2022-06-19 <![CDATA[ Evaluating the differential expression of TAM family receptors and efferocytosis activities in differentiated and polarized THP-1 macrophage ]]> https://biorxiv.org/content/10.1101/2022.06.21.497076v1?rss=1 Chamberland, M. Farrell, B. Yeh, J. T.- H. 2022-06-21 doi:10.1101/2022.06.21.497076 Cold Spring Harbor Laboratory Press 2022-06-21 <![CDATA[ Gene expression as phenotype - Many small-step changes leading to little long-term phenotypic evolution ]]> https://biorxiv.org/content/10.1101/2022.06.24.497468v1?rss=1 Lin, P. Lu, G.-A. Liufu, Z.-Q. Zhao, Y. Ruan, Y.-S. Wu, C.-I. Wen, H.-J. 2022-06-28 doi:10.1101/2022.06.24.497468 Cold Spring Harbor Laboratory Press 2022-06-28 <![CDATA[ Diversity and task-dependence of task representations in V1 during freely-moving decisions ]]> https://biorxiv.org/content/10.1101/2022.07.06.498845v1?rss=1 Zhang, A. Zador, A. M. 2022-07-07 doi:10.1101/2022.07.06.498845 Cold Spring Harbor Laboratory Press 2022-07-07 <![CDATA[ Establishing Physalis as a new Solanaceae model system enables genetic reevaluation of the inflated calyx syndrome ]]> https://biorxiv.org/content/10.1101/2022.07.29.502011v1?rss=1 He, J. Alonge, M. Ramakrishnan, S. Benoit, M. Soyk, S. Reem, N. Hendelman, A. Van Eck, J. Schatz, M. Lippman, Z. 2022-07-30 doi:10.1101/2022.07.29.502011 Cold Spring Harbor Laboratory Press 2022-07-30 <![CDATA[ Expansion Sequencing of RNA Barcoded Neurons in the Mammalian Brain: Progress and Implications for Molecularly Annotated Connectomics ]]> https://biorxiv.org/content/10.1101/2022.07.31.502046v1?rss=1 Goodwin, D. R. Vaughan, A. Leible, D. Alon, S. Henry, G. L. Cheng, A. V. Chen, X. Zhang, R. Xue, A. G. Wassie, A. T. Sinha, A. Bando, Y. Kajita, A. Marblestone, A. H. Zador, A. M. Boyden, E. S. Church, G. M. Kohman, R. E. 2022-07-31 doi:10.1101/2022.07.31.502046 Cold Spring Harbor Laboratory Press 2022-07-31 <![CDATA[ Primary Somatosensory Cortex Bidirectionally Modulates Sensory Gain and Nociceptive Behavior in a Layer-Specific Manner ]]> https://biorxiv.org/content/10.1101/2022.08.02.502350v1?rss=1 Ziegler, K. Burghardt, J. Folkard, R. Gonzalez, A. Antharvedi-Goda, S. Martin-Cortecero, J. Isaias-Camacho, E. Kaushalya, S. Tan, L. L. Kuner, T. Kuner, R. Mease, R. Groh, A. 2022-08-03 doi:10.1101/2022.08.02.502350 Cold Spring Harbor Laboratory Press 2022-08-03 <![CDATA[ Intratumoral heterogeneity and clonal evolution induced by HPV integration ]]> https://biorxiv.org/content/10.1101/2022.08.11.503647v1?rss=1 Akagi, K. Symer, D. E. Mahmoud, M. Jiang, B. Goodwin, S. Wangsa, D. Li, Z. Xiao, W. Dunn, J. D. McCombie, R. Ried, T. Coombes, K. R. Sedlazeck, F. J. Gillison, M. L. 2022-08-13 doi:10.1101/2022.08.11.503647 Cold Spring Harbor Laboratory Press 2022-08-13 <![CDATA[ Lipids Maintain Genomic Stability and Developmental Potency of Murine Pluripotent Stem Cells ]]> https://biorxiv.org/content/10.1101/2022.08.12.503780v1?rss=1 Wen, D. Zhong, L. Gordillo, M. Wang, X. Qin, Y. Huang, Y. Soshnev, A. Kumar, R. Nanjangud, G. James, D. Allis, C. D. Evans, T. Carey, B. 2022-08-15 doi:10.1101/2022.08.12.503780 Cold Spring Harbor Laboratory Press 2022-08-15 <![CDATA[ Single-cell transcriptomics of resected human traumatic brain injury tissues reveals acute activation of endogenous retroviruses in oligodendrocytes ]]> https://biorxiv.org/content/10.1101/2022.09.07.506982v1?rss=1 Garza, R. Sharma, Y. Atacho, D. Hamdeh, S. A. Jonsson, M. E. Ingelsson, M. Jern, P. Hammell, M. G. Englund, E. Jakobsson, J. Marklund, N. 2022-09-09 doi:10.1101/2022.09.07.506982 Cold Spring Harbor Laboratory Press 2022-09-09 <![CDATA[ Comparative transcriptomics reveals human-specific cortical features ]]> https://biorxiv.org/content/10.1101/2022.09.19.508480v1?rss=1 Jorstad, N. L. Song, J. H. T. Exposito-Alonso, D. Suresh, H. Castro, N. Krienen, F. M. Yanny, A. M. Close, J. Gelfand, E. Travaglini, K. J. Basu, S. Beaudin, M. Bertagnolli, D. Crow, M. Ding, S.-L. Eggermont, J. Glandon, A. Goldy, J. Kroes, T. Long, B. McMillen, D. Pham, T. Rimorin, C. Siletti, K. Somasundaram, S. Tieu, M. Torkelson, A. Ward, K. Feng, G. Hopkins, W. D. Hollt, T. Keene, C. D. Linnarsson, S. McCarroll, S. A. Lelieveldt, B. P. Sherwood, C. C. Smith, K. Walsh, C. A. Dobin, A. Gillis, J. Lein, E. S. Hodge, R. D. Bakken, T. E. 2022-09-19 doi:10.1101/2022.09.19.508480 Cold Spring Harbor Laboratory Press 2022-09-19 <![CDATA[ Conserved coexpression at single cell resolution across primate brains ]]> https://biorxiv.org/content/10.1101/2022.09.20.508736v1?rss=1 Suresh, H. Crow, M. Jorstad, N. Hodge, R. Lein, E. Dobin, A. Bakken, T. Gillis, J. 2022-09-22 doi:10.1101/2022.09.20.508736 Cold Spring Harbor Laboratory Press 2022-09-22 <![CDATA[ Circadian rhythm orthologs drive pulses of heterochronic miRNA transcription in C. elegans ]]> https://biorxiv.org/content/10.1101/2022.09.26.509508v1?rss=1 Kinney, B. Sahu, S. Stec, N. Hills-Muckey, K. Adams, D. Wang, J. Jaremako, M. Joshua-Tor, L. Keil, W. Hammell, C. M. 2022-09-26 doi:10.1101/2022.09.26.509508 Cold Spring Harbor Laboratory Press 2022-09-26 <![CDATA[ Ten new high-quality genome assemblies for diverse bioenergy sorghum genotypes ]]> https://biorxiv.org/content/10.1101/2022.09.26.509520v1?rss=1 Voelker, W. G. Krishnan, K. Chougule, K. Alexander, L. C. Lu, Z. Olson, A. Ware, D. Songsomboon, K. Ponce, C. M. Brenton, Z. Boatwright, J. L. Cooper, E. A. 2022-09-27 doi:10.1101/2022.09.26.509520 Cold Spring Harbor Laboratory Press 2022-09-27 <![CDATA[ Transcriptional regulation and repressive condensates modulate a proliferative-invasive cellular switch in vivo ]]> https://biorxiv.org/content/10.1101/2022.09.30.510381v1?rss=1 Medwig-Kinney, T. N. Kinney, B. A. Martinez, M. A. Q. Yee, C. Sirota, S. S. Mullarkey, A. A. Somineni, N. Hippler, J. Zhang, W. Shen, K. Hammell, C. M. Pani, A. M. Matus, D. Q. 2022-10-01 doi:10.1101/2022.09.30.510381 Cold Spring Harbor Laboratory Press 2022-10-01 <![CDATA[ Designed active-site library reveals thousands of functional GFP variants ]]> https://biorxiv.org/content/10.1101/2022.10.11.511732v1?rss=1 16,000 unique designs encoding as many as eight active-site mutations. Many designs exhibit substantial and useful diversity in functional thermostability (up to 96 {degrees}C), fluorescence lifetime, and quantum yield. By eliminating incompatible active-site mutations, htFuncLib generates a large diversity of functional sequences. We envision that htFuncLib will be useful for one-shot optimization of activity in enzymes, binders, and other proteins. ]]> Weinstein, J. Y. Aldaravi, C. M. G. Lipsh-Sokolik, R. Hoch, S. Y. Liebermann, D. Nevo, R. Weissman, H. Petrovich-Kopitman, E. Margulies, D. Ivankov, D. McCandlish, D. Fleishman, S. J. 2022-10-11 doi:10.1101/2022.10.11.511732 Cold Spring Harbor Laboratory Press 2022-10-11 <![CDATA[ An expandable FLP-ON::TIR1 system for precise spatiotemporal protein degradation in C. elegans ]]> https://biorxiv.org/content/10.1101/2022.10.14.512315v1?rss=1 Xiao, Y. Yee, C. Martinez, M. A. Q. Zhao, C. Z. Zhang, W. Shen, K. Matus, D. Q. Hammell, C. M. 2022-10-16 doi:10.1101/2022.10.14.512315 Cold Spring Harbor Laboratory Press 2022-10-16 <![CDATA[ Model-based characterization of the equilibrium dynamics of transcription initiation and promoter-proximal pausing in human cells ]]> https://biorxiv.org/content/10.1101/2022.10.19.512929v1?rss=1 Zhao, Y. Liu, L. Siepel, A. 2022-10-21 doi:10.1101/2022.10.19.512929 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ Translesion DNA synthesis polymerase kappa functions in the nucleolar stress response ]]> https://biorxiv.org/content/10.1101/2022.10.27.513845v1?rss=1 Paul, S. Rebok, A. Cifani, P. Paul, A. Pappin, D. Huang, T. T. Spratt, T. E. 2022-10-27 doi:10.1101/2022.10.27.513845 Cold Spring Harbor Laboratory Press 2022-10-27 <![CDATA[ The BRAIN Initiative Cell Census Data Ecosystem: A User's Guide ]]> https://biorxiv.org/content/10.1101/2022.10.26.513573v1?rss=1 BICCN Data Ecosytem Collaboration, Hawrylycz, M. J. Martone, M. E. Hof, P. R. Lein, E. S. Regev, A. Ascoli, G. A. A. Bjaalie, J. G. Dong, H.-W. Ghosh, S. S. Gillis, J. Hertzano, R. Haynor, D. R. Kim, Y. Liu, Y. Miller, J. A. Mitra, P. P. Mukamel, E. Osumi-Sutherland, D. Peng, H. Ray, P. L. Sanchez, R. Ropelewski, A. Scheuermann, R. H. Tan, S. Z. K. Tickle, T. Tilgner, H. Varghese, M. Wester, B. White, O. Aevermann, B. Allemang, D. Ament, S. Athey, T. L. Baker, P. M. Baker, C. Baker, K. S. Bandrowski, A. Bishwakarma, P. Carr, A. Chen, M. Choudhury, R. 2022-10-30 doi:10.1101/2022.10.26.513573 Cold Spring Harbor Laboratory Press 2022-10-30 <![CDATA[ Breast cancer progression and metastasis to lymph nodes reveals cancer cell plasticity and MHC class II-mediated immune regulation ]]> https://biorxiv.org/content/10.1101/2022.10.30.514441v1?rss=1 Lei, P.-J. Pereira, E. Andersson, P. Amoozgar, Z. Wijnbergen, J. W. V. O'Melia, M. J. Zhou, H. Chatterjee, S. Ho, W. W. Posada, J. M. Kumar, A. S. Morita, S. Chuang, C. Ergin, I. Jones, D. Huang, P. Beyaz, S. Padera, T. P. 2022-11-01 doi:10.1101/2022.10.30.514441 Cold Spring Harbor Laboratory Press 2022-11-01 <![CDATA[ Evolution-inspired augmentations improve deep learning for regulatory genomics ]]> https://biorxiv.org/content/10.1101/2022.11.03.515117v1?rss=1 Lee, N. K. Tang, Z. Toneyan, S. Koo, P. K. 2022-11-04 doi:10.1101/2022.11.03.515117 Cold Spring Harbor Laboratory Press 2022-11-04 <![CDATA[ Transcriptomic cytoarchitecture reveals principles of human neocortex organization ]]> https://biorxiv.org/content/10.1101/2022.11.06.515349v1?rss=1 Jorstad, N. L. Close, J. Johansen, N. Yanny, A. M. Barkan, E. R. Travaglini, K. J. Bertagnolli, D. Campos, J. Casper, T. Crichton, K. Dee, N. Ding, S.-L. Gelfand, E. Goldy, J. Hirschstein, D. Kroll, M. Kunst, M. Lathia, K. Long, B. Martin, N. McMillen, D. Pham, T. Rimorin, C. Ruiz, A. Shapovalova, N. Shehata, S. Siletti, K. Somasundaram, S. Sulc, J. Tieu, M. Torkelson, A. Tung, H. Ward, K. Callaway, E. M. Hof, P. R. Keene, C. D. Levi, B. P. Linnarsson, S. Mitra, P. P. Smith, K. Hodge, R. D. Bakken, T. E. Lein, E. S. 2022-11-06 doi:10.1101/2022.11.06.515349 Cold Spring Harbor Laboratory Press 2022-11-06 <![CDATA[ Modular cell type organization of cortical areas revealed by in situ sequencing ]]> https://biorxiv.org/content/10.1101/2022.11.06.515380v1?rss=1 Chen, X. Fischer, S. Zhang, A. Gillis, J. Zador, A. 2022-11-06 doi:10.1101/2022.11.06.515380 Cold Spring Harbor Laboratory Press 2022-11-06 <![CDATA[ A cortical circuit for orchestrating oromanual food manipulation ]]> https://biorxiv.org/content/10.1101/2022.12.03.518964v1?rss=1 An, X. Matho, K. S. Li, Y. Mohan, H. Xu, X. H. Whishaw, I. Kepecs, A. Huang, Z. J. 2022-12-03 doi:10.1101/2022.12.03.518964 Cold Spring Harbor Laboratory Press 2022-12-03 <![CDATA[ A circuit from the locus coeruleus to the anterior cingulate cortex modulates offspring interactions in mice ]]> https://biorxiv.org/content/10.1101/2022.12.04.519053v1?rss=1 Corona, A. Choe, J. Munoz-Castaneda, R. Osten, P. Shea, S. D. 2022-12-04 doi:10.1101/2022.12.04.519053 Cold Spring Harbor Laboratory Press 2022-12-04 <![CDATA[ Snakeobjects: an object-oriented workflow management system ]]> https://biorxiv.org/content/10.1101/2022.12.08.519599v1?rss=1 Yamrom, B. Lee, Y.-h. Marks, S. Chorbadjiev, L. Meyer, H. V. Iossifov, I. 2022-12-12 doi:10.1101/2022.12.08.519599 Cold Spring Harbor Laboratory Press 2022-12-12 <![CDATA[ An improved reference of the grapevine genome supports reasserting the origin of the PN40024 highly-homozygous genotype ]]> https://biorxiv.org/content/10.1101/2022.12.21.521434v1?rss=1 Velt, A. Frommer, B. Blanc, S. Holtgräwe, D. Duchene, E. Dumas, V. Grimplet, J. Hugueney, P. Lahaye, M. Kim, C. Matus, J. T. Navarro-Paya, D. Orduna, L. Tello-Ruiz, M. K. Vitulo, N. Ware, D. Rustenholz, C. 2022-12-22 doi:10.1101/2022.12.21.521434 Cold Spring Harbor Laboratory Press 2022-12-22 <![CDATA[ Specificity, synergy, and mechanisms of splice-modifying drugs ]]> https://biorxiv.org/content/10.1101/2022.12.30.522303v1?rss=1 Ishigami, Y. Wong, M. S. Marti-Gomez, C. Ayaz, A. Kooshkbaghi, M. Hanson, S. McCandlish, D. M. Krainer, A. R. Kinney, J. B. 2022-12-31 doi:10.1101/2022.12.30.522303 Cold Spring Harbor Laboratory Press 2022-12-31 <![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[ Area postrema neurons mediate interleukin-6 function in cancer-associated cachexia ]]> https://biorxiv.org/content/10.1101/2023.01.12.523716v1?rss=1 Li, B. Sun, Q. van de Lisdonk, D. Ferrer, M. Gegenhuber, B. Wu, M. Tollkuhn, J. Janowitz, T. 2023-01-13 doi:10.1101/2023.01.12.523716 Cold Spring Harbor Laboratory Press 2023-01-13 <![CDATA[ Cryptochromes and UBP12/13 deubiquitinases antagonistically regulate DNA damage response in Arabidopsis ]]> https://biorxiv.org/content/10.1101/2023.01.15.524001v1?rss=1 Hu, Y. Rosado, D. Lindback, L. N. Micko, J. Pedmale, U. V. 2023-01-16 doi:10.1101/2023.01.15.524001 Cold Spring Harbor Laboratory Press 2023-01-16 <![CDATA[ Light and temperature regulate m6A-RNA modification to regulate growth in plants ]]> https://biorxiv.org/content/10.1101/2023.01.17.524395v1?rss=1 Artz, O. Ackermann, A. Taylor, L. J. Koo, P. Pedmale, U. V. 2023-01-17 doi:10.1101/2023.01.17.524395 Cold Spring Harbor Laboratory Press 2023-01-17 <![CDATA[ High-throughput sequencing of macaque basolateral amygdala projections reveals dissociable connectional motifs with frontal cortex ]]> https://biorxiv.org/content/10.1101/2023.01.18.524407v1?rss=1 Zeisler, Z. R. London, L. Janssen, W. G. Fredericks, J. M. Elorette, C. Fujimoto, A. Zhan, H. Russ, B. E. Clem, R. L. Hof, P. R. Stoll, F. M. Rudebeck, P. H. 2023-01-18 doi:10.1101/2023.01.18.524407 Cold Spring Harbor Laboratory Press 2023-01-18 <![CDATA[ Identification of glioblastoma stem cell-associated lncRNAs using single-cell RNA-sequencing datasets ]]> https://biorxiv.org/content/10.1101/2023.01.20.524887v1?rss=1 Hazra, R. Utama, R. Naik, P. Dobin, A. Spector, D. 2023-01-21 doi:10.1101/2023.01.20.524887 Cold Spring Harbor Laboratory Press 2023-01-21 <![CDATA[ Neural dynamics in the rodent motor cortex enables flexible control of vocal timing ]]> https://biorxiv.org/content/10.1101/2023.01.23.525252v1?rss=1 Banerjee, A. Chen, F. Druckmann, S. Long, M. A. 2023-01-23 doi:10.1101/2023.01.23.525252 Cold Spring Harbor Laboratory Press 2023-01-23 <![CDATA[ Duck pan-genome reveals two transposon-derived structural variations caused bodyweight enlarging and white plumage phenotype formation during evolution ]]> https://biorxiv.org/content/10.1101/2023.01.28.526061v1?rss=1 Wang, K. Hua, G. Li, J. Yang, Y. Zhang, C. Yang, L. Hu, X. Scheben, A. Wu, Y. Gong, P. Zhang, S. Fan, Y. Zeng, T. Lu, L. Gong, Y. Jiang, R. Sun, G. Tian, Y. Kang, X. Hu, H. Li, W. 2023-01-30 doi:10.1101/2023.01.28.526061 Cold Spring Harbor Laboratory Press 2023-01-30 <![CDATA[ Selective deletion of Methyl CpG binding protein 2 from parvalbumin interneurons in the auditory cortex delays the onset of maternal retrieval in mice ]]> https://biorxiv.org/content/10.1101/2023.01.30.526321v1?rss=1 Rupert, D. D. Pagliaro, A. H. Choe, J. Shea, S. D. 2023-01-31 doi:10.1101/2023.01.30.526321 Cold Spring Harbor Laboratory Press 2023-01-31 <![CDATA[ Stable sound decoding despite modulated sound representation in the auditory cortex ]]> https://biorxiv.org/content/10.1101/2023.01.31.526457v1?rss=1 Funamizu, A. Marbach, F. Zador, A. M. 2023-02-02 doi:10.1101/2023.01.31.526457 Cold Spring Harbor Laboratory Press 2023-02-02 <![CDATA[ Histone demethylase KDM2A is a selective vulnerability of cancers relying on alternative telomere maintenance ]]> https://biorxiv.org/content/10.1101/2023.02.10.528023v1?rss=1 Li, F. Wang, Y. Hwang, I. Janng, J.-Y. Zhou, L. Deng, Z. Yu, E. Y. Cai, Y. Wu, C. Han, Z. Huang, Y.-H. Huang, X. Zhang, L. Yao, J. Lue, N. Lieberman, P. Ying, H. Paik, J. Zheng, H. 2023-02-11 doi:10.1101/2023.02.10.528023 Cold Spring Harbor Laboratory Press 2023-02-11 <![CDATA[ Mutation and selection induce correlations between selection coefficients and mutation rates ]]> https://biorxiv.org/content/10.1101/2023.02.13.528299v1?rss=1 Gitschlag, B. L. Cano, A. V. Payne, J. L. McCandlish, D. M. Stoltzfus, A. 2023-02-14 doi:10.1101/2023.02.13.528299 Cold Spring Harbor Laboratory Press 2023-02-14 <![CDATA[ Ketogenic diet promotes tumor ferroptosis but induces relative corticosterone deficiency that accelerates cachexia ]]> https://biorxiv.org/content/10.1101/2023.02.17.528937v1?rss=1 View larger version (24K): org.highwire.dtl.DTLVardef@613bb6org.highwire.dtl.DTLVardef@19746a4org.highwire.dtl.DTLVardef@9ef652org.highwire.dtl.DTLVardef@3db934_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LIKetogenic diet delays tumor growth but accelerates cancer cachexia and shortens survival C_LIO_LIIn the tumor, accumulation of lipid peroxidation products results in saturation of the GSH detoxifying pathway and ferroptotic death of cancer cells C_LIO_LIIn the host organism, systemic redox state imbalance causes NADPH depletion, GDF-15 elevations, and relative corticosterone deficiency C_LIO_LIDexamethasone coadministration with ketogenic diet delays onset of cancer cachexia by improving food intake, glucose homeostasis and utilization of nutritional substrates C_LI ]]> Ferrer, M. Mourikis, N. Davidson, E. E. Kleeman, S. O. Zaccaria, M. Habel, J. Rubino, R. Flint, T. R. Connell, C. M. Lukey, M. White, E. P. Coll, A. P. Venkitaraman, A. R. Janowitz, T. 2023-02-18 doi:10.1101/2023.02.17.528937 Cold Spring Harbor Laboratory Press 2023-02-18 <![CDATA[ The axon guidance cue SEMA3A promotes the aggressive phenotype of basal-like PDAC ]]> https://biorxiv.org/content/10.1101/2023.02.25.529923v1?rss=1 Lupo, F. Pezzini, F. Fiorini, E. Adamo, A. Veghini, L. Bevere, M. Frusteri, C. Delfino, P. D'Agosto, S. Andreani, S. Piro, G. Malinova, A. De Sanctis, F. Pasini, D. Lawlor, R. T. Hwang, C.-i. Carbone, C. Amelio, I. Bailey, P. Bronte, V. Tuveson, D. Scarpa, A. Ugel, S. Corbo, V. 2023-02-26 doi:10.1101/2023.02.25.529923 Cold Spring Harbor Laboratory Press 2023-02-26 <![CDATA[ Domain-adaptive neural networks improve supervised machine learning based on simulated population genetic data ]]> https://biorxiv.org/content/10.1101/2023.03.01.529396v1?rss=1 Mo, Z. Siepel, A. 2023-03-01 doi:10.1101/2023.03.01.529396 Cold Spring Harbor Laboratory Press 2023-03-01 <![CDATA[ L1 retrotransposons drive human neuronal transcriptome complexity and functional diversification ]]> https://biorxiv.org/content/10.1101/2023.03.04.531072v1?rss=1 Garza, R. Atacho, D. Adami, A. Gerdes, P. Vinod, M. Hsieh, P. Karlsson, O. Horvath, V. Johansson, P. A. Pandiloski, N. Matas, J. Quaegebeur, A. Kouli, A. Sharma, Y. Jonsson, M. E. Monni, E. Englund, E. Eichler, E. E. Gale Hammell, M. Barker, R. A. Kokaia, Z. Douse, C. H. Jakobsson, J. 2023-03-06 doi:10.1101/2023.03.04.531072 Cold Spring Harbor Laboratory Press 2023-03-06 <![CDATA[ Antibody-directed extracellular proximity biotinylation reveals Contactin-1 regulates axo-axonic innervation of axon initial segments. ]]> https://biorxiv.org/content/10.1101/2023.03.06.531378v1?rss=1 Ogawa, Y. Lim, B. George, S. Oses-Prieto, J. Rasband, J. Eshed-Eisenbach, Y. Nair, S. Boata, F. Peles, E. Burlingame, A. Van Aelst, L. Rasband, M. N. 2023-03-06 doi:10.1101/2023.03.06.531378 Cold Spring Harbor Laboratory Press 2023-03-06 <![CDATA[ The cell type composition of the adult mouse brain revealed by single cell and spatial genomics ]]> https://biorxiv.org/content/10.1101/2023.03.06.531307v1?rss=1 Langlieb, J. Sachdev, N. Balderrama, K. Nadaf, N. Raj, M. Murray, E. Webber, J. Vanderburg, C. Gazestani, V. Tward, D. Mezias, C. Li, X. Norton, T. Mitra, P. P. Chen, F. Macosko, E. 2023-03-08 doi:10.1101/2023.03.06.531307 Cold Spring Harbor Laboratory Press 2023-03-08 <![CDATA[ Optimizing Short-format Training: an International Consensus on Effective, Inclusive, and Career-spanning Professional Development in the Life Sciences and Beyond ]]> https://biorxiv.org/content/10.1101/2023.03.10.531570v1?rss=1 Williams, J. J. Tractenberg, R. E. Batut, B. Becker, E. A. Brown, A. M. Burke, M. L. Busby, B. Cooch, N. K. Dillman, A. A. Donovan, S. S. Doyle, M. A. van Gelder, C. W. G. Hall, C. R. Hertweck, K. L. Jordan, K. L. Jungck, J. R. Latour, A. R. Lindvall, J. M. Lloret-Llinares, M. McDowell, G. S. Morris, R. Mourad, T. Nisselle, A. Ordonez, P. Paladin, L. Palagi, P. M. Sukhai, M. A. Teal, T. K. Woodley, L. 2023-03-13 doi:10.1101/2023.03.10.531570 Cold Spring Harbor Laboratory Press 2023-03-13 <![CDATA[ The maize PLASTID TERMINAL OXIDASE (PTOX) gene controls the carotenoid content of kernels. ]]> https://biorxiv.org/content/10.1101/2023.03.13.532334v1?rss=1 Nie, Y. Wang, H. Zhang, G. Ding, H. Han, B. Liu, L. Shi, J. Du, J. Li, X. Li, X. Zhao, Y. Zhang, X. Liu, C. Weng, J. Li, X. Zhang, X. Zhao, X. Pan, G. Jackson, D. Wu, Q. Zhang, Z. 2023-03-14 doi:10.1101/2023.03.13.532334 Cold Spring Harbor Laboratory Press 2023-03-14 <![CDATA[ Plasma cells in human pancreatic ductal adenocarcinoma secrete antibodies to self-antigens ]]> https://biorxiv.org/content/10.1101/2023.03.20.533453v1?rss=1 Yao, M. Preall, J. Yeh, J. Pappin, D. Cifani, P. Zhao, Y. Z. Shen, S. Moresco, P. He, B. Patel, H. Habowski, A. King, D. Raphael, K. Rishi, A. Sejpal, D. Weiss, M. Tuveson, D. Fearon, D. 2023-03-23 doi:10.1101/2023.03.20.533453 Cold Spring Harbor Laboratory Press 2023-03-23 <![CDATA[ Preservation of co-expression defines the primary tissue fidelity of human neural organoids ]]> https://biorxiv.org/content/10.1101/2023.03.31.535112v1?rss=1 Werner, J. Gillis, J. 2023-03-31 doi:10.1101/2023.03.31.535112 Cold Spring Harbor Laboratory Press 2023-03-31 <![CDATA[ Assessing Microbial Diversity in Soil Samples Along the Potomac River: Implications for Environmental Health ]]> https://biorxiv.org/content/10.1101/2023.03.31.535185v1?rss=1 Taraboletti, A. A. King, A. Dixon, Y. Orr, O. Parnell, C. Watson, Y. Nash, B. Esimai, C. Ude, G. 2023-04-01 doi:10.1101/2023.03.31.535185 Cold Spring Harbor Laboratory Press 2023-04-01 <![CDATA[ Preclinical Screening of Splice-Switching Antisense Oligonucleotides in PDAC Organoids ]]> https://biorxiv.org/content/10.1101/2023.03.31.535161v1?rss=1 Wan, L. Kral, A. J. Voss, D. Krainer, A. 2023-04-03 doi:10.1101/2023.03.31.535161 Cold Spring Harbor Laboratory Press 2023-04-03 <![CDATA[ The ENCODE Uniform Analysis Pipelines ]]> https://biorxiv.org/content/10.1101/2023.04.04.535623v1?rss=1 Hitz, B. C. Lee, J.-W. Jolanki, O. Kagda, M. S. Graham, K. Sud, P. Gabdank, I. Strattan, J. S. Sloan, C. A. Dreszer, T. Rowe, L. D. Podduturi, N. R. Malladi, V. S. Chan, E. T. Davidson, J. M. Ho, M. Miyasato, S. Simison, M. Tanaka, F. Luo, Y. Whaling, I. Lin, K. Jou, J. Hong, E. L. Lee, B. T. Sandstrom, R. Rynes, E. Nelson, J. Nishida, A. Ingersoll, A. Buckley, M. Frerker, M. Kim, D. S. Boley, N. Trout, D. Dobin, A. Rahmanian, S. Wyman, D. Balderrama-Gutierrez, G. Reese, F. Durand, N. C. Dudchenko, O. Weisz, D. Rao, S. S. P. Blackburn, A. Gkountarou 2023-04-06 doi:10.1101/2023.04.04.535623 Cold Spring Harbor Laboratory Press 2023-04-06 <![CDATA[ Engrailed-1 Promotes Pancreatic Cancer Metastasis ]]> https://biorxiv.org/content/10.1101/2023.04.10.536259v1?rss=1 Xu, J. Roe, J. S. Lee, E. Tonelli, C. Somerville, T. Yao, M. Milazzo, J. Tiriac, H. Kolarzyk, A. Lee, E. Grem, J. Lazenby, A. Grunkemeyer, J. Hollingsworth, M. Borowsky, A. D. Park, Y. Vakoc, C. Tuveson, D. Hwang, C.-i. 2023-04-12 doi:10.1101/2023.04.10.536259 Cold Spring Harbor Laboratory Press 2023-04-12 <![CDATA[ p73 activates transcriptional signatures of basal lineage identity and ciliogenesis in pancreatic ductal adenocarcinoma ]]> https://biorxiv.org/content/10.1101/2023.04.20.537667v1?rss=1 Hur, S. K. Somerville, T. D. D. Wu, X. S. Maia-Silva, D. Demerdash, O. E. Tuveson, D. A. Notta, F. Vakoc, C. R. 2023-04-21 doi:10.1101/2023.04.20.537667 Cold Spring Harbor Laboratory Press 2023-04-21 <![CDATA[ Evaluating possible maternal effect lethality of Naa10 knockout mice, and modulation of phenotypes for embryonic and neonatal lethality by genetic background and environment ]]> https://biorxiv.org/content/10.1101/2023.04.27.538618v1?rss=1 Lyon, G. Longo, J. Garcia, A. Inusa, F. Marchi, E. Shi, D. Doerfel, M. Arnesen, T. Aldabe, R. Lyons, S. K. Nashat, M. Bolton, D. 2023-04-27 doi:10.1101/2023.04.27.538618 Cold Spring Harbor Laboratory Press 2023-04-27 <![CDATA[ TDP-43 pathology in Drosophila induces glial-cell type specific toxicity that can be ameliorated by knock-down of SF2/SRSF1. ]]> https://biorxiv.org/content/10.1101/2023.05.04.539439v1?rss=1 Krupp, S. Tam, O. Hammell, M. G. dubnau, j. 2023-05-05 doi:10.1101/2023.05.04.539439 Cold Spring Harbor Laboratory Press 2023-05-05 <![CDATA[ Identification of pan-cancer/testis genes and validation of therapeutic targeting in triple-negative breast cancer: Lin28a- and Siglece-based vaccination induces anti-tumor immunity and inhibits metastasis ]]> https://biorxiv.org/content/10.1101/2023.05.09.539617v1?rss=1 Carter, J. A. Matta, B. Battaglia, J. Somerville, C. Harris, B. D. LaPan, M. Atwal, G. S. Barnes, B. J. 2023-05-10 doi:10.1101/2023.05.09.539617 Cold Spring Harbor Laboratory Press 2023-05-10 <![CDATA[ Comparative analysis of gonadal hormone receptor expression in the house mouse, meadow vole, and prairie vole brain ]]> https://biorxiv.org/content/10.1101/2023.05.12.540606v1?rss=1 Tollkuhn, J. Denney, K. A. Wu, M. V. Sun, S. Moon, S. 2023-05-13 doi:10.1101/2023.05.12.540606 Cold Spring Harbor Laboratory Press 2023-05-13 <![CDATA[ Latent circuit inference from heterogeneous neural responses during cognitive tasks ]]> https://biorxiv.org/content/10.1101/2022.01.23.477431v1?rss=1 Langdon, C. Engel, T. A. 2022-01-24 doi:10.1101/2022.01.23.477431 Cold Spring Harbor Laboratory Press 2022-01-24 <![CDATA[ Massive Multiplexing of Spatially Resolved Single Neuron Projections with Axonal BARseq ]]> https://biorxiv.org/content/10.1101/2023.02.18.528865v1?rss=1 8,000 mouse primary auditory cortex neurons from a single brain. We identified major cell types based on projection targets and axonal trajectory. The large sample size enabled us to systematically quantify the projections of intratelencephalic (IT) neurons, and revealed that individual IT neurons project to different layers in an area-dependent fashion. Axonal BARseq is a powerful technique for studying the heterogeneity of single neuronal projections at high throughput within individual brains. ]]> Yuan, L. Chen, X. Zhan, H. Gilbert, H. L. Zador, A. M. 2023-02-18 doi:10.1101/2023.02.18.528865 Cold Spring Harbor Laboratory Press 2023-02-18 <![CDATA[ Gene recoding by synonymous mutations creates promiscuous intragenic transcription initiation in mycobacteria ]]> https://biorxiv.org/content/10.1101/2023.03.17.532606v1?rss=1 Hegelmeyer, N. K. Previti, M. L. Andrade, J. Utama, R. Sejour, R. J. Gardin, J. Muller, S. Ketchum, S. Yurovsky, A. Futcher, B. Goodwin, S. Ueberheide, B. Seeliger, J. 2023-03-17 doi:10.1101/2023.03.17.532606 Cold Spring Harbor Laboratory Press 2023-03-17 <![CDATA[ Allele pairing at Sun1-enriched domains at the nuclear periphery via T1A3 tandem DNA repeats ]]> https://biorxiv.org/content/10.1101/2023.04.07.536031v1?rss=1 Balasooriya, G. I. Spector, D. L. 2023-04-07 doi:10.1101/2023.04.07.536031 Cold Spring Harbor Laboratory Press 2023-04-07 <![CDATA[ Stable heteroplasmy at the single cell level is facilitated by inter-cellular exchange of mtDNA ]]> https://biorxiv.org/content/10.1101/007005v1?rss=1 90%) mtDNA and its ability to detect rare variants is limited only by sequencing depth, providing unprecedented sensitivity and specificity. Using Mseek, we confirmed the ubiquity of heteroplasmy by analyzing mtDNA from a diverse set of cell lines and human samples. Applying Mseek to colonies derived from single cells, we find heteroplasmy is stably maintained in individual daughter cells over multiple cell divisions. We hypothesized that the stability of heteroplasmy could be facilitated by inter-cellular exchange of mtDNA. We explicitly demonstrate this exchange by co-culturing cell lines with distinct mtDNA haplotypes. Our results shed new light on the maintenance of heteroplasmy and provide a novel platform to investigate features of heteroplasmy in normal and diseased states. ]]> Anitha D Jayaprakash Erica Benson Swapna Gone Raymond Liang Jaehee Shim Luca Lambertini Masoud M Toloue Mike Wigler Stuart Aaronson Ravi Sachidanandam 2014-07-10 doi:10.1101/007005 Cold Spring Harbor Laboratory Press 2014-07-10 <![CDATA[ Statistical mechanics of multistable perception ]]> https://biorxiv.org/content/10.1101/008177v1?rss=1 Gurinder Singh Atwal 2014-08-19 doi:10.1101/008177 Cold Spring Harbor Laboratory Press 2014-08-19 <![CDATA[ Mutational biases influence parallel adaptation ]]> https://biorxiv.org/content/10.1101/114694v1?rss=1 Stoltzfus, A. McCandlish, D. M. 2017-03-07 doi:10.1101/114694 Cold Spring Harbor Laboratory Press 2017-03-07 <![CDATA[ Naturally-segregating Variation at Ugt86Dd Contributes to Nicotine Resistance in Drosophila melanogaster ]]> https://biorxiv.org/content/10.1101/134429v1?rss=1 Highfill, C. Tran, J. Nguyen, S. Moldenhauer, T. Wang, X. Macdonald, S. J. 2017-05-05 doi:10.1101/134429 Cold Spring Harbor Laboratory Press 2017-05-05 <![CDATA[ OPRM1 A118G and serum β-endorphin interact with sex and digit ratio (2D:4D) to influence risk and course of alcohol dependence ]]> https://biorxiv.org/content/10.1101/200196v1?rss=1 Gegenhuber, J. B. Weinland, C. Kornhuber, J. Muehle, C. Lenz, B. 2017-10-09 doi:10.1101/200196 Cold Spring Harbor Laboratory Press 2017-10-09 <![CDATA[ Sox2 and canonical Wnt signaling interact to activate a developmental checkpoint coordinating morphogenesis with mesodermal fate acquisition ]]> https://biorxiv.org/content/10.1101/2020.01.29.924050v1?rss=1 Kinney, B. A. Row, R. H. Tseng, Y.-J. Weidmann, M. D. Knaut, H. Martin, B. L. 2020-01-30 doi:10.1101/2020.01.29.924050 Cold Spring Harbor Laboratory Press 2020-01-30 <![CDATA[ HflX controls hypoxia-induced non-replicating persistence in slow growing mycobacteria ]]> https://biorxiv.org/content/10.1101/2020.03.13.990168v1?rss=1 NGAN, J. Y. G. PASUNOOTI, S. TSE, W. MENG, W. NGAN, S. F. C. NG, S. W. JAAFAR, M. T. JIA, H. CHO, S. L. S. LIM, J. KOH, H. Q. V. ABDULGHANI, N. PETHE, K. Sze, K. S. Lescar, J. Alonso, S. 2020-03-15 doi:10.1101/2020.03.13.990168 Cold Spring Harbor Laboratory Press 2020-03-15 <![CDATA[ Linkage mapping and QTL analysis of flowering time using ddRAD sequencing with genotype error correction in Brassica napus ]]> https://biorxiv.org/content/10.1101/2020.06.26.162966v1?rss=1 Scheben, A. Severn-Ellis, A. Patel, D. Pradhan, A. Rae, S. Batley, J. Edwards, D. 2020-06-26 doi:10.1101/2020.06.26.162966 Cold Spring Harbor Laboratory Press 2020-06-26 <![CDATA[ Imd pathway-specific immune assays reveal NF-κB stimulation by viral RNA PAMPs in Aedes aegypti Aag2 cells ]]> https://biorxiv.org/content/10.1101/2020.06.30.179879v1?rss=1 Russell, T. A. Ayaz, A. Davidson, A. D. Fernandez-Sesma, A. Maringer, K. 2020-06-30 doi:10.1101/2020.06.30.179879 Cold Spring Harbor Laboratory Press 2020-06-30 <![CDATA[ Molecular architecture of the developing mouse brain ]]> https://biorxiv.org/content/10.1101/2020.07.02.184051v1?rss=1 La Manno, G. Siletti, K. Furlan, A. Gyllborg, D. Vinsland, E. Langseth, C. Khven, I. Johnsson, A. Nilsson, M. Lonnerberg, P. Linnarsson, S. 2020-07-03 doi:10.1101/2020.07.02.184051 Cold Spring Harbor Laboratory Press 2020-07-03 <![CDATA[ Protective Plant Immune Responses are Elicited by Bacterial Outer Membrane Vesicles ]]> https://biorxiv.org/content/10.1101/2020.07.24.220160v1?rss=1 McMillan, H. M. Zebell, S. G. Ristaino, J. B. Dong, X. Kuehn, M. 2020-07-24 doi:10.1101/2020.07.24.220160 Cold Spring Harbor Laboratory Press 2020-07-24 <![CDATA[ The claustrum-medial prefrontal cortex network controls attentional set-shifting ]]> https://biorxiv.org/content/10.1101/2020.10.14.339259v1?rss=1 Fodoulian, L. Gschwend, O. Huber, C. Mutel, S. Salazar, R. Leone, R. Renfer, J.-R. Ekundayo, K. Rodriguez, I. Carleton, A. 2020-10-15 doi:10.1101/2020.10.14.339259 Cold Spring Harbor Laboratory Press 2020-10-15 <![CDATA[ Mice alternate between discrete strategies during perceptual decision-making ]]> https://biorxiv.org/content/10.1101/2020.10.19.346353v1?rss=1 Ashwood, Z. C. Roy, N. A. Stone, I. R. International Brain Laboratory, T. Churchland, A. K. Pouget, A. Pillow, J. W. 2020-10-21 doi:10.1101/2020.10.19.346353 Cold Spring Harbor Laboratory Press 2020-10-21 <![CDATA[ Cancer phylogenetics using single-cell RNA-seq data ]]> https://biorxiv.org/content/10.1101/2021.01.07.425804v1?rss=1 Moravec, J. C. Lanfear, R. Spector, D. Diermeier, S. Gavryushkin, A. 2021-01-08 doi:10.1101/2021.01.07.425804 Cold Spring Harbor Laboratory Press 2021-01-08 <![CDATA[ Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL) ]]> https://biorxiv.org/content/10.1101/2021.04.22.436044v1?rss=1 Schatz, M. C. Philippakis, A. A. Afgan, E. Banks, E. Carey, V. J. Carroll, R. J. Culotti, A. Ellrott, K. Goecks, J. Grossman, R. L. Hall, I. Hansen, K. D. Lawson, J. Leek, J. T. O'Donnell Luria, A. Mosher, S. Morgan, M. Nekrutenko, A. O'Connor, B. D. Osborn, K. Paten, B. Patterson, C. Tan, F. J. Overby Taylor, C. Vessio, J. Waldron, L. D. Wang, T. Wuichet, K. AnVIL Team, 2021-04-23 doi:10.1101/2021.04.22.436044 Cold Spring Harbor Laboratory Press 2021-04-23 <![CDATA[ Key kinematic features in early training predict performance of adult female mice in a single pellet reaching and grasping task ]]> https://biorxiv.org/content/10.1101/2021.05.07.442851v1?rss=1 Mykins, M. Wade, E. An, X. Lau, B. Y. B. Krishnan, K. 2021-05-09 doi:10.1101/2021.05.07.442851 Cold Spring Harbor Laboratory Press 2021-05-09 <![CDATA[ A complete reference genome improves analysis of human genetic variation ]]> https://biorxiv.org/content/10.1101/2021.07.12.452063v1?rss=1 Aganezov, S. Yan, S. M. Soto, D. C. Kirsche, M. Zarate, S. Avdeyev, P. Taylor, D. J. Shafin, K. Shumate, A. Xiao, C. Wagner, J. McDaniel, J. Olson, N. D. Sauria, M. E. G. Vollger, M. R. Rhie, A. Meredith, M. Martin, S. Lee, J. Koren, S. Rosenfeld, J. Paten, B. Layer, R. Chin, C.-S. Sedlazeck, F. J. Hansen, N. F. Miller, D. E. Phillippy, A. M. Miga, K. H. McCoy, R. C. Dennis, M. Y. Zook, J. M. Schatz, M. C. 2021-07-13 doi:10.1101/2021.07.12.452063 Cold Spring Harbor Laboratory Press 2021-07-13 <![CDATA[ Arf6 anchors Cdr2 nodes at the cell cortex to control cell size at division ]]> https://biorxiv.org/content/10.1101/2021.08.17.456680v1?rss=1 Opalko, H. E. Miller, K. E. Kim, H.-S. Vargas-Garcia, C. A. Singh, A. Keogh, M.-C. Moseley, J. B. 2021-08-17 doi:10.1101/2021.08.17.456680 Cold Spring Harbor Laboratory Press 2021-08-17 <![CDATA[ QTL analysis of vegetative phase change in natural accessions of Arabidopsis thaliana ]]> https://biorxiv.org/content/10.1101/2021.10.27.465806v1?rss=1 Doody, E. Zha, Y. He, J. Poethig, S. 2021-10-28 doi:10.1101/2021.10.27.465806 Cold Spring Harbor Laboratory Press 2021-10-28 <![CDATA[ Genetic architecture of spatially complex color patterning in hybrid Mimulus ]]> https://biorxiv.org/content/10.1101/2022.04.29.490035v1?rss=1 Cooley, A. M. Schlutius, C. Matthews, M. Zheng, X. Thomas, D. Edger, P. Platts, A. George, L. Williams, A. LaFountain, A. Hundley, D. Yuan, Y.-w. Twyford, A. D. Puzey, J. D. 2022-05-01 doi:10.1101/2022.04.29.490035 Cold Spring Harbor Laboratory Press 2022-05-01 <![CDATA[ Phosphorylation of the Smooth Muscle Master Splicing Regulator RBPMS Regulates its Splicing Activity ]]> https://biorxiv.org/content/10.1101/2022.08.11.503562v1?rss=1 Barnhart, M. D. Yang, Y. Nakagaki-Silva, E. E. Hammond, T. H. Pizzinga, M. Gooding, C. Stott, K. Smith, C. 2022-08-12 doi:10.1101/2022.08.11.503562 Cold Spring Harbor Laboratory Press 2022-08-12 <![CDATA[ Tissue-Like 3D Standard and Protocols for Microscope Quality Management ]]> https://biorxiv.org/content/10.1101/2022.08.14.503777v1?rss=1 Abrams, B. Pengo, T. Deagle, R. C. Vuillemin, N. Wee, T. L. Callahan, L. M. Smith, M. A. Kubow, K. E. Girard, A.-M. Rappoport, J. Z. Bayles, C. J. Cameron, L. A. Cole, R. Brown, C. M. 2022-08-15 doi:10.1101/2022.08.14.503777 Cold Spring Harbor Laboratory Press 2022-08-15 <![CDATA[ Synthetic maize centromeres transmit chromosomes across generations ]]> https://biorxiv.org/content/10.1101/2022.09.19.508542v1?rss=1 Dawe, R. K. Gent, J. I. Zeng, Y. Zhang, H. Fu, F.-F. Wang, N. Kim, D. W. Swentowsky, K. W. Liu, J. Piri, R. D. 2022-09-19 doi:10.1101/2022.09.19.508542 Cold Spring Harbor Laboratory Press 2022-09-19 <![CDATA[ Ubiquitination steers SRF3 plasma membrane nano-organization to specify signaling outputs ]]> https://biorxiv.org/content/10.1101/2022.10.28.514292v1?rss=1 Platre, M. P. Gleason, M. F. Brent, L. Cao, M. Zhang, L. Satbhai, S. B. Neveu, J. Vert, G. Busch, W. 2022-10-31 doi:10.1101/2022.10.28.514292 Cold Spring Harbor Laboratory Press 2022-10-31 <![CDATA[ Root Walker: an automated pipeline for large scale quantification of early root growth responses at high spatial and temporal resolution ]]> https://biorxiv.org/content/10.1101/2022.11.16.516796v1?rss=1 Platre, M. P. Halvorson, Z. Mehta, P. Brent, L. Matias, G. F. Faizi, K. Busch, W. 2022-11-17 doi:10.1101/2022.11.16.516796 Cold Spring Harbor Laboratory Press 2022-11-17 <![CDATA[ Integrative proteogenomics using ProteomeGenerator2 ]]> https://biorxiv.org/content/10.1101/2023.01.04.522774v1?rss=1 Kwok, N. Aretz, Z. Takao, S. Ser, Z. Cifani, P. Kentsis, A. 2023-01-04 doi:10.1101/2023.01.04.522774 Cold Spring Harbor Laboratory Press 2023-01-04 <![CDATA[ Loss of secondary motor cortex neurons in chronic neuropathic pain ]]> https://biorxiv.org/content/10.1101/2023.01.05.522932v1?rss=1 Das Gupta, A. Zheng, H. Asan, L. John, J. Kaushalya, S. Beretta, C. Kuner, R. Knabbe, J. Kuner, T. 2023-01-05 doi:10.1101/2023.01.05.522932 Cold Spring Harbor Laboratory Press 2023-01-05 <![CDATA[ Mechanism of an alternative splicing switch mediated by cell-specific and general splicing regulators ]]> https://biorxiv.org/content/10.1101/2023.01.23.525191v1?rss=1 Smith, C. W. J. Yang, Y. Lee, G. Nakagaki-Silva, E. E. Huang, Y. Peacey, M. Partridge, R. Gooding, C. 2023-01-23 doi:10.1101/2023.01.23.525191 Cold Spring Harbor Laboratory Press 2023-01-23 <![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[ Improved genome assembly and annotation for the rock pigeon (Columba livia) ]]> https://biorxiv.org/content/10.1101/220947v1?rss=1 Holt, C. Campbell, M. Keays, D. Edelman, N. Kapusta, A. Maclary, E. Domyan, E. Suh, A. Warrenb, W. Yandell, M. Gilbert, T. Shapiro, M. D. 2017-11-21 doi:10.1101/220947 Cold Spring Harbor Laboratory Press 2017-11-21 <![CDATA[ Non-parametric and semi-parametric support estimation using SEquential RESampling random walks on biomolecular sequences ]]> https://biorxiv.org/content/10.1101/292078v1?rss=1 Wang, W. Smith, J. Hejase, H. Liu, K. J. 2018-03-30 doi:10.1101/292078 Cold Spring Harbor Laboratory Press 2018-03-30 <![CDATA[ Molecular architecture of the mouse nervous system ]]> https://biorxiv.org/content/10.1101/294918v1?rss=1 Zeisel, A. Hochgerner, H. Lonnerberg, P. Johnsson, A. Memic, F. van der Zwan, J. Haring, M. Braun, E. Borm, L. La Manno, G. Codeluppi, S. Furlan, A. Skene, N. Harris, K. D. Hjerling Leffler, J. Arenas, E. Ernfors, P. Marklund, U. Linnarsson, S. 2018-04-05 doi:10.1101/294918 Cold Spring Harbor Laboratory Press 2018-04-05 <![CDATA[ Representation Learning of Genomic Sequence Motifs with Convolutional Neural Networks ]]> https://biorxiv.org/content/10.1101/362756v1?rss=1 Koo, P. K. Eddy, S. R. 2018-07-08 doi:10.1101/362756 Cold Spring Harbor Laboratory Press 2018-07-08 <![CDATA[ Illuminating spatial A-to-I RNA editing signatures within the Drosophila brain ]]> https://biorxiv.org/content/10.1101/370296v1?rss=1 Sapiro, A. L. Shmueli, A. Henry, G. L. Li, Q. Shalit, T. Yaron, O. Paas, Y. Li, J. B. Shohat-Ophir, G. 2018-07-16 doi:10.1101/370296 Cold Spring Harbor Laboratory Press 2018-07-16 <![CDATA[ In vivo glucoregulation and tissue-specific glucose uptake in female Akt substrate 160 kDa knockout rats ]]> https://biorxiv.org/content/10.1101/777284v1?rss=1 ZHENG, X. Arias, E. Qi, N. Saunders, T. Cartee, G. 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Martienssen, R. A. 2023-05-30 doi:10.1101/2023.05.27.542553 Cold Spring Harbor Laboratory Press 2023-05-30 <![CDATA[ High-throughput confocal airy beam oblique light-sheet tomography of brain-wide imaging at single-cell resolution ]]> https://biorxiv.org/content/10.1101/2023.06.04.543586v1?rss=1 Qi, X. Castaneda, R. M. Narasimhan, A. Ding, L. Chen, X. Elowsky, C. Palmer, J. Drewes, R. Sun, J. Mizrachi, J. Peng, H. Wu, Z. Osten, P. 2023-06-06 doi:10.1101/2023.06.04.543586 Cold Spring Harbor Laboratory Press 2023-06-06 <![CDATA[ CyVerse: Cyberinfrastructure for Open Science ]]> https://biorxiv.org/content/10.1101/2023.06.16.545223v1?rss=1 Swetnam, T. L. Antin, P. B. Bartelme, R. Bucksch, A. Camhy, D. Chism, G. Choi, I. Cooksey, A. M. Cosi, M. Cowen, C. Culshaw-Maurer, M. Davey, R. Davey, S. Devisetty, U. Edgin, T. Edmonds, A. Fedorov, D. Frady, J. Fonner, J. Gillan, J. K. Hossain, I. Joyce, B. Lang, K. Lee, T. Littin, S. Mcewen, I. Merchant, N. Micklos, D. Nelson, A. Ramsey, A. Roberts, S. Sarando, P. Skidmore, E. Song, J. Sprinkle, M. M. Srinivasan, S. Strootman, J. D. Stryeck, S. Tuteja, R. Vaughn, M. Wali, M. Wall, M. Walls, R. Wang, L. Wickizer, T. Williams, J. Wregglesworth, J. 2023-06-19 doi:10.1101/2023.06.16.545223 Cold Spring Harbor Laboratory Press 2023-06-19 <![CDATA[ Protein evolvability under rewired genetic codes ]]> https://biorxiv.org/content/10.1101/2023.06.20.545706v1?rss=1 Rozhonova, H. Marti-Gomez, C. McCandlish, D. M. Payne, J. L. 2023-06-23 doi:10.1101/2023.06.20.545706 Cold Spring Harbor Laboratory Press 2023-06-23 <![CDATA[ HPC-based genome variant calling workflow (HPC-GVCW) ]]> https://biorxiv.org/content/10.1101/2023.06.25.546420v1?rss=1 Zhou, Y. Kathiresan, N. Yu, Z. Rivera, L. F. Thimma, M. Manickam, K. Chebotarov, D. Mauleon, R. Chougule, K. Wei, S. Gao, T. Green, C. D. Zuccolo, A. Zhang, J. Ware, D. McNally, K. L. Wing, R. A. 2023-06-26 doi:10.1101/2023.06.25.546420 Cold Spring Harbor Laboratory Press 2023-06-26 <![CDATA[ Engaged decision-makers align spontaneous movements to stereotyped task demands ]]> https://biorxiv.org/content/10.1101/2023.06.26.546404v1?rss=1 Yin, C. Melin, M. Rojas-Bowe, G. Couto, J. Sun, X. Gluf, S. Kostiuk, A. Musall, S. Churchland, A. K. 2023-06-26 doi:10.1101/2023.06.26.546404 Cold Spring Harbor Laboratory Press 2023-06-26 <![CDATA[ Stochastic coding: a conserved feature of odor representations and its implications for odor discrimination ]]> https://biorxiv.org/content/10.1101/2023.06.27.546757v1?rss=1 Srinivasan, S. Daste, S. Modi, M. Turner, G. Fleischmann, A. Navlakha, S. 2023-06-29 doi:10.1101/2023.06.27.546757 Cold Spring Harbor Laboratory Press 2023-06-29 <![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[ Chromatin remodeling of histone H3 variants underlies epigenetic inheritance of DNA methylation ]]> https://biorxiv.org/content/10.1101/2023.07.11.548598v1?rss=1 Lee, S. C. Adams, D. W. Ipsaro, J. J. Cahn, J. Lynn, J. Kim, H.-S. Berube, B. Major, V. Calarco, J. P. LeBlanc, C. Bhattacharjee, S. Ramu, U. Grimanelli, D. Jacob, Y. Voigt, P. Joshua-Tor, L. Martienssen, R. A. 2023-07-11 doi:10.1101/2023.07.11.548598 Cold Spring Harbor Laboratory Press 2023-07-11 <![CDATA[ Teosinte Pollen Drive guides maize domestication and evolution by RNAi ]]> https://biorxiv.org/content/10.1101/2023.07.12.548689v1?rss=1 Berube, B. Ernst, E. Cahn, J. Roche, B. de Santis Alves, C. Lynn, J. Scheben, A. Siepel, A. Ross-Ibarra, J. Kermicle, J. Martienssen, R. A. 2023-07-13 doi:10.1101/2023.07.12.548689 Cold Spring Harbor Laboratory Press 2023-07-13 <![CDATA[ The dynamics and geometry of choice in premotor cortex ]]> https://biorxiv.org/content/10.1101/2023.07.22.550183v1?rss=1 Genkin, M. Shenoy, K. V. Chandrasekaran, C. Engel, T. A. 2023-07-25 doi:10.1101/2023.07.22.550183 Cold Spring Harbor Laboratory Press 2023-07-25 <![CDATA[ Sexual coordination in a whole-brain map of prairie-vole pair-bonding ]]> https://biorxiv.org/content/10.1101/2023.07.26.550685v1?rss=1 Gustison, M. L. Munoz-Castaneda, R. Osten, P. Phelps, S. M. 2023-07-28 doi:10.1101/2023.07.26.550685 Cold Spring Harbor Laboratory Press 2023-07-28 <![CDATA[ Dendritic, delayed, and stochastic CaMKII activation underlies behavioral time scale plasticity in CA1 synapses ]]> https://biorxiv.org/content/10.1101/2023.08.01.549180v1?rss=1 Jain, A. Nakahata, Y. Watabe, T. Rusina, P. South, K. E. Adachi, K. Yan, L. Simorowski, N. Furukawa, H. Yasuda, R. 2023-08-01 doi:10.1101/2023.08.01.549180 Cold Spring Harbor Laboratory Press 2023-08-01 <![CDATA[ Restoring adiponectin via rosiglitazone ameliorates tissue wasting in mice with lung cancer. ]]> https://biorxiv.org/content/10.1101/2023.07.31.551241v1?rss=1 Langer, H. T. Ramsamooj, S. Dantas, E. Murthy, A. Ahmed, M. Hwang, S.-K. Grover, R. Pozovskiy, R. Liang, R. J. Queiroz, A. L. Brown, J. C. White, E. P. Janowitz, T. Goncalves, M. D. 2023-08-02 doi:10.1101/2023.07.31.551241 Cold Spring Harbor Laboratory Press 2023-08-02 <![CDATA[ Retrotransposon addiction promotes centromere function via epigenetically activated small RNAs ]]> https://biorxiv.org/content/10.1101/2023.08.02.551486v1?rss=1 Shimada, A. Cahn, J. Ernst, E. Lynn, J. Grimanelli, D. Henderson, I. R. Kakutani, T. Martienssen, R. A. 2023-08-02 doi:10.1101/2023.08.02.551486 Cold Spring Harbor Laboratory Press 2023-08-02 <![CDATA[ The genomes and epigenomes of aquatic plants (Lemnaceae) promote triploid hybridization and clonal reproduction ]]> https://biorxiv.org/content/10.1101/2023.08.02.551673v1?rss=1 Ernst, E. Abramson, B. Acosta, K. Hoang, P. T. Mateo-Elizalde, C. Schubert, V. Pasaribu, B. Hartwick, N. Colt, K. Aylward, A. J. Ramu, U. Birchler, J. A. Schubert, I. Lam, E. Michael, T. P. Martienssen, R. A. 2023-08-05 doi:10.1101/2023.08.02.551673 Cold Spring Harbor Laboratory Press 2023-08-05 <![CDATA[ Using deep long-read RNAseq in Alzheimer's disease brain to assess clinical relevance of RNA isoform diversity ]]> https://biorxiv.org/content/10.1101/2023.08.06.552162v1?rss=1 Aguzzoli Heberle, B. Brandon, J. A. Page, M. L. Nations, K. A. Dikobe, K. I. White, B. J. Gordon, L. A. Fox, G. A. Wadsworth, M. E. Doyle, P. H. Fox, E. J. Shantaraman, A. Ryten, M. Goodwin, S. Ghiban, E. Wappel, R. Mavruk-Eskpelivan, S. Miller, J. B. Seyfried, N. Nelson, P. T. Fryer, J. D. Ebbert, M. T. W. 2023-08-07 doi:10.1101/2023.08.06.552162 Cold Spring Harbor Laboratory Press 2023-08-07 <![CDATA[ Integrated high-confidence and high-throughput approaches for quantifying synapse engulfment by oligodendrocyte precursor cells ]]> https://biorxiv.org/content/10.1101/2023.08.24.554663v1?rss=1 Kahng, J. A. Xavier, A. M. Ferro, A. Auguste, Y. S. S. Cheadle, L. 2023-08-25 doi:10.1101/2023.08.24.554663 Cold Spring Harbor Laboratory Press 2023-08-25 <![CDATA[ Fast updating feedback from piriform cortex to the olfactory bulb relays multimodal reward contingency signals during rule-reversal ]]> https://biorxiv.org/content/10.1101/2023.09.12.557267v1?rss=1 Trejo, D. H. Ciuparu, A. Garcia da Silva, P. Velasquez, C. M. Rebouillat, B. Gross, M. D. Davis, M. B. Muresan, R. C. Albeanu, D. F. 2023-09-13 doi:10.1101/2023.09.12.557267 Cold Spring Harbor Laboratory Press 2023-09-13 <![CDATA[ Olfactory learning modulates a neural circuit mediating innate odor-guided behavior in Drosophila ]]> https://biorxiv.org/content/10.1101/2023.09.20.558596v1?rss=1 Campetella, F. Huber, R. Klappenbach, M. Wernecke, C. Locatelli, F. Felsenberg, J. Hansson, B. S. Knaden, M. Sachse, S. 2023-09-22 doi:10.1101/2023.09.20.558596 Cold Spring Harbor Laboratory Press 2023-09-22 <![CDATA[ Metabotropic signaling within somatostatin interneurons regulates thalamocortical inputs during development ]]> https://biorxiv.org/content/10.1101/2023.09.21.558862v1?rss=1 Dwivedi, D. Dumontier, D. Sherer, M. Lin, S. Mirow, A. M. Qiu, Y. Xu, Q. Liebman, S. A. Joseph, D. Datta, S. R. Fishell, G. Pouchelon, G. 2023-09-22 doi:10.1101/2023.09.21.558862 Cold Spring Harbor Laboratory Press 2023-09-22 <![CDATA[ Inhibiting Glutamine Metabolism Blocks Coronavirus Replication in Mammalian Cells ]]> https://biorxiv.org/content/10.1101/2023.09.27.559756v1?rss=1 Greene, K. S. Choi, A. Chen, M. Yang, N. Li, R. Qiu, Y. Lukey, M. J. Rojas, K. S. Shen, J. Wilson, K. F. Katt, W. P. Whittaker, G. R. Cerione, R. A. 2023-09-28 doi:10.1101/2023.09.27.559756 Cold Spring Harbor Laboratory Press 2023-09-28 <![CDATA[ ecDNA amplification of MYC drives intratumor copy-number heterogeneity and adaptation to stress in PDAC ]]> https://biorxiv.org/content/10.1101/2023.09.27.559717v1?rss=1 Malinova, A. Schreyer, D. Fiorini, E. Pasini, D. Bevere, M. D'Agosto, S. Andreani, S. Lupo, F. Veghini, L. Grimaldi, S. Pedron, S. Nourse, C. Salvia, R. Malleo, G. Ruzzenente, A. Guglielmi, A. Milella, M. Lawlor, R. T. Luchini, C. Pilarsky, C. Scarpa, A. Tuveson, D. Bailey, P. Corbo, V. 2023-09-29 doi:10.1101/2023.09.27.559717 Cold Spring Harbor Laboratory Press 2023-09-29 <![CDATA[ Single-cell transcription mapping of murine and human mammary organoids responses to female hormones ]]> https://biorxiv.org/content/10.1101/2023.09.28.559971v1?rss=1 Ruiz-Ortiz, J. Lewis, S. M. Ciccone, M. F. Chatterjee, D. Henry, S. Siepel, A. Dos Santos, C. O. 2023-09-29 doi:10.1101/2023.09.28.559971 Cold Spring Harbor Laboratory Press 2023-09-29 <![CDATA[ High-throughput single-nucleus hybrid sequencing reveals genome-transcriptome correlations in cancer ]]> https://biorxiv.org/content/10.1101/2023.10.04.560973v1?rss=1 Li, S. Alexander, J. Kendall, J. Andrews, P. Rose, E. Orjuela, H. Park, S. Podszus, C. Shanley, L. Ma, R. Ranade, N. Ronemus, M. Rishi, A. Donoho, D. L. Goldberg, G. L. Levy, D. Wigler, M. 2023-10-06 doi:10.1101/2023.10.04.560973 Cold Spring Harbor Laboratory Press 2023-10-06 <![CDATA[ Population variability in X-chromosome inactivation across 9 mammalian species ]]> https://biorxiv.org/content/10.1101/2023.10.17.562732v1?rss=1 Werner, J. Hover, J. Gillis, J. 2023-10-19 doi:10.1101/2023.10.17.562732 Cold Spring Harbor Laboratory Press 2023-10-19 <![CDATA[ Master transcription factor binding sites are necessary for early replication control element activity ]]> https://biorxiv.org/content/10.1101/2023.10.22.563497v1?rss=1 Turner, J. L. Gilbert, D. M. Ay, F. Hinojosa-Gonzalez, L. Vouzas, A. Sasaki, T. Fitch, C. A. Brown, A. N. Alexander, K. E. Soto, M. S. Chakraborty, A. 2023-10-23 doi:10.1101/2023.10.22.563497 Cold Spring Harbor Laboratory Press 2023-10-23 <![CDATA[ Marker-based CRISPR screening reveals a MED12-p63 interaction that activates basal identity in pancreatic ductal adenocarcinoma ]]> https://biorxiv.org/content/10.1101/2023.10.24.563848v1?rss=1 Maia-Silva, D. Schier, A. C. Skopelitis, D. Kechejian, V. Alpsoy, A. Liverpool, J. Taatjes, D. J. Vakoc, C. R. 2023-10-27 doi:10.1101/2023.10.24.563848 Cold Spring Harbor Laboratory Press 2023-10-27 <![CDATA[ A sub-set of guanine- and cytosine-rich genes are actively transcribed at the nuclear Lamin B1 region ]]> https://biorxiv.org/content/10.1101/2023.10.28.564411v1?rss=1 Balasooriya, G. I. Wee, T. L. Spector, D. 2023-10-28 doi:10.1101/2023.10.28.564411 Cold Spring Harbor Laboratory Press 2023-10-28 <![CDATA[ Utility of AlphaMissense predictions in Asparagine Synthetase deficiency variant classification ]]> https://biorxiv.org/content/10.1101/2023.10.30.564808v1?rss=1 Staklinski, S. J. Scheben, A. J. Siepel, A. Kilberg, M. S. 2023-11-02 doi:10.1101/2023.10.30.564808 Cold Spring Harbor Laboratory Press 2023-11-02 <![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[ Interpreting cis-regulatory mechanisms from genomic deep neural networks using surrogate models ]]> https://biorxiv.org/content/10.1101/2023.11.14.567120v1?rss=1 Seitz, E. McCandlish, D. M. Kinney, J. B. Koo, P. K. 2023-11-16 doi:10.1101/2023.11.14.567120 Cold Spring Harbor Laboratory Press 2023-11-16 <![CDATA[ Preserved particulate organic carbon is likely derived from the subsurface sulfidic photic zone of the Proterozoic Ocean: evidence from a modern, oxygen-deficient lake ]]> https://biorxiv.org/content/10.1101/2023.11.19.567733v1?rss=1 2.7 m) particulate organic carbon values (813CPOC) from meromictic Fayetteville Green Lake, NY, USA. The high-O2 Calvin-Benson-Bassham (CBB) gene (cbbL) was most abundant in the <2.7 m size fraction in shallow oxic and deep hypoxic waters, corresponding with cyanobacterial populations. The low-O2 CBB gene (cbbM) was most abundant near the lower oxycline boundary in the larger size fraction, coincident with purple sulfur bacteria populations. The reverse citric acid cycle gene (aclB) was equally abundant in both size fractions in the deepest photic zone, coinciding with green sulfur bacteria populations. Methane coenzyme reductase A (mcrA), of anaerobic methane cyclers, was most abundant at the lower oxycline boundary in both size fractions, coinciding with Methanoregula populations. 813CPOC values overlapped with the high-O2 CBB fixation range except for two negative excursions near the lower oxycline boundary, likely reflecting assimilation of isotopically-depleted groundwater-derived inorganic carbon by autotrophs and acetate oxidation by sulfate-reducers. Throughout aphotic waters, 813CPOC values of the large size fraction became 13C-enriched, likely reflecting abundant purple sulfur bacterial aggregates. Microalgal-like isotopic signatures corresponded with increases in cbbL, cbbM and aclB, and enrichment of exopolymer-rich prokaryotic photoautotrophs aggregates. Results suggest that 813CPOC values of preserved sediments from areas of the Proterozoic Ocean with sulfidic photic zones may reflect a mixture of alternate carbon-fixing populations exported from the deep photic zone, challenging the paradigm that sedimentary stable carbon isotope values predominantly reflect oxygenic photosynthesis from surface waters. ]]> Cohen, A. B. Taylor, G. T. Henkes, G. Weber, F. Christensen, L. N. Yagudaeva, M. Lo, E. McCormick, M. 2023-11-19 doi:10.1101/2023.11.19.567733 Cold Spring Harbor Laboratory Press 2023-11-19 <![CDATA[ Compact deep neural network models of visual cortex ]]> https://biorxiv.org/content/10.1101/2023.11.22.568315v1?rss=1 Cowley, B. R. Stan, P. L. Pillow, J. W. Smith, M. A. 2023-11-23 doi:10.1101/2023.11.22.568315 Cold Spring Harbor Laboratory Press 2023-11-23 <![CDATA[ Anatomical insights into the vascular lay-out of the barley rachis: implications for transport and spikelet connection ]]> https://biorxiv.org/content/10.1101/2023.11.23.568454v1?rss=1 Rutten, T. Thirulogachandar, V. Huang, Y. Shanmugaraj, N. Koppolu, R. Ortleb, S. Hensel, G. Kumlehn, J. Melzer, M. Schnurbusch, T. 2023-11-23 doi:10.1101/2023.11.23.568454 Cold Spring Harbor Laboratory Press 2023-11-23 <![CDATA[ copepodTCR: Identification of Antigen-Specific T Cell Receptors with combinatorial peptide pooling ]]> https://biorxiv.org/content/10.1101/2023.11.28.569052v1?rss=1 Kovaleva, V. A. Pattinson, D. J. Barton, C. Chapin, S. R. Minerva, A. A. Richards, K. A. Sant, A. J. Thomas, P. G. Pogorelyy, M. V. Meyer, H. V. 2023-11-29 doi:10.1101/2023.11.28.569052 Cold Spring Harbor Laboratory Press 2023-11-29 <![CDATA[ Coexpression enhances cross-species integration of scRNA-seq across diverse plant species ]]> https://biorxiv.org/content/10.1101/2023.11.28.569145v1?rss=1 Passalacqua, M. J. Gillis, J. 2023-11-30 doi:10.1101/2023.11.28.569145 Cold Spring Harbor Laboratory Press 2023-11-30 <![CDATA[ Unraveling the Phenotypic States of Human innate-like T Cells: Comparative Insights with Conventional T Cells and Mouse Models ]]> https://biorxiv.org/content/10.1101/2023.12.07.570707v1?rss=1 Loh, L. Carcy, S. Krovi, H. S. Domenico, J. Spengler, A. Lin, Y. Torres, J. D. Palmer, W. Norman, P. J. Stone, M. Brunetti, T. Meyer, H. V. Gapin, L. 2023-12-08 doi:10.1101/2023.12.07.570707 Cold Spring Harbor Laboratory Press 2023-12-08 <![CDATA[ AI without networks ]]> https://biorxiv.org/content/10.1101/2023.12.09.570922v1?rss=1 Mitra, P. P. Sire, C. 2023-12-09 doi:10.1101/2023.12.09.570922 Cold Spring Harbor Laboratory Press 2023-12-09 <![CDATA[ The blobulator: a webtool for identification andvisual exploration of hydrophobic modularity inprotein sequences ]]> https://biorxiv.org/content/10.1101/2024.01.15.575761v1?rss=1 Pitman, C. Santiago-McRae, E. Lohia, R. Bassi, K. Joseph, T. T. Hansen, M. E. B. Brannigan, G. 2024-01-16 doi:10.1101/2024.01.15.575761 Cold Spring Harbor Laboratory Press 2024-01-16 <![CDATA[ Mammalian SWI/SNF complex activity regulates POU2F3 and constitutes a targetable dependency in small cell lung cancer ]]> https://biorxiv.org/content/10.1101/2024.01.21.576304v1?rss=1 Duplaquet, L. So, K. Ying, A. W. Li, X. Li, Y. Qiu, X. Li, R. Singh, S. Wu, X. S. Liu, Q. Qi, J. Somerville, T. D. D. Heiling, H. Mazzola, E. Lee, Y. Zoller, T. Vakoc, C. R. Doench, J. G. Forrester, W. C. Abrams, T. Long, H. W. Niederst, M. J. Kadoch, C. Oser, M. G. 2024-01-24 doi:10.1101/2024.01.21.576304 Cold Spring Harbor Laboratory Press 2024-01-24 <![CDATA[ Early dynamics of excitation and inhibition maintain late frequency tuning in auditory cortex ]]> https://biorxiv.org/content/10.1101/2024.01.26.577483v1?rss=1 Reid, A. P. Hromadka, T. Zador, A. M. 2024-01-27 doi:10.1101/2024.01.26.577483 Cold Spring Harbor Laboratory Press 2024-01-27 <![CDATA[ Convergent evolution of plant prickles is drivenby repeated gene co-option over deep time ]]> https://biorxiv.org/content/10.1101/2024.02.21.581474v1?rss=1 Satterlee, J. W. Alonso, D. Gramazio, P. Jenike, K. M. He, J. Arrones, A. Villanueva, G. Plazas, M. Ramakrishnan, S. Benoit, M. Gentile, I. Hendelman, A. Shohat, H. Fitzgerald, B. Robitaille, G. M. Green, Y. Swartwood, K. Passalacqua, M. J. Gagnon, E. Hilgenhof, R. Huggins, T. D. Eizenga, G. C. Gur, A. Rutten, T. Stein, N. Yao, S. Bellot, C. Bendahmane, M. Frary, A. Knapp, S. Sarkinen, T. Gillis, J. Van Eck, J. Schatz, M. C. Eshed, Y. Prohens, J. Vilanova, S. Lippman, Z. B. 2024-02-22 doi:10.1101/2024.02.21.581474 Cold Spring Harbor Laboratory Press 2024-02-22 <![CDATA[ MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication. ]]> https://biorxiv.org/content/10.1101/2024.02.22.581585v1?rss=1 Cahn, J. Regulski, M. Lynn, J. Ernst, E. de Santis Alves, C. Ramakrishnan, S. Chougule, K. Wei, S. Lu, Z. Xu, X. Drenkow, J. Kramer, M. Seetharam, A. Hufford, M. B. McCombie, W. R. Ware, D. Jackson, D. Schatz, M. C. Gingeras, T. R. Martienssen, R. A. 2024-02-23 doi:10.1101/2024.02.22.581585 Cold Spring Harbor Laboratory Press 2024-02-23 <![CDATA[ Orderly specification and precise laminar deployment of cortical glutamatergic projection neuron types through intermediate progenitors ]]> https://biorxiv.org/content/10.1101/2024.03.01.582863v1?rss=1 Huilgol, D. Levine, J. M. Galbavy, W. Wang, B.-S. Huang, Z. J. 2024-03-02 doi:10.1101/2024.03.01.582863 Cold Spring Harbor Laboratory Press 2024-03-02 <![CDATA[ Large-scale single-cell profiling of stem cells uncovers redundant regulators of shoot development and yield trait variation ]]> https://biorxiv.org/content/10.1101/2024.03.04.583414v1?rss=1 Xu, X. Passalacqua, M. Rice, B. Demesa-Arevalo, E. Kojima, M. Takebayashi, Y. Harris, B. Sakakibara, H. Gallavotti, A. Gillis, J. Jackson, D. 2024-03-06 doi:10.1101/2024.03.04.583414 Cold Spring Harbor Laboratory Press 2024-03-06 <![CDATA[ The cytokine receptor Fn14 is a molecular brake on neuronal activity that mediates circadian function in vivo ]]> https://biorxiv.org/content/10.1101/2024.04.02.587786v1?rss=1 Ferro, A. Arshad, A. Boyd, L. Stanley, T. Berisha, A. Vrudhula, U. Gomez, A. M. Borniger, J. C. Cheadle, L. M. 2024-04-02 doi:10.1101/2024.04.02.587786 Cold Spring Harbor Laboratory Press 2024-04-02 <![CDATA[ Establishing neuroanatomical correspondences across mouse and marmoset brain structures ]]> https://biorxiv.org/content/10.1101/2024.05.06.592808v1?rss=1 Mezias, C. Huo, B. Bota, M. Jayakumar, J. Mitra, P. P. 2024-05-08 doi:10.1101/2024.05.06.592808 Cold Spring Harbor Laboratory Press 2024-05-08 <![CDATA[ A 3D whole-face movement analysis system to uncover underlying physiology in mice ]]> https://biorxiv.org/content/10.1101/2024.05.07.593051v1?rss=1 Daruwalla, K. Martin, I. N. Frankel, A. Naglic, D. Ahmad, Z. Hou, X. H. 2024-05-08 doi:10.1101/2024.05.07.593051 Cold Spring Harbor Laboratory Press 2024-05-08 <![CDATA[ The structural landscape of Microprocessor Mediated pri-let-7 miRNAs processing ]]> https://biorxiv.org/content/10.1101/2024.05.09.593372v1?rss=1 Garg, A. Shang, R. Cvetanovic, T. Lai, E. C. Joshua-Tor, L. 2024-05-09 doi:10.1101/2024.05.09.593372 Cold Spring Harbor Laboratory Press 2024-05-09 <![CDATA[ It only takes seconds for a human monoclonal autoantibody to inhibit N-methyl-D-aspartate receptors ]]> https://biorxiv.org/content/10.1101/2024.05.28.595700v1?rss=1 Yang, S. Heckmann, J. Taha, A. Gao, S. Steinke, S. Hust, M. Pruess, H. Furukawa, H. Geis, C. Heckmann, M. Yu-Strzelczyk, J. 2024-06-01 doi:10.1101/2024.05.28.595700 Cold Spring Harbor Laboratory Press 2024-06-01 <![CDATA[ Cross-species plant genomes modeling at single nucleotide resolution using a pre-trained DNA language model ]]> https://biorxiv.org/content/10.1101/2024.06.04.596709v1?rss=1 Zhai, J. Gokaslan, A. Schiff, Y. Berthel, A. Liu, Z.-Y. Miller, Z. R. Scheben, A. Stitzer, M. C. Romay, C. Buckler, E. S. Kuleshov, V. 2024-06-05 doi:10.1101/2024.06.04.596709 Cold Spring Harbor Laboratory Press 2024-06-05 <![CDATA[ Directionality bias is necessary to explain spatiotemporal progression of pathology in mouse models of tauopathy ]]> https://biorxiv.org/content/10.1101/2024.06.04.597478v1?rss=1 Torok, J. Mezias, C. Raj, A. 2024-06-06 doi:10.1101/2024.06.04.597478 Cold Spring Harbor Laboratory Press 2024-06-06 <![CDATA[ A single-cell transcriptomic atlas of sensory-dependent gene expression in developing mouse visual cortex ]]> https://biorxiv.org/content/10.1101/2024.06.25.600673v1?rss=1 Xavier, A. M. Lin, Q. Kang, C. J. Cheadle, L. 2024-06-26 doi:10.1101/2024.06.25.600673 Cold Spring Harbor Laboratory Press 2024-06-26 <![CDATA[ A side-by-side comparison of variant function measurements using deep mutational scanning and base editing ]]> https://biorxiv.org/content/10.1101/2024.06.30.601444v1?rss=1 Sokirniy, I. Inam, H. McCandlish, D. Pritchard, J. R. 2024-07-01 doi:10.1101/2024.06.30.601444 Cold Spring Harbor Laboratory Press 2024-07-01 <![CDATA[ Exploring the genetic and epigenetic underpinnings of early-onset cancers: Variant prioritization for long read whole genome sequencing from family cancer pedigrees ]]> https://biorxiv.org/content/10.1101/2024.06.27.601096v1?rss=1 Kramer, M. Goodwin, S. Wappel, R. Borio, M. Offit, K. Feldman, D. R. Stadler, Z. K. McCombie, W. R. 2024-07-02 doi:10.1101/2024.06.27.601096 Cold Spring Harbor Laboratory Press 2024-07-02 <![CDATA[ Reticulate leaf venation in Pilea peperomioides is a Voronoi diagram ]]> https://biorxiv.org/content/10.1101/2024.07.01.601217v1?rss=1 Zheng, X. Venezia, M. Blum, E. Pedmale, U. V. Jackson, D. Prusinkiewicz, P. Navlakha, S. 2024-07-03 doi:10.1101/2024.07.01.601217 Cold Spring Harbor Laboratory Press 2024-07-03 <![CDATA[ The microRNA156/SPL9 module mediates auxin response to facilitate apical hook maintenance in Arabidopsis ]]> https://biorxiv.org/content/10.1101/2024.07.16.603710v1?rss=1 Pierdona, F. G. Silva, A. J. M. Vicente, M. H. Taylor, L. Pedmale, U. V. Nogueira, F. T. S. 2024-07-19 doi:10.1101/2024.07.16.603710 Cold Spring Harbor Laboratory Press 2024-07-19 <![CDATA[ A disinhibitory basal forebrain to cortex projection supports sustained attention ]]> https://biorxiv.org/content/10.1101/2024.07.22.604711v1?rss=1 Li, S.-J. Hangya, B. Gupta, U. Fischer, K. B. Sturgill, J. F. Callaway, E. M. Kepecs, A. 2024-07-23 doi:10.1101/2024.07.22.604711 Cold Spring Harbor Laboratory Press 2024-07-23 <![CDATA[ Dynorphin modulates motivation through a pallido-amygdala cholinergic circuit ]]> https://biorxiv.org/content/10.1101/2024.07.31.605785v1?rss=1 Li, B. Sun, Q. Liu, M. Guan, W. Xiao, X. Dong, C. Bruchas, M. Zweifel, L. Li, Y. Tian, L. 2024-07-31 doi:10.1101/2024.07.31.605785 Cold Spring Harbor Laboratory Press 2024-07-31 <![CDATA[ Inferring polygenic negative selection underlying an individual trait as a distribution of fitness effects (DFEs) from GWAS summary statistics ]]> https://biorxiv.org/content/10.1101/2024.07.29.601707v1?rss=1 Xue, A. T. Huang, Y.-f. Siepel, A. 2024-08-02 doi:10.1101/2024.07.29.601707 Cold Spring Harbor Laboratory Press 2024-08-02 <![CDATA[ Restoring transient connectivity during development improves dysfunctions in fragile X mice ]]> https://biorxiv.org/content/10.1101/2024.09.08.611918v1?rss=1 Dumontier, D. Liebman, S. A. Le, V.-H. George, S. Valdemar, D. Van Aelst, L. Pouchelon, G. 2024-09-09 doi:10.1101/2024.09.08.611918 Cold Spring Harbor Laboratory Press 2024-09-09 <![CDATA[ Spontaneously regenerative corticospinal neurons in mice ]]> https://biorxiv.org/content/10.1101/2024.09.09.612115v1?rss=1 Fait, B. W. Cotto, B. Murakami, T. C. Hagemann-Jensen, M. Zhan, H. Freivald, C. Turbek, I. Gao, Y. Yao, Z. Way, S. W. Zeng, H. Tasic, B. Steward, O. Heintz, N. Schmidt, E. F. 2024-09-12 doi:10.1101/2024.09.09.612115 Cold Spring Harbor Laboratory Press 2024-09-12 <![CDATA[ Solanum pan-genomics and pan-genetics reveal paralogs as contingencies in crop engineering ]]> https://biorxiv.org/content/10.1101/2024.09.10.612244v1?rss=1 Benoit, M. Jenike, K. M. Satterlee, J. W. Ramakrishnan, S. Gentile, I. Hendelman, A. Passalacqua, M. J. Suresh, H. Shohat, H. Robitaille, G. M. Fitzgerald, B. Alonge, M. M. Wang, X. Santos, R. He, J. Ou, S. Golan, H. Green, Y. Swartwood, K. Sierra, G. P. Orejuela, A. Fornaguera, F. Goodwin, S. McCombie, W. R. Kizito, E. B. Gagnon, E. Knapp, S. Sarkinen, T. Frary, A. Gillis, J. Van Eck, J. Schatz, M. C. Lippman, Z. B. 2024-09-14 doi:10.1101/2024.09.10.612244 Cold Spring Harbor Laboratory Press 2024-09-14 <![CDATA[ Selective expansion of motor cortical projections in the evolution of vocal novelty ]]> https://biorxiv.org/content/10.1101/2024.09.13.612752v1?rss=1 Isko, E. C. Harpole, C. E. Zheng, X. M. Zhan, H. Davis, M. B. Zador, A. M. Banerjee, A. 2024-09-14 doi:10.1101/2024.09.13.612752 Cold Spring Harbor Laboratory Press 2024-09-14 <![CDATA[ A brain-body feedback loop driving HPA-axis dysfunction in breast cancer ]]> https://biorxiv.org/content/10.1101/2024.09.13.612923v1?rss=1 Gomez, A. Wu, Y. Zhang, C. Boyd, L. Wee, T. L. Gewolb, J. Amor, C. Cheadle, L. M. Borniger, J. C. 2024-09-14 doi:10.1101/2024.09.13.612923 Cold Spring Harbor Laboratory Press 2024-09-14 <![CDATA[ Eigengene reveals invariant global spatial patterns across mouse and fish brain development ]]> https://biorxiv.org/content/10.1101/2024.09.19.613507v1?rss=1 Kerstjens, S. Engert, F. Zador, A. M. Douglas, R. J. 2024-09-20 doi:10.1101/2024.09.19.613507 Cold Spring Harbor Laboratory Press 2024-09-20 <![CDATA[ Medicago truncatula CORYNE regulates inflorescence meristem branching, nutrient signaling, and arbuscular mycorrhizal symbiosis ]]> https://biorxiv.org/content/10.1101/2024.09.20.614181v1?rss=1 Orosz, J. Lin, E. X. Lindsay, P. L. Kappes, M. Bashyal, S. Everett, H. Gautam, C. K. Jackson, D. Mueller, L. M. 2024-09-23 doi:10.1101/2024.09.20.614181 Cold Spring Harbor Laboratory Press 2024-09-23 <![CDATA[ GRAS Family Transcription Factor Binding Behaviors in Sorghum bicolor, Oyrza, and Maize ]]> https://biorxiv.org/content/10.1101/2024.09.23.614502v1?rss=1 Gladman, N. P. Kumari, S. Fahey, A. Regulski, M. Ware, D. 2024-09-25 doi:10.1101/2024.09.23.614502 Cold Spring Harbor Laboratory Press 2024-09-25 <![CDATA[ GeTMoR: Simultaneous genomic, transcriptomic, andmorphological profiling of rare single cells ]]> https://biorxiv.org/content/10.1101/2024.09.29.615279v1?rss=1 Prabakar, R. K. Schmidt, M. J. Kuhn, P. Hicks, J. 2024-10-01 doi:10.1101/2024.09.29.615279 Cold Spring Harbor Laboratory Press 2024-10-01 <![CDATA[ Brain Structural Organization Revealed by Unbiased Cell-Type Distribution Clustering ]]> https://biorxiv.org/content/10.1101/2024.10.02.615922v1?rss=1 Munoz-Castaneda, R. Palaniswamy, R. Palmer, J. Drewes, R. Elowsky, C. Hirokawa, K. E. Cain, N. Venkataraju, K. U. Harris, J. A. Osten, P. 2024-10-03 doi:10.1101/2024.10.02.615922 Cold Spring Harbor Laboratory Press 2024-10-03 <![CDATA[ Quantitative proteomic mass spectrometry of protein kinases to determine dynamic heterogeneity of the human kinome ]]> https://biorxiv.org/content/10.1101/2024.10.04.614143v1?rss=1 300 kinases in a single LC-MS experiment using ten micrograms protein from human tissues including biopsies. This enables absolute quantitation of kinase protein abundance at attomole-femtomole expression levels, requiring no kinase enrichment and less than ten micrograms of starting protein from flash-frozen and formalin fixed paraffin embedded tissues. Breast cancer biopsies, organoids, and cell lines were analyzed using the SureQuant method, demonstrating the heterogeneity of kinase protein expression across and within breast cancer clinical subtypes. Kinome quantitation was coupled with nanoscale phosphoproteomics, providing a feasible method for novel clinical diagnosis and understanding of patient kinome responses to treatment. ]]> East, M. P. Sprung, R. W. Okumu, D. O. Olivares-Quintero, J. F. Joisa, C. U. Chen, X. Zhang, Q. Erdmann-Gilmore, P. Mi, Y. Sciaky, N. Malone, J. P. Bhatia, S. McCabe, I. C. Xu, Y. Sutcliffe, M. D. Luo, J. Spears, P. A. Perou, C. M. Earp, H. S. Carey, L. A. Yeh, J. J. Spector, D. L. Gomez, S. M. Spanheimer, P. M. Townsend, R. R. Johnson, G. L. 2024-10-04 doi:10.1101/2024.10.04.614143 Cold Spring Harbor Laboratory Press 2024-10-04 <![CDATA[ A fitness distribution law for amino-acid replacements ]]> https://biorxiv.org/content/10.1101/2024.10.11.617952v1?rss=1 Sun, M. Stoltzfus, A. McCandlish, D. M. 2024-10-15 doi:10.1101/2024.10.11.617952 Cold Spring Harbor Laboratory Press 2024-10-15 <![CDATA[ Diversity of ancestral brainstem noradrenergic neurons across species and multiple biological factors ]]> https://biorxiv.org/content/10.1101/2024.10.14.618224v1?rss=1 Kelberman, M. A. Rodberg, E. Arabzadeh, E. Bair-Marshall, C. J. Berridge, C. W. Berrocoso, E. Breton-Provencher, V. Chandler, D. J. Che, A. Davy, O. Devilbiss, D. M. Downs, A. M. Drummond, G. Dvorkin, R. Fazlali, Z. Froemke, R. C. Glennon, E. Gold, J. I. Ito, H. Jiang, X. Johansen, J. P. Kaye, A. P. Kim, J. R. Kuo, C.-c. Liu, R.-j. Liu, Y. Llorca-Torralba, M. McCall, J. G. McElligott, Z. A. McKinney, A. M. Miguelez, C. Min, M.-Y. Nowlan, A. C. Omrani, M. Pickering, A. E. Poe, G. R. Ranjbar-Slamloo, Y. Razquin, J. Rodenkirch, C. Sales, A. C. Satyasambit, 2024-10-16 doi:10.1101/2024.10.14.618224 Cold Spring Harbor Laboratory Press 2024-10-16 <![CDATA[ Ductal pancreatic cancer interception by FGFR2 abrogation ]]> https://biorxiv.org/content/10.1101/2024.10.16.618726v1?rss=1 Tonelli, C. Deschenes, A. Gaeth, V. Jensen, A. Vithlani, N. Yao, M. A. Zhao, Z. Park, Y. Tuveson, D. 2024-10-18 doi:10.1101/2024.10.16.618726 Cold Spring Harbor Laboratory Press 2024-10-18 <![CDATA[ Antagonizing cis-regulatory elements of a conserved flowering gene mediate developmental robustness ]]> https://biorxiv.org/content/10.1101/2024.11.03.621740v1?rss=1 Lanctot, A. Hendelman, A. Udilovich, P. Robitaille, G. M. Lippman, Z. 2024-11-05 doi:10.1101/2024.11.03.621740 Cold Spring Harbor Laboratory Press 2024-11-05 <![CDATA[ Uncertainty-aware genomic deep learning with knowledge distillation ]]> https://biorxiv.org/content/10.1101/2024.11.13.623485v1?rss=1 Zhou, J. Rizzo, K. Tang, Z. Koo, P. K. 2024-11-15 doi:10.1101/2024.11.13.623485 Cold Spring Harbor Laboratory Press 2024-11-15 <![CDATA[ Dynamic consensus-building between neocortical areas via long-range connections ]]> https://biorxiv.org/content/10.1101/2024.11.27.625691v1?rss=1 Javadzadeh, M. Schimel, M. Hofer, S. B. Ahmadian, Y. Hennequin, G. 2024-11-27 doi:10.1101/2024.11.27.625691 Cold Spring Harbor Laboratory Press 2024-11-27 <![CDATA[ Temporal and Spatial Characterization of CUL3KLHL20-driven Targeted Degradation of BET family, BRD Proteins by the Macrocycle-based Degrader BTR2004 ]]> https://biorxiv.org/content/10.1101/2024.12.07.627262v1?rss=1 Yeh, J. Fechtmeyer, P. 2024-12-07 doi:10.1101/2024.12.07.627262 Cold Spring Harbor Laboratory Press 2024-12-07 <![CDATA[ A three-dimensional histological cell atlas of the developing human brain ]]> https://biorxiv.org/content/10.1101/2024.12.17.628811v1?rss=1 Jayakumar, J. Sivaprakasam, M. Verma, R. Bota, M. Joseph, J. Mulay, S. Kumutha, J. Srinivasan, C. S, S. S, L. Kumar, H. E. Bhaduri, A. Nowakowski, T. J. Roy, P. K. Savoia, S. Banerjee, S. Tward, D. Mitra, P. P. 2024-12-18 doi:10.1101/2024.12.17.628811 Cold Spring Harbor Laboratory Press 2024-12-18 <![CDATA[ Weight Transfer in the Reinforcement Learning Model of Songbird Acquisition ]]> https://biorxiv.org/content/10.1101/2024.12.30.628217v1?rss=1 Tran, K. Koulakov, A. 2024-12-30 doi:10.1101/2024.12.30.628217 Cold Spring Harbor Laboratory Press 2024-12-30 <![CDATA[ LIN-67 functionally interacts with heterochronic miRNAs and regulates developmental timing in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2024.12.31.630947v1?rss=1 Medley, J. C. Perales, R. Gaete Humada, B. Doerfel, K. Levine, A. Panzade, G. Hammell, C. M. Zinovyeva, A. 2025-01-02 doi:10.1101/2024.12.31.630947 Cold Spring Harbor Laboratory Press 2025-01-02 <![CDATA[ Diurnal Modulation of Locus Coeruleus Noradrenergic Neurons in Anesthetized Adult Male Rats ]]> https://biorxiv.org/content/10.1101/2025.01.06.631545v1?rss=1 Rae, R. J. Baker, N. L. Irwin, Z. T. Shea, S. D. McMahon, L. L. 2025-01-07 doi:10.1101/2025.01.06.631545 Cold Spring Harbor Laboratory Press 2025-01-07 <![CDATA[ Volatile-suppressed peptide signaling enhances volatile responses in plant-plant interactions ]]> https://biorxiv.org/content/10.1101/2025.01.20.634011v1?rss=1 Wang, L. Hoefer, S. Jimenez-Sandoval, P. Yu, H. Spiegelhalder, R. Waterman, J. M. Hurni, L. Hu, L. Liu, L. Jackson, D. Raissig, M. Erb, M. 2025-01-23 doi:10.1101/2025.01.20.634011 Cold Spring Harbor Laboratory Press 2025-01-23 <![CDATA[ Extensive genome evolution distinguishes maize within a stable tribe of grasses ]]> https://biorxiv.org/content/10.1101/2025.01.22.633974v1?rss=1 Stitzer, M. C. Seetharam, A. S. Scheben, A. Hsu, S.-K. Schulz, A. J. AuBuchon-Elder, T. El-Walid, M. Ferebee, T. H. Hale, C. O. La, T. Liu, Z.-Y. McMorrow, S. J. Minx, P. Phillips, A. Syring, M. Wrightsman, T. Zhai, J. Pasquet, R. McAllister, C. Malcomber, S. Traiperm, P. Layton, D. Zhong, J. Costich, D. E. Dawe, R. K. Fengler, K. Harris, C. Irelan, Z. Llaca, V. Parakkal, P. Zastrow-Hayes, G. Woodhouse, M. R. Cannon, E. K. Portwood, J. Andorf, C. M. Albert, P. S. Birchler, J. A. Siepel, A. Ross-Ibarra, J. Romay, M. C. Kellogg, E. Buckler, E. S. Hufford 2025-01-24 doi:10.1101/2025.01.22.633974 Cold Spring Harbor Laboratory Press 2025-01-24 <![CDATA[ An evolutionarily conserved mechanism for reformatting odor concentration in early olfactory circuits ]]> https://biorxiv.org/content/10.1101/2025.01.23.634259v1?rss=1 Shen, Y. Banerjee, A. Albeanu, D. F. Navlakha, S. 2025-01-24 doi:10.1101/2025.01.23.634259 Cold Spring Harbor Laboratory Press 2025-01-24 <![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[ Non-Canonical Role of DNA Mismatch Repair on Sensory Processing in Mice ]]> https://biorxiv.org/content/10.1101/2025.02.13.638164v1?rss=1 Oviedo, H. V. Rahman, S. N. Neophytou, D. Oviedo-Gray, S. Vuong, B. Q. 2025-02-17 doi:10.1101/2025.02.13.638164 Cold Spring Harbor Laboratory Press 2025-02-17 <![CDATA[ A pan-gene catalogue of Asian cultivated rice ]]> https://biorxiv.org/content/10.1101/2025.02.17.638606v1?rss=1 Contreras-Moreira, B. Sharma, E. Saraf, S. Naamati, G. Gupta, P. Elser, J. Chebotarov, D. Chougule, K. Lu, Z. Wei, S. Olson, A. Tsang, I. Lodha, D. Zhou, Y. Yu, Z. Zhao, W. Zhang, J. Amberkar, S. Sue-Ob, K. Martin, M. McNally, K. L. Ware, D. Sun, Z. Deutsch, E. W. Copetti, D. Wing, R. A. Jaiswal, P. Dyer, S. Jones, A. R. 2025-02-23 doi:10.1101/2025.02.17.638606 Cold Spring Harbor Laboratory Press 2025-02-23 <![CDATA[ Triploidy is prominent in the duckweed Lemna minor complex ]]> https://biorxiv.org/content/10.1101/2025.02.18.638736v1?rss=1 Michael, T. P. Hoang, P. T. N. Abramson, B. W. Mamerto, A. Pasaribu, B. Ernst, E. Allsing, N. Braglia, L. Petrus, S. Fuchs, J. Schubert, V. Hartwick, N. Wang, M. Lensink, M. Duong, T. Colt, K. Bog, M. Sree, K. S. Morello, L. Appenroth, K. J. Schubert, I. Martienssen, R. A. Lam, E. 2025-02-23 doi:10.1101/2025.02.18.638736 Cold Spring Harbor Laboratory Press 2025-02-23 <![CDATA[ Autophagy Suppresses CCL2 to Preserve Appetite and Prevent Lethal Cachexia ]]> https://biorxiv.org/content/10.1101/2025.02.20.638910v1?rss=1 Ibrahim, M. Gomez-Jenkins, M. Scheinfeld, A. Zhao, Z. Lopes, E. C. Sawant, A. Hu, Z. S. Dharani, A. Sun, M. Siddiqui, S. Mirek, E. T. Saliba, J. A. Lattime, E. Su, X. Janowitz, T. Goncalves, M. Dunn, S. Pritykin, Y. Anthony, T. Rabinowitz, J. White, E. 2025-02-24 doi:10.1101/2025.02.20.638910 Cold Spring Harbor Laboratory Press 2025-02-24 <![CDATA[ Small Molecule Modulators of TOX protein to Re-invigorate T cell Activity ]]> https://biorxiv.org/content/10.1101/2025.03.03.641115v1?rss=1 Wu, B. Chang, H. J. Singh, P. Hostetler, A. Xiang, Y. Guo, S. Wang, F. Y. Zhong, J. J. Leifer, B. S. Schiavoni, R. P. Choudhary, A. Westcott, P. M. K. Koehler, A. N. 2025-03-10 doi:10.1101/2025.03.03.641115 Cold Spring Harbor Laboratory Press 2025-03-10 <![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[ Inference and visualization of complexgenotype-phenotype with gpmap-tools ]]> https://biorxiv.org/content/10.1101/2025.03.09.642267v1?rss=1 Marti-Gomez, C. Zhou, J. Chen, W.-C. Kinney, J. B. McCandlish, D. M. 2025-03-13 doi:10.1101/2025.03.09.642267 Cold Spring Harbor Laboratory Press 2025-03-13 <![CDATA[ Pathogenic Viruses, Genome Integrations, and Viral::Human Chimeric Transcripts Detected by VirusIntegrationFinder Across >30k Human Tumor and Normal Samples ]]> https://biorxiv.org/content/10.1101/2025.03.10.642430v1?rss=1 Haas, B. J. Van Arsdale, A. Dobin, A. Brown, M. Gould, J. Georgescu, C. Agosta, E. Baulande, S. Jamail, I. Kamal, M. Bieche, I. Lenz, J. Montagna, C. Al'Khafaji, A. 2025-03-13 doi:10.1101/2025.03.10.642430 30k Human Tumor and Normal Samples]]> Cold Spring Harbor Laboratory Press 2025-03-13 <![CDATA[ LetA defines a structurally distinct transporter family involved in lipid trafficking ]]> https://biorxiv.org/content/10.1101/2025.03.21.644421v1?rss=1 Santarossa, C. C. Li, Y. Yousef, S. Hasdemir, H. S. Rodriguez, C. C. Haase, M. B. Baek, M. Coudray, N. Pavek, J. G. Focke, K. N. Silverberg, A. L. Bautista, C. Yeh, J. Marty, M. Baker, D. Tajkhorshid, E. Ekiert, D. C. Bhabha, G. 2025-03-22 doi:10.1101/2025.03.21.644421 Cold Spring Harbor Laboratory Press 2025-03-22 <![CDATA[ Genome sequence assembly and annotation of MATA and MATB strains of Yarrowia lipolytica ]]> https://biorxiv.org/content/10.1101/2025.03.24.645116v1?rss=1 Zali, N. El Demerdash, O. Chougule, K. Lu, J. Ware, D. Stillman, B. 2025-03-25 doi:10.1101/2025.03.24.645116 Cold Spring Harbor Laboratory Press 2025-03-25 <![CDATA[ Parametric Modulation of a Shared Midbrain Circuit Drives Distinct Vocal Modes in a Singing Mouse ]]> https://biorxiv.org/content/10.1101/2025.04.04.647309v1?rss=1 Zheng, X. M. Harpole, C. E. Davis, M. B. Banerjee, A. 2025-04-05 doi:10.1101/2025.04.04.647309 Cold Spring Harbor Laboratory Press 2025-04-05 <![CDATA[ Extreme mobility creates contrasting patterns of panmixia, isolation-by-distance and hybridization in four flying-fox species (Pteropus) ]]> https://biorxiv.org/content/10.1101/2025.04.06.647431v1?rss=1 Scheben, A. McKeown, A. Walsh, T. Westcott, D. A. Metcalfe, S. S. Vanderduys, E. P. Webber, B. L. 2025-04-10 doi:10.1101/2025.04.06.647431 Cold Spring Harbor Laboratory Press 2025-04-10 <![CDATA[ Splice-switching ASOs targeting an Alu-derived exon in the AURKA 5'UTR collapse an SRSF1-AURKA-MYC oncogenic circuit in pancreatic cancer ]]> https://biorxiv.org/content/10.1101/2025.04.14.648775v1?rss=1 Kral, A. J. Jia, L. Sim, G. Wan, L. Krainer, A. R. 2025-04-15 doi:10.1101/2025.04.14.648775 Cold Spring Harbor Laboratory Press 2025-04-15 <![CDATA[ On learning functions over biological sequence space: relating Gaussian process priors, regularization, and gauge fixing ]]> https://biorxiv.org/content/10.1101/2025.04.26.650699v1?rss=1 Petti, S. Marti-Gomez, C. Kinney, J. B. Zhou, J. McCandlish, D. M. 2025-04-30 doi:10.1101/2025.04.26.650699 Cold Spring Harbor Laboratory Press 2025-04-30 <![CDATA[ 3D multimodal histological atlas and coordinate framework for the mouse brain and head ]]> https://biorxiv.org/content/10.1101/2025.04.30.650246v1?rss=1 Tward, D. J. Flannery, P. J. Savoia, S. Mezias, C. Banerjee, S. Richman, M. Lodato, B. O'Rourke, J. R. Balani, S. Arima, K. Washington, S. Coronado-Leija, R. Zhang, J. Mitra, P. P. 2025-05-01 doi:10.1101/2025.04.30.650246 Cold Spring Harbor Laboratory Press 2025-05-01 <![CDATA[ Effect of plant tissue culture parameters on the ploidy level of Physalis grisea, Solanum lycopersicum, and Solanum prinophyllum regenerants ]]> https://biorxiv.org/content/10.1101/2025.05.01.651681v1?rss=1 Van Eck, J. Swartwood, K. Green, Y. Gentile, I. Lippman, Z. B. 2025-05-03 doi:10.1101/2025.05.01.651681 Cold Spring Harbor Laboratory Press 2025-05-03 <![CDATA[ Skeletonization of neuronal processes using Discrete Morse techniques from computational topology ]]> https://biorxiv.org/content/10.1101/2025.05.12.653477v1?rss=1 Banerjee, S. Stam, C. Tward, D. J. Savoia, S. Wang, Y. Mitra, P. P. 2025-05-15 doi:10.1101/2025.05.12.653477 Cold Spring Harbor Laboratory Press 2025-05-15 <![CDATA[ Sustained Glucose Turnover Flux Distinguishes Cancer Cachexia from Nutrient Limitation ]]> https://biorxiv.org/content/10.1101/2025.05.15.654370v1?rss=1 Kwon, Y. Y. Liang, Y. Gomez-Jenkins, M. Ahmed, M. Jiang, G. Hsiang, J. Lewis, D. Janowitz, T. Goncalves, M. D. White, E. Hui, S. 2025-05-20 doi:10.1101/2025.05.15.654370 Cold Spring Harbor Laboratory Press 2025-05-20 <![CDATA[ Targeting Neutrophil Extracellular Traps to inhibit Colon Cancer Tumor Necrosis and Metastasis ]]> https://biorxiv.org/content/10.1101/2025.05.30.657122v1?rss=1 Gazzara, E. Adrover, J. M. Lui, A. Han, S. Aminzada, Z. Bhandari, N. Sivetz, N. Shirue, V. S. Shergill, B. S. Curtis, M. B. George, S. C. Cicala, A. Rishi, A. Chung, C. Devoe, C. Huang, H. Weiss, M. Lou, E. Tuveson, D. A. Beyaz, S. Westcott, P. M. K. Egeblad, M. Gholami, S. 2025-06-03 doi:10.1101/2025.05.30.657122 Cold Spring Harbor Laboratory Press 2025-06-03 <![CDATA[ Crosslinked CXCR4 Signals Decreased Motility and Increased Adhesion of T Cells ]]> https://biorxiv.org/content/10.1101/2025.06.04.652236v1?rss=1 Pearson, J. Yang, J.-I. Krivitsky, S. Kelley, Z. Fearon, D. T. 2025-06-05 doi:10.1101/2025.06.04.652236 Cold Spring Harbor Laboratory Press 2025-06-05 <![CDATA[ Oncogenic and tumor-suppressive forces converge on a progenitor-orchestrated niche to shape early tumorigenesis ]]> https://biorxiv.org/content/10.1101/2025.06.10.656791v1?rss=1 Reyes, J. Del Priore, I. Chaikovsky, A. C. Pasnuri, N. Elhossiny, A. M. Krause, T. Moorman, A. Snopkowski, C. Takizawa, M. Burdziak, C. Ratnayeke, N. Masillioni, I. Ho, Y.-J. Chaligne, R. Romesser, P. B. Filliol, A. Nawy, T. Morris, J. P. Zhao, Z. Di Magliano, M. P. Alonso-Curbelo, D. Pe'er, D. Lowe, S. W. 2025-06-12 doi:10.1101/2025.06.10.656791 Cold Spring Harbor Laboratory Press 2025-06-12 <![CDATA[ Positive genetic interactions: high impact, but underrepresented in theliterature ]]> https://biorxiv.org/content/10.1101/2025.06.25.661621v1?rss=1 Sun, M. McCandlish, D. M. 2025-06-28 doi:10.1101/2025.06.25.661621 Cold Spring Harbor Laboratory Press 2025-06-28 <![CDATA[ GAME: Genomic API for Model Evaluation ]]> https://biorxiv.org/content/10.1101/2025.07.04.663250v1?rss=1 Luthra, I. Priyadarshi, S. Guo, R. Mahieu, L. Kempynck, N. Dooley, D. Penzar, D. Vorontsov, I. Sheng, Y. Tu, X. Klie, A. Drusinsky, S. Floren, A. Armand, E. Alasoo, K. Seelig, G. Tewhey, R. Koo, P. Agarwal, V. Gosai, S. Pinello, L. White, M. A. Lal, A. Zeitlinger, J. Pollard, K. S. Libbrecht, M. Carter, H. Mostafavi, S. Kulakovskiy, I. Hsiao, W. Aerts, S. Zhou, J. de Boer, C. G. 2025-07-08 doi:10.1101/2025.07.04.663250 Cold Spring Harbor Laboratory Press 2025-07-08 <![CDATA[ FLYWCH transcription factors act in a LIN-42/Period autoregulatory loop during gonad migration in C. elegans ]]> https://biorxiv.org/content/10.1101/2025.07.10.664215v1?rss=1 Kinney, B. Menjivar-Hernandez, J. Koitz, F. Grinevich, D. Madonna Baselios, M. Hammell, C. M. Gordon, K. L. 2025-07-11 doi:10.1101/2025.07.10.664215 Cold Spring Harbor Laboratory Press 2025-07-11 <![CDATA[ Novel reactivity phenotype mediates long-term consequences of cocaine exposure during adolescence and adulthood in male Sprague-Dawley rats. ]]> https://biorxiv.org/content/10.1101/2025.07.10.664140v1?rss=1 Maldonado-Devincci, A. M. Amante, R. A. Raudales, R. Micheal, L. A. Badanich, K. A. Kirstein, C. L. 2025-07-15 doi:10.1101/2025.07.10.664140 Cold Spring Harbor Laboratory Press 2025-07-15 <![CDATA[ Fine-tuning RIPENING INHIBITOR (RIN) expression by introducing allelic mutations in its promoter using CRISPR/Cas9 multiplex editing ]]> https://biorxiv.org/content/10.1101/2025.07.14.664838v1?rss=1 Zhou, J. Yang, C.-L. Beckles, D. M. 2025-07-18 doi:10.1101/2025.07.14.664838 Cold Spring Harbor Laboratory Press 2025-07-18 <![CDATA[ Growth Cost and Transport Efficiency Tradeoffs Define Root System Optimization Across Varying Developmental Stages and Environments in Arabidopsis ]]> https://biorxiv.org/content/10.1101/2025.07.25.666579v1?rss=1 Faizi, K. Mehta, P. Maida, A. Humphreys, T. Berrigan, E. McKee-Reid, L. McCorkell, R. Tagade, A. Rumbelow, J. Showalter, J. Brent, L. Coroenne, C. Rigaud, A. Chandrasekhar, A. Navlakha, S. Martin, A. Pradal, C. Lee, S. Busch, W. Platre, M. P. 2025-07-26 doi:10.1101/2025.07.25.666579 Cold Spring Harbor Laboratory Press 2025-07-26 <![CDATA[ Structural and mechanistic insights into Dis3L2 mediated degradation of structured RNA ]]> https://biorxiv.org/content/10.1101/2025.08.01.668158v1?rss=1 Matos, R. G. Garg, A. Costa, S. M. Pereira, P. Arraiano, C. M. Joshua-Tor, L. Viegas, S. C. 2025-08-02 doi:10.1101/2025.08.01.668158 Cold Spring Harbor Laboratory Press 2025-08-02 <![CDATA[ Antagonistic interactions between CLAVATA receptors shape maize ear development ]]> https://biorxiv.org/content/10.1101/2025.08.04.667500v1?rss=1 Lindsay, P. L. Xu, F. Liu, L. Boumpas, P. Reyes, A. Je, B. I. Ogawa-Ohnishi, M. Man, J. Skopelitis, T. Matsubayashi, Y. Bartlett, M. Xu, S.-L. Jackson, D. 2025-08-06 doi:10.1101/2025.08.04.667500 Cold Spring Harbor Laboratory Press 2025-08-06 <![CDATA[ GHIST 2024: The 1st Genomic History Inference Strategies Tournament ]]> https://biorxiv.org/content/10.1101/2025.08.05.668560v1?rss=1 Struck, T. J. Vaughn, A. H. Daigle, A. Ray, D. D. Noskova, E. Sequeira, J. J. Antonets, S. Alekseevskaya, E. Grigoreva, E. Raines, E. McMaster, E. S. Kovacs, T. G. L. Ragsdale, A. P. Moreno-Estrada, A. Lotterhos, K. E. Siepel, A. Gutenkunst, R. N. 2025-08-11 doi:10.1101/2025.08.05.668560 Cold Spring Harbor Laboratory Press 2025-08-11 <![CDATA[ A quantitative framework for predicting odor intensity across molecule and mixtures ]]> https://biorxiv.org/content/10.1101/2025.08.08.668954v1?rss=1 Pellegrino, R. Samoilova, K. Ihara, Y. Andres, M. Singh, V. Gerkin, R. C. Koulakov, A. Mainland, J. D. 2025-08-12 doi:10.1101/2025.08.08.668954 Cold Spring Harbor Laboratory Press 2025-08-12 <![CDATA[ Non-catalytic and catalytic TREHALOSE-6-PHOSPHATE SYNTHASES interact with RAMOSA3 to control maize development. ]]> https://biorxiv.org/content/10.1101/2025.08.09.669499v1?rss=1 Tran, T. Claeys, H. Abraham Juarez, M. J. Vi, L. S. Xu, X. Michalski, K. Chou, T. H. Iohannes, S. D. Boumpas, P. Williams, Z. Sheppard, S. Griffiths, C. Paul, M. Furukawa, H. Jackson, D. 2025-08-12 doi:10.1101/2025.08.09.669499 Cold Spring Harbor Laboratory Press 2025-08-12 <![CDATA[ MYC-Driven Activation of USP39 Enhances SRSF1 Stability and Promotes PDAC Progression ]]> https://biorxiv.org/content/10.1101/2025.08.22.671882v1?rss=1 Ma, B. Kral, A. Zhang, X. Singh, N. Deschenes, A. Cifani, P. Park, Y. Tuveson, D. Krainer, A. Wan, L. 2025-08-28 doi:10.1101/2025.08.22.671882 Cold Spring Harbor Laboratory Press 2025-08-28 <![CDATA[ APEX2 and TurboID define unique subcellular proteomes ]]> https://biorxiv.org/content/10.1101/2025.09.04.673741v1?rss=1 Battison, A. S. Balsbaugh, J. L. Borniger, J. C. 2025-09-06 doi:10.1101/2025.09.04.673741 Cold Spring Harbor Laboratory Press 2025-09-06 <![CDATA[ JSP1 Regulates Neutrophil Adhesion via Integrin-SRC Signaling in Vascular Inflammation ]]> https://biorxiv.org/content/10.1101/2025.09.04.674122v1?rss=1 Li, L. Tonks, N. K. 2025-09-06 doi:10.1101/2025.09.04.674122 Cold Spring Harbor Laboratory Press 2025-09-06 <![CDATA[ Discovery and shaping of decision strategies using adversarial stimuli in rats ]]> https://biorxiv.org/content/10.1101/2025.09.09.675127v1?rss=1 Zhang, A. Zador, A. M. 2025-09-11 doi:10.1101/2025.09.09.675127 Cold Spring Harbor Laboratory Press 2025-09-11 <![CDATA[ Tumor Genotype Dictates Mitochondrial and Immune Vulnerabilities in Liver Cancer ]]> https://biorxiv.org/content/10.1101/2025.09.10.675369v1?rss=1 Unlu, G. Millet, A. Wangdu, K. Donne, R. Erdal, R. DelGaudio, N. L. Uygur, B. Shah, V. Cho, K. Fecke, A. Cansiz, F. Tarcan, Z. C. Isay-Del Viscio, M. Kilic, E. Kurth, I. Molina, H. Sickmann, A. Basturk, O. Patti, G. Beyaz, S. Smith, K. W. Lujambio, A. Tasdogan, A. Tavazoie, S. F. Birsoy, K. 2025-09-11 doi:10.1101/2025.09.10.675369 Cold Spring Harbor Laboratory Press 2025-09-11 <![CDATA[ Bayesian inference of tissue-migration histories in metastatic cancer from cell-lineage tracing data ]]> https://biorxiv.org/content/10.1101/2025.09.09.668633v1?rss=1 Staklinski, S. J. Scheben, A. Brault, L. M. Hassett, R. Serio, R. N. Xing, J. Nowak, D. G. Siepel, A. 2025-09-12 doi:10.1101/2025.09.09.668633 Cold Spring Harbor Laboratory Press 2025-09-12 <![CDATA[ RiboCop surveils pre-rRNA processing by Dicer in cellular quiescence ]]> https://biorxiv.org/content/10.1101/2025.09.16.676644v1?rss=1 Roche, B. Martienssen, R. A. 2025-09-18 doi:10.1101/2025.09.16.676644 Cold Spring Harbor Laboratory Press 2025-09-18 <![CDATA[ A deep-time landscape of plant cis-regulatory sequence evolution ]]> https://biorxiv.org/content/10.1101/2025.09.17.676453v1?rss=1 Amundson, K. R. Hendelman, A. Ciren, D. Yang, H. de Neve, A. E. Tal, S. Sulema, A. Jackson, D. Barlett, M. E. Lippman, Z. B. Efroni, I. 2025-09-19 doi:10.1101/2025.09.17.676453 Cold Spring Harbor Laboratory Press 2025-09-19 <![CDATA[ Gut microbiota as a modulator of circadian neural development in the honey bee model. ]]> https://biorxiv.org/content/10.1101/2025.09.30.678393v1?rss=1 KORU, Y. B. Beer, K. Ruggieri, A. A. Rodriguez-Cordero, J. A. Aviles-Rios, E. Anderson, M. Citron-Rodriguez, E. A. Montes-Mercado, A. De Jesus-Cortes, H. Giannoni-Guzman, M. A. Perez Claudio, E. Courtney, E. C. Andujar-Sierra, C. L. Strubbe-Nieves, A. Ortiz-Alvarado, Y. Doke, M. A. Ortiz-Zuazaga, H. Moore, D. Giordano, R. Ghezzi, A. Scheiner, R. Giray, T. Agosto-Rivera, J. L. 2025-10-02 doi:10.1101/2025.09.30.678393 Cold Spring Harbor Laboratory Press 2025-10-02 <![CDATA[ Hepatic ceramide synthesis links systemic inflammation to organelle dysfunction in cancer ]]> https://biorxiv.org/content/10.1101/2025.10.01.679814v1?rss=1 Liu, Y. Miao, T. Wang, A. Ezequiel, D. Kim, A.-R. Zhang, Z. Sun, X. Binari, R. Asara, J. M. Hu, Y. Goncalves, M. Janowitz, T. Perrimon, N. 2025-10-03 doi:10.1101/2025.10.01.679814 Cold Spring Harbor Laboratory Press 2025-10-03 <![CDATA[ Uncovering the Mechanistic Landscape of Regulatory DNA with Deep Learning ]]> https://biorxiv.org/content/10.1101/2025.10.07.681052v1?rss=1 Seitz, E. McCandlish, D. M. Kinney, J. B. Koo, P. 2025-10-08 doi:10.1101/2025.10.07.681052 Cold Spring Harbor Laboratory Press 2025-10-08 <![CDATA[ Multiplexed cytokine and antigen mRNA administration generates durable anti-tumor immunity against pancreatic cancer ]]> https://biorxiv.org/content/10.1101/2025.10.13.681939v1?rss=1 Parikh, C. N. DeMarco, K. D. Kane, G. I. Bhalerao, N. Dinnell, R. W. Ma, B. Giwa, H. K. Zhao, Z. Zhou, L. Murphy, K. C. Chibaya, L. Mori, H. Qiao, Y. Lewis, B. C. Xue, W. Pitarresi, J. R. Atukorale, P. U. Ruscetti, M. 2025-10-14 doi:10.1101/2025.10.13.681939 Cold Spring Harbor Laboratory Press 2025-10-14 <![CDATA[ 3' Nucleotide Asymmetry Directs miRNA Strand Selection ]]> https://biorxiv.org/content/10.1101/2025.10.15.682714v1?rss=1 Medley, J. C. Kurosu Moriya, S. Ouyang, H. Crawshaw, H. Zhang, S. Y. Panzade, G. Sydzyik, W. J. Sydzyik, J. T. Bhandari, M. Hammell, C. M. Zinovyeva, A. 2025-10-16 doi:10.1101/2025.10.15.682714 Cold Spring Harbor Laboratory Press 2025-10-16 <![CDATA[ CD8 T cells mediate immunosurveillance for neoantigen+ epithelial stem cells in the colon ]]> https://biorxiv.org/content/10.1101/2025.10.19.683142v1?rss=1 Buck, J. Iyer, N. R. Fagerberg, E. Micevic, G. He, J. St. Denis, K. Shah, V. Blackburn, H. N. Venkatesan, S. Attanasio, J. Hunt, B. G. Dalrymple, A. Konnikova, L. Beyaz, S. Damo, M. Booth, C. J. Connolly, K. A. Joshi, N. S. 2025-10-19 doi:10.1101/2025.10.19.683142 Cold Spring Harbor Laboratory Press 2025-10-19 <![CDATA[ JAK1/2 Inhibition Delays Cachexia and Improves Survival through Increased Food Intake ]]> https://biorxiv.org/content/10.1101/2025.10.21.683287v1?rss=1 Dantas, E. C. Murthy, A. Kim, J. Ahmed, T. Ahmed, M. Perrier, T. Ramsamooj, S. Nathoo, I. Kniess Debarba, L. Lima Queiroz, A. Li, S. Ersoy, B. Ferrer, M. Goldstein, I. C. Gao, J. Lam, T. Nagler, M. Malbari, M. Altorki, N. Cararo Lopes, E. Gomez Jenkins, M. Das, T. Jamal-Hanjani, M. White, E. Janowitz, T. Goncalves, M. 2025-10-22 doi:10.1101/2025.10.21.683287 Cold Spring Harbor Laboratory Press 2025-10-22 <![CDATA[ Identification and Validation of an inhibitor of the protein kinases PIM and DYRK ]]> https://biorxiv.org/content/10.1101/2025.10.22.683941v1?rss=1 Bencze, G. Venkataramani, P. Elkayam, E. Rivera, K. D. Garg, A. Szabadkai, I. Orfi, L. Joshua-Tor, L. Pappin, D. Tonks, N. K. 2025-10-22 doi:10.1101/2025.10.22.683941 Cold Spring Harbor Laboratory Press 2025-10-22 <![CDATA[ Macropinocytosis enables metabolic recycling of extracellular DNA in cancer cells ]]> https://biorxiv.org/content/10.1101/2025.10.22.684010v1?rss=1 Yang, W.-H. Stamatatos, O. T. Michalopoulou, E. Sann, A. Cifani, P. Van Aelst, L. Cross, J. R. Wee, T.-L. Lukey, M. J. 2025-10-23 doi:10.1101/2025.10.22.684010 Cold Spring Harbor Laboratory Press 2025-10-23 <![CDATA[ NOVEL SMALL-MOLECULE INHIBITORS OF THE PROTEIN KINASE DYRK: POTENTIAL THERAPEUTIC CANDIDATES IN CANCER ]]> https://biorxiv.org/content/10.1101/2025.11.05.686653v1?rss=1 Venkataramani, P. Elkayam, E. Garg, A. Cheng, K. F. Altiti, A. He, M. Thakur, K. Michalopoulou, E. Gonzalez, C. Van Aelst, L. Pappin, D. Joshua-Tor, L. Al-Abed, Y. Tonks, N. K. 2025-11-06 doi:10.1101/2025.11.05.686653 Cold Spring Harbor Laboratory Press 2025-11-06 <![CDATA[ Order code in the olfactory system. ]]> https://biorxiv.org/content/10.1101/2025.11.16.688691v1?rss=1 Samoilova, K. Harvey, J. S. Nakayama, H. Rinberg, D. Koulakov, A. 2025-11-17 doi:10.1101/2025.11.16.688691 Cold Spring Harbor Laboratory Press 2025-11-17 <![CDATA[ plinkQC: An Integrated Tool for Ancestry Inference, Sample Selection, and Quality Control in Population Genetics ]]> https://biorxiv.org/content/10.1101/2025.11.25.690541v1?rss=1 Syed, M. Walter, C. Meyer, H. V. 2025-11-28 doi:10.1101/2025.11.25.690541 Cold Spring Harbor Laboratory Press 2025-11-28 <![CDATA[ A clinical-stage oncology compound selectively targets drug-resistant cancers ]]> https://biorxiv.org/content/10.1101/2025.11.26.690878v1?rss=1 Long, K. Bhattacharjee, D. Newman-Stonebraker, S. H. Suhr, S. Mercado, B. Q. Tighe, A. Romero, L. Thompson, S. L. Sausville, E. L. John, K. M. Julian, L. Mishra, S. Klingbeil, O. Gupta, P. Bhatt, U. Gao, A. C. Ricardo, S. Vakoc, C. R. Bornhauser, B. C. Corsello, S. M. Taylor, S. S. Holland, P. L. Sheltzer, J. M. 2025-11-30 doi:10.1101/2025.11.26.690878 Cold Spring Harbor Laboratory Press 2025-11-30 <![CDATA[ Weakest link epistasis and the geometry of genetic load ]]> https://biorxiv.org/content/10.64898/2025.12.08.693057v1?rss=1 Labourel, F. Bansept, F. McCandlish, D. M. 2025-12-09 doi:10.64898/2025.12.08.693057 Cold Spring Harbor Laboratory Press 2025-12-09 <![CDATA[ GaugeFixer: overcoming parameter non-identifiability in models of sequence-function relationships ]]> https://biorxiv.org/content/10.64898/2025.12.08.693054v1?rss=1 Marti-Gomez, C. McCandlish, D. M. Kinney, J. B. 2025-12-10 doi:10.64898/2025.12.08.693054 Cold Spring Harbor Laboratory Press 2025-12-10 <![CDATA[ Non-apoptotic death of the C. elegans linker cell is primed by MYRF-1 activation of pqn-41/polyQ ]]> https://biorxiv.org/content/10.64898/2025.12.08.693091v1?rss=1 Yarychkivska, O. Liu, S. Horowitz, L. B. Newland, S. Wu, P. Mittal, S. Tamura, S. Novosolova, T. Ritter, D. F. Lu, Y. Ercan, S. Hammell, C. Shaham, S. 2025-12-11 doi:10.64898/2025.12.08.693091 Cold Spring Harbor Laboratory Press 2025-12-11 <![CDATA[ Sparse, random sampling is sufficient for central tolerance ]]> https://biorxiv.org/content/10.64898/2025.12.09.693230v1?rss=1 Meyer, H. V. Dasgupta, S. Banerjee, A. Lin, Y. Prabakar, R. K. Chapin, S. R. Kiingsford, C. Navlakha, S. 2025-12-12 doi:10.64898/2025.12.09.693230 Cold Spring Harbor Laboratory Press 2025-12-12 <![CDATA[ Rehabilitation drives functional reorganization of intact corticospinal-supraspinal projections following partial spinal cord injury ]]> https://biorxiv.org/content/10.64898/2025.12.12.694014v1?rss=1 Bonanno, J. L. Trivedi, S. O'Brien, C. F. Saha, S. Cafferty, W. B. J. 2025-12-16 doi:10.64898/2025.12.12.694014 Cold Spring Harbor Laboratory Press 2025-12-16 <![CDATA[ High-Fidelity Tuning of Olfactory Mixture Distances in the Perceptual Space of Smell Through a Community Effort ]]> https://biorxiv.org/content/10.64898/2025.12.13.694160v1?rss=1 Satarifard, V. Sisson, L. Han, Y. Ilidio, P. Hladis, M. Lalis, M. Song, X. Yin, W. Ravia, A. Zheng, C. X. Andreoletti, G. Albrecht, J. Pellegrino, R. Wang, Z. Yang, S. D'hondt, R. Ghinis, A. de Boer, J. Nakano, F. K. Gharahighehi, A. DREAM Olfactory Mixtures Prediction Consortium, Sanchez-Lengeling, B. Keller, A. Vosshall, L. B. Fiorucci, S. Tewari, A. Topin, J. Vens, C. Bjorkman, M. Kragic, D. Sobel, N. Christakis, N. A. Mainland, J. D. Meyer, P. 2025-12-16 doi:10.64898/2025.12.13.694160 Cold Spring Harbor Laboratory Press 2025-12-16 <![CDATA[ The plant circadian clock exerts stronger control over the diel proteome than the transcriptome ]]> https://biorxiv.org/content/10.64898/2025.12.19.695194v1?rss=1 Mehta, D. Talasila, M. Lau, Z. X. Rodriguez Gallo, M. C. Li, Q. Zhong, Y. Muzumdar, S. Li, R. Luo, W. J. Lau, V. Pasha, A. Lock, S. Ezer, D. Provart, N. J. Uhrig, R. G. 2025-12-22 doi:10.64898/2025.12.19.695194 Cold Spring Harbor Laboratory Press 2025-12-22 <![CDATA[ NW-flex: flexible-block sequence alignment for short tandem repeats ]]> https://biorxiv.org/content/10.64898/2025.12.22.695990v1?rss=1 Yu, Z. Levy, D. 2025-12-24 doi:10.64898/2025.12.22.695990 Cold Spring Harbor Laboratory Press 2025-12-24 <![CDATA[ A foundational model for joint sequence-function multi-species modeling at scale for long-range genomic prediction ]]> https://biorxiv.org/content/10.64898/2025.12.22.695963v1?rss=1 Boshar, S. Evans, B. Tang, Z. Picard, A. Adel, Y. Lorbeer, F. K. Rajesh, C. Karch, T. Sidbon, S. Emms, D. Mendoza-Revilla, J. Al-Ani, F. Seitz, E. Schiff, Y. Bornachot, Y. Hernandez, A. Lopez, M. Laterre, A. Beguir, K. Koo, P. Kuleshov, V. Stark, A. de Almeida, B. P. Pierrot, T. 2025-12-25 doi:10.64898/2025.12.22.695963 Cold Spring Harbor Laboratory Press 2025-12-25 <![CDATA[ Variational Inference with Node Embeddings (VINE) for Scalable Bayesian Phylogenetics ]]> https://biorxiv.org/content/10.64898/2025.12.24.696405v1?rss=1 Siepel, A. Hassett, R. Staklinski, S. J. 2025-12-26 doi:10.64898/2025.12.24.696405 Cold Spring Harbor Laboratory Press 2025-12-26 <![CDATA[ Frizzled 6 Drives EMT and Stromal Remodeling Downstream of SP1 in Basal-like Pancreatic Cancer ]]> https://biorxiv.org/content/10.64898/2025.12.31.697213v1?rss=1 Stevens, P. D. Giannotta, C. S. Spires, E. C. Diegel, C. R. Zhong, Z. A. Madaj, Z. J. Olson, S. I. Dawood, M. H. Honabarger, A. Caligiuri, G. Tuveson, D. A. Hostetter, G. B. Williams, B. O. 2026-01-01 doi:10.64898/2025.12.31.697213 Cold Spring Harbor Laboratory Press 2026-01-01 <![CDATA[ Targeting EZH2 Oncogenic Splicing: Decoding the Regulatory Network and Antisense Correction ]]> https://biorxiv.org/content/10.64898/2026.01.07.697981v1?rss=1 Islam, M. R. Nagar, P. McNaughton, N. Heeamoni, S. A. Hasan, M. M. Kandel, S. Tsakiroglou, P. Dalton, W. B. Abdel-Wahab, O. Krainer, A. R. Rahman, M. A. 2026-01-08 doi:10.64898/2026.01.07.697981 Cold Spring Harbor Laboratory Press 2026-01-08 <![CDATA[ 3'-tRNA Fragments Target Domesticated LTR-Retrotransposons ]]> https://biorxiv.org/content/10.64898/2026.01.22.698655v1?rss=1 Peacey, M. Steinberg, J. I. Schorn, A. J. 2026-01-22 doi:10.64898/2026.01.22.698655 Cold Spring Harbor Laboratory Press 2026-01-22 <![CDATA[ A developmental timer coordinates organism-wide microRNA transcription ]]> https://biorxiv.org/content/10.64898/2026.01.21.700890v1?rss=1 Wu, P. Wang, J. Pryor, B. Valentino, I. Ritter, D. F. Loel, K. Kinney, J. Ercan, S. Joshua-Tor, L. Hammell, C. M. 2026-01-23 doi:10.64898/2026.01.21.700890 Cold Spring Harbor Laboratory Press 2026-01-23 <![CDATA[ How the olfactory bulb maintains stable odor manifolds amid adaptation and representational drift ]]> https://biorxiv.org/content/10.64898/2026.01.23.701335v1?rss=1 Zheng, C. X. Yu, B. Navlakha, S. Koulakov, A. 2026-01-25 doi:10.64898/2026.01.23.701335 Cold Spring Harbor Laboratory Press 2026-01-25 <![CDATA[ Maternal-fetal immune conflict contributes to male-specific impairments in a mouse model of neurodevelopmental disorders ]]> https://biorxiv.org/content/10.64898/2026.02.02.703351v1?rss=1 Sanchez-Martin, I. Kukreja, B. Henderson, P. Lin, Q. DiMartino, D. Bagan, V. Park, J. Kalish, B. T. Cheadle, L. 2026-02-03 doi:10.64898/2026.02.02.703351 Cold Spring Harbor Laboratory Press 2026-02-03 <![CDATA[ A neofunctionalized flowering antagonist created an evolutionary contingency that channeled Solanaceae adaptation ]]> https://biorxiv.org/content/10.64898/2026.02.20.707063v1?rss=1 Shohat, H. Ciren, D. Arrones, A. Gentile, I. Ramakrishnan, S. Hendelman, A. Jenike, K. M. Brown, N. L. Luna-Ramos, J. Passalacqua, M. J. Satterlee, J. W. Fitzgerald, B. Baraja-Fonseca, V. Robitaille, G. M. Seman, B. M. Gillis, J. Van Eck, J. Prohens, J. Schatz, M. C. Lippman, Z. B. 2026-02-21 doi:10.64898/2026.02.20.707063 Cold Spring Harbor Laboratory Press 2026-02-21 <![CDATA[ Development and evaluation of a cost-effective, mid-density SNP array as a sorghum community genotyping resource ]]> https://biorxiv.org/content/10.64898/2026.02.20.706663v1?rss=1 90% for most samples and markers), low missing data, and accurate resolution of population structure consistent with prior whole-genome studies. In comparative genomic prediction analyses, the mid-density array performed equivalently to high-density genotype-by-sequencing (GBS) platforms for key traits such as grain yield and plant height across multi-environment trials. Designed for broad utility in breeding pipelines, the array enables marker-assisted selection, genomic prediction, identity verification, and germplasm quality control. Moreover, its adoption by the USDA National Plant Germplasm System facilitates the curation of genebanks and the management of core collections. This community-driven genotyping platform offers a scalable, reproducible, and customizable tool to support molecular breeding in sorghum and underscores the value of targeted marker systems in resource-optimized crop improvement programs. ]]> Kumar, V. Klein, R. R. Kaufman, B. Winans, N. D. Crozier, D. Rooney, W. L. Harrison, M. Hayes, C. Tello-Ruiz, M. K. Gladman, N. P. Olson, C. Burow, G. Sexton-Bowser, S. Punnuri, S. Knoll, J. Dahlberg, J. Ware, D. 2026-02-23 doi:10.64898/2026.02.20.706663 Cold Spring Harbor Laboratory Press 2026-02-23 <![CDATA[ Evolution of Origin Sequence and Recognition for Licensing of Eukaryotic DNA Replication ]]> https://biorxiv.org/content/10.64898/2026.03.10.710760v1?rss=1 Bauer, J. Zali, N. Chouhan, O. P. Demerdash, O. E. Loell, K. Kinney, J. B. Joshua-Tor, L. W. Stillman, B. 2026-03-10 doi:10.64898/2026.03.10.710760 Cold Spring Harbor Laboratory Press 2026-03-10 <![CDATA[ Single-library chromosome-scale diploid assemblies of vole genomes resolve a species-specific duplication implicated in pair bonding ]]> https://biorxiv.org/content/10.64898/2026.03.13.711624v1?rss=1 Abuelanin, M. Kaya, G. Lake, J. A. Lambert, C. Wu, M. V. Berendzen, K. Krasheninnikova, K. Wood, J. M. Solomon, N. G. Donaldson, Z. R. Bales, K. L. Howe, K. Korlach, J. Manoli, D. S. Tollkuhn, J. Dennis, M. Y. 2026-03-17 doi:10.64898/2026.03.13.711624 Cold Spring Harbor Laboratory Press 2026-03-17 <![CDATA[ Diverse high-fat diets drive multi-omic reprogramming that persists after dietary reversal ]]> https://biorxiv.org/content/10.64898/2026.03.17.708620v1?rss=1 Van Camp, A. G. Park, J. Ozcelik, E. Eskiocak, O. Ozler, K. A. Papciak, K. Subhash, S. Alwaseem, H. Ergin, I. Chung, C. Shah, V. Yueh, B. Fein, M. R. Durmaz, C. Mozsary, C. Kilic, E. Garipcan, A. Damle, N. Najjar, D. Nelson, T. M. Ryon, K. A. Butler, D. J. Patel, C. J. Thaiss, C. A. Birsoy, K. Mason, C. E. Meydan, C. Tierney, B. T. Beyaz, S. 2026-03-19 doi:10.64898/2026.03.17.708620 Cold Spring Harbor Laboratory Press 2026-03-19 <![CDATA[ TEsingle enables locus-specific transposable element expression analysis at single-cell resolution ]]> https://biorxiv.org/content/10.64898/2026.03.19.712984v1?rss=1 Forcier, T. Cheng, E. Tam, O. H. Wunderlich, C. Castilla-Vallmanya, L. Jones, J. L. Quaegebeur, A. Barker, R. A. Jakobsson, J. Gale Hammell, M. 2026-03-22 doi:10.64898/2026.03.19.712984 Cold Spring Harbor Laboratory Press 2026-03-22 <![CDATA[ Structural dynamics between Argonaute-2 and CK1α promote target RNA release in microRNA-mediated silencing ]]> https://biorxiv.org/content/10.64898/2026.03.23.713669v1?rss=1 Garg, A. Braviner, L. Axhemi, A. Bibel, B. Joshua-Tor, L. 2026-03-25 doi:10.64898/2026.03.23.713669 Cold Spring Harbor Laboratory Press 2026-03-25 <![CDATA[ Patient-derived organoid xenografts reveal the multifaceted role of the lncRNA MALAT1 in breast cancer progression ]]> https://biorxiv.org/content/10.64898/2026.04.02.716096v1?rss=1 Aggarwal, D. Russo, S. Anderson, K. Floyd, T. Utama, R. Rouse, J. A. Naik, P. Pawlak, S. Iyer, S. V. Kramer, M. Satpathy, S. Wilkinson, J. E. Gao, Q. Bhatia, S. Arun, G. Akerman, M. McCombie, W. R. Revenko, A. Kostroff, K. Spector, D. L. 2026-04-03 doi:10.64898/2026.04.02.716096 Cold Spring Harbor Laboratory Press 2026-04-03 <![CDATA[ Exon-Skipping Antisense Oligonucleotides for H3.3K27M-Altered Diffuse Midline Glioma Therapy ]]> https://biorxiv.org/content/10.64898/2026.04.03.715131v1?rss=1 Yang, L. Zhang, Q. Wilkinson, J. E. Krainer, A. R. 2026-04-04 doi:10.64898/2026.04.03.715131 Cold Spring Harbor Laboratory Press 2026-04-04 <![CDATA[ Mount Fuji's stubby peak: the genotypic density of additive landscapes near maximal fitness ]]> https://biorxiv.org/content/10.64898/2026.04.02.716185v1?rss=1 Kinney, J. B. 2026-04-06 doi:10.64898/2026.04.02.716185 Cold Spring Harbor Laboratory Press 2026-04-06 <![CDATA[ Genetic background shapes AI-predicted variant effects ]]> https://biorxiv.org/content/10.64898/2026.04.04.715328v1?rss=1 Schilder, B. M. Liu, Z. Desmarais, J. J. Laub, D. Rahimi, F. Sethi, P. Pereira, L. A. Sun, M. M. Kinney, J. B. McCandlish, D. M. Zhou, J. Koo, P. K. 2026-04-07 doi:10.64898/2026.04.04.715328 Cold Spring Harbor Laboratory Press 2026-04-07 <![CDATA[ AI predictions and the expansion of scientific frontiers: Evidence from structural biology ]]> https://biorxiv.org/content/10.64898/2026.04.06.716821v1?rss=1 Sun, M. Choi, S. Yin, Y. 2026-04-07 doi:10.64898/2026.04.06.716821 Cold Spring Harbor Laboratory Press 2026-04-07