Differences in firing efficiency, chromatin, and transcription underlie the developmental plasticity of the Arabidopsis DNA replication origins

Celina Costas,Crisanto Gutierrez,Irene Aragüez,Joana Sequeira-Mendes,Jordi Morata,Josep M. Casacuberta,Ramon Peiró,Raul Mendez-Giraldez,Ugo Bastolla,Zaida Vergara

A new approach for rare variation collapsing on functional protein domains implicates specific genic regions in ALS

Aaron D. Gitler,Andrew Allen,Brittany N. Lasseigne,Charles J. Wolock,Cristiane de Araujo Martins Moreno,David B. Goldstein,Elizabeth T. Cirulli,Guy A. Rouleau,Hemali Phatnani,Matthew B. Harms,Neil A. Shneider,Richard M. Myers,Robert H. Brown Jr,Sahar Gelfman,Sarah Dugger,Slavé Petrovski,Tim Harris,Tom Maniatis,Zhong Ren

Identification of regulatory elements from nascent transcription using dREG

Charles G. Danko,Lauren A. Choate,Tinyi Chu,Zhong Wang

Efficient and unique cobarcoding of second-generation sequencing reads from long DNA molecules enabling cost-effective and accurate sequencing, haplotyping, and de novo assembly

Andrei Alexeev,Ao Chen,Brock A. Peters,Chongjun Xu,Christian Villarosa,Dan Chen,Darlene Nguyen,Ellis Anderson,Fei Fan,Han K. Lam,He Wang,Huanming Yang,Jia Sophie Liu,Jian Wang,Jingbo Tang,Jingwan Wang,Karsten Kristiansen,Linying Wang,Michelle Ka Yan Wu,Nina Barua,Ou Wang,Qing Mao,Radoje Drmanac,Rebecca Yu Zhang,Robert Chin,Scott Gablenz,Snezana Drmanac,Staci Nguyen,Wenlan Tian,Wenwei Zhang,Xiao Liu,Xiaofang Cheng,Xiaojuan Qi,Xun Xu,Yan Zou,Yinlong Xie,Yuhui Sun,Yujun Zhou,Yuliang Dong

Exome-wide assessment of the functional impact and pathogenicity of multinucleotide mutations

Brown rat demography reveals pre-commensal structure in eastern Asia before expansion into Southeast Asia

Emily E. Puckett,Jason Munshi-South

A virome-wide clonal integration analysis platform for discovering cancer viral etiology

Arvis Sulovari,Dawei Li,Jason Kost,Jian Cao,Nathalie Wong,Winnie S. Liang,Xun Chen

Long-read single-molecule maps of the functional methylome

Alex,Alex R. Hastie,Assaf Grunwald,Br,Dmitry Torchinsky,Elmar Weinhold,Eric Vilain,Ernest T. Lam,Felix Gularek,Gil Nifker,Han Cao,Hayk Barseghyan,Hila Sharim,Jeff Reifenberger,Jonathan Pevsner,Kathryn R. Wagner,Matyas Juhasz,Miguel Almalvez,Rani Arielly,Sapir Margalit,Sreetama Sen Ch,Surajit Bhattacharya,Tslil Gabrieli,Yael Michaeli,Yi-Wen Chen,Yuval Ebenstein,er Liu,on Dufault,ra

The accessible chromatin landscape of the murine hippocampus at single-cell resolution

Andrew C. Adey,Cole Trapnell,Frank J. Steemers,Gail M,Hannah A. Pliner,John R. Sinnamon,Kristof A. Torkenczy,Michael W. Linhoff,Ryan M. Mulqueen,Sarah A. Vitak,el

Hormone-control regions mediate steroid receptor–dependent genome organization

A. Silvina Nacht,Enrique Vidal,Fran？ois Le Dily,Gaetano Verde,Guillermo P. Vicent,Javier Quilez,José Carbonell-Caballero,José Luis Villanueva-Ca？as,Lara Isabel De Llobet,Miguel Beato,Priyanka Sharma,Roberto Ferrari,Roni H.G. Wright,Yasmina Cuartero

Corrigendum: RNA-DNA hybrid (R-loop) immunoprecipitation mapping: an analytical workflow to evaluate inherent biases

Anett Mázló,Beáta Boros-Oláh,Gábor Halmos,László Halász,Lóránt Székv？lgyi,Tímea Kuik-Rózsa,Zsolt Karányi,ágnes Mosolygó-L,éva Nagy,éva Rajnav？lgyi,éva Sipos

Human papillomavirus and the landscape of secondary genetic alterations in oral cancers

Amit D. Agrawal,Anne-Katrin Emde,Benjamin J. Swanson,Birgit Stache-Crain,Bo Jiang,David E. Symer,Heather M. Geiger,Jingfeng Li,Keiko Akagi,Kevin R. Coombes,Mark Zucker,Maura L. Gillison,Nicolas Robine,Robert K.L. Pickard,Weihong Xiao

Comparison and assessment of family- and population-based genotype imputation methods in large pedigrees

Alej,Ehsan Ullah,Ellen M. Wijsman,Halima Bensmail,Khalid Kunji,Mohamad Saad,Mostafa M. Abbas,Raghvendra Mall,ro Q. Nato Jr

Coexpression patterns define epigenetic regulators associated with neurological dysfunction

Aaron R. Quinlan,Hans T. Bjornsson,James M. Havrilla,Kasper D. Hansen,Le,Peter F. Hickey,ros Boukas

GenTree, an integrated resource for analyzing the evolution and function of primate-specific coding genes

Bin Z. He,Chunyan Chen,Daqi Yu,Ge Gao,Hao Shen,Hua Chen,Manyuan Long,Shilei Zhao,Shuai Jiang,Xi Chen,Yan Fu,Yi Shao,Yong E. Zhang,Zhenglin Zhu,Zhiqiang Gao

Improved discovery of genetic interactions using CRISPRiSeq across multiple environments

Adam Dziulko,Gavin Sherlock,Justin D. Smith,Mia Jaffe,Robert P. St.Onge,Sasha F. Levy

Beta-binomial modeling of CRISPR pooled screen data identifies target genes with greater sensitivity and fewer false negatives

Huda Y. Zoghbi,Hyun-Hwan Jeong,Maxime W.C. Rousseaux,Seon Young Kim,Zh,ong Liu

The C. elegans embryonic transcriptome with tissue, time, and alternative splicing resolution

Adam D. Warner,Brent Ewing,LaDeana W. Hillier,Louis Gevirtzman,Robert H. Waterston

A massively parallel 3′ UTR reporter assay reveals relationships between nucleotide content, sequence conservation, and mRNA destabilization

Adam J. Litterman,David J. Erle,Hani Goodarzi,John D. Gagnon,K. Mark Ansel,Olivier Le Tonqueze,Robin Kageyama,Wenxue Zhao

Genome-wide reconstitution of chromatin transactions reveals that RSC preferentially disrupts H2AZ-containing nucleosomes

Andreas H. Ehrensberger,Aylin Cakiroglu,Bradley R. Cairns,Cedric R. Clapier,Elodie Darbo,Jesper Q. Svejstrup,Nicholas M. Luscombe

Corrigendum: Inherited DNA methylation primes the establishment of accessible chromatin during genome activation

Guifen Liu,Shengen Hu,Wen Wang,Xiangxiu Wang,Yong Zhang

Most chromatin interactions are not in linkage disequilibrium

Katherine S. Pollard,Sean Whalen

Turnover of ribosome-associated transcripts from de novo ORFs produces gene-like characteristics available for de novo gene emergence in wild yeast populations

Alex,Christian R. L,Isabelle Gagnon-Arsenault,Isabelle Hatin,Johan Hallin,Lou Nielly-Thibault,Olivier Namy,re K. Dubé,ry,éléonore Dur

One minute analysis of 200 histone posttranslational modifications by direct injection mass spectrometry

Andrew J. Andrews,Benjamin A. Garcia,Hee Jong Kim,Julia Pinheiro Chagas da Cunha,Katarzyna Kulej,Kevin A. Janssen,Laura M. Agosto,Mariana Lopes,Simone Sidoli,Yekaterina Kori,Zuo-Fei Yuan

Diversification and collapse of a telomere elongation mechanism

Bastien Saint-Le,Mia T. Levine,Son C. Nguyen,re

Ribosomal DNA harbors an evolutionarily conserved clock of biological aging

Bernardo Lemos,Meng Wang

PepQuery enables fast, accurate, and convenient proteomic validation of novel genomic alterations

Bing Zhang,Bo Wen,Xiaojing Wang

High-throughput functional analysis of lncRNA core promoters elucidates rules governing tissue specificity

Chiara Gerhardinger,James C. Lee,John L. Rinn,Kaia Mattioli,Marta Melé,Philipp G. Maass,Pieter-Jan Volders

Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells

Aaron Watters,Aviv Madar,Dan R. Littman,Dayanne M. Castro,Emily R. Miraldi,Jason A. Hall,June-Yong Lee,Maria Ciofani,Maria Pokrovskii,Nicholas De Veaux,Nick Carriero,Richard Bonneau

Dynamics of cardiomyocyte transcriptome and chromatin landscape demarcates key events of heart development

Aleks,Cecilia L. Winata,Jordan A. Ramilowski,Karim Abu Nahia,Katarzyna Piwocka,Katarzyna Z. Kedzierska,Kosuke Hashimoto,Lukasz Bugajski,Maciej Migdal,Michal Pawlak,Piero Carninci,ra Marconi

The circular RNome of primary breast cancer

Adam Butler,Alain Viari,Alastair M. Thompson,Andrea L. Richardson,Andrew P. Futreal,Angelo Paradiso,Anieta M. Sieuwerts,Anne Vincent-Salomon,Anne van Galen,Anne-Lise B？rresen-Dale,Annegien Broeks,Carlos Caldas,Christine Desmedt,Colin A. Purdie,F. Germán Rodríguez-González,Fred C.G.J. Sweep,Ga？ten MacGrogan,Gert G.G.M. van den Eynden,Helen R. Davies,Hendrik G. Stunnenberg,Johan Staaf,John A. Foekens,John W.M. Martens,Jorunn Eyfjord,Katharina Uhr,Marc J. van de Vijver,Marcel Smid,Michelle van der Vlugt-Daane,Mike Stratton,Paul N. Span,Peter T. Simpson,Roberto Salgado,Sancha Martin,Saskia M. Wilting,Serena Nik-Zainal,Steven Van Laere,Stian Knappskog,Sunil R. Lakhani,Tari King,Vanja de Weerd,Wendy J.C. Prager-Van der Smissen

Transposon insertional mutagenesis in Saccharomyces uvarum reveals trans-acting effects influencing species-dependent essential genes

Adam P. Arkin,Amy A. Caudy,Blake T. Hovde,Celia Payen,Frances Cheong,Jeffrey M. Skerker,Maitreya J. Dunham,Monica R. Sanchez,Rachel B. Brem,Sarah Bissonnette

Laboratory validation of a clinical metagenomic sequencing assay for pathogen detection in cerebrospinal fluid

Becky Fung,Charles Y. Chiu,Danielle Ingebrigtsen,Doug Stryke,Elizabeth Pham,Erik Samayoa,John A. Leake,Kevin Messacar,Rick Pesano,Roberta DeBiasi,S,Samia N. Naccache,Samuel Dominguez,Scot Federman,Shaun Arevalo,Steve Miller,Walter Lorizio,William J. Bolosky,ra M. Paff

Anchor: trans-cell type prediction of transcription factor binding sites

Daniel Quang,Hongyang Li,Yuanfang Guan

Transcription factor activity and nucleosome organization in mitosis

Agnès Dubois,Alex,Elena Gallego,Inma Gonzalez,Michel Cohen-Tannoudji,Nancy Gutierrez,Nick Owens,Nicola Festuccia,Pablo Navarro,S,Thaleia Papadopoulou,oermel-Pournin,ra Tachtsidi,rine V

Systematic interrogation of human promoters

Adina Weinberger,Eilon Sharon,Eran Segal,Ronit Nir,Shai Lubliner,Shira Weingarten-Gabbay,Yael Kalma

CTCF sites display cell cycle–dependent dynamics in factor binding and nucleosome positioning

Anders S. Hansen,Job Dekker,Marlies E. Oomen,Xavier Darzacq,Yu Liu

Corrigendum: Initiation of mtDNA transcription is followed by pausing, and diverges across human cell types and during evolution

Amit Blumberg,Anshul Kundaje,Charles G. Danko,Dan Mishmar,Edward J. Rice

Corrigendum: H3K4me1 marks DNA regions hypomethylated during aging in human stem and differentiated cells

Agustín F. Fernández,Alex,Anouk Mentink,Antonella Carella,Cecilia Ferrero,Clara Bueno,Corrado Fagnani,Emanuela Medda,Estela G. Tora？o,Fabian Claire,Flor M. Pérez-Campo,Gustavo F. Bayón,Isabel Cubillo,Jan de Boer,Javier García-Castro,Jesús Delgado-Calle,José A. Riancho,Katia Mareschi,Lorenza Nisticò,Manel Esteller,Maria A. Stazi,Mario F. Fraga,María G. García,Pablo Martinez-Camblor,Pablo Menéndez,Rocío G. Urdinguio,S,Sebastián Moran,Sonia Brescianini,Virgilia Toccaceli,ra Petrus-Reurer,ra Stolzing

The origins and evolution of chromosomes, dosage compensation, and mechanisms underlying venom regulation in snakes

Andrew B. Corbin,Balan Ramesh,Blair W. Perry,Cara F. Smith,Daren C. Card,Drew R. Schield,Esther Betrán,Giulia M. Pasquesi,Heath Blackmon,Jeffery P. Demuth,Jesse M. Meik,Marc Tollis,Nicole R. Hales,Richard H. Adams,Stephen P. Mackessy,Todd A. Castoe

Experimental and pan-cancer genome analyses reveal widespread contribution of acrylamide exposure to carcinogenesis in humans

Adriana Heguy,Alexis Robitaille,Alvin W.T. Ng,Claire Renard,Frederick A. Bel,James McKay,Jiri Zavadil,Kathryn Z. Guyton,Liacine Bouaoun,Magali Olivier,Manuraj P,Maria Zhivagui,Martha R. Stampfer,Maude Ardin,Michael Korenjak,Mona I. Churchwell,Monica Hollstein,Stephanie Villar,Steven G. Rozen,Vincent Cahais,ey

Analysis of 100 high-coverage genomes from a pedigreed captive baboon colony

Betsy Ferguson,Deborah E. Newman,Jacqueline A. Robinson,Jeannie Chan,Jeffrey D. Wall,Jeremy P. Glenn,Laura A. Cox,Saurabh Belsare,Shifra Birnbaum

A chromosome-scale assembly of the axolotl genome

Drew Hardy,Jeramiah J. Smith,Melissa C. Keinath,Nataliya Timoshevskaya,S. R,Vladimir A. Timoshevskiy,al Voss

Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks

Alex,Anastasia A. Proskuryakova,Anastasia I. Kulemzina,Anna V. Kukekova,Denis M. Larkin,Guojie Zhang,Harris A. Lewin,Jaebum Kim,Jennifer L. Johnson,Jian Ma,Marta Farré,Oliver A. Ryder,Polina L. Perelman,Qiye Li,Stephen J. O'Brien,Warren E. Johnson,Wesley C. Warren,Yang Zhang,Yang Zhou,Yingqi Xiong,er S. Graphodatsky

Detection of vancomycin-resistant Enterococcus faecium hospital-adapted lineages in municipal wastewater treatment plants indicates widespread distribution and release into the environment

Beth Blane,Carolyne Horner,Catherine Ludden,Danesh Moradigarav,Direk Limmathurotsakul,Francesc Coll,Jukka Cor,Julian Parkhill,Kathy E. Raven,Nicholas M. Brown,Plamena Naydenova,Sharon J. Peacock,Theodore Gouliouris,er

Chromatin architecture reorganization during neuronal cell differentiation in Drosophila genome

Keerthi T. Chathoth,Nicolae Radu Zabet

Remodeling of epigenome and transcriptome landscapes with aging in mice reveals widespread induction of inflammatory responses

Anne Brunet,Anshul Kundaje,Ben W. Dulken,Bérénice A. Benayoun,Elizabeth A. Pollina,Itamar Harel,Kerriann M. Casey,Param Priya Singh,Salah Mahmoudi

CG dinucleotides enhance promoter activity independent of DNA methylation

Arnaud R. Krebs,Christiane Wirbelauer,Dirk Schübeler,Dominik Hartl,Lukas Burger,Luke Isbel,Ralph S. Gr,Tuncay Baubec

TET2 binding to enhancers facilitates transcription factor recruitment in hematopoietic cells

George S. Vassiliou,Ivan Berest,Jesper Christensen,Judith B. Zaugg,Kasper D. Rasmussen,Koutarou Nishimura,Kristian Helin,Lucía Simón-Carrasco,Marianne T. Pedersen,S,ra Keβler

MicroRNAs reinforce repression of PRC2 transcriptional targets independently and through a feed-forward regulatory network

Haridha Shivram,Steven V. Le,Vishwanath R. Iyer