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

Convergent recombination cessation between mating-type genes and centromeres in selfing anther-smut fungi

Alodie Snirc,Fantin Carpentier,Marco A. Coelho,Michael E. Hood,Ricardo C. Rodríguez de la Vega,Sara Branco,Tatiana Giraud

Kinetics of Xist-induced gene silencing can be predicted from combinations of epigenetic and genomic features

Annalisa Marsico,Benjamin Foret,Chong-Jian Chen,Christel Picard,Edda G. Schulz,Edith Heard,Ilona Dunkel,Iris Jonkers,John T. Lis,Julie Chaumeil,Laurène Syx,Lisa Barros de Andrade e Sousa

Diversification and collapse of a telomere elongation mechanism

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

Comprehensive, integrated, and phased whole-genome analysis of the primary ENCODE cell line K562

Alex,Alexej Abyzov,Bo Zhou,Dimitri Perrin,Giltae Song,Hanlee P. Ji,John M. Bell,Joseph G. Arthur,Michael S. Haney,Noa Ben-Efraim,Noah Spies,Rajini R. Haraksingh,Reenal Pattni,Seunggyu Byeon,Stephanie U. Greer,Steve S. Ho,Wing H. Wong,Xianglong Zhang,Xiaowei Zhu,er E. Urban

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

Mapping global and local coevolution across 600 species to identify novel homologous recombination repair genes

Alex,Alon Lalezari,Anna Mellul,Arash Samiei,Aviad Zick,Dana Sherill-Rofe,Dolev Rahat,Idit Bloch,Irene Guberman,Maya Braun,Michal Goldberg,Ruslan Sadreyev,Steven Findlay,Yuval Tabach,re Orthwein

Identification of a primitive intestinal transcription factor network shared between esophageal adenocarcinoma and its precancerous precursor state

Andrew D. Sharrocks,Connor Rogerson,Edward Britton,Neil Hanley,Sarah Withey,Yeng S. Ang

Erratum: Deep experimental profiling of microRNA diversity, deployment, and evolution across the Drosophila genus

Adam Siepel,Alex,Alex S. Flynt,Eric C. Lai,Jaaved Mohammed,Matthew DeCruz,Md Mosharrof Hossain Mondal,ra M. Panzarino

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

Bayesian-based noninvasive prenatal diagnosis of single-gene disorders

Artem Danilevsky,Avital Polsky,Chen Raff,David Golan,Guy Shapira,Lina Basel-Salmon,Noam Shomron,Reut Tomashov Matar,Tom Rabinowitz

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

Orientation-aware plasma cell-free DNA fragmentation analysis in open chromatin regions informs tissue of origin

Brigette B.Y. Ma,Hao Sun,Henry L.Y. Chan,John Wong,K.C. Allen Chan,Kun Sun,Paul B.S. Lai,Peiyong Jiang,Rossa W.K. Chiu,Simon S.M. Ng,Stephen L. Chan,Suk Hang Cheng,Tak Y. Leung,Timothy H.T. Cheng,Tony S.K. Mok,Vincent W.S. Wong,Y.M. Dennis Lo

Single-cell sequencing of primate preimplantation embryos reveals chromosome elimination via cellular fragmentation and blastomere exclusion

Andrew Adey,Brittany L. Daughtry,Byung Park,Jimi L. Rosenkrantz,Kimberly A. Nevonen,Kristof A. Torkenczy,Lina Gao,Lucia Carbone,Melissa Yan,Nash Redmayne,Nathan H. Lazar,Shawn L. Chavez,Suzanne S. Fei

Large-scale discovery of mouse transgenic integration sites reveals frequent structural variation and insertional mutagenesis

Cathleen Lutz,Elissa J. Chesler,Erik Splinter,Hao He,Jacqueline K. White,Juliet Ndukum,Karen Svenson,Laura G. Reinholdt,Leslie O. Goodwin,Max van Min,Michael Sasner,Rachel Urban,Robert E. Braun,Stephen A. Murray,Tiffany L. Davis,Vivek Kumar,Vivek M. Philip

An AR-ERG transcriptional signature defined by long-range chromatin interactomes in prostate cancer cells

Charlie L. Heng,Edwin Cheung,Guoliang Li,Huay Mei Poh,Huy Hoang Do,John T. Lis,Kern Rei Chng,Leighton J. Core,Manolis Kellis,Mei Hui Liu,Nicola Rinaldi,Shaojiang Cai,Shreyas Lingadahalli,Si Kee Tan,Wing-Kin Sung,Xiaoan Ruan,Yijun Ruan,Ying Ying Sung,Zhizhuo Zhang,Zikai Chen

Systematic interrogation of human promoters

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

Fast and flexible bacterial genomic epidemiology with PopPUNK

Gerry Tonkin-Hill,Jeffrey N. Weiser,John A. Lees,Jukka Cor,Rebecca A. Gladstone,Simon R. Harris,Stephanie W. Lo,Stephen D. Bentley,er

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

Identification of human silencers by correlating cross-tissue epigenetic profiles and gene expression

Brendan F. Miller,Di Huang,Hanna M. Petrykowska,Ivan Ovcharenko,Laura Elnitski

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

Resolving the full spectrum of human genome variation using Linked-Reads

Adam Lowe,Adrian Fehr,Alvaro Martinez Barrio,Andrew Price,Andrew Wei Xu,Ariel Royall,Bill Lin,Brendan Galvin,Cass,Christopher Hindson,Christopher J. O'Keefe,Claudia Catalanotti,Daniel MacArthur,David Stafford,Deanna M. Church,Elise Ruark,Esty Holt,Francesca Meschi,Haynes Heaton,Heather Ordonez,Ian T. Fiddes,Indira Wu,Jamie Marshall,Jill Herschleb,Jorge Bernate,Josh Delaney,Kamila Belhocine,Keith Bjornson,Michael Schnall-Levin,Monkol Lek,Nazneen Rahman,Nikka Keivanfar,Patrick Marks,Pranav Patel,Preyas Shah,Rajiv Bharadwaj,Sarah Garcia,Shamoni Maheshwari,Shazia Mahamdallie,Sheila Seal,Sofia Kyriazopoulou-Panagiotopoulou,Stephen Williams,Susanna Jett,Tony Makarewicz,ra B. Jabara

Chromatin architecture reorganization during neuronal cell differentiation in Drosophila genome

Keerthi T. Chathoth,Nicolae Radu Zabet

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

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

DNA (de)methylation in embryonic stem cells controls CTCF-dependent chromatin boundaries

Achim Breiling,Christopher T. Clarkson,Frank Lyko,Graeme J. Thorn,Günter Raddatz,Karsten Rippe,Laura Wiehle,Vladimir B. Teif

Guide Positioning Sequencing identifies aberrant DNA methylation patterns that alter cell identity and tumor-immune surveillance networks

Baolong Zhang,Cizhong Jiang,Dan Zou,Feizhen Wu,Hongbo Yang,Huaibing Luo,Jin Li,Lina Peng,Ming Gao,Peng Xu,Qingping Zou,Shaoliang Peng,Shihua Dong,Ting Wang,Wei Li,Wenqiang Yu,Xin Hu,Yan Li,Yanping Xi,Ying Liang

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

Daniel Quang,Hongyang Li,Yuanfang Guan

A dynamic and integrated epigenetic program at distal regions orchestrates transcriptional responses to VEGFA

Bing Zhang,Daniel S. Day,Fang Zhang,Guo-cheng Yuan,Huangying Le,Huijing Yu,Jiahuan Chen,Jingfang Wang,Kun Sun,Pengyi Yan,Peter J. Park,Sara P. Garcia,Sean M. Stevens,Shiyan Wang,Weiting Wei,William T. Pu,Xiaodong Liang,Xusheng Luo,Yan Zhang,Zeguang Han,Zhi-jie Liu,Zixuan Li

Pathogenicity and selective constraint on variation near splice sites

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

Accelerated rates of large-scale mutations in the presence of copper and nickel

Frédéric J.J. Chain,James K. Bull,Jullien M. Flynn,Melania E. Cristescu

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

Defining TP53 pioneering capabilities with competitive nucleosome binding assays

Michael J. Buck,Xinyang Yu

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

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

Cohesin occupancy and composition at enhancers and promoters are linked to DNA replication origin proximity in Drosophila

Dale Dorsett,Maria Gause,Michelle Pherson,Ziva Misulovin

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

New guidelines for DNA methylome studies regarding 5-hydroxymethylcytosine for understanding transcriptional regulation

Alfred S.L. Cheng,Kevin Y. Yip,Le Li,Qiong Wu,Yuwei Gao

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