Expanded encyclopaedias of DNA elements in the human and mouse genomes
Federico Abascal(Wellcome Sanger Institute), Reyes Acosta(Altius Institute for Biomedical Sciences), Nicholas J. Addleman(Stanford University), Jessika Adrian(Stanford University), Veena Afzal(Lawrence Berkeley National Laboratory), Rizi Ai(University of California San Diego), Bronwen Aken(European Bioinformatics Institute), Jennifer A. Akiyama(Lawrence Berkeley National Laboratory), Omar Al Jammal(National Institutes of Health), Henry Amrhein(California Institute of Technology), Stacie M. Anderson(National Institutes of Health), Gregory R. Andrews(University of Massachusetts Chan Medical School), Igor Antoshechkin(California Institute of Technology), Kristin Ardlie(Broad Institute), Joel Armstrong(University of California, Santa Cruz), Matthew Astley(Wellcome Sanger Institute), Budhaditya Banerjee(Brigham and Women's Hospital), Amira Barkal(California Institute for Regenerative Medicine), If H. A. Barnes(European Bioinformatics Institute), Iros Barozzi(Lawrence Berkeley National Laboratory), Daniel Barrell(European Bioinformatics Institute), Gemma Barson(Wellcome Sanger Institute), Daniel J. Bates(Altius Institute for Biomedical Sciences), Ulugbek K. Baymuradov(Stanford University), Cassandra Bazile(Massachusetts Institute of Technology), M Beer(Johns Hopkins University), Samantha Beik(Broad Institute), M. A. Bender(Fred Hutch Cancer Center), Ruth Bennett(European Bioinformatics Institute), Louis Philip Benoit Bouvrette(Université de Montréal), B Bernstein(Broad Institute), Andrew Berry(European Bioinformatics Institute), Anand Bhaskar(Stanford University), Alexandra Bignell(European Bioinformatics Institute), Steven M. Blue(University of California San Diego), David M. Bodine(National Institutes of Health), Carles A. Boix(Massachusetts Institute of Technology), Nathan Boley(Stanford University), Tyler Borrman(University of Massachusetts Chan Medical School), Beatrice Borsari(Universitat Pompeu Fabra), Alan P. Boyle(University of Michigan), Laurel A. Brandsmeier(HudsonAlpha Institute for Biotechnology), Alessandra Breschi(Universitat Pompeu Fabra), Emery H. Bresnick(University of Wisconsin–Madison), Jason A. Brooks(University of Massachusetts Chan Medical School), Michael Buckley(Altius Institute for Biomedical Sciences), Christopher B. Burge(Massachusetts Institute of Technology), Rachel Byron(Fred Hutch Cancer Center), Eileen Cahill(National Institutes of Health), Lingling Cai(Tongji University), Lulu Cao(Stanford University), Mark Carty(Memorial Sloan Kettering Cancer Center), Rosa G. Castanon(Salk Institute for Biological Studies), Andres Castillo(Altius Institute for Biomedical Sciences), Hassan Chaı̈b(Stanford University), Esther T. Chan(Stanford University), Daniel R. Chee(Altius Institute for Biomedical Sciences), Sora Chee(University of California San Diego), Hao Chen(University of Massachusetts Chan Medical School), Huaming Chen(Salk Institute for Biological Studies), Jiayu Chen(University of California San Diego), Songjie Chen(Stanford University), J. Michael Cherry(Stanford University), Surya B. Chhetri(HudsonAlpha Institute for Biotechnology), Jyoti S. Choudhary(Institute of Cancer Research), Jacqueline Chrast(University of Lausanne), Dongjun Chung(The Ohio State University), Declan Clarke(Yale University), Neal Cody(Université de Montréal), Candice J. Coppola(HudsonAlpha Institute for Biotechnology), Julie Coursen(National Institutes of Health), Anthony D’Ippolito(Duke University), Stephen Dalton(University of Georgia), Cassidy Danyko(Cold Spring Harbor Laboratory), Claire Davidson(European Bioinformatics Institute), José Dávila-Velderrain(Massachusetts Institute of Technology), Carrie Davis(Cold Spring Harbor Laboratory), Job Dekker(University of Massachusetts Chan Medical School), Alden Deran(University of California, Santa Cruz), Gilberto DeSalvo(California Institute of Technology), Gloria Despacio-Reyes(Wellcome Sanger Institute), Colin N. Dewey(University of Wisconsin–Madison), Diane E. Dickel(Lawrence Berkeley National Laboratory), Morgan Diegel(Altius Institute for Biomedical Sciences), Mark Diekhans(University of California, Santa Cruz), Vishnu Dileep(Florida State University), Bo Ding(University of California San Diego), Sarah Djebali(Universitat Pompeu Fabra), Alexander Dobin(Cold Spring Harbor Laboratory), Daniel Domı́nguez(Massachusetts Institute of Technology), Sarah Donaldson(European Bioinformatics Institute), Jörg Drenkow(Cold Spring Harbor Laboratory), Timothy R. Dreszer(Stanford University), Yotam Drier(MGH Institute of Health Professions), Michael O. Duff(Institute for Systems Biology), Douglass Dunn(Altius Institute for Biomedical Sciences), Catharine Eastman(Stanford University), Joseph R. Ecker(Salk Institute for Biological Studies), Matthew D. Edwards(Massachusetts Institute of Technology), Nicole El-Ali(University of California, Irvine), Shaimae I. Elhajjajy(University of Massachusetts Chan Medical School), Keri Elkins(University of California San Diego), Andrew Emili(University of Toronto), Charles B. Epstein(Broad Institute), Rachel C. Evans(HudsonAlpha Institute for Biotechnology), Iakes Ezkurdia(Centro de Investigación en Red en Enfermedades Cardiovasculares), Kaili Fan(University of Massachusetts Chan Medical School), Peggy Farnham(University of Southern California), Nina Farrell(Broad Institute), Elise A. Feingold(National Institutes of Health), Anne-Maud Ferreira(University of Lausanne), Katherine Fisher-Aylor(California Institute of Technology), Stephen Fitzgerald(Wellcome Sanger Institute), Paul Flicek(European Bioinformatics Institute), Chuan-Sheng Foo(Institute for Infocomm Research), Kevin Fortier(University of Massachusetts Chan Medical School), Adam Frankish(European Bioinformatics Institute), Peter Freese(Massachusetts Institute of Technology), Shaliu Fu(Tongji University), Xiang‐Dong Fu(University of California San Diego), Y. Fu(University of Massachusetts Chan Medical School), Y. Fukuda(Lawrence Berkeley National Laboratory), Mariateresa Fulciniti(Dana-Farber Cancer Institute), Alister P. W. Funnell(Altius Institute for Biomedical Sciences), Idan Gabdank(Stanford University), Timur R. Galeev(Yale University), Mingshi Gao(University of Massachusetts Chan Medical School), Carlos García Girón(European Bioinformatics Institute), Tyler H. Garvin(Lawrence Berkeley National Laboratory), Chelsea Gelboin-Burkhart(University of California San Diego), Grigorios Georgolopoulos(Altius Institute for Biomedical Sciences), Mark Gerstein(Yale University), Belinda Giardine(Pennsylvania State University), David K. Gifford(Massachusetts Institute of Technology), David M. Gilbert(Florida State University), Daniel A. Gilchrist(National Institutes of Health), Shawn Gillespie(MGH Institute of Health Professions), T Gingeras(Cold Spring Harbor Laboratory), Peng Gong(Yale University), Álvaro González(Memorial Sloan Kettering Cancer Center), José M. González(European Bioinformatics Institute), Peter J. Good, Alon Goren(Broad Institute), David U. Gorkin(University of California San Diego), Brenton R. Graveley(Institute for Systems Biology), Michael R. Gray(Wellcome Sanger Institute), Jack Greenblatt(University of Toronto), Ed Griffiths(Wellcome Sanger Institute), Mark Groudine(Fred Hutch Cancer Center), Fabian Grubert(Stanford University), Mengting Gu(Yale University), Roderic Guigó(Universitat Pompeu Fabra), Hongbo Guo(University of Toronto), Yuming Guo(Massachusetts Institute of Technology), Yuchun Guo(Massachusetts Institute of Technology), Gamze Gürsoy(Yale University), María Gutiérrez‐Arcelus(Brigham and Women's Hospital), Jessica Halow(Altius Institute for Biomedical Sciences), Ross C. Hardison(Pennsylvania State University), Matthew P. Hardy(European Bioinformatics Institute), Manoj Hariharan(Salk Institute for Biological Studies), Arif Harmanci(Yale University), Anne Harrington(Lawrence Berkeley National Laboratory), Jennifer Harrow, Tatsunori Hashimoto(Massachusetts Institute of Technology), Richard Hasz(Gift of Life Michigan), Meital Hatan(Broad Institute), Eric Haugen(Altius Institute for Biomedical Sciences), James E. Hayes(Icahn School of Medicine at Mount Sinai), Peng He(Salk Institute for Biological Studies), Yupeng He(Salk Institute for Biological Studies), Nastaran Heidari(Stanford University), David N. Hendrickson(Broad Institute), Elisabeth F. Heuston(National Institutes of Health), Jason A. Hilton(Stanford University), Benjamin C. Hitz(Stanford University), Abigail Hochman(Massachusetts Institute of Technology), Cory Holgren(University of Chicago), Lei Hou(Massachusetts Institute of Technology), Shuyu Hou(Tongji University), Yun-Hua Esther Hsiao(University of California, Los Angeles), Shanna Hsu(Broad Institute), Hui Huang(University of California San Diego), Tim Hubbard(Guy's Hospital), Jack Huey(University of Massachusetts Chan Medical School), Timothy R. Hughes(University of Toronto), Toby Hunt(European Bioinformatics Institute), Sean Ibarrientos(Altius Institute for Biomedical Sciences), Robbyn Issner(Broad Institute), Mineo Iwata(Altius Institute for Biomedical Sciences), Osagie Izuogu(European Bioinformatics Institute), Tommi Jaakkola(Massachusetts Institute of Technology), Nader Jameel(University of Chicago), Camden Jansen(University of California, Irvine), Lixia Jiang(Stanford University), Peng Jiang(Dana-Farber Cancer Institute), Audra Johnson(Altius Institute for Biomedical Sciences), Rory Johnson(Universitat Pompeu Fabra), Irwin Jungreis(Massachusetts Institute of Technology), Madhura Kadaba(University of Chicago), Maya Kasowski(Stanford University), Mary Kasparian(University of Chicago), Momoe Kato(Lawrence Berkeley National Laboratory), Rajinder Kaul(University of Washington), Trupti Kawli(Stanford University), Mike Kay(European Bioinformatics Institute), Judith C. Keen(American Society for Radiation Oncology), Sündüz Keleş(University of Wisconsin–Madison), Cheryl A. Keller(Pennsylvania State University), David R. Kelley(Harvard University Press), Manolis Kellis(Broad Institute), Pouya Kheradpour(Massachusetts Institute of Technology), Daniel Sunwook Kim(Stanford University), Anthony Kirilusha(California Institute of Technology), Robert J. Klein(Icahn School of Medicine at Mount Sinai), Birgit Knoechel(Dana-Farber Cancer Institute), Samantha Kuan(University of California San Diego), Michael Kulik(University of Georgia), Sushant Kumar(Yale University), Anshul Kundaje(Stanford University), Tanya Kutyavin(Altius Institute for Biomedical Sciences), Julien Lagarde(Universitat Pompeu Fabra), Bryan R. Lajoie(University of Massachusetts Chan Medical School), Nicole Lambert(Massachusetts Institute of Technology), John Lazar(Altius Institute for Biomedical Sciences), Ah Young Lee(University of California San Diego), Donghoon Lee(Yale University), Elizabeth Lee(Lawrence Berkeley National Laboratory), Jin‐Wook Lee(Stanford University), Kristen Lee(Altius Institute for Biomedical Sciences), Christina S. Leslie(Memorial Sloan Kettering Cancer Center), Shawn Levy(HudsonAlpha Institute for Biotechnology), Bin Li(University of California San Diego), Hairi Li(University of California San Diego), Nan Li(University of California San Diego), Shantao Li(Yale University), Xiang-Rui Li(Tongji University), Yang Li(Stanford University), Ying Li(Tongji University), Yining Li(Stanford University), Yue Li(Massachusetts Institute of Technology), Jin Lian(Yale University), Maxwell W. Libbrecht(Simon Fraser University), Shin Lin(Stanford University), Yiing Lin(Washington University in St. Louis), Dianbo Liu(Massachusetts Institute of Technology), Jason Liu(Yale University), Peng Liu(University of Wisconsin–Madison), Tingting Liu(Penn State Milton S. Hershey Medical Center), X. Shirley Liu(Dana-Farber Cancer Institute), Yan Liu(Tongji University), Yaping Liu(Massachusetts Institute of Technology), Maria Long(Pennsylvania State University), Shaoke Lou(Yale University), Jane Loveland(European Bioinformatics Institute), Aiping Lu(Tongji University), Yuheng Lu(Memorial Sloan Kettering Cancer Center), Éric Lécuyer(McGill University), Lijia Ma(University of Chicago), Mark Mackiewicz(HudsonAlpha Institute for Biotechnology), Brandon J. Mannion(Lawrence Berkeley National Laboratory), Michael Mannstadt(MGH Institute of Health Professions), Deepa Manthravadi(Wellcome Sanger Institute), Georgi K. Marinov(California Institute of Technology), Fergal J. Martin(European Bioinformatics Institute), Eugenio Mattei(University of Massachusetts Chan Medical School), Kenneth McCue(California Institute of Technology), Megan McEown(HudsonAlpha Institute for Biotechnology), Graham McVicker(Salk Institute for Biological Studies), Sarah K. Meadows(HudsonAlpha Institute for Biotechnology), Alex Meissner(Max Planck Institute for Molecular Genetics), Eric M. Mendenhall(HudsonAlpha Institute for Biotechnology), C. Luke Messer(HudsonAlpha Institute for Biotechnology), Wouter Meuleman(Altius Institute for Biomedical Sciences), Clifford A. Meyer(Dana-Farber Cancer Institute), Steve Miller(Wellcome Sanger Institute), Matthew G. Milton(University of Chicago), Tejaswini Mishra(Stanford University), Dianna E. Moore(HudsonAlpha Institute for Biotechnology), Helen M. Moore(National Institutes of Health), Jill E. Moore(University of Massachusetts Chan Medical School), Samuel H. Moore(National Institutes of Health), Jennifer Moran(University of Chicago), A Mortazavi(University of California, San Francisco), Jonathan M. Mudge(European Bioinformatics Institute), Nikhil Munshi(Dana-Farber Cancer Institute), Rabi Murad(University of California, Irvine), R Myers(HudsonAlpha Institute for Biotechnology), Vivek Nandakumar(Altius Institute for Biomedical Sciences), Preetha Nandi(National Institutes of Health), Anil Narasimha(Stanford University), Aditi K. Narayanan(Stanford University), Hannah Naughton(National Institutes of Health), Fábio C. P. Navarro(Yale University), Patrick A. Navas(Altius Institute for Biomedical Sciences), Jurijs Nazarovs(University of Wisconsin–Madison), Jemma Nelson(Altius Institute for Biomedical Sciences), Shane Neph(Altius Institute for Biomedical Sciences), Fidencio Neri(Altius Institute for Biomedical Sciences), Joseph R. Nery(Salk Institute for Biological Studies), Amy R. Nesmith(HudsonAlpha Institute for Biotechnology), J. Scott Newberry(HudsonAlpha Institute for Biotechnology), Kimberly M. Newberry(HudsonAlpha Institute for Biotechnology), Vu N. Ngo(University of California San Diego), Rosy Nguyen(HudsonAlpha Institute for Biotechnology), Thai B. Nguyen(University of California San Diego), Tung Nguyen(University of California San Diego), Andrew Nishida(Altius Institute for Biomedical Sciences), William Stafford Noble(University of Washington), Catherine S. Novak(Lawrence Berkeley National Laboratory), Eva Maria Novoa(Massachusetts Institute of Technology), Briana Nuñez(National Institutes of Health), Charles W. O’Donnell(Massachusetts Institute of Technology), Sara Olson(Institute for Systems Biology), Kathrina C. Onate(Stanford University), Ericka Otterman(Altius Institute for Biomedical Sciences), Hakan Özadam(University of Massachusetts Chan Medical School), Michael Pagan(National Institutes of Health), Tsultrim Palden(Massachusetts Institute of Technology), Xinghua Pan(Yale University), Yong‐Jin Park(Massachusetts Institute of Technology), E. Christopher Partridge(HudsonAlpha Institute for Biotechnology), Benedict Paten(University of California, Santa Cruz), Florencia Pauli(HudsonAlpha Institute for Biotechnology), Michael J. Pazin(National Institutes of Health), Baikang Pei(Yale University), L Pennacchio(Lawrence Berkeley National Laboratory), Alexendar R. Perez(Memorial Sloan Kettering Cancer Center), Emily Perry(European Bioinformatics Institute), Dmitri D. Pervouchine(Universitat Pompeu Fabra), Nishigandha Phalke(University of Massachusetts Chan Medical School), Quan Pham(Lawrence Berkeley National Laboratory), Doug Phanstiel(University of North Carolina at Chapel Hill), Ingrid Plajzer-Frick(Lawrence Berkeley National Laboratory), Henry Pratt(University of California San Diego), Henry Pratt(University of Massachusetts Chan Medical School), Sebastian Preißl(University of California San Diego), Jonathan K. Pritchard(Stanford University), Yuri Pritykin(Memorial Sloan Kettering Cancer Center), Michael Purcaro(University of Massachusetts Chan Medical School), Qian Qin(Harvard University), Giovanni Quinones-Valdez(University of California, Los Angeles), Ines Rabano(University of California San Diego), Ernest Radovani(University of Toronto), Anil Raj(Stanford University), Nisha Rajagopal(Brigham and Women's Hospital), Oren Ram(Broad Institute), Lucia Ramirez(Stanford University), Ricardo N. Ramírez(University of California, Irvine), Dylan M. Rausch(MGH Institute of Health Professions), Soumya Raychaudhuri(Brigham and Women's Hospital), Joseph J. Raymond(Broad Institute), Rozita Razavi(University of Toronto), Timothy E. Reddy(Duke University), Thomas Reimonn(University of Massachusetts Chan Medical School), Bing Ren(University of California San Diego), Alexandre Reymond(University of Lausanne), Alex Reynolds(Altius Institute for Biomedical Sciences), Suhn K. Rhie(University of Southern California), John L. Rinn(University of Colorado Boulder), Miguel N. Rivera(MGH Institute of Health Professions), Juan Carlos Rivera-Mulia(Florida State University), Brian S. Roberts(HudsonAlpha Institute for Biotechnology), José Manuel Rodrı́guez(Centro de Investigación en Red en Enfermedades Cardiovasculares), Joel Rozowsky(Yale University), Russell J.H. Ryan(MGH Institute of Health Professions), Eric Rynes(Altius Institute for Biomedical Sciences), Denis Salins(Stanford University), Richard Sandstrom(Altius Institute for Biomedical Sciences), Takayo Sasaki(Florida State University), Shashank Sathe(University of California San Diego), Daniel Savic(St. Jude Children's Research Hospital), Alexandra Scavelli(Cold Spring Harbor Laboratory), Jonathan Scheiman(Harvard University), Christoph N. Schlaffner(Wellcome Sanger Institute), Jeffery A. Schloss(National Institutes of Health), Frank W. Schmitges(University of Toronto), Lei Hoon See(Cold Spring Harbor Laboratory), Anurag Sethi(Yale University), Manu Setty(Memorial Sloan Kettering Cancer Center), Anthony Shafer(Altius Institute for Biomedical Sciences), Shuo Shan(University of Massachusetts Chan Medical School), Eilon Sharon(Stanford University), Quan Shen(Yale University), Yin Shen(University of California, San Francisco), Richard I. Sherwood(Brigham and Women's Hospital), Minyi Shi(Stanford University), Sunyoung Shin(The University of Texas at Dallas), Noam Shoresh(Broad Institute), Kyle Siebenthall(Altius Institute for Biomedical Sciences), Cristina Sisu(Yale University), Teri Slifer(Stanford University), Cricket A. Sloan(Stanford University), Anna Marie Smith(Leidos (United States)), Valentina Snetkova(Lawrence Berkeley National Laboratory), M Snyder, Damek V. Spacek(Stanford University), Sharanya Srinivasan(Brigham and Women's Hospital), Rohith Srivas(Stanford University), George Stamatoyannopoulos(University of Washington Medical Center), J Stamatoyannopoulos(University of Washington), Rebecca Stanton(University of California San Diego), Dave Steffan(University of Chicago), Sandra Stehling-Sun(Altius Institute for Biomedical Sciences), J. Seth Strattan(Stanford University), Amanda Su(Massachusetts Institute of Technology), Balaji Sundararaman(University of California San Diego), Marie‐Marthe Suner(European Bioinformatics Institute), Tahin Syed(Massachusetts Institute of Technology), Matt Szynkarek(University of Chicago), Forrest Y. Tanaka(Stanford University), Danielle Tenen(Broad Institute), Mingxiang Teng(Moffitt Cancer Center), Jeffrey A. Thomas(National Disease Research Interchange), Dave Toffey(University of Chicago), Michael L. Tress(Spanish National Cancer Research Centre), Diane Trout(California Institute of Technology), Gosia Trynka(Wellcome Sanger Institute), Junko Tsuji(University of Massachusetts Chan Medical School), Sean A. Upchurch(California Institute of Technology), Oana Ursu(Stanford University), Barbara Uszczyńska-Ratajczak(International Institute of Molecular and Cell Biology), Mia C. Uziel(Broad Institute), Alfonso Valencia(Spanish National Cancer Research Centre), Benjamin Van Biber(Altius Institute for Biomedical Sciences), Arjan G. van der Velde(Boston University), Eric L. Van Nostrand(University of California San Diego), Yekaterina Vaydylevich(National Institutes of Health), Jesús Vázquez(Centro de Investigación en Red en Enfermedades Cardiovasculares), Alec Victorsen(University of Chicago), Jost Vielmetter(California Institute of Technology), Jeff Vierstra(Altius Institute for Biomedical Sciences), Axel Visel(University of California, Merced), Anna Vlasova(Universitat Pompeu Fabra), Christopher M. Vockley(Duke University), Simona Volpi(National Institutes of Health), Shinny Vong(Altius Institute for Biomedical Sciences), Hao Wang(Altius Institute for Biomedical Sciences), Mengchi Wang(University of California San Diego), Qin Wang(Tongji University), Ruth Wang(University of California San Diego), Tao Wang(University of California San Diego), Wei Wang(University of California San Diego), Xiaofeng Wang(Montreal Clinical Research Institute), Yanli Wang(Penn State Milton S. Hershey Medical Center), Nathaniel Watson(Stanford University), Xintao Wei(Institute for Systems Biology), Zhijie Wei(Tongji University), Hendrik Weisser(Wellcome Sanger Institute), Sherman M. Weissman(Yale University), Rene Welch(University of Wisconsin–Madison), Robert E. Welikson(Altius Institute for Biomedical Sciences), Zhiping Weng(Boston University), Harm-Jan Westra(Brigham and Women's Hospital), John W. Whitaker(University of California San Diego), Collin C. White(HudsonAlpha Institute for Biotechnology), Kevin P. White(Tempus Labs (United States)), André Wildberg(University of California San Diego), Brian A. Williams(California Institute of Technology), David Wine(Broad Institute), Heather Witt(University of Southern California), B Wold(California Institute of Technology), Maxim Y. Wolf(Massachusetts Institute of Technology), James C. Wright(Wellcome Sanger Institute), Rui Xiao(University of California San Diego), Xinshu Xiao(University of California, Los Angeles), Jie Xu(Penn State Milton S. Hershey Medical Center), Jinrui Xu(Yale University), Koon-Kiu Yan(Yale University), Yongqi Yan(Altius Institute for Biomedical Sciences), Hongbo Yang(Penn State Milton S. Hershey Medical Center), Xinqiong Yang(Stanford University), Yiwen Yang(University of California, Los Angeles), Galip Gürkan Yardımcı(University of Washington), Brian A. Yee(University of California San Diego), G Yeo(University of California San Diego), Taylor Young(University of Massachusetts Chan Medical School), Tianxiong Yu(Tongji University), Feng Yue(Penn State Milton S. Hershey Medical Center), Chris Zaleski(Cold Spring Harbor Laboratory), Chongzhi Zang(Dana-Farber Cancer Institute), Haoyang Zeng(Massachusetts Institute of Technology), Weihua Zeng(University of California, Irvine), Daniel R. Zerbino(European Bioinformatics Institute), Jie Zhai(Stanford University), Lijun Zhan(Penn State Milton S. Hershey Medical Center), Ye Zhan(University of Massachusetts Chan Medical School), Bo Zhang(Penn State Milton S. Hershey Medical Center), Jialing Zhang(Yale University), Jing Zhang(Yale University), Kai Zhang(University of California San Diego), Lijun Zhang(Penn State Milton S. Hershey Medical Center), Peng Zhang(Tongji University), Qi Zhang(University of Nebraska–Lincoln), Xiao‐Ou Zhang(University of Massachusetts Chan Medical School), Yanxiao Zhang(University of California San Diego), Zhizhuo Zhang(Massachusetts Institute of Technology), Yuan Zhao(University of California San Diego), Zheng Ye(University of Wisconsin–Madison), Guoqing Zhong(University of Toronto), Xiaoqiao Zhou(National Institutes of Health), Yun Zhu(University of California San Diego), Jared Zimmerman(Florida State University), Jill E. Moore(University of Massachusetts Chan Medical School), Michael Purcaro(University of Massachusetts Chan Medical School), Henry Pratt(University of Massachusetts Chan Medical School), Charles B. Epstein(Broad Institute), Noam Shoresh(Broad Institute), Jessika Adrian(Stanford University), Trupti Kawli(Stanford University), Carrie Davis(Cold Spring Harbor Laboratory), Alexander Dobin(Cold Spring Harbor Laboratory), Rajinder Kaul(University of Washington), Jessica Halow(Altius Institute for Biomedical Sciences), Eric L. Van Nostrand(University of California San Diego), Peter Freese(Massachusetts Institute of Technology), David U. Gorkin(University of California San Diego), Yin Shen(University of California, San Francisco), Yupeng He(Salk Institute for Biological Studies), Mark Mackiewicz(HudsonAlpha Institute for Biotechnology), Florencia Pauli(HudsonAlpha Institute for Biotechnology), Brian A. Williams(California Institute of Technology), A Mortazavi(University of California, San Francisco), Cheryl A. Keller(Pennsylvania State University), Xiao‐Ou Zhang(University of Massachusetts Chan Medical School), Shaimae I. Elhajjajy(University of Massachusetts Chan Medical School), Jack Huey(University of Massachusetts Chan Medical School), Diane E. Dickel(Lawrence Berkeley National Laboratory), Valentina Snetkova(Lawrence Berkeley National Laboratory), Xintao Wei(Institute for Systems Biology), Xiaofeng Wang(Montreal Clinical Research Institute), Juan Carlos Rivera-Mulia(Florida State University), Joel Rozowsky(Yale University), Jing Zhang(Yale University), Surya B. Chhetri(HudsonAlpha Institute for Biotechnology), Jialing Zhang(Yale University), Alec Victorsen(University of Chicago), Kevin P. White(Tempus Labs (United States)), Axel Visel(University of California, Merced), G Yeo(University of California San Diego), Christopher B. Burge(Montreal Clinical Research Institute), Éric Lécuyer(Florida State University), David M. Gilbert(Florida State University), Job Dekker(University of Massachusetts Chan Medical School), John Rinn(University of Alabama in Huntsville), Eric M. Mendenhall(Salk Institute for Biological Studies), Joseph R. Ecker(Salk Institute for Biological Studies), Manolis Kellis(Broad Institute), Robert J. Klein(University of Washington), William Stafford Noble(Stanford University), Anshul Kundaje(Universitat Pompeu Fabra), Roderic Guigó(University of Southern California), Peggy Farnham(Stanford University), J. Michael Cherry(HudsonAlpha Institute for Biotechnology), R Myers(University of California San Diego), Bing Ren(Institute for Systems Biology), Brenton R. Graveley(Yale University), Mark B. Gerstein(University of California, Berkeley), L Pennacchio, M Snyder(Broad Institute), Bradley E. Bernstein(California Institute of Technology), B Wold(Pennsylvania State University), Ross C. Hardison(Cold Spring Harbor Laboratory), T Gingeras(University of Washington), J Stamatoyannopoulos(Boston University), Zhiping Weng
Cited by 2,552Open Access
Abstract
Abstract The human and mouse genomes contain instructions that specify RNAs and proteins and govern the timing, magnitude, and cellular context of their production. To better delineate these elements, phase III of the Encyclopedia of DNA Elements (ENCODE) Project has expanded analysis of the cell and tissue repertoires of RNA transcription, chromatin structure and modification, DNA methylation, chromatin looping, and occupancy by transcription factors and RNA-binding proteins. Here we summarize these efforts, which have produced 5,992 new experimental datasets, including systematic determinations across mouse fetal development. All data are available through the ENCODE data portal ( https://www.encodeproject.org ), including phase II ENCODE 1 and Roadmap Epigenomics 2 data. We have developed a registry of 926,535 human and 339,815 mouse candidate cis -regulatory elements, covering 7.9 and 3.4% of their respective genomes, by integrating selected datatypes associated with gene regulation, and constructed a web-based server (SCREEN; http://screen.encodeproject.org ) to provide flexible, user-defined access to this resource. Collectively, the ENCODE data and registry provide an expansive resource for the scientific community to build a better understanding of the organization and function of the human and mouse genomes.
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