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Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, Sandstrom R, Ma Z, Davis C, Pope BD, Shen Y, Pervouchine DD, Djebali S, Thurman RE, Kaul R, Rynes E, Kirilusha A, Marinov GK, Williams BA, Trout D, Amrhein H, Fisher-Aylor K, Antoshechkin I, DeSalvo G, See LH, Fastuca M, Drenkow J, Zaleski C, Dobin A, Prieto P, Lagarde J, Bussotti G, Tanzer A, Denas O, Li K, Bender MA, Zhang M, Byron R, Groudine MT, McCleary D, Pham L, Ye Z, Kuan S, Edsall L, Wu YC, Rasmussen MD, Bansal MS, Kellis M, Keller CA, Morrissey CS, Mishra T, Jain D, Dogan N, Harris RS, Cayting P, Kawli T, Boyle AP, Euskirchen G, Kundaje A, Lin S, Lin Y, Jansen C, Malladi VS, Cline MS, Erickson DT, Kirkup VM, Learned K, Sloan CA, Rosenbloom KR, Lacerda de Sousa B, Beal K, Pignatelli M, Flicek P, Lian J, Kahveci T, Lee D, Kent WJ, Ramalho Santos M, Herrero J, Notredame C, Johnson A, Vong S, Lee K, Bates D, Neri F, Diegel M, Canfield T, Sabo PJ, Wilken MS, Reh TA, Giste E, Shafer A, Kutyavin T, Haugen E, Dunn D, Reynolds AP, Neph S, Humbert R, Hansen RS, De Bruijn M, Selleri L, Rudensky A, Josefowicz S, Samstein R, Eichler EE, Orkin SH, Levasseur D, Papayannopoulou T, Chang KH, Skoultchi A, Gosh S, Disteche C, Treuting P, Wang Y, Weiss MJ, Blobel GA, Cao X, Zhong S, Wang T, Good PJ, Lowdon RF, Adams LB, Zhou XQ, Pazin MJ, Feingold EA, Wold B, Taylor J, Mortazavi A, Weissman SM, Stamatoyannopoulos JA, Snyder MP, Guigo R, Gingeras TR, Gilbert DM, Hardison RC, Beer MA, Ren B. A comparative encyclopedia of DNA elements in the mouse genome. Nature 2015;515:355-64. [PMID: 25409824 PMCID: PMC4266106 DOI: 10.1038/nature13992] [Citation(s) in RCA: 1135] [Impact Index Per Article: 126.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 10/24/2014] [Indexed: 12/11/2022]

Affiliation(s)

Feng Yue 1] Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA. [2] Department of Biochemistry and Molecular Biology, College of Medicine, The Pennsylvania State University, Hershey, Pennsylvania 17033, USA
Yong Cheng Department of Genetics, Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA
Alessandra Breschi Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, 08003 Barcelona, Catalonia, Spain
Jeff Vierstra Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
Weisheng Wu Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
Tyrone Ryba Department of Biological Science, 319 Stadium Drive, Florida State University, Tallahassee, Florida 32306-4295, USA
Richard Sandstrom Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
Zhihai Ma Department of Genetics, Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA
Carrie Davis Functional Genomics, Cold Spring Harbor Laboratory, Bungtown Road, Cold Spring Harbor, New York 11724, USA
Benjamin D Pope Department of Biological Science, 319 Stadium Drive, Florida State University, Tallahassee, Florida 32306-4295, USA
Yin Shen Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA
Dmitri D Pervouchine Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, 08003 Barcelona, Catalonia, Spain
Sarah Djebali Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, 08003 Barcelona, Catalonia, Spain
Robert E Thurman Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
Rajinder Kaul Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
Eric Rynes Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
Anthony Kirilusha Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
Georgi K Marinov Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
Brian A Williams Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
Diane Trout Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
Henry Amrhein Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
Katherine Fisher-Aylor Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
Igor Antoshechkin Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
Gilberto DeSalvo Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
Lei-Hoon See Functional Genomics, Cold Spring Harbor Laboratory, Bungtown Road, Cold Spring Harbor, New York 11724, USA
Meagan Fastuca Functional Genomics, Cold Spring Harbor Laboratory, Bungtown Road, Cold Spring Harbor, New York 11724, USA
Jorg Drenkow Functional Genomics, Cold Spring Harbor Laboratory, Bungtown Road, Cold Spring Harbor, New York 11724, USA
Chris Zaleski Functional Genomics, Cold Spring Harbor Laboratory, Bungtown Road, Cold Spring Harbor, New York 11724, USA
Alex Dobin Functional Genomics, Cold Spring Harbor Laboratory, Bungtown Road, Cold Spring Harbor, New York 11724, USA
Pablo Prieto Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, 08003 Barcelona, Catalonia, Spain
Julien Lagarde Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, 08003 Barcelona, Catalonia, Spain
Giovanni Bussotti Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, 08003 Barcelona, Catalonia, Spain
Andrea Tanzer 1] Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, 08003 Barcelona, Catalonia, Spain. [2] Department of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Waehringerstrasse 17/3/303, A-1090 Vienna, Austria
Olgert Denas Departments of Biology and Mathematics and Computer Science, Emory University, O. Wayne Rollins Research Center, 1510 Clifton Road NE, Atlanta, Georgia 30322, USA
Kanwei Li Departments of Biology and Mathematics and Computer Science, Emory University, O. Wayne Rollins Research Center, 1510 Clifton Road NE, Atlanta, Georgia 30322, USA
M A Bender 1] Department of Pediatrics, University of Washington, Seattle, Washington 98195, USA. [2] Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
Miaohua Zhang Basic Science Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
Rachel Byron Basic Science Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
Mark T Groudine 1] Basic Science Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA. [2] Department of Radiation Oncology, University of Washington, Seattle, Washington 98195, USA
David McCleary Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA
Long Pham Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA
Zhen Ye Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA
Samantha Kuan Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA
Lee Edsall Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA
Yi-Chieh Wu Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA
Matthew D Rasmussen Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA
Mukul S Bansal Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA
Manolis Kellis 1] Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA. [2] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
Cheryl A Keller Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
Christapher S Morrissey Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
Tejaswini Mishra Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
Deepti Jain Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
Nergiz Dogan Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
Robert S Harris Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
Philip Cayting Department of Genetics, Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA
Trupti Kawli Department of Genetics, Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA
Alan P Boyle Department of Genetics, Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA
Ghia Euskirchen Department of Genetics, Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA
Anshul Kundaje Department of Genetics, Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA
Shin Lin Department of Genetics, Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA
Yiing Lin Department of Genetics, Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA
Camden Jansen Department of Developmental and Cell Biology, University of California, Irvine, Irvine, California 92697, USA
Venkat S Malladi Department of Genetics, Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA
Melissa S Cline Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, California 95064, USA
Drew T Erickson Department of Genetics, Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA
Vanessa M Kirkup Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, California 95064, USA
Katrina Learned Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, California 95064, USA
Cricket A Sloan Department of Genetics, Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA
Kate R Rosenbloom Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, California 95064, USA
Beatriz Lacerda de Sousa Departments of Obstetrics/Gynecology and Pathology, and Center for Reproductive Sciences, University of California San Francisco, San Francisco, California 94143, USA
Kathryn Beal European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Miguel Pignatelli European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Paul Flicek European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Jin Lian Yale University, Department of Genetics, PO Box 208005, 333 Cedar Street, New Haven, Connecticut 06520-8005, USA
Tamer Kahveci Computer &Information Sciences &Engineering, University of Florida, Gainesville, Florida 32611, USA
Dongwon Lee McKusick-Nathans Institute of Genetic Medicine and Department of Biomedical Engineering, Johns Hopkins University, 733 N. Broadway, BRB 573 Baltimore, Maryland 21205, USA
W James Kent Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, California 95064, USA
Miguel Ramalho Santos Departments of Obstetrics/Gynecology and Pathology, and Center for Reproductive Sciences, University of California San Francisco, San Francisco, California 94143, USA
Javier Herrero 1] European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. [2] Bill Lyons Informatics Centre, UCL Cancer Institute, University College London, London WC1E 6DD, UK
Cedric Notredame Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, 08003 Barcelona, Catalonia, Spain
Audra Johnson Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
Shinny Vong Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
Kristen Lee Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
Daniel Bates Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
Fidencio Neri Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
Morgan Diegel Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
Theresa Canfield Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
Peter J Sabo Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
Matthew S Wilken Department of Biological Structure, University of Washington, HSB I-516, 1959 NE Pacific Street, Seattle, Washington 98195, USA
Thomas A Reh Department of Biological Structure, University of Washington, HSB I-516, 1959 NE Pacific Street, Seattle, Washington 98195, USA
Erika Giste Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
Anthony Shafer Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
Tanya Kutyavin Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
Eric Haugen Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
Douglas Dunn Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
Alex P Reynolds Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
Shane Neph Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
Richard Humbert Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
R Scott Hansen Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
Marella De Bruijn MRC Molecular Haemotology Unit, University of Oxford, Oxford OX3 9DS, UK
Licia Selleri Department of Cell and Developmental Biology, Weill Cornell Medical College, New York, New York 10065, USA
Alexander Rudensky HHMI and Ludwig Center at Memorial Sloan Kettering Cancer Center, Immunology Program, Memorial Sloan Kettering Cancer Canter, New York, New York 10065, USA
Steven Josefowicz HHMI and Ludwig Center at Memorial Sloan Kettering Cancer Center, Immunology Program, Memorial Sloan Kettering Cancer Canter, New York, New York 10065, USA
Robert Samstein HHMI and Ludwig Center at Memorial Sloan Kettering Cancer Center, Immunology Program, Memorial Sloan Kettering Cancer Canter, New York, New York 10065, USA
Evan E Eichler Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
Stuart H Orkin Dana Farber Cancer Institute, Harvard Medical School, Cambridge, Massachusetts 02138, USA
Dana Levasseur University of Iowa Carver College of Medicine, Department of Internal Medicine, Iowa City, Iowa 52242, USA
Thalia Papayannopoulou Division of Hematology, Department of Medicine, University of Washington, Seattle, Washington 98195, USA
Kai-Hsin Chang University of Iowa Carver College of Medicine, Department of Internal Medicine, Iowa City, Iowa 52242, USA
Arthur Skoultchi Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
Srikanta Gosh Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
Christine Disteche Department of Pathology, University of Washington, Seattle, Washington 98195, USA
Piper Treuting Department of Comparative Medicine, University of Washington, Seattle, Washington 98195, USA
Yanli Wang Bioinformatics and Genomics program, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
Mitchell J Weiss Department of Hematology, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
Gerd A Blobel 1] Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA. [2] Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
Xiaoyi Cao Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
Sheng Zhong Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
Ting Wang Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63108, USA
Peter J Good NHGRI, National Institutes of Health, 5635 Fishers Lane, Bethesda, Maryland 20892-9307, USA
Rebecca F Lowdon NHGRI, National Institutes of Health, 5635 Fishers Lane, Bethesda, Maryland 20892-9307, USA
Leslie B Adams NHGRI, National Institutes of Health, 5635 Fishers Lane, Bethesda, Maryland 20892-9307, USA
Xiao-Qiao Zhou NHGRI, National Institutes of Health, 5635 Fishers Lane, Bethesda, Maryland 20892-9307, USA
Michael J Pazin NHGRI, National Institutes of Health, 5635 Fishers Lane, Bethesda, Maryland 20892-9307, USA
Elise A Feingold NHGRI, National Institutes of Health, 5635 Fishers Lane, Bethesda, Maryland 20892-9307, USA
Barbara Wold Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
James Taylor Departments of Biology and Mathematics and Computer Science, Emory University, O. Wayne Rollins Research Center, 1510 Clifton Road NE, Atlanta, Georgia 30322, USA
Ali Mortazavi Department of Developmental and Cell Biology, University of California, Irvine, Irvine, California 92697, USA
Sherman M Weissman Yale University, Department of Genetics, PO Box 208005, 333 Cedar Street, New Haven, Connecticut 06520-8005, USA
John A Stamatoyannopoulos Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
Michael P Snyder Department of Genetics, Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA
Roderic Guigo Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, 08003 Barcelona, Catalonia, Spain
Thomas R Gingeras Functional Genomics, Cold Spring Harbor Laboratory, Bungtown Road, Cold Spring Harbor, New York 11724, USA
David M Gilbert Department of Biological Science, 319 Stadium Drive, Florida State University, Tallahassee, Florida 32306-4295, USA
Ross C Hardison Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
Michael A Beer McKusick-Nathans Institute of Genetic Medicine and Department of Biomedical Engineering, Johns Hopkins University, 733 N. Broadway, BRB 573 Baltimore, Maryland 21205, USA
Bing Ren Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA

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Fisher K, Ozdemir A, Kwan G, Pepke S, Kirilusha A, DeSalvo G, Stathopoulos A, Wold B. Investigating ChIP-seq derived candidate cis-regulatory regions in two different developmental systems. Dev Biol 2010. [DOI: 10.1016/j.ydbio.2010.05.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]

Williams B, Mortazavil A, Kirilusha A, Fisher K, Marinov G, DeSalvo G, McCue K, Wold B. 18-P012 The muscle gene regulatory network. Mech Dev 2009. [DOI: 10.1016/j.mod.2009.06.779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]