ENCODE Project Consortium ENCODE Project Scientific Management: National Human Genome Research Institute E. A. Feingold,1 P. J. Good,1 M. S. Guyer,1 S. Kamholz,1 L. Liefer,1 K. Wetterstrand,1 F. S. Collins2 Initial ENCODE Pilot Phase Participants: Affymetrix, Inc. T. R. Gingeras,3 D. Kampa,3 E. A. Sekinger,4 J. Cheng,3 H. Hirsch,4 S. Ghosh,3 Z. Zhu,5 S. Patel,3 A. Piccolboni,3 A. Yang,4 H. Tammana,3 S. Bekiranov,3 P. Kapranov,3 R. Harrison,5 G. Church,5 K. Struhl4; Ludwig Institute for Cancer Research B. Ren,6 T. H. Kim,6 L. O. Barrera,6 C. Qu,6 S. Van Calcar,6 R. Luna,7 C. K. Glass,7 M. G. Rosenfeld8; Municipal Institute of Medical Research R. Guigó,9 S. E. Antonarakis,10 E. Birney,11 M. Brent,12 L. Pachter,13 A. Reymond,10,14 E. T. Dermitzakis,15 C. Dewey,16 D. Keefe,11 F. Denoeud,9 J. Lagarde,9 J. Ashurst,15 T. Hubbard,15 J. J. Wesselink,9 R. Castelo,9 E. Eyras9; Stanford University R. M. Myers,17 A. Sidow,17,18 S. Batzoglou,19 N. D. Trinklein,17 S. J. Hartman,17 S. F. Aldred,17 E. Anton,17 D. I. Schroeder,20 S. S. Marticke,17 L. Nguyen,17 J. Schmutz,21 J. Grimwood,21 M. Dickson,21 G. M. Cooper,17 E. A. Stone,17 G. Asimenos,19 M. Brudno19; University of Virginia A. Dutta,22 N. Karnani,22 C. M. Taylor,22,23 H. K. Kim,22 G. Robins23; University of Washington G. Stamatoyannopoulos,24,25 J. A. Stamatoyannopoulos,26 M. Dorschner,26 P. Sabo,26 M. Hawrylycz,26 R. Humbert,26 J. Wallace,26 M. Yu,24 P. A. Navas,24 M. McArthur,26 W. S. Noble25; Wellcome Trust Sanger Institute I. Dunham,15 C. M. Koch,15 R. M. Andrews,15 G. K. Clelland,15 S. Wilcox,15 J. C. Fowler,15 K. D. James,15 P. Groth,15 O. M. Dovey,15 P. D. Ellis,15 V. L. Wraight,15 A. J. Mungall,15 P. Dhami,15 H. Fiegler,15 C. F. Langford,15 N. P. Carter,15 D. Vetrie15; Yale University M. Snyder,27 G. Euskirchen,27 A. E. Urban,27 U. Nagalakshmi,27 J. Rinn,27 G. Popescu,27 P. Bertone,27 S. Hartman,27 J. Rozowsky,28 O. Emanuelsson,28 T. Royce,28 S. Chung,28 M. Gerstein,28 Z. Lian,29 J. Lian,29 Y. Nakayama,29 S. Weissman,29 V. Stolc,27,30 W. Tongprasit,31 H. Sethi31 Additional ENCODE Pilot Phase Participants: British Columbia Cancer Agency Genome Sciences Centre S. Jones,32 M. Marra,32 H. Shin,32 J. Schein32; Broad Institute M. Clamp,33 K. Lindblad-Toh,33 J. Chang,33 D. B. Jaffe,33 M. Kamal,33 E. S. Lander,33 T. S. Mikkelsen,33 J. Vinson,33 M. C. Zody33; Children’s Hospital Oakland Research Institute P. J. de Jong,34 K. Osoegawa,34 M. Nefedov,34 B. Zhu34; National Human Genome Research Institute/Computational Genomics Unit A. D. Baxevanis,35 T. G. Wolfsberg35; National Human Genome Research Institute/Molecular Genetics Section F. S. Collins,35 G. E. Crawford,35 J. Whittle,35 I. E. Holt,35 T. J. Vasicek,36 D. Zhou,36 S. Luo36; NIH Intramural Sequencing Center/National Human Genome Research Institute E. D. Green,37 G. G. Bouffard,37 E. H. Margulies,37 M. E. Portnoy,37 N. F. Hansen,37 P. J. Thomas,37 J. C. McDowell,37 B. Maskeri,37 A. C. Young,37 J. R. Idol,37 R. W. Blakesley37; National Library of Medicine G. Schuler38; Pennsylvania State University W. Miller,39,40,41 R. Hardison,39,42 L. Elnitski,39,41 P. Shah39,41; The Institute for Genomic Research S. L. Salzberg,43 M. Pertea,43 W. H. Majoros43; University of California, Santa Cruz D. Haussler,44,45 D. Thomas,44 K. R. Rosenbloom,44 H. Clawson,44 A. Siepel,44 W. J. Kent44 ENCODE Technology Development Phase Participants: Boston University Z. Weng,46,47 S. Jin,46,47 A. Halees,46 H. Burden,46,47 U. Karaoz,46 Y. Fu,46 Y. Yu,46,47 C. Ding,46 C. R. Cantor46,47; Massachusetts General Hospital R. E. Kingston,5,48 J. Dennis5,48; NimbleGen Systems, Inc. R. D. Green,49 M. A. Singer,49 T. A. Richmond,49 J. E. Norton,49 P. J Farnham,50 M. J. Oberley,51 D. R. Inman51; NimbleGen Systems, Inc. M. R. McCormick,49 H. Kim,52 C. L. Middle,49 M. C. Pirrung52; University of California, San Diego X. D. Fu,7 Y. S. Kwon,7 Z. Ye7; University of Massachusetts Medical School J. Dekker,53 T. M. Tabuchi,53 N. Gheldof,53 J. Dostie,53 S. C. Harvey54 Affiliations for Participants 1Division of Extramural Research, National Human Genome Research Institute, Bethesda, MD 20892–9305, USA. 2Office of the Director, National Human Genome Research Institute, Bethesda, MD 20892, USA. 3Affymetrix, Inc., Santa Clara, CA 92024, USA. 4Dept of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA. 5Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. 6Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA 92093–0653, USA. 7Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093–0651, USA. 8Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093, USA. 9Grup de Recerca en Informàtica Biomèdica, Institut Municipal d’Investigació Mèdica and Centre de Regulació Genòmica, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain. 10Department of Genetic Medicine and Development, University of Geneva Medical School and University Hospitals of Geneva, 1211 Geneva, Switzerland. 11European Bioinformatics Institute, Hinxton, Cambridge, UK. 12Laboratory for Computational Genomics, Washington University, St. Louis, MO 63130, USA. 13Department of Mathematics, University of California, Berkeley, Berkeley, CA 94720, USA. 14Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland. 15The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK. 16Department of Electrical Engineering and Computer Science, University of California, Berkeley, Berkeley, CA 94720, USA. 17Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA. 18Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA. 19Department of Computer Science, Stanford University, Stanford, CA 94305, USA. 20Biomedical Informatics Program, Stanford University School of Medicine, Stanford, CA 94305, USA. 21Stanford Human Genome Center, Stanford University School of Medicine, Stanford, CA 94305, USA. 22Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA. 23Department of Computer Science, University of Virginia, Charlottesville, VA 22908, USA. 24Division of Medical Genetics, University of Washington, Seattle, WA 98195, USA. 25Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA. 26Regulome, Seattle, WA 98121, USA. 27Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA. 28Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA. 29Department of Genetics, Yale University, New Haven, CT 06520, USA. 30Center for Nanotechnology, NASA Ames Research Center, Moffett Field, CA 94036, USA. 31Eloret Corporation, NASA Ames Research Center, Sunnyvale, CA 94087, USA. 32Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada. 33Broad Institute, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02141, USA. 34Children’s Hospital Oakland Research Institute, Oakland, CA 94609–1673, USA. 35Genome Technology Branch, Division of Intramural Research, National Human Genome Research Institute, Bethesda, MD 20892–8002, USA. 36Lynx Therapeutics, Inc., Hayward, CA 94545, USA. 37NISC Comparative Sequencing Program, Genome Technology Branch and NIH Intramural Sequencing Center (NISC), National Human Genome Research Institute, Bethesda, MD 20892, USA. 38National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20892, USA. 39Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, PA 16802, USA. 40Department of Biology, Pennsylvania State University, University Park, PA 16802, USA. 41Department of Computer Science, Pennsylvania State University, University Park, PA 16802, USA. 42Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA. 43The Institute for Genomic Research, Rockville, MD 20850, USA. 44Genome Bioinformatics Group, Center for Biomolecular Science and Engineering, Baskin School of Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA. 45Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA. 46Bioinformatics Program, Boston University, Boston, MA 02215, USA. 47Biomedical Engineering Department, Boston University, Boston, MA 02215, USA. 48Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA. 49NimbleGen Systems, Inc., Madison, WI 53711, USA. 50Department of Medical Pharmacology, University of California, Davis Genome Center, Davis, CA 95616–8816, USA. 51University of Wisconsin Medical School, Madison, WI 53706, USA. 52Department of Chemistry, Duke University, Durham, NC 27708, USA. 53Program in Gene Function and Expression, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605– 2324, USA. 54School of Biology, Georgia Institute of Technology, Atlanta, GA 30332–0230, USA. .