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The ENCyclopedia Of DNA Elements (ENCODE) Project aims to identifyall functional elements in the human genome sequence. The pilotphase of the Project is focused on a specified 30 megabases(1%) of the human genome sequence and is organized as an internationalconsortium of computational and laboratory-based scientistsworking to develop and apply high-throughput approaches fordetecting all sequence elements that confer biological function.The results of this pilot phase will guide future efforts toanalyze the entire human genome.
ENCODE Project Scientific Management: National Human GenomeResearch Institute (E. A. Feingold, P. J. Good, M. S. Guyer,S. Kamholz, L. Liefer, K. Wetterstrand, F. S. Collins).InitialENCODE Pilot Phase Participants: Affymetrix, Inc. (T. R. Gingeras,D. Kampa, E. A. Sekinger, J. Cheng, H. Hirsch, S. Ghosh, Z.Zhu, S. Patel, A. Piccolboni, A. Yang, H. Tammana, S. Bekiranov,P. Kapranov, R. Harrison, G. Church, K. Struhl); Ludwig Institutefor Cancer Research (B. Ren, T. H. Kim, L. O. Barrera, C. Qu,S. Van Calcar, R. Luna, C. K. Glass, M. G. Rosenfeld); MunicipalInstitute of Medical Research (R. Guigo, S. E. Antonarakis,E. Birney, M. Brent, L. Pachter, A. Reymond, E. T. Dermitzakis,C. Dewey, D. Keefe, F. Denoeud, J. Lagarde, J. Ashurst, T. Hubbard,J. J. Wesselink, R. Castelo, E. Eyras); Stanford University(R. M. Myers, A. Sidow, S. Batzoglou, N. D. Trinklein, S. J.Hartman, S. F. Aldred, E. Anton, D. I. Schroeder, S. S. Marticke,L.Nguyen, J.Schmutz, J.Grimwood, M.Dickson, G. M. Cooper, E.A. Stone, G. Asimenos, M. Brudno); University of Virginia (A.Dutta,N.Karnani, C.M.Taylor, H. K. Kim, G. Robins); University ofWashington (G. Stamatoyannopoulos, J. A. Stamatoyannopoulos,M. Dorschner, P. Sabo, M. Hawrylycz, R. Humbert, J. Wallace,M. Yu, P. A. Navas, M. McArthur, W. S. Noble); Wellcome TrustSanger Institute (I. Dunham, C. M. Koch, R.M.Andrews, G.K.Clelland,S.Wilcox, J.C.Fowler, K.D. James, P. Groth, O. M. Dovey, P.D. Ellis, V. L. Wraight, A. J. Mungall, P. Dhami, H. Fiegler,C. F. Langford, N. P. Carter, D. Vetrie); Yale University (M.Snyder, G. Euskirchen, A. E. Urban, U. Nagalakshmi, J. Rinn,G. Popescu, P. Bertone, S.Hartman, J. Rozowsky, O. Emanuelsson,T. Royce, S. Chung, M. Gerstein, Z. Lian, J. Lian, Y. Nakayama,S. Weissman, V.Stolc, W.Tongprasit, H.Sethi). Additional ENCODEPilot Phase Participants: British Columbia Cancer Agency GenomeSciences Centre (S. Jones, M. Marra, H. Shin, J. Schein); BroadInstitute (M. Clamp, K. Lindblad-Toh, J. Chang, D. B. Jaffe,M. Kamal, E. S. Lander, T. S. Mikkelsen, J. Vinson, M. C. Zody);Children's Hospital Oakland Research Institute (P.J.deJong,K.Osoegawa, M.Nefedov, B.Zhu); National Human Genome ResearchInstitute/Computational Genomics Unit (A. D. Baxevanis, T. G.Wolfsberg); National Human Genome Research Institute/MolecularGenetics Section (F. S. Collins, G. E. Crawford, J. Whittle,I. E. Holt, T. J. Vasicek, D. Zhou, S. Luo); NIH IntramuralSequencing Center/National Human Genome Research Institute (E.D. Green, G. G. Bouffard, E. H. Margulies, M. E. Portnoy, N.F. Hansen, P. J. Thomas, J. C. McDowell, B. Maskeri, A. C. Young,J. R. Idol, R. W. Blakesley); National Library of Medicine (G.Schuler); Pennsylvania State University (W. Miller, R. Hardison,L. Elnitski, P. Shah); The Institute for Genomic Research (S.L. Salzberg, M. Pertea, W. H. Majoros); University of California,Santa Cruz (D. Haussler, D. Thomas, K. R. Rosenbloom, H. Clawson,A. Siepel, W. J. Kent). ENCODE Technology Development PhaseParticipants: Boston University (Z. Weng, S. Jin, A. Halees,H. Burden, U. Karaoz, Y. Fu, Y. Yu, C. Ding, C. R. Cantor);Massachusetts General Hospital (R. E. Kingston, J. Dennis);NimbleGen Systems, Inc.(R.D.Green, M.A.Singer, T.A. Richmond,J.E.Norton, P.JFarnham, M.J.Oberley, D.R. Inman); NimbleGenSystems, Inc. (M. R. McCormick, H. Kim, C. L. Middle, M. C.Pirrung); University of California, San Diego (X. D. Fu, Y.S. Kwon, Z. Ye); University of Massachusetts Medical School(J. Dekker, T. M. Tabuchi, N. Gheldof, J. Dostie, S. C. Harvey).
To whom correspondence should be addressed. E-mail: elise_feingold{at}nih.gov
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PNAS
103, 19824-19829
|Abstract »|Full Text »|PDF »
A supervised hidden markov model framework for efficiently segmenting tiling array data in transcriptional and chIP-chip experiments: systematically incorporating validated biological knowledge.
J. Du, J. S. Rozowsky, J. O. Korbel, Z. D. Zhang, T. E. Royce, M. H. Schultz, M. Snyder, and M. Gerstein (2006)
Bioinformatics
22, 3016-3024
|Abstract »|Full Text »|PDF »
1%) of the human genome sequence and is organized as an international consortium of computational and laboratory-based scientists working to develop and apply high-throughput approaches for detecting all sequence elements that confer biological function. The results of this pilot phase will guide future efforts to analyze the entire human genome. 
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