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Science 22 October 2004:
Vol. 306. no. 5696, pp. 636 - 640
DOI: 10.1126/science.1105136
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The ENCODE (ENCyclopedia Of DNA Elements) Project

The ENCODE Project Consortium*{dagger}

The ENCyclopedia Of DNA Elements (ENCODE) Project aims to identify all functional elements in the human genome sequence. The pilot phase of the Project is focused on a specified 30 megabases (~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.

* Affiliations for all members of the ENCODE Consortium can be found on Science Online at www.sciencemag.org/cgi/content/full/306/5696/636/DC1.


ENCODE Project Scientific Management: National Human Genome Research Institute (E. A. Feingold, P. J. Good, M. S. Guyer, S. Kamholz, L. Liefer, K. Wetterstrand, F. S. Collins).Initial ENCODE 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 Institute for Cancer Research (B. Ren, T. H. Kim, L. O. Barrera, C. Qu, S. Van Calcar, R. Luna, C. K. Glass, M. G. Rosenfeld); Municipal Institute 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 of Washington (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 Trust Sanger 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 ENCODE Pilot Phase Participants: British Columbia Cancer Agency Genome Sciences Centre (S. Jones, M. Marra, H. Shin, J. Schein); Broad Institute (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 Research Institute/Computational Genomics Unit (A. D. Baxevanis, T. G. Wolfsberg); National Human Genome Research Institute/Molecular Genetics Section (F. S. Collins, G. E. Crawford, J. Whittle, I. E. Holt, T. J. Vasicek, D. Zhou, S. Luo); NIH Intramural Sequencing 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 Phase Participants: 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); NimbleGen Systems, 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).

{dagger} To whom correspondence should be addressed. E-mail: elise_feingold{at}nih.gov

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PNAS 104, 3067-3072
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E. J. Pritham and C. Feschotte (2007)
PNAS 104, 1895-1900
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Multiple sequence alignment: In pursuit of homologous DNA positions.
S. Kumar and A. Filipski (2007)
Genome Res. 17, 127-135
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Genome Res. 17, 231-239
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The UCSC genome browser database: update 2007.
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Ensembl 2007.
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M. J. Chaisson, B. J. Raphael, and P. A. Pevzner (2006)
PNAS 103, 19824-19829
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J. Du, J. S. Rozowsky, J. O. Korbel, Z. D. Zhang, T. E. Royce, M. H. Schultz, M. Snyder, and M. Gerstein (2006)
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L. Elnitski, V. X. Jin, P. J. Farnham, and S. J.M. Jones (2006)
Genome Res. 16, 1455-1464
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Unraveling transcription regulatory networks by protein-DNA and protein-protein interaction mapping.
A. J.M. Walhout (2006)
Genome Res. 16, 1445-1454
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A computational genomics approach to identify cis-regulatory modules from chromatin immunoprecipitation microarray data--A case study using E2F1.
V. X. Jin, A. Rabinovich, S. L. Squazzo, R. Green, and P. J. Farnham (2006)
Genome Res. 16, 1585-1595
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Chromosome Conformation Capture Carbon Copy (5C): A massively parallel solution for mapping interactions between genomic elements.
J. Dostie, T. A. Richmond, R. A. Arnaout, R. R. Selzer, W. L. Lee, T. A. Honan, E. D. Rubio, A. Krumm, J. Lamb, C. Nusbaum, et al. (2006)
Genome Res. 16, 1299-1309
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Mapping of the juxtacentromeric heterochromatin-euchromatin frontier of human chromosome 21.
C. Grunau, J. Buard, M.-E. Brun, and A. De Sario (2006)
Genome Res. 16, 1198-1207
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A genome-wide study of preferential amplification/hybridization in microarray-based pooled DNA experiments.
H.-C. Yang, Y.-J. Liang, M.-C. Huang, L.-H. Li, C.-H. Lin, J.-Y. Wu, Y.-T. Chen, and C.S.J. Fann (2006)
Nucleic Acids Res. 34, e106
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Activation of Receptor Activator of NF-{kappa}B Ligand Gene Expression by 1,25-Dihydroxyvitamin D3 Is Mediated through Multiple Long-Range Enhancers..
S. Kim, M. Yamazaki, L. A. Zella, N. K. Shevde, and J. W. Pike (2006)
Mol. Cell. Biol. 26, 6469-6486
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Navigating the HapMap.
M. R. Barnes (2006)
Brief Bioinform 7, 211-224
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Chromosome-wide, allele-specific analysis of the histone code on the human X chromosome.
C. M. Valley, L. M. Pertz, B. S. Balakumaran, and H. F. Willard (2006)
Hum. Mol. Genet. 15, 2335-2347
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Multiplex sequencing of paired-end ditags (MS-PET): a strategy for the ultra-high-throughput analysis of transcriptomes and genomes.
P. Ng, J. J.S. Tan, H. S. Ooi, Y. L. Lee, K. P. Chiu, M. J. Fullwood, K. G. Srinivasan, C. Perbost, L. Du, W.-K. Sung, et al. (2006)
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