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Perspectives on ENCODE

Author

Listed:
  • Michael P. Snyder

    (Stanford University
    Stanford School of Medicine)

  • Thomas R. Gingeras

    (Cold Spring Harbor Laboratory)

  • Jill E. Moore

    (University of Massachusetts Medical School, Program in Bioinformatics and Integrative Biology)

  • Zhiping Weng

    (University of Massachusetts Medical School, Program in Bioinformatics and Integrative Biology
    Tongji University
    Bioinformatics Program, Boston University)

  • Mark B. Gerstein

    (Yale University)

  • Bing Ren

    (University of California, San Diego
    University of California, San Diego)

  • Ross C. Hardison

    (The Pennsylvania State University)

  • John A. Stamatoyannopoulos

    (Altius Institute for Biomedical Sciences
    University of Washington
    University of Washington)

  • Brenton R. Graveley

    (Institute for Systems Genomics, UConn Health)

  • Elise A. Feingold

    (National Institutes of Health)

  • Michael J. Pazin

    (National Institutes of Health)

  • Michael Pagan

    (National Institutes of Health)

  • Daniel A. Gilchrist

    (National Institutes of Health)

  • Benjamin C. Hitz

    (Stanford University)

  • J. Michael Cherry

    (Stanford University)

  • Bradley E. Bernstein

    (Massachusetts General Hospital and Harvard Medical School)

  • Eric M. Mendenhall

    (University of Alabama in Huntsville
    HudsonAlpha Institute for Biotechnology)

  • Daniel R. Zerbino

    (European Bioinformatics Institute, Wellcome Genome Campus)

  • Adam Frankish

    (European Bioinformatics Institute, Wellcome Genome Campus)

  • Paul Flicek

    (European Bioinformatics Institute, Wellcome Genome Campus)

  • Richard M. Myers

    (HudsonAlpha Institute for Biotechnology)

Abstract

The Encylopedia of DNA Elements (ENCODE) Project launched in 2003 with the long-term goal of developing a comprehensive map of functional elements in the human genome. These included genes, biochemical regions associated with gene regulation (for example, transcription factor binding sites, open chromatin, and histone marks) and transcript isoforms. The marks serve as sites for candidate cis-regulatory elements (cCREs) that may serve functional roles in regulating gene expression1. The project has been extended to model organisms, particularly the mouse. In the third phase of ENCODE, nearly a million and more than 300,000 cCRE annotations have been generated for human and mouse, respectively, and these have provided a valuable resource for the scientific community.

Suggested Citation

  • Michael P. Snyder & Thomas R. Gingeras & Jill E. Moore & Zhiping Weng & Mark B. Gerstein & Bing Ren & Ross C. Hardison & John A. Stamatoyannopoulos & Brenton R. Graveley & Elise A. Feingold & Michael , 2020. "Perspectives on ENCODE," Nature, Nature, vol. 583(7818), pages 693-698, July.
    • Handle: RePEc:nat:nature:v:583:y:2020:i:7818:d:10.1038_s41586-020-2449-8
    DOI: 10.1038/s41586-020-2449-8
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    Cited by:

    1. H. Serhat Tetikol & Deniz Turgut & Kubra Narci & Gungor Budak & Ozem Kalay & Elif Arslan & Sinem Demirkaya-Budak & Alexey Dolgoborodov & Duygu Kabakci-Zorlu & Vladimir Semenyuk & Amit Jain & Brandi N., 2022. "Pan-African genome demonstrates how population-specific genome graphs improve high-throughput sequencing data analysis," Nature Communications, Nature, vol. 13(1), pages 1-11, December.

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