[go: up one dir, main page]
More Web Proxy on the site http://driver.im/
Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Perspective
  • Published:

Perspectives on ENCODE

Nature volume 583, pages 693–698 (2020)Cite this article

Subjects

An Author Correction to this article was published on 26 April 2022

This article has been updated

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.

Access through your institution
Buy or subscribe

This is a preview of subscription content, access via your institution

Access options

Access through your institution

Buy this article

  • Purchase on SpringerLink
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Fig. 1: ENCODE assays by year.
Fig. 2: Progress in annotating the human genome.
Fig. 3: Publications using ENCODE data.
Fig. 4: An overview of the mouse ENCODE Project in the current phase.

Similar content being viewed by others

Change history

References

  1. Kellis, M. et al. Defining functional DNA elements in the human genome. Proc. Natl Acad. Sci. USA 111, 6131–6138 (2014).

    Article  ADS  CAS  Google Scholar 

  2. ENCODE Project Consortium. The ENCODE (ENCyclopedia Of DNA Elements) Project. Science 306, 636–640 (2004).

    Article  ADS  Google Scholar 

  3. Lindblad-Toh, K. et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature 478, 476–482 (2011).

    Article  CAS  Google Scholar 

  4. Waterston, R. H. et al. Initial sequencing and comparative analysis of the mouse genome. Nature 420, 520–562 (2002).

    Article  ADS  CAS  Google Scholar 

  5. ENCODE Project Consortium. A user’s guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol. 9, e1001046 (2011).

    Article  Google Scholar 

  6. Birney, E. et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447, 799–816 (2007). The results of the pilot phase of ENCODE included extensive functional assays across a selected one per cent of the human genome with experiments conducted on a variety of cell lines and largely with array-based technology.

    Article  ADS  CAS  Google Scholar 

  7. ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57–74 (2012). The results of the second phase of ENCODE were based mostly on a large number of genome-wide assays that leveraged high-throughput sequencing technologies and were done across two ‘tier one’ cell lines with large-scale assays across several hundred cell and tissue types.

    Article  ADS  Google Scholar 

  8. The ENCODE Project Consortium et al. Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature https://doi.org/10.1038/s41586-020-2493-4 (2020).

  9. Partridge, E. C. et al. Occupancy maps of 208 chromatin-associated proteins in one human cell type. Nature https://doi.org/10.1038/s41586-020-2023-4 (2020).

  10. Meuleman, W. Index and biological spectrum of human DNase I hypersensitive sites. Nature https://doi.org/10.1038/s41586-020-XXXX-X (2020).

  11. Vierstra, J. et al. Global reference mapping of human transcription factor footprints. Nature https://doi.org/10.1038/s41586-020-2528-x (2020). 

  12. Breschi, A. et al. A limited set of transcriptional programs define major cell types. Preprint at https://doi.org/10.1101/857169 (2020).

  13. Grubert, F. et al. Landscape of cohesin-mediated chromatin loops in the human genome. Nature https://doi.org/10.1038/s41586-020-2151-x (2020).

  14. Van Nostrand, E. L. et al. A large-scale binding and functional map of human RNA binding proteins. Nature https://doi.org/10.1038/s41586-020-2077-3 (2020).

  15. Wang, Z., Gerstein, M. & Snyder, M. RNA-seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet. 10, 57–63 (2009).

    Article  CAS  Google Scholar 

  16. Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L. & Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-seq. Nat. Methods 5, 621–628 (2008).

    Article  CAS  Google Scholar 

  17. Johnson, D. S., Mortazavi, A., Myers, R. M. & Wold, B. Genome-wide mapping of in vivo protein–DNA interactions. Science 316, 1497–1502 (2007).

    Article  ADS  CAS  Google Scholar 

  18. Robertson, G. et al. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat. Methods 4, 651–657 (2007).

    Article  CAS  Google Scholar 

  19. Iyer, V. R. et al. Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature 409, 533–538 (2001).

    Article  ADS  CAS  Google Scholar 

  20. Ren, B. et al. Genome-wide location and function of DNA binding proteins. Science 290, 2306–2309 (2000).

    Article  ADS  CAS  Google Scholar 

  21. Landt, S. G. et al. ChIP–seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res. 22, 1813–1831 (2012). A consortium-wide effort to standardize performance, quality control and outputs of ChIP–seq experiments, including validation of antibodies, to facilitate experimental reproducibllity and data utility.

    Article  CAS  Google Scholar 

  22. Sundararaman, B. et al. Resources for the comprehensive discovery of functional RNA elements. Mol. Cell 61, 903–913 (2016).

    Article  CAS  Google Scholar 

  23. Maurano, M. T. et al. Systematic localization of common disease-associated variation in regulatory DNA. Science 337, 1190–1195 (2012).

    Article  ADS  CAS  Google Scholar 

  24. Schaub, M. A., Boyle, A. P., Kundaje, A., Batzoglou, S. & Snyder, M. Linking disease associations with regulatory information in the human genome. Genome Res. 22, 1748–1759 (2012).

    Article  CAS  Google Scholar 

  25. Yue, F. et al. A comparative encyclopedia of DNA elements in the mouse genome. Nature 515, 355–364 (2014). Results of a large-scale effort of the mouse ENCODE consortium, presenting regulatory and transcript maps of the mouse.

    Article  ADS  CAS  Google Scholar 

  26. Gerstein, M. B. et al. Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science 330, 1775–1787 (2010).

    Article  ADS  CAS  Google Scholar 

  27. The modENCODE Consortium et al. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science 330, 1787–1797 (2010).

    Article  Google Scholar 

  28. Kudron, M. M. et al. The ModERN Resource: genome-wide binding profiles for hundreds of Drosophila and Caenorhabditis elegans transcription factors. Genetics 208, 937–949 (2018).

    Article  CAS  Google Scholar 

  29. Gorkin, D. U. et al. An atlas of dynamic chromatin landscapes in mouse fetal development. Nature https://doi.org/10.1038/s41586-020-2093-3 (2020).

  30. He, P. A. The changing mouse embryo transcriptome at whole tissue and single-cell resolution. Nature https://doi.org/10.1038/s41586-020-XXXX-X (2020).

  31. He, Y. et al. Spatiotemporal DNA methylome dynamics of the developing mouse fetus. Nature https://doi.org/10.1038/s41586-020-2119-x (2020).

  32. Cheng, Y. et al. Principles of regulatory information conservation between mouse and human. Nature 515, 371–375 (2014).

    Article  ADS  CAS  Google Scholar 

  33. Stefflova, K. et al. Cooperativity and rapid evolution of cobound transcription factors in closely related mammals. Cell 154, 530–540 (2013).

    Article  CAS  Google Scholar 

  34. Keilwagen, J., Posch, S. & Grau, J. Accurate prediction of cell type-specific transcription factor binding. Genome Biol. 20, 9 (2019).

    Article  Google Scholar 

  35. Tang, F., Lao, K. & Surani, M. A. Development and applications of single-cell transcriptome analysis. Nat. Methods 8 (Suppl), S6–S11 (2011).

    Article  CAS  Google Scholar 

  36. Buenrostro, J. D. et al. Single-cell chromatin accessibility reveals principles of regulatory variation. Nature 523, 486–490 (2015).

    Article  ADS  CAS  Google Scholar 

  37. Hu, B. C.; HuBMAP Consortium. The human body at cellular resolution: the NIH Human Biomolecular Atlas Program. Nature 574, 187–192 (2019).

    Article  ADS  Google Scholar 

  38. Regev, A. et al. The human cell atlas. eLife 6, e27041 (2017).

    Article  Google Scholar 

  39. Rhoads, A. & Au, K. F. PacBio sequencing and its applications. Genomics Proteomics Bioinformatics 13, 278–289 (2015).

    Article  Google Scholar 

  40. Arnold, C. D. et al. Genome-wide quantitative enhancer activity maps identified by STARR-seq. Science 339, 1074–1077 (2013).

    Article  ADS  CAS  Google Scholar 

  41. Klein, J. C., Chen, W., Gasperini, M. & Shendure, J. Identifying novel enhancer elements with CRISPR-based screens. ACS Chem. Biol. 13, 326–332 (2018).

    Article  CAS  Google Scholar 

  42. Harrow, J. et al. GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res. 22, 1760–1774 (2012).

    Article  CAS  Google Scholar 

  43. Paudyal, A. et al. The novel mouse mutant, chuzhoi, has disruption of Ptk7 protein and exhibits defects in neural tube, heart and lung development and abnormal planar cell polarity in the ear. BMC Dev. Biol. 10, 87 (2010).

    Article  Google Scholar 

Download references

Acknowledgements

We thank S. Moore, E. Cahill, M. Kellis and J. Li for their assistance, and B. Wold for helpful comments. This work was supported by grants from the NIH: U01HG007019, U01HG007033, U01HG007036, U01HG007037, U41HG006992, U41HG006993, U41HG006994, U41HG006995, U41HG006996, U41HG006997, U41HG006998, U41HG006999, U41HG007000, U41HG007001, U41HG007002, U41HG007003, U41HG007234, U54HG006991, U54HG006997, U54HG006998, U54HG007004, U54HG007005, U54HG007010 and UM1HG009442.

Author information

Authors and Affiliations

  1. Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA

    Nicholas J. Addleman, Jessika Adrian, Ulugbek K. Baymuradov, Anand Bhaskar, Nathan Boley, Lulu Cao, Hassan Chaib, Esther T. Chan, Songjie Chen, J. Michael Cherry, Timothy R. Dreszer, Idan Gabdank, Fabian Grubert, Nastaran Heidari, Jason A. Hilton, Benjamin C. Hitz, Lixia Jiang, Maya Kasowski, Trupti Kawli, Daniel Sunwook Kim, Anshul Kundaje, Jin Wook Lee, Yang I. Li, Yining Li, Shin Lin, Tejaswini Mishra, Anil M. Narasimha, Aditi K. Narayanan, Kathrina C. Onate, Jonathan K. Pritchard, Anil Raj, Lucia Ramirez, Denis N. Salins, Eilon Sharon, Minyi Shi, Teri Slifer, Cricket A. Sloan, Michael P. Snyder, Damek V. Spacek, Rohith Srivas, J. Seth Strattan, Forrest Y. Tanaka, Oana Ursu, Nathaniel K. Watson, Xinqiong Yang, Jie Zhai, Michael P. Snyder, Benjamin C. Hitz & J. Michael Cherry

  2. Cardiovascular Institute, Stanford School of Medicine, Stanford, CA, USA

    Michael P. Snyder & Michael P. Snyder

  3. Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA

    Cassidy Danyko, Carrie A. Davis, Alexander Dobin, Thomas R. Gingeras, Alexandra Scavelli, Lei Hoon See, Chris Zaleski & Thomas R. Gingeras

  4. University of Massachusetts Medical School, Program in Bioinformatics and Integrative Biology, Worcester, MA, USA

    Gregory R. Andrews, Tyler Borrman, Jason A. Brooks, Hao Chen, Shaimae I. Elhajjajy, Kaili Fan, Kevin Fortier, Yu Fu, Mingshi Gao, Jack Huey, Eugenio Mattei, Jill E. Moore, Nishigandha N. Phalke, Henry E. Pratt, Michael J. Purcaro, Thomas M. Reimonn, Shuo Shan, Junko Tsuji, Arjan G. van der Velde, Zhiping Weng, Taylor Young, Xiao-Ou Zhang, Jill E. Moore & Zhiping Weng

  5. Department of Thoracic Surgery, Clinical Translational Research Center, Shanghai Pulmonary Hospital, The School of Life Sciences and Technology, Tongji University, Shanghai, China

    Lingling Cai, Shaliu Fu, Shuyu Hou, Xiangrui Li, Ying Li, Yan Liu, Aiping Lu, Qin Wang, Zhijie Wei, Zhiping Weng, Tianxiong Yu, Peng Zhang & Zhiping Weng

  6. Bioinformatics Program, Boston University, Boston, MA, USA

    Hao Chen, Arjan G. van der Velde, Zhiping Weng & Zhiping Weng

  7. Yale University, New Haven, CT, USA

    Declan Clarke, Timur Galeev, Mark B. Gerstein, Mengting Gu, Gamze Gursoy, Arif Harmanci, Sushant Kumar, Donghoon Lee, Jason Liu, Shaoke Lou, Fabio C. P. Navarro, Baikang Pei, Joel Rozowsky, Anurag Sethi, Cristina Sisu, Jinrui Xu, Koon-Kiu Yan, Jing Zhang & Mark B. Gerstein

  8. Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA, USA

    Sora Chee, David U. Gorkin, Hui Huang, Samantha Kuan, Ah Young Lee, Bin Li, Sebastian Preissl, Bing Ren, Yin Shen, Yanxiao Zhang, Yuan Zhao & Bing Ren

  9. Center for Epigenomics, University of California, San Diego, La Jolla, CA, USA

    David U. Gorkin, Bing Ren & Bing Ren

  10. Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA

    Belinda M. Giardine, Ross C. Hardison, Cheryl A. Keller, Maria Long & Ross C. Hardison

  11. Altius Institute for Biomedical Sciences, Seattle, WA, USA

    Reyes Acosta, Daniel Bates, Michael Buckley, Andres Castillo, Daniel R. Chee, Morgan Diegel, Douglass Dunn, Alister P. W. Funnell, Grigorios Georgolopoulos, Jessica Halow, Eric Haugen, Sean Ibarrientos, Mineo Iwata, Audra Johnson, Rajinder Kaul, Tanya Kutyavin, John Lazar, Kristen Lee, Wouter Meuleman, Vivek Nandakumar, Patrick Navas, Jemma Nelson, Shane Neph, Fidencio Jun Neri, Andrew Nishida, Ericka Otterman, Alex Reynolds, Eric Rynes, Richard Sandstrom, Anthony Shafer, Kyle Siebenthall, John A. Stamatoyannopoulos, Sandra Stehling-Sun, Benjamin Van Biber, Jeff Vierstra, Shinny Vong, Hao Wang, Robert E. Welikson, Yongqi Yan & John A. Stamatoyannopoulos

  12. Department of Genome Sciences, University of Washington, Seattle, WA, USA

    William S. Noble, John A. Stamatoyannopoulos, Galip Gürkan Yardımcı & John A. Stamatoyannopoulos

  13. Department of Medicine, University of Washington, Seattle, WA, USA

    Rajinder Kaul, John A. Stamatoyannopoulos & John A. Stamatoyannopoulos

  14. Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT, USA

    Michael O. Duff, Brenton R. Graveley, Sara Olson, Xintao Wei, Lijun Zhan & Brenton R. Graveley

  15. National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA

    Omar Al Jammal, Eileen Cahill, Julie Coursen, Elise A. Feingold, Daniel A. Gilchrist, Samuel H. Moore, Preetha Nandi, Hannah Naughton, Briana Nuñez, Michael Pagan, Michael J. Pazin, Jeffery A. Schloss, Yekaterina Vaydylevich, Simona Volpi, Xiao-Qiao Zhou, Elise A. Feingold, Michael J. Pazin, Michael Pagan & Daniel A. Gilchrist

  16. Broad Institute and Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA

    Bradley E. Bernstein & Bradley E. Bernstein

  17. Biological Sciences, University of Alabama in Huntsville, Huntsville, AL, USA

    Surya B. Chhetri, Candice J. Coppola, Eric M. Mendenhall & Eric M. Mendenhall

  18. HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA

    Laurel A. Brandsmeier, Surya B. Chhetri, Candice J. Coppola, Rachel C. Evans, Shawn Levy, Mark Mackiewicz, Megan McEown, Sarah K. Meadows, Eric M. Mendenhall, Christopher L. Messer, Dianna E. Moore, Richard M. Myers, Amy R. Nesmith, J. Scott Newberry, Kimberly M. Newberry, Rosy Nguyen, E. Christopher Partridge, Florencia Pauli-Behn, Brian Roberts, Collin White, Eric M. Mendenhall & Richard M. Myers

  19. European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK

    Bronwen Aken, If H. A. Barnes, Daniel Barrell, Ruth Bennett, Andrew Berry, Alexandra Bignell, Claire Davidson, Sarah Donaldson, Paul Flicek, Adam Frankish, Carlos Garcia Giron, Jose M. Gonzalez, Matthew Hardy, Toby Hunt, Osagie Izuogu, Michael Kay, Jane Loveland, Fergal J. Martin, Jonathan M. Mudge, Emily H. Perry, Marie-Marthe Suner, Daniel R. Zerbino, Daniel R. Zerbino, Adam Frankish & Paul Flicek

  20. The Broad Institute of Harvard and MIT, Cambridge, MA, USA

    Kristin G. Ardlie, Samantha Beik, Charles B. Epstein, Nina Farrell, Alon Goren, Meital Hatan, David Hendrickson, Shanna Hsu, Robbyn Issner, Irwin Jungreis, Manolis Kellis, Oren Ram, Joseph Raymond, Noam Shoresh, Danielle Tenen, Mia C. Uziel, Christopher M. Vockley & David Wine

  21. MGH, Boston, MA, USA

    Yotam Drier, Shawn Gillespie, Michael Mannstadt, Dylan Rausch, Miguel Rivera & Russell Ryan

  22. Dana-Farber Cancer Institute, Boston, MA, USA

    Mariateresa Fulciniti, Birgit Knoechel & Nikhil Munshi

  23. Harvard Medical School, Boston, MA, USA

    Qian Qin & Jonathan Scheiman

  24. Boston Children’s Hospital, Boston, MA, USA

    Birgit Knoechel

  25. Harvard University, Cambridge, MA, USA

    David Kelley

  26. Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA

    Carles Boix, Jose Davila-Velderrain, Matthew D. Edwards, David K. Gifford, Yuchun Guo, Tatsunori B. Hashimoto, Lei Hou, Tommi Jaakkola, Irwin Jungreis, Manolis Kellis, Pouya Kheradpour, Yue Li, Dianbo Liu, Yaping Liu, Eva Maria Novoa, Charles W. O’Donnell, Yongjin Park, Tahin Syed, Maxim Wolf, Haoyang Zeng & Zhizhuo Zhang

  27. Max Planck Institute for Molecular Genetics, Department of Genome Regulation, Berlin, Germany

    Alex Meissner

  28. University of Colorado Boulder, Boulder, CO, USA

    John Rinn

  29. Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology and Universitat Pompeu Fabra, Barcelona, Spain

    Beatrice Borsari, Alessandra Breschi, Sarah Djebali, Roderic Guigó, Rory Johnson, Julien Lagarde, Dmitri D. Pervouchine, Barbara Uszczynska-Ratajczak & Anna Vlasova

  30. IRSD, Université de Toulouse, INSERM, INRA, ENVT, UPS, U1220, CHU Purpan, CS60039, Toulouse, France

    Sarah Djebali

  31. Skolkovo Institute for Science and Technology, Moscow, Russia

    Dmitri D. Pervouchine

  32. Functional Genomics, Cold Spring Harbor Laboratory, Woodbury, NY, USA

    Jorg Drenkow

  33. Department of Clinical Research, University of Bern, Bern, Switzerland

    Rory Johnson

  34. International Institute of Molecular and Cell Biology, Warsaw, Poland

    Barbara Uszczynska-Ratajczak

  35. Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA

    Cassandra Bazile, Christopher B. Burge, Daniel Dominguez, Abigail Hochman, Nicole J. Lambert, Tsultrim Palden & Amanda Su

  36. Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, Stem Cell Program, Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA

    Steven M. Blue, Keri Elkins, Chelsea Anne Gelboin-Burkhart, Thai B. Nguyen, Gabriel A. Pratt, Ines Rabano, Shashank Sathe, Rebecca Stanton, Balaji Sundararaman, Eric L. Van Nostrand, Ruth Wang, Brian A. Yee & Gene W. Yeo

  37. Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, Quebec, Canada

    Louis Philip Benoit Bouvrette, Neal A. L. Cody, Eric Lécuyer & Xiaofeng Wang

  38. Division of Experimental Medicine, McGill University, Quebec, Canada

    Louis Philip Benoit Bouvrette, Neal A. L. Cody, Eric Lécuyer & Xiaofeng Wang

  39. Institut de Recherches Cliniques de Montréal (IRCM), Montréal, Quebec, Canada

    Louis Philip Benoit Bouvrette, Neal A. L. Cody, Eric Lécuyer & Xiaofeng Wang

  40. Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA, USA

    Peter Freese

  41. Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, San Diego, CA, USA

    Jia-Yu Chen, Xiang-Dong Fu, Hairi Li & Rui Xiao

  42. Department of Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN, USA

    Daniel Savic

  43. Division of Biology, California Institute of Technology, Pasadena, CA, USA

    Henry Amrhein, Igor Antoshechkin, Gilberto DeSalvo, Katherine Fisher-Aylor, Peng He, Anthony Kirilusha, Georgi K. Marinov, Kenneth McCue, Diane E. Trout, Sean A. Upchurch, Jost Vielmetter, Brian A. Williams & Barbara Wold

  44. National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA

    Stacie M. Anderson, David M. Bodine & Elisabeth F. Heuston

  45. Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA

    Timothy E. Reddy

  46. Center for Genomic and Computational Biology, Duke University, Durham, NC, USA

    Anthony M. D’Ippolito & Timothy E. Reddy

  47. Biological Sciences, University of California, Irvine, Irvine, CA, USA

    Nicole El-Ali, Camden Jansen, Ali Mortazavi, Rabi Murad, Ricardo N. Ramirez & Weihua Zeng

  48. Salk Institute for Biological Studies, La Jolla, CA, USA

    Rosa G. Castanon, Huaming Chen, Joseph R. Ecker, Manoj Hariharan, Yupeng He, Graham McVicker & Joseph R. Nery

  49. Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA

    Veena Afzal, Jennifer A. Akiyama, Iros Barozzi, Diane E. Dickel, Yoko Fukuda-Yuzawa, Tyler H. Garvin, Anne Harrington, Momoe Kato, Elizabeth Lee, Brandon J. Mannion, Catherine S. Novak, Len A. Pennacchio, Quan Pham, Ingrid Plajzer-Frick, Valentina Snetkova & Axel Visel

  50. Department of Chemistry and Biochemistry, Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA

    Bo Ding, Nan Li, Vu Ngo, Tung Nguyen, Mengchi Wang, Tao Wang, Wei Wang, John W. Whitaker, Andre Wildberg, Kai Zhang & Yun Zhu

  51. Institute for Human Genetics, Department of Neurology, University of California, San Francisco, San Francisco, CA, USA

    Yin Shen

  52. Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA

    Feng Yue

  53. Penn State Health Milton S. Hershey Medical Center, Hershey, PA, USA

    Tingting Liu, Yanli Wang, Jie Xu, Hongbo Yang, Feng Yue, Bo Zhang & Lijun Zhang

  54. US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA

    Len A. Pennacchio & Axel Visel

  55. School of Natural Sciences, University of California, Merced, Merced, CA, USA

    Axel Visel

  56. Comparative Biochemistry Program, University of California, Berkeley, CA, USA

    Len A. Pennacchio

  57. Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA, USA

    Joseph R. Ecker

  58. Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA

    Alan P. Boyle

  59. Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA

    Alan P. Boyle

  60. Department of Molecular and Cellular Physiology, School of Medicine, Stanford University, Palo Alto, CA, USA

    Catharine Eastman

  61. Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada

    Andrew Emili, Jack F. Greenblatt, Hongbo Guo, Timothy R. Hughes, Ernest Radovani & Guoqing Zhong

  62. Department of Genetics, School of Medicine, Yale University, New Haven, CT, USA

    Peng Gong, Jin Lian, Xinghua Pan, Quan Shen, Sherman M. Weissman & Jialing Zhang

  63. Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA

    Peggy J. Farnham, Yu Guo, Suhn K. Rhie & Heather N. Witt

  64. Department of Radiation Oncology, School of Medicine, Stanford University, Palo Alto, CA, USA

    Nastaran Heidari

  65. Department of Human Genetics, Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL, USA

    Cory Holgren, Nader Jameel, Madhura Kadaba, Mary Kasparian, Lijia Ma, Matthew G. Milton, Jennifer Moran, Dave Steffan, Matt Szynkarek, Dave Toffey & Alec Victorsen

  66. Division of General Surgery, Section of Transplant Surgery, School of Medicine, Washington University, St. Louis, MO, USA

    Yiing Lin

  67. Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China

    Xinghua Pan

  68. Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Guangzhou, China

    Xinghua Pan

  69. Department of Cell Biology & Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA

    Doug H. Phanstiel

  70. Thurston Arthritis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA

    Doug H. Phanstiel

  71. Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada

    Jack F. Greenblatt, Rozita Razavi & Frank W. Schmitges

  72. School of Medicine, Jiangsu University, Zhenjiang, China

    Quan Shen

  73. Department of Molecular Genetics, Donnelly Centre, University of Toronto, Toronto, Ontario, Canada

    Timothy R. Hughes

  74. Tempus Labs, Chicago, IL, USA

    Kevin P. White

  75. Department of Medicine, University of Washington, Seattle, WA, USA

    George Stamatoyannopoulos

  76. Fred Hutchinson Cancer Research Center, Seattle, WA, USA

    M. A. Bender, Rachel Byron & Mark T. Groudine

  77. HHMI and Program in Systems Biology, University of Massachusetts Medical School, Albert Sherman Center, Worcester, MA, USA

    Job Dekker, Bryan R. Lajoie, Hakan Ozadam & Ye Zhan

  78. University of Massachusetts Amherst, Amherst, MA, USA

    Yu Fu

  79. Institute for Infocomm Research, Singapore, Singapore

    Chuan Sheng Foo

  80. Simon Fraser University, Burnaby, British Columbia, Canada

    Maxwell W. Libbrecht

  81. Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA

    Peng Jiang, X. Shirley Liu, Clifford Meyer & Chongzhi Zang

  82. Department of Data Sciences, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, MA, USA

    Peng Jiang, X. Shirley Liu, Clifford Meyer & Chongzhi Zang

  83. Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA

    Chongzhi Zang

  84. Molecular Pathology Unit & Cancer Center, Boston, MA, USA

    Qian Qin

  85. Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, USA

    Mingxiang Teng

  86. Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA

    Amira A. Barkal

  87. Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA

    Budhaditya Banerjee, Maria Gutierrez-Arcelus, Nisha Rajagopal, Soumya Raychaudhuri, Richard I. Sherwood, Sharanya Srinivasan & Harm-Jan Westra

  88. Department of Statistics, Medical Sciences Center, Madison, WI, USA

    Sunduz Keles, Jurijs Nazarovs & Ye Zheng

  89. Department of Biostatistics and Medical Informatics, Madison, WI, USA

    Colin N. Dewey, Sunduz Keles, Peng Liu & Rene Welch

  90. Department of Mathematical Sciences, University of Texas at Dallas, Richardson, TX, USA

    Sunyoung Shin

  91. Department of Statistics, University of Nebraska-Lincoln, Lincoln, NE, USA

    Qi Zhang

  92. Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA

    Dongjun Chung

  93. Department of Cell and Regenerative Biology, UW-Madison Blood Research Program, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA

    Emery H. Bresnick

  94. Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA

    James E. Hayes & Robert J. Klein

  95. Wellcome Sanger Institute, Cambridge, UK

    Federico Abascal, Matthew Astley, Gemma Barson, Gloria Despacio-Reyes, Stephen Fitzgerald, Michael Gray, Ed Griffiths, Deepa Manthravadi, Steve Miller, Christoph Schlaffner, Gosia Trynka, Hendrik Weisser & James Wright

  96. Program in Computational Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA

    Mark Carty, Alvaro Gonzalez, Christina S. Leslie, Yuheng Lu, Alexander R. Perez, Yuri Pritykin & Manu Setty

  97. 610 Charles E. Young Drive S, Terasaki Life Sciences Building, Room 2000E, Los Angeles, CA, USA

    Yun-Hua E. Hsiao, Giovanni Quinones-Valdez, Xinshu Xiao & Yi-Wen Yang

  98. McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA

    Michael A. Beer

  99. Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA

    Michael A. Beer

  100. University of California, Santa Cruz, Santa Cruz, CA, USA

    Joel Armstrong, Alden Deran, Mark Diekhans & Benedict Paten

  101. Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland

    Jacqueline Chrast, Anne-Maud Ferreira & Alexandre Reymond

  102. Centro Nacional de Investigaciones Cardiovasculares (CNIC) and CIBER de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain

    Iakes Ezkurdia & Jesus Vazquez

  103. Spanish National Cancer Research Centre (CNIO), Madrid, Spain

    Jose Manuel Rodriguez, Michael L. Tress & Alfonso Valencia

  104. Brunel University London, London, UK

    Cristina Sisu

  105. King’s College London, Guy’s Hospital, London, UK

    Tim J. Hubbard

  106. ELIXIR Hub, Wellcome Genome Campus, Cambridge, UK

    Jennifer L. Harrow

  107. Institute of Cancer Research, London, UK

    Jyoti S. Choudhary

  108. Department of Biological Science, Florida State University, Tallahassee, FL, USA

    Vishnu Dileep, David M. Gilbert, Juan Carlos Rivera-Mulia, Takayo Sasaki & Jared Zimmerman

  109. Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Medical School, Minneapolis, MN, USA

    Juan Carlos Rivera-Mulia

  110. Center for Vaccines and Immunology University of Georgia, Athens, GA, USA

    Michael J. Kulik

  111. Center for Molecular Medicine and Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA

    Stephen Dalton

  112. Gift of Life Donor Program, Philadelphia, PA, USA

    Richard D. Hasz

  113. American Society for Radiation Oncology, Arlington, VA, USA

    Judith C. Keen

  114. National Cancer Institute, National Institutes of Health, Bethesda, MD, USA

    Helen M. Moore

  115. Leidos Biomedical, Inc, Frederick, MD, USA

    Anna Smith

  116. National Disease Research Interchange (NDRI), Philadelphia, PA, USA

    Jeffrey A. Thomas

  117. 4407 Puller Drive, Kensington, MD, USA

    Peter Good

  118. Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA

    Rizi Ai

  119. Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA

    Shantao Li

Authors
  1. Michael P. Snyder
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Thomas R. Gingeras
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Jill E. Moore
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Zhiping Weng
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Mark B. Gerstein
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Bing Ren
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Ross C. Hardison
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. John A. Stamatoyannopoulos
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Brenton R. Graveley
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Elise A. Feingold
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Michael J. Pazin
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Michael Pagan
    View author publications

    You can also search for this author in PubMed Google Scholar

  13. Daniel A. Gilchrist
    View author publications

    You can also search for this author in PubMed Google Scholar

  14. Benjamin C. Hitz
    View author publications

    You can also search for this author in PubMed Google Scholar

  15. J. Michael Cherry
    View author publications

    You can also search for this author in PubMed Google Scholar

  16. Bradley E. Bernstein
    View author publications

    You can also search for this author in PubMed Google Scholar

  17. Eric M. Mendenhall
    View author publications

    You can also search for this author in PubMed Google Scholar

  18. Daniel R. Zerbino
    View author publications

    You can also search for this author in PubMed Google Scholar

  19. Adam Frankish
    View author publications

    You can also search for this author in PubMed Google Scholar

  20. Paul Flicek
    View author publications

    You can also search for this author in PubMed Google Scholar

  21. Richard M. Myers
    View author publications

    You can also search for this author in PubMed Google Scholar

Consortia

The ENCODE Project Consortium

  • Federico Abascal
  • , Reyes Acosta
  • , Nicholas J. Addleman
  • , Jessika Adrian
  • , Veena Afzal
  • , Bronwen Aken
  • , Rizi Ai
  • , Jennifer A. Akiyama
  • , Omar Al Jammal
  • , Henry Amrhein
  • , Stacie M. Anderson
  • , Gregory R. Andrews
  • , Igor Antoshechkin
  • , Kristin G. Ardlie
  • , Joel Armstrong
  • , Matthew Astley
  • , Budhaditya Banerjee
  • , Amira A. Barkal
  • , If H. A. Barnes
  • , Iros Barozzi
  • , Daniel Barrell
  • , Gemma Barson
  • , Daniel Bates
  • , Ulugbek K. Baymuradov
  • , Cassandra Bazile
  • , Michael A. Beer
  • , Samantha Beik
  • , M. A. Bender
  • , Ruth Bennett
  • , Louis Philip Benoit Bouvrette
  • , Bradley E. Bernstein
  • , Andrew Berry
  • , Anand Bhaskar
  • , Alexandra Bignell
  • , Steven M. Blue
  • , David M. Bodine
  • , Carles Boix
  • , Nathan Boley
  • , Tyler Borrman
  • , Beatrice Borsari
  • , Alan P. Boyle
  • , Laurel A. Brandsmeier
  • , Alessandra Breschi
  • , Emery H. Bresnick
  • , Jason A. Brooks
  • , Michael Buckley
  • , Christopher B. Burge
  • , Rachel Byron
  • , Eileen Cahill
  • , Lingling Cai
  • , Lulu Cao
  • , Mark Carty
  • , Rosa G. Castanon
  • , Andres Castillo
  • , Hassan Chaib
  • , Esther T. Chan
  • , Daniel R. Chee
  • , Sora Chee
  • , Hao Chen
  • , Huaming Chen
  • , Jia-Yu Chen
  • , Songjie Chen
  • , J. Michael Cherry
  • , Surya B. Chhetri
  • , Jyoti S. Choudhary
  • , Jacqueline Chrast
  • , Dongjun Chung
  • , Declan Clarke
  • , Neal A. L. Cody
  • , Candice J. Coppola
  • , Julie Coursen
  • , Anthony M. D’Ippolito
  • , Stephen Dalton
  • , Cassidy Danyko
  • , Claire Davidson
  • , Jose Davila-Velderrain
  • , Carrie A. Davis
  • , Job Dekker
  • , Alden Deran
  • , Gilberto DeSalvo
  • , Gloria Despacio-Reyes
  • , Colin N. Dewey
  • , Diane E. Dickel
  • , Morgan Diegel
  • , Mark Diekhans
  • , Vishnu Dileep
  • , Bo Ding
  • , Sarah Djebali
  • , Alexander Dobin
  • , Daniel Dominguez
  • , Sarah Donaldson
  • , Jorg Drenkow
  • , Timothy R. Dreszer
  • , Yotam Drier
  • , Michael O. Duff
  • , Douglass Dunn
  • , Catharine Eastman
  • , Joseph R. Ecker
  • , Matthew D. Edwards
  • , Nicole El-Ali
  • , Shaimae I. Elhajjajy
  • , Keri Elkins
  • , Andrew Emili
  • , Charles B. Epstein
  • , Rachel C. Evans
  • , Iakes Ezkurdia
  • , Kaili Fan
  • , Peggy J. Farnham
  • , Nina Farrell
  • , Elise A. Feingold
  • , Anne-Maud Ferreira
  • , Katherine Fisher-Aylor
  • , Stephen Fitzgerald
  • , Paul Flicek
  • , Chuan Sheng Foo
  • , Kevin Fortier
  • , Adam Frankish
  • , Peter Freese
  • , Shaliu Fu
  • , Xiang-Dong Fu
  • , Yu Fu
  • , Yoko Fukuda-Yuzawa
  • , Mariateresa Fulciniti
  • , Alister P. W. Funnell
  • , Idan Gabdank
  • , Timur Galeev
  • , Mingshi Gao
  • , Carlos Garcia Giron
  • , Tyler H. Garvin
  • , Chelsea Anne Gelboin-Burkhart
  • , Grigorios Georgolopoulos
  • , Mark B. Gerstein
  • , Belinda M. Giardine
  • , David K. Gifford
  • , David M. Gilbert
  • , Daniel A. Gilchrist
  • , Shawn Gillespie
  • , Thomas R. Gingeras
  • , Peng Gong
  • , Alvaro Gonzalez
  • , Jose M. Gonzalez
  • , Peter Good
  • , Alon Goren
  • , David U. Gorkin
  • , Brenton R. Graveley
  • , Michael Gray
  • , Jack F. Greenblatt
  • , Ed Griffiths
  • , Mark T. Groudine
  • , Fabian Grubert
  • , Mengting Gu
  • , Roderic Guigó
  • , Hongbo Guo
  • , Yu Guo
  • , Yuchun Guo
  • , Gamze Gursoy
  • , Maria Gutierrez-Arcelus
  • , Jessica Halow
  • , Ross C. Hardison
  • , Matthew Hardy
  • , Manoj Hariharan
  • , Arif Harmanci
  • , Anne Harrington
  • , Jennifer L. Harrow
  • , Tatsunori B. Hashimoto
  • , Richard D. Hasz
  • , Meital Hatan
  • , Eric Haugen
  • , James E. Hayes
  • , Peng He
  • , Yupeng He
  • , Nastaran Heidari
  • , David Hendrickson
  • , Elisabeth F. Heuston
  • , Jason A. Hilton
  • , Benjamin C. Hitz
  • , Abigail Hochman
  • , Cory Holgren
  • , Lei Hou
  • , Shuyu Hou
  • , Yun-Hua E. Hsiao
  • , Shanna Hsu
  • , Hui Huang
  • , Tim J. Hubbard
  • , Jack Huey
  • , Timothy R. Hughes
  • , Toby Hunt
  • , Sean Ibarrientos
  • , Robbyn Issner
  • , Mineo Iwata
  • , Osagie Izuogu
  • , Tommi Jaakkola
  • , Nader Jameel
  • , Camden Jansen
  • , Lixia Jiang
  • , Peng Jiang
  • , Audra Johnson
  • , Rory Johnson
  • , Irwin Jungreis
  • , Madhura Kadaba
  • , Maya Kasowski
  • , Mary Kasparian
  • , Momoe Kato
  • , Rajinder Kaul
  • , Trupti Kawli
  • , Michael Kay
  • , Judith C. Keen
  • , Sunduz Keles
  • , Cheryl A. Keller
  • , David Kelley
  • , Manolis Kellis
  • , Pouya Kheradpour
  • , Daniel Sunwook Kim
  • , Anthony Kirilusha
  • , Robert J. Klein
  • , Birgit Knoechel
  • , Samantha Kuan
  • , Michael J. Kulik
  • , Sushant Kumar
  • , Anshul Kundaje
  • , Tanya Kutyavin
  • , Julien Lagarde
  • , Bryan R. Lajoie
  • , Nicole J. Lambert
  • , John Lazar
  • , Ah Young Lee
  • , Donghoon Lee
  • , Elizabeth Lee
  • , Jin Wook Lee
  • , Kristen Lee
  • , Christina S. Leslie
  • , Shawn Levy
  • , Bin Li
  • , Hairi Li
  • , Nan Li
  • , Shantao Li
  • , Xiangrui Li
  • , Yang I. Li
  • , Ying Li
  • , Yining Li
  • , Yue Li
  • , Jin Lian
  • , Maxwell W. Libbrecht
  • , Shin Lin
  • , Yiing Lin
  • , Dianbo Liu
  • , Jason Liu
  • , Peng Liu
  • , Tingting Liu
  • , X. Shirley Liu
  • , Yan Liu
  • , Yaping Liu
  • , Maria Long
  • , Shaoke Lou
  • , Jane Loveland
  • , Aiping Lu
  • , Yuheng Lu
  • , Eric Lécuyer
  • , Lijia Ma
  • , Mark Mackiewicz
  • , Brandon J. Mannion
  • , Michael Mannstadt
  • , Deepa Manthravadi
  • , Georgi K. Marinov
  • , Fergal J. Martin
  • , Eugenio Mattei
  • , Kenneth McCue
  • , Megan McEown
  • , Graham McVicker
  • , Sarah K. Meadows
  • , Alex Meissner
  • , Eric M. Mendenhall
  • , Christopher L. Messer
  • , Wouter Meuleman
  • , Clifford Meyer
  • , Steve Miller
  • , Matthew G. Milton
  • , Tejaswini Mishra
  • , Dianna E. Moore
  • , Helen M. Moore
  • , Jill E. Moore
  • , Samuel H. Moore
  • , Jennifer Moran
  • , Ali Mortazavi
  • , Jonathan M. Mudge
  • , Nikhil Munshi
  • , Rabi Murad
  • , Richard M. Myers
  • , Vivek Nandakumar
  • , Preetha Nandi
  • , Anil M. Narasimha
  • , Aditi K. Narayanan
  • , Hannah Naughton
  • , Fabio C. P. Navarro
  • , Patrick Navas
  • , Jurijs Nazarovs
  • , Jemma Nelson
  • , Shane Neph
  • , Fidencio Jun Neri
  • , Joseph R. Nery
  • , Amy R. Nesmith
  • , J. Scott Newberry
  • , Kimberly M. Newberry
  • , Vu Ngo
  • , Rosy Nguyen
  • , Thai B. Nguyen
  • , Tung Nguyen
  • , Andrew Nishida
  • , William S. Noble
  • , Catherine S. Novak
  • , Eva Maria Novoa
  • , Briana Nuñez
  • , Charles W. O’Donnell
  • , Sara Olson
  • , Kathrina C. Onate
  • , Ericka Otterman
  • , Hakan Ozadam
  • , Michael Pagan
  • , Tsultrim Palden
  • , Xinghua Pan
  • , Yongjin Park
  • , E. Christopher Partridge
  • , Benedict Paten
  • , Florencia Pauli-Behn
  • , Michael J. Pazin
  • , Baikang Pei
  • , Len A. Pennacchio
  • , Alexander R. Perez
  • , Emily H. Perry
  • , Dmitri D. Pervouchine
  • , Nishigandha N. Phalke
  • , Quan Pham
  • , Doug H. Phanstiel
  • , Ingrid Plajzer-Frick
  • , Gabriel A. Pratt
  • , Henry E. Pratt
  • , Sebastian Preissl
  • , Jonathan K. Pritchard
  • , Yuri Pritykin
  • , Michael J. Purcaro
  • , Qian Qin
  • , Giovanni Quinones-Valdez
  • , Ines Rabano
  • , Ernest Radovani
  • , Anil Raj
  • , Nisha Rajagopal
  • , Oren Ram
  • , Lucia Ramirez
  • , Ricardo N. Ramirez
  • , Dylan Rausch
  • , Soumya Raychaudhuri
  • , Joseph Raymond
  • , Rozita Razavi
  • , Timothy E. Reddy
  • , Thomas M. Reimonn
  • , Bing Ren
  • , Alexandre Reymond
  • , Alex Reynolds
  • , Suhn K. Rhie
  • , John Rinn
  • , Miguel Rivera
  • , Juan Carlos Rivera-Mulia
  • , Brian Roberts
  • , Jose Manuel Rodriguez
  • , Joel Rozowsky
  • , Russell Ryan
  • , Eric Rynes
  • , Denis N. Salins
  • , Richard Sandstrom
  • , Takayo Sasaki
  • , Shashank Sathe
  • , Daniel Savic
  • , Alexandra Scavelli
  • , Jonathan Scheiman
  • , Christoph Schlaffner
  • , Jeffery A. Schloss
  • , Frank W. Schmitges
  • , Lei Hoon See
  • , Anurag Sethi
  • , Manu Setty
  • , Anthony Shafer
  • , Shuo Shan
  • , Eilon Sharon
  • , Quan Shen
  • , Yin Shen
  • , Richard I. Sherwood
  • , Minyi Shi
  • , Sunyoung Shin
  • , Noam Shoresh
  • , Kyle Siebenthall
  • , Cristina Sisu
  • , Teri Slifer
  • , Cricket A. Sloan
  • , Anna Smith
  • , Valentina Snetkova
  • , Michael P. Snyder
  • , Damek V. Spacek
  • , Sharanya Srinivasan
  • , Rohith Srivas
  • , George Stamatoyannopoulos
  • , John A. Stamatoyannopoulos
  • , Rebecca Stanton
  • , Dave Steffan
  • , Sandra Stehling-Sun
  • , J. Seth Strattan
  • , Amanda Su
  • , Balaji Sundararaman
  • , Marie-Marthe Suner
  • , Tahin Syed
  • , Matt Szynkarek
  • , Forrest Y. Tanaka
  • , Danielle Tenen
  • , Mingxiang Teng
  • , Jeffrey A. Thomas
  • , Dave Toffey
  • , Michael L. Tress
  • , Diane E. Trout
  • , Gosia Trynka
  • , Junko Tsuji
  • , Sean A. Upchurch
  • , Oana Ursu
  • , Barbara Uszczynska-Ratajczak
  • , Mia C. Uziel
  • , Alfonso Valencia
  • , Benjamin Van Biber
  • , Arjan G. van der Velde
  • , Eric L. Van Nostrand
  • , Yekaterina Vaydylevich
  • , Jesus Vazquez
  • , Alec Victorsen
  • , Jost Vielmetter
  • , Jeff Vierstra
  • , Axel Visel
  • , Anna Vlasova
  • , Christopher M. Vockley
  • , Simona Volpi
  • , Shinny Vong
  • , Hao Wang
  • , Mengchi Wang
  • , Qin Wang
  • , Ruth Wang
  • , Tao Wang
  • , Wei Wang
  • , Xiaofeng Wang
  • , Yanli Wang
  • , Nathaniel K. Watson
  • , Xintao Wei
  • , Zhijie Wei
  • , Hendrik Weisser
  • , Sherman M. Weissman
  • , Rene Welch
  • , Robert E. Welikson
  • , Zhiping Weng
  • , Harm-Jan Westra
  • , John W. Whitaker
  • , Collin White
  • , Kevin P. White
  • , Andre Wildberg
  • , Brian A. Williams
  • , David Wine
  • , Heather N. Witt
  • , Barbara Wold
  • , Maxim Wolf
  • , James Wright
  • , Rui Xiao
  • , Xinshu Xiao
  • , Jie Xu
  • , Jinrui Xu
  • , Koon-Kiu Yan
  • , Yongqi Yan
  • , Hongbo Yang
  • , Xinqiong Yang
  • , Yi-Wen Yang
  • , Galip Gürkan Yardımcı
  • , Brian A. Yee
  • , Gene W. Yeo
  • , Taylor Young
  • , Tianxiong Yu
  • , Feng Yue
  • , Chris Zaleski
  • , Chongzhi Zang
  • , Haoyang Zeng
  • , Weihua Zeng
  • , Daniel R. Zerbino
  • , Jie Zhai
  • , Lijun Zhan
  • , Ye Zhan
  • , Bo Zhang
  • , Jialing Zhang
  • , Jing Zhang
  • , Kai Zhang
  • , Lijun Zhang
  • , Peng Zhang
  • , Qi Zhang
  • , Xiao-Ou Zhang
  • , Yanxiao Zhang
  • , Zhizhuo Zhang
  • , Yuan Zhao
  • , Ye Zheng
  • , Guoqing Zhong
  • , Xiao-Qiao Zhou
  • , Yun Zhu
  •  & Jared Zimmerman

Contributions

The role of the NHGRI Project Management Group in the preparation of this paper was limited to coordination and scientific management of the ENCODE consortium. All other authors contributed to the concepts, writing and/or revisions of this manuscript.

Corresponding author

Correspondence to Michael P. Snyder.

Ethics declarations

Competing interests

B.E.B. declares outside interests in Fulcrum Therapeutics, 1CellBio, HiFiBio, Arsenal Biosciences, Cell Signaling Technologies, BioMillenia, and Nohla Therapeutics. P.F. is a member of the Scientific Advisory Boards of Fabric Genomics, Inc. and Eagle Genomics, Ltd. M.P.S. is cofounder and scientific advisory board member of Personalis, SensOmics, Mirvie, Qbio, January, Filtricine, and Genome Heart. He serves on the scientific advisory board of these companies and Genapsys and Jupiter. Z.W. is a cofounder of Rgenta Therapeutics and she serves on its scientific advisory board. R.M.M. is an advisor to DNAnexus and Decheng Capital, and has outside interests in IMIDomics, Accuragen and ReadCoor, Inc. The authors declare no other competing financial interests.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data figures and tables

Extended Data Fig. 1 ENCODE timeline.

Pilot phase: September 2003–September 2007; ENCODE 2: September 2007–September 2012; ENCODE 3: September 2012–January 2017; ENCODE 4: February 2017–present; modENCODE: April 2007–April 2012; mouse ENCODE: 2009–2012.

Supplementary information

Supplementary Information

This file contains the full author list for The ENCODE Project Consortium, and Supplementary Note 1 (Useful URLs).

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

The ENCODE Project Consortium., Snyder, M.P., Gingeras, T.R. et al. Perspectives on ENCODE. Nature 583, 693–698 (2020). https://doi.org/10.1038/s41586-020-2449-8

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41586-020-2449-8

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing