ArticleNature2020
Expanded encyclopaedias of DNA elements in the human and mouse genomes.
Erratum issuedOpen access · hybridAbstract read
In one paragraph
Article in Nature, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 1,503 papers.
0numbers the graph read from it
0cells of the map it votes in
1,503citing papers in PubMed
111.1field-weighted citation impact, top 1% of its field
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
1,503 citing papers in PubMed, 2,490 citations in OpenAlex.
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- Epigenetic dynamics of human spermatogenesis and their dysregulation in non-obstructive azoospermia.Protein & cell · 2026Article
- Single-Nucleus Multi-Omic Atlas Maps Regulatory Architecture and Non-Coding Variant Effects across Adult Human Tissues.bioRxiv : the preprint server for biology · 2026Article
- Epigenetic regulation of DPP4 receptor expression by NONO enables replication of MERS-CoV.bioRxiv : the preprint server for biology · 2026Article
- FFPE-CUTAC: A Single Assay, Multiple Layers.bioRxiv : the preprint server for biology · 2026Article
- GenART: Reading the genome's language with adaptive "words".Cell reports methods · 2026Article
- Non-Coding Negative Regulatory Features in Livestock Genomes: Functional Annotation and Causal Validation.Animals : an open access journal from MDPI · 2026Review
1,443 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
64 authors at 20 institutions in 9 countries.
ENCODE Project Consortium
Jill E Moore *University of Massachusetts Medical School, Program in Bioinformatics and Integrative Biology, Worcester, MA, USA.ORCID http://orcid.org/0000-0002-3023-0806
Michael J Purcaro *University of Massachusetts Medical School, Program in Bioinformatics and Integrative Biology, Worcester, MA, USA.ORCID http://orcid.org/0000-0002-4735-4215
Henry E Pratt *University of Massachusetts Medical School, Program in Bioinformatics and Integrative Biology, Worcester, MA, USA.
Charles B Epstein *The Broad Institute of Harvard and MIT, Cambridge, MA, USA.ORCID http://orcid.org/0000-0001-8358-8345
Noam Shoresh *The Broad Institute of Harvard and MIT, Cambridge, MA, USA.
Jessika Adrian *Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA.
Trupti Kawli *Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA.
Carrie A Davis *Cold Spring Harbor Laboratory, Functional Genomics, Cold Spring Harbor, NY, USA.
Alexander Dobin *Cold Spring Harbor Laboratory, Functional Genomics, Cold Spring Harbor, NY, USA.
Rajinder Kaul *Altius Institute for Biomedical Sciences, Seattle, WA, USA.ORCID http://orcid.org/0000-0002-7895-9284
Jessica Halow *Altius Institute for Biomedical Sciences, Seattle, WA, USA.
Eric L Van Nostrand *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.
Peter Freese *Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
David U Gorkin *Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0003-4944-4107
Yin Shen *Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0001-9901-5613
Yupeng He *Genomics Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
Mark Mackiewicz *HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.ORCID http://orcid.org/0000-0002-7088-1902
Florencia Pauli-Behn *HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
Brian A WilliamsDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
Ali MortazaviDepartment of Developmental and Cell Biology, University of California Irvine, Irvine, CA, USA.ORCID http://orcid.org/0000-0002-4259-6362
Cheryl A KellerDepartment of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.ORCID http://orcid.org/0000-0001-6594-0245
Xiao-Ou ZhangUniversity of Massachusetts Medical School, Program in Bioinformatics and Integrative Biology, Worcester, MA, USA.
Shaimae I ElhajjajyUniversity of Massachusetts Medical School, Program in Bioinformatics and Integrative Biology, Worcester, MA, USA.
Jack HueyUniversity of Massachusetts Medical School, Program in Bioinformatics and Integrative Biology, Worcester, MA, USA.
Diane E DickelEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.ORCID http://orcid.org/0000-0001-5497-6824
Valentina SnetkovaEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
Xintao WeiDepartment of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT, USA.
Xiaofeng WangDépartement de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, Quebec, Canada.
Juan Carlos Rivera-MuliaDepartment of Biological Science, Florida State University, Tallahassee, FL, USA.ORCID http://orcid.org/0000-0002-7566-3875
Joel RozowskyYale University, New Haven, CT, USA.ORCID http://orcid.org/0000-0002-3565-0762
Jing ZhangYale University, New Haven, CT, USA.
Surya B ChhetriHudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
Jialing ZhangDepartment of Genetics, School of Medicine, Yale University, New Haven, CT, USA.
Alec VictorsenDepartment of Human Genetics, Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL, USA.
Kevin P WhiteTempus Labs, Chicago, IL, USA.
Axel ViselEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.ORCID http://orcid.org/0000-0002-4130-7784
Gene W YeoDepartment 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.ORCID http://orcid.org/0000-0002-0799-6037
Christopher B BurgeDepartment of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.ORCID http://orcid.org/0000-0001-9047-5648
Eric LécuyerDépartement de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, Quebec, Canada.
David M GilbertDepartment of Biological Science, Florida State University, Tallahassee, FL, USA.ORCID http://orcid.org/0000-0001-8087-9737
Job DekkerHHMI and Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA, USA.ORCID http://orcid.org/0000-0001-5631-0698
John RinnUniversity of Colorado Boulder, Boulder, CO, USA.ORCID http://orcid.org/0000-0002-7231-7539
Eric M MendenhallHudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.ORCID http://orcid.org/0000-0002-7395-6295
Joseph R EckerGenomics Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.ORCID http://orcid.org/0000-0001-5799-5895
Manolis KellisThe Broad Institute of Harvard and MIT, Cambridge, MA, USA.ORCID http://orcid.org/0000-0001-7113-9630
Robert J KleinDepartment of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.ORCID http://orcid.org/0000-0003-3539-5391
William S NobleDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
Anshul KundajeDepartment of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA.ORCID http://orcid.org/0000-0003-3084-2287
Roderic GuigóBioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology and Universitat Pompeu Fabra, Barcelona, Spain.
Peggy J FarnhamDepartment of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.ORCID http://orcid.org/0000-0003-4469-7914
J Michael CherryDepartment of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA. cherry@stanford.edu.ORCID http://orcid.org/0000-0001-9163-5180
Richard M MyersHudsonAlpha Institute for Biotechnology, Huntsville, AL, USA. rmyers@hudsonalpha.org.
Bing RenCenter for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA. biren@ucsd.edu.ORCID http://orcid.org/0000-0002-5435-1127
Brenton R GraveleyDepartment of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT, USA. graveley@uchc.edu.
Mark B GersteinYale University, New Haven, CT, USA. mark@gersteinlab.org.
Len A PennacchioEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. lapennacchio@lbl.gov.ORCID http://orcid.org/0000-0002-8748-3732
Michael P SnyderDepartment of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA. mpsnyder@stanford.edu.ORCID http://orcid.org/0000-0003-0784-7987
Bradley E BernsteinBroad Institute and Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA. Bernstein.Bradley@mgh.harvard.edu.ORCID http://orcid.org/0000-0002-5726-6278
Barbara WoldDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA. woldb@caltech.edu.
Ross C HardisonDepartment of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA. rch8@psu.edu.ORCID http://orcid.org/0000-0003-4084-7516
Thomas R GingerasCold Spring Harbor Laboratory, Functional Genomics, Cold Spring Harbor, NY, USA. gingeras@cshl.edu.
John A StamatoyannopoulosAltius Institute for Biomedical Sciences, Seattle, WA, USA. jstam@altius.org.
Zhiping WengUniversity of Massachusetts Medical School, Program in Bioinformatics and Integrative Biology, Worcester, MA, USA. zhiping.weng@umassmed.edu.ORCID http://orcid.org/0000-0002-3032-7966
Stanford University · USUniversity of California San Diego · USAltius Institute for Biomedical Sciences · USUniversity of Massachusetts Chan Medical School · USMassachusetts Institute of Technology · USYale University · USHudsonAlpha Institute for Biotechnology · USEuropean Bioinformatics Institute · GBBroad Institute · USNational Institutes of Health · USLawrence Berkeley National Laboratory · USCalifornia Institute of Technology · USWellcome Sanger Institute · GBUniversity of Chicago · USCold Spring Harbor Laboratory · USSalk Institute for Biological Studies · USTongji University · CNUniversitat Pompeu Fabra · ESFlorida State University · USPenn State Milton S. Hershey Medical Center · US
Funding
X-RAY CRYSTALLOGRAPHYP30CA008748 · NCI · SLOAN-KETTERING INSTITUTE FOR CANCER RES · PI Hongbiao Carl Lekaye · 1985 to 2026
$347.4MSingle-Cell Biology Shared ResourceP30CA045508 · NCI · COLD SPRING HARBOR LABORATORY · PI John Edward Moses · 1987 to 2026
$118.9MViral Vector Core (VVC)P30CA014195 · NCI · SALK INSTITUTE FOR BIOLOGICAL STUDIES · PI Reuben Shaw · 1985 to 2026
$82.8MINSTITUTIONAL TRAINING GRANT IN GENOME SCIENCET32HG000044 · NHGRI · STANFORD UNIVERSITY · PI MICHAEL P. SNYDER · 1995 to 2026
$32.2MA Data Coordinating Center for ENCODEU24HG009397 · NHGRI · STANFORD UNIVERSITY · PI CHERRY, J. MICHAEL · 2017 to 2023
$26.0MPRODUCTION CENTER FOR MAPPING REGULATORY REGIONS OF THE HUMAN GENOMEUM1HG009442 · NHGRI · STANFORD UNIVERSITY · PI SNYDER, MICHAEL P. · 2017 to 2021
$20.1MToward a comprehensive functional annotation of the human genomeU54HG006998 · NHGRI · HUDSON-ALPHA INSTITUTE FOR BIOTECHNOLOGY · PI MYERS, RICHARD M · 2012 to 2016
$17.5MA Data Coordinating Center for ENCODEU41HG006992 · NHGRI · STANFORD UNIVERSITY · PI CHERRY, J. MICHAEL · 2012 to 2016
$16.6MStructural Annotation of the Human GenomeR01HG003143 · NHGRI · UNIV OF MASSACHUSETTS MED SCH WORCESTER · PI Job Dekker · 2003 to 2026
$15.4MProduction Center for Mapping Regulatory Regions of the Human GenomeU54HG006996 · NHGRI · STANFORD UNIVERSITY · PI SNYDER, MICHAEL P. · 2012 to 2016
$14.6MCenter for Mammalian Regulatory GenomicsU54HG006997 · NHGRI · LUDWIG INSTITUTE FOR CANCER RES LTD · PI REN, BING · 2012 to 2016
$14.3MComprhensive analysis of functional RNA elements encoded in the human genomeU54HG007005 · NHGRI · UNIVERSITY OF CONNECTICUT SCH OF MED/DNT · PI GRAVELEY, BRENTON R. · 2012 to 2017
$12.5MNCI NIH HHS P30 CA008748NCI NIH HHS P30 CA014195NCI NIH HHS P30 CA045508NHGRI NIH HHS F32 HG006993NHGRI NIH HHS K99 HG009530NHGRI NIH HHS R01 HG003143NHGRI NIH HHS R01 HG012367NHGRI NIH HHS T32 HG000044NHGRI NIH HHS U01 HG007019NHGRI NIH HHS U01 HG007033NHGRI NIH HHS U01 HG007036NHGRI NIH HHS U01 HG007037NHGRI NIH HHS U01 HG009380NHGRI NIH HHS U01 HG009431NHGRI NIH HHS U24 HG009446NHGRI NIH HHS U41 HG006992NHGRI NIH HHS U41 HG007000NHGRI NIH HHS U54 HG006991NHGRI NIH HHS U54 HG006994NHGRI NIH HHS U54 HG006996NHGRI NIH HHS U54 HG006997NHGRI NIH HHS U54 HG006998NHGRI NIH HHS U54 HG007002NHGRI NIH HHS U54 HG007004NHGRI NIH HHS U54 HG007005NHGRI NIH HHS U54 HG007010NHGRI NIH HHS UM1 HG009390NHGRI NIH HHS UM1 HG009411NHGRI NIH HHS UM1 HG009442NIDDK NIH HHS R01 DK068634NIDDK NIH HHS R24 DK106766NIDDK NIH HHS R37 DK050107NIGMS NIH HHS R01 GM083337NIGMS NIH HHS T32 GM087237
Abstract
The human and mouse genomes contain instructions that specify RNAs and proteins and govern the timing, magnitude, and cellular context of their production. To better delineate these elements, phase III of the Encyclopedia of DNA Elements (ENCODE) Project has expanded analysis of the cell and tissue repertoires of RNA transcription, chromatin structure and modification, DNA methylation, chromatin looping, and occupancy by transcription factors and RNA-binding proteins. Here we summarize these efforts, which have produced 5,992 new experimental datasets, including systematic determinations across mouse fetal development. All data are available through the ENCODE data portal (https://www.encodeproject.org), including phase II ENCODE
Indexed as
Databases, GeneticGenomicsMolecular Sequence AnnotationRegistriesAnimalsChromatinDeoxyribonuclease IDNADNA FootprintingDNA MethylationDNA Replication TimingGenomeGenome, HumanHistonesHumansMiceChromatinDeoxyribonuclease IDNAHistonesRNA-Binding ProteinsTransposases
Identifiers
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