ArticleResearch square2023
The ENCODE Uniform Analysis Pipelines.
Open access · greenAbstract readPreprint
In one paragraph
Article in Research square, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
–field-weighted citation impact
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
2 citing papers in PubMed, 38 citations in OpenAlex.
- Benchmarking genome choice in functional genomics analyses.Nature communications · 2026Article
- Tracing the evolution of sequencing into the era of genomic medicine.Nature reviews. Genetics · 2025Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
60 authors at 12 institutions in 3 countries.
Benjamin C HitzDepartment of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
Jin-Wook LeeDepartment of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
Otto JolankiDepartment of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
Meenakshi S KagdaDepartment of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.ORCID 0000-0003-0545-0185
Keenan GrahamDepartment of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
Paul SudDepartment of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
Idan GabdankDepartment of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
J Seth StrattanDepartment of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
Cricket A SloanDepartment of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
Timothy DreszerDepartment of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
Laurence D RoweDepartment of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
Nikhil R PodduturiDepartment of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
Venkat S MalladiDepartment of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
Esther T ChanDepartment of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.ORCID 0000-0002-2406-2623
Jean M DavidsonDepartment of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
Marcus HoDepartment of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
Stuart MiyasatoDepartment of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
Matt SimisonDepartment of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
Forrest TanakaDepartment of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
Yunhai LuoDepartment of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
Ian WhalingDepartment of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
Eurie L HongDepartment of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
Brian T LeeGenomics Institute, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA.ORCID 0000-0001-6382-9738
Richard SandstromAltius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA.
Eric RynesAltius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA.
Jemma NelsonAltius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA.
Andrew NishidaAltius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA.
Alyssa IngersollAltius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA.
Michael BuckleyAltius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA.
Mark FrerkerAltius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA.
Daniel S KimDepartment of Genetics, Department of Computer Science, Stanford University, 240 Pasteur Drive, Palo Alto, CA 94304, USA.
Nathan BoleyDepartment of Genetics, Department of Computer Science, Stanford University, 240 Pasteur Drive, Palo Alto, CA 94304, USA.ORCID 0000-0001-7114-2450
Diane TroutDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125 USA.ORCID 0000-0002-4928-5532
Alex DobinCold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
Sorena RahmanianCenter for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA.
Dana WymanCenter for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA.
Gabriela Balderrama-GutierrezCenter for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA.
Fairlie ReeseCenter for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA.
Neva C DurandBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA.ORCID 0009-0006-5647-2623
Olga DudchenkoThe Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
David WeiszThe Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
Suhas S P RaoThe Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
Alyssa BlackburnThe Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
Dimos GkountaroulisThe Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
Mahdi SadrThe Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
Moshe OlshanskyBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Yossi EliazThe Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
Dat NguyenThe Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.ORCID 0000-0001-7330-7028
Ivan BochkovThe Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
Muhammad Saad ShamimThe Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.ORCID 0000-0002-2600-5147
Ragini MahajanCenter for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA.
Erez AidenBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Tom GingerasCold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
Simon HeathCNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain. Universitat Pompeu Fabra, Barcelona, Spain.
Martin HirstMicheal Smith Laboratories, University of British Columbia, British Columbia, Canada.ORCID 0000-0001-9136-9054
W James KentGenomics Institute, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
Anshul KundajeDepartment of Genetics, Department of Computer Science, Stanford University, 240 Pasteur Drive, Palo Alto, CA 94304, USA.ORCID 0000-0003-3084-2287
Ali MortazaviCenter for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA.ORCID 0000-0002-4259-6362
Barbara WoldDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125 USA.ORCID 0000-0003-3235-8130
J Michael CherryDepartment of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
Stanford University · USBaylor College of Medicine · USAltius Institute for Biomedical Sciences · USUniversity of California, Irvine · USBroad Institute · USCalifornia Institute of Technology · USCold Spring Harbor Laboratory · USUniversity of California, Santa Cruz · USCentre for Genomic Regulation · ESRice University · USUniversity of British Columbia · CAUniversity of California, Berkeley · US
Funding
A Data Coordinating Center for ENCODEU24HG009397 · NHGRI · STANFORD UNIVERSITY · PI CHERRY, J. MICHAEL · 2017 to 2023
$26.0MNovel algorithm development, user support and maintenance for STARR01HG009318 · NHGRI · COLD SPRING HARBOR LABORATORY · PI DOBIN, ALEXANDER · 2017 to 2021
$2.4MNHGRI NIH HHS R01 HG009318NHGRI NIH HHS U24 HG009397
Abstract
The Encyclopedia of DNA elements (ENCODE) project is a collaborative effort to create a comprehensive catalog of functional elements in the human genome. The current database comprises more than 19000 functional genomics experiments across more than 1000 cell lines and tissues using a wide array of experimental techniques to study the chromatin structure, regulatory and transcriptional landscape of the
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analysis pipelinesNGS analysissoftware
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What OpenQuestion holds
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.