ArticlebioRxiv : the preprint server for biology2023
An encyclopedia of enhancer-gene regulatory interactions in the human genome.
Open access · greenAbstract readPreprint
In one paragraph
Article in bioRxiv : the preprint server for biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
0numbers the graph read from it
0cells of the map it votes in
3citing 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
3 citing papers in PubMed, 109 citations in OpenAlex.
- EPInformer: scalable and integrative prediction of gene expression from promoter-enhancer sequences with multimodal epigenomic profiles.Nature communications · 2026Article
- Modeling nascent transcription from chromatin landscape and structure with CLASTER.Genome biology · 2026Article
- The exit from naive pluripotency: a platform for the study of enhancer mechanistics.Biochemical Society transactions · 2025Review
Corrections and comments
- Updated by
Authors and funding
41 authors at 15 institutions in 4 countries.
Andreas R GschwindDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.ORCID 0000-0002-0769-6907
Kristy S MualimDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Alireza KarbalaygharehComputational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
Maya U ShethDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Kushal K DeyComputational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
Evelyn JagodaThe Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Ramil N NurtdinovCentre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain.
Wang XiDepartment of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
Anthony S TanDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Hank JonesDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.ORCID 0009-0007-3220-3098
X Rosa MaDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
David YaoDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.ORCID 0000-0002-2232-524X
Joseph NasserBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0001-5941-5751
Žiga AvsecGoogle DeepMind, London, UK.ORCID 0000-0002-7790-8936
Benjamin T JamesBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0002-6228-055X
Muhammad S ShamimThe Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.ORCID 0000-0002-2600-5147
Neva C DurandGene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0009-0006-5647-2623
Suhas S P RaoThe Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
Ragini MahajanThe Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
Benjamin R DoughtyDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.ORCID 0000-0003-0447-4468
Kalina AndreevaDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.ORCID 0000-0002-5206-532X
Jacob C UlirschBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Kaili FanProgram in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA.ORCID 0000-0002-8723-7902
Elizabeth M PerezBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Tri C NguyenDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.ORCID 0000-0002-5141-5228
David R KelleyCalico Life Sciences, South San Francisco, CA, USA.ORCID 0000-0001-7782-3548
Hilary K FinucaneDepartment of Medicine, Massachusetts General Hospital, Boston, MA, USA.
Jill E MooreProgram in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA.
Zhiping WengProgram in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA.ORCID 0000-0002-3032-7966
Manolis KellisBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0001-7113-9630
Michael C BassikDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Alkes L PriceDepartment of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
Michael A BeerDepartment of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA.ORCID 0000-0001-9955-3809
Roderic GuigóCentre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain.ORCID 0000-0002-5738-4477
John A StamatoyannopoulosAltius Institute for Biomedical Sciences, Seattle, WA, USA.
Erez Lieberman AidenBroad Institute of MIT and Harvard, Cambridge, MA, USA.
William J GreenleafDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.ORCID 0000-0003-1409-3095
Christina S LeslieMemorial Sloan Kettering Cancer Center, New York, NY, USA.ORCID 0000-0002-4571-5910
Lars M SteinmetzDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.ORCID 0000-0002-3962-2865
Anshul KundajeDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.ORCID 0000-0003-3084-2287
Jesse M EngreitzDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.ORCID 0000-0002-5754-1719
Broad Institute · USLucile Packard Children's Hospital · USStanford University · USMemorial Sloan Kettering Cancer Center · USBaylor College of Medicine · USCentre for Genomic Regulation · ESHarvard University · USJohns Hopkins University · USUniversity of Massachusetts Chan Medical School · USCarnegie Institution for Science · USEnzo Life Sciences (United States) · USEuropean Molecular Biology Laboratory · DEFred Hutch Cancer Center · USGoogle DeepMind (United Kingdom) · GBUniversity of California, San Francisco · US
Funding
X-RAY CRYSTALLOGRAPHYP30CA008748 · NCI · SLOAN-KETTERING INSTITUTE FOR CANCER RES · PI SELWYN M VICKERS · 1985 to 2026
$347.4MINSTITUTIONAL 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
$26.0MA Data Coordinating Center for ENCODEU41HG006992 · NHGRI · STANFORD UNIVERSITY · PI CHERRY, J. MICHAEL · 2012 to 2016
$16.6MStanford Center for Connecting DNA Variants to Function and PhenotypeUM1HG011972 · NHGRI · STANFORD UNIVERSITY · PI JESSE M ENGREITZ, THOMAS QUERTERMOUS · 2021 to 2026
$10.5MEDAC: ENCODE Data Analysis CenterU24HG009446 · NHGRI · UNIV OF MASSACHUSETTS MED SCH WORCESTER · PI GERSTEIN, MARK BENDER, WENG, ZHIPING · 2017 to 2022
$10.4MDeciphering the Genomics of Gene Network Regulation of T Cell and Fibroblast States in Autoimmune InflammationU01HG012103 · NHGRI · SLOAN-KETTERING INST CAN RESEARCH · PI Christina S Leslie, Alexander Y Rudensky · 2021 to 2026
$7.5MHigh-throughput systematic characterization of regulatory element functionUM1HG009436 · NHGRI · STANFORD UNIVERSITY · PI BASSIK, MICHAEL C, GREENLEAF, WILLIAM JAMES · 2017 to 2021
$5.4MPredicting the impact of genetic variants, genes and pathways on human DiseaseU01HG012009 · NHGRI · BRIGHAM AND WOMEN'S HOSPITAL · PI ALKES L PRICE, Soumya Raychaudhuri · 2021 to 2026
$4.2MPredicting context-specific molecular and phenotypic effects of genetic variation through the lens of the cis-regulatory codeU01HG012069 · NHGRI · STANFORD UNIVERSITY · PI Anshul Kundaje · 2021 to 2026
$3.9MEncoding genomic architecture in the encyclopedia: linking DNA elements, chromatin state, and gene expression in 3DU01HG009395 · NHGRI · SLOAN-KETTERING INST CAN RESEARCH · PI LESLIE, CHRISTINA S · 2017 to 2021
$3.7MDecoding the regulatory architecture of the human genome across cell types, individuals and diseaseU01HG009431 · NHGRI · STANFORD UNIVERSITY · PI PRITCHARD, JONATHAN K · 2017 to 2021
$3.5MNCI NIH HHS P30 CA008748NHGRI NIH HHS K99 HG009917NHGRI NIH HHS R00 HG009917NHGRI NIH HHS R00 HG012203NHGRI NIH HHS R01 HG012367NHGRI NIH HHS R35 HG011324NHGRI NIH HHS T32 HG000044NHGRI NIH HHS U01 HG009380NHGRI NIH HHS U01 HG009395NHGRI NIH HHS U01 HG009431NHGRI NIH HHS U01 HG012009NHGRI NIH HHS U01 HG012069NHGRI NIH HHS U01 HG012103NHGRI NIH HHS U24 HG009397NHGRI NIH HHS U24 HG009446NHGRI NIH HHS U41 HG006992NHGRI NIH HHS UM1 HG009436NHGRI NIH HHS UM1 HG011972
Abstract
Identifying transcriptional enhancers and their target genes is essential for understanding gene regulation and the impact of human genetic variation on disease
Identifiers
What OpenQuestion holds
Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390
Registered trials
None linked
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.