ArticleNature2025
Massively parallel characterization of transcriptional regulatory elements.
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Article in Nature, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 86 papers.
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86citing papers in PubMed
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Who cites it
86 citing papers in PubMed.
- N-terminal fusion length: The key to reliable and context-preserving regulatory sequence characterization.Synthetic and systems biotechnology · 2027Article
- The gene-regulatory evolution of the human skeleton.Nature · 2026Article
- AlphaGenome Atlas:medRxiv : the preprint server for health sciences · 2026Article
- Uniform processing and analysis of IGVF massively parallel reporter assay data with MPRAsnakeflow.Genome research · 2026Article
- Multichannel genomic recording of biological information with ENGRAM.Nature protocols · 2026Review
- Article
- Toward generalizable and interpretable AI in regulatory genomics.Nature genetics · 2026Review
- Opportunities for artificial intelligence and synthetic biology in designing living drug delivery systems.Advanced drug delivery reviews · 2026Review
- Massively parallel characterization and predictive modelling of neuronal regulatory variation.bioRxiv : the preprint server for biology · 2026Article
- Lentiviral single-cell MPRA of synthetic enhancers reveals motif affinity-based encoding of cell state specificity.Genome biology · 2026Article
- The Encyclopedia of DNA Elements.bioRxiv : the preprint server for biology · 2026Article
- Identifying severe COVID-19 risk variants modulating enhancer reporter activity in lung cells.PLoS genetics · 2026Article
- Deciphering key factors of active learning performance in biomolecular design.Bioinformatics (Oxford, England) · 2026Article
- Inference of fitness landscapes with heterogeneous patterns of epistasis across sites.bioRxiv : the preprint server for biology · 2026Article
- Expression-linked promoter selection (ELiPS) engineers short, strong ubiquitous promoters for gene therapy applications.bioRxiv : the preprint server for biology · 2026Article
- Intrinsic promoter responsiveness dictates sensitivity to transcriptional activation by enhancers.bioRxiv : the preprint server for biology · 2026Article
- A comparative survey of functional evidence use in hearing and vision loss genetics.Communications medicine · 2026Article
- Autoimmune non-coding variants perturb transcription factor-cofactor complex assembly linked to enhancer activity.bioRxiv : the preprint server for biology · 2026Article
- An in vivo parallelized reporter assay to uncover tissue-specific splicing regulatory sequences in a multicellular animal.Nucleic acids research · 2026Article
- Massively parallel reporter assay-informed modeling improves prediction of context-specific enhancer-gene regulatory interactions.Nucleic acids research · 2026Article
26 more citing papers are in PubMed but not listed here.
Corrections and comments
- Update of
Authors and funding
17 authors.
Vikram Agarwal *Department of Genome Sciences, University of Washington, Seattle, WA, USA. vikram.agarwal@sanofi.com.ORCID 0000-0001-8148-952X
Fumitaka Inoue *Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA.ORCID 0000-0003-0657-434X
Max SchubachBerlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany.ORCID 0000-0002-2032-6679
Dmitry PenzarVavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia.
Beth K MartinDepartment of Genome Sciences, University of Washington, Seattle, WA, USA.
Pyaree Mohan DashBerlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany.
Pia KeukeleireInstitute of Human Genetics, University Medical Center Schleswig-Holstein, University of Lübeck, Lübeck, Germany.ORCID 0000-0002-8828-636X
Zicong ZhangInstitute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan.ORCID 0000-0003-1444-5054
Ajuni SohotaDepartment of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA.
Jingjing ZhaoDepartment of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA.
Ilias Georgakopoulos-SoaresInstitute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA.ORCID 0000-0003-3641-1488
William S NobleDepartment of Genome Sciences, University of Washington, Seattle, WA, USA.ORCID 0000-0001-7283-4715
Galip Gürkan YardımcıDepartment of Genome Sciences, University of Washington, Seattle, WA, USA.
Ivan V KulakovskiyVavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia.ORCID 0000-0002-6554-8128
Martin KircherBerlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany.ORCID 0000-0001-9278-5471
Jay ShendureDepartment of Genome Sciences, University of Washington, Seattle, WA, USA. shendure@uw.edu.ORCID 0000-0002-1516-1865
Nadav AhituvDepartment of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA. nadav.ahituv@ucsf.edu.ORCID 0000-0002-7434-8144
Funding
RESEARCH TRAINING IN HEMATOLOGYT32HL007093 · NHLBI · UNIVERSITY OF WASHINGTON · PI Janis L Abkowitz · 1985 to 2026
$13.9MEDAC: ENCODE Data Analysis CenterU24HG009446 · NHGRI · UNIV OF MASSACHUSETTS MED SCH WORCESTER · PI GERSTEIN, MARK BENDER, WENG, ZHIPING · 2017 to 2022
$10.4MMassively parallel characterization of variants and elements impacting transcriptional regulation in dynamic cellular systemsUM1HG011966 · NHGRI · UNIVERSITY OF WASHINGTON · PI Nadav Ahituv, Jay Ashok Shendure · 2021 to 2026
$9.7MMassively parallel reporter assays and genome editing of ENCODE predicted regulatory elementsUM1HG009408 · NHGRI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI AHITUV, NADAV, SHENDURE, JAY ASHOK · 2017 to 2021
$7.6MNHGRI NIH HHS U24 HG009446NHGRI NIH HHS UM1 HG009408NHGRI NIH HHS UM1 HG011966NHLBI NIH HHS T32 HL007093
Abstract
The human genome contains millions of candidate cis-regulatory elements (cCREs) with cell-type-specific activities that shape both health and many disease states
Indexed as
Gene Expression RegulationHigh-Throughput Nucleotide SequencingRegulatory Elements, TranscriptionalEnhancer Elements, GeneticGenes, ReporterGenome, HumanHumansK562 CellsLentivirusNucleotide MotifsOrgan SpecificityPromoter Regions, Genetic
Identifiers
What Socratic holds
Textmetadata
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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 Socratic graph.