ArticleNature2025
Multiscale footprints reveal the organization of cis-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 39 papers.
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39citing papers in PubMed
–field-weighted citation impact
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Who cites it
39 citing papers in PubMed.
- Flow Orchestrated Regulatory Genomics Engine (FORGE): A Configurable Nextflow Pipeline for End-to-End snMultiome Analysis.bioRxiv : the preprint server for biology · 2026Article
- Fruit-Specific Promoters in Plants: Advances, Regulatory Mechanisms and Applications in Plant Biotechnology.Plants (Basel, Switzerland) · 2026Review
- CroCoNet: a framework for the quantitative comparison of gene regulatory networks across species.Genome biology · 2026Article
- Translating genome-wide association studies at multiple scales: Drug target prioritization, cellular architectures, and organ imaging.Cell genomics · 2026Review
- YY1 in hematopoietic stem cells: epigenetic regulation, chromatin architecture, and aging.Current opinion in hematology · 2026Review
- Systemic epigenetic dysregulation as a driver of ageing and a therapeutic target.Nature reviews. Molecular cell biology · 2026Review
- Robust footprinting with sample-specific Tn5 bias correction for bulk and single cell ATAC-seq.Nature communications · 2026Article
- 3D genome architecture and epigenetic regulation of lineage identity in advanced prostate cancer.Endocrinology · 2026Review
- Cell-specific dedifferentiation inbioRxiv : the preprint server for biology · 2026Article
- Informational blueprints reveal condition-dependent gene regulatory architectures.bioRxiv : the preprint server for biology · 2026Article
- CREsted: modeling genomic and synthetic cell-type-specific enhancers across tissues and species.Nature methods · 2026Article
- Spatially decoding genotype-associated epigenetic landscapes in human lymphoma FFPE tissues via epi-Patho-DBiT.Nature communications · 2026Article
- Article
- Transcription factor collaboration enables precise T cell state engineering.bioRxiv : the preprint server for biology · 2026Article
- Article
- Article
- Epigenetic memory of colitis promotes tumour growth.Nature · 2026Article
- A Cytosine Deaminase-Based Genomic Footprinting Assay (cFOOT-seq) for Detecting Transcription Factor Occupancy.Bio-protocol · 2026Article
- Interplay between circadian and other transcription factors-Implications for cycling transcriptome reprogramming.FEBS letters · 2026Review
- Lineage-specific evolution of regulatory landscapes in a polyploid plant and its diploid progenitors.bioRxiv : the preprint server for biology · 2026Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
22 authors.
Yan Hu *Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0002-8435-6586
Max A Horlbeck *Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0002-3875-871X
Ruochi Zhang *Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0002-1103-5044
Sai MaGene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0002-9785-7929
Rojesh ShresthaGene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Vinay K KarthaGene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Fabiana M DuarteGene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Conrad HockGene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Rachel E SavageGene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Ajay LabadeGene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0003-1348-8220
Heidi KletzienDepartment of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
Alia MelikiGene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Andrew CastilloGene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Neva C DurandGene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0009-0006-5647-2623
Eugenio MatteiGene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0002-8889-658X
Lauren J AndersonGene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0009-0001-5180-6122
Tristan TayGene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Andrew S EarlGene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0002-5732-954X
Noam ShoreshGene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Charles B EpsteinGene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0001-8358-8345
Amy J WagersDepartment of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
Jason D BuenrostroGene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA. jason_buenrostro@harvard.edu.ORCID 0000-0001-9958-3987
Funding
Transcriptional and epigenetic heterogeneity of stem/progenitor cellsP01HL131477 · NHLBI · MASSACHUSETTS GENERAL HOSPITAL · PI LEONARD Ira ZON · 2017 to 2026
$24.6MA Foundational Resource of Functional Elements, TF footprints and Gene Regulatory InteractionsUM1HG011986 · NHGRI · BROAD INSTITUTE, INC. · PI BRADLEY Evan BERNSTEIN, Jason Daniel Buenrostro · 2021 to 2026
$13.3MTRAINING GRANT IN GENETICST32GM007748 · NIGMS · HARVARD UNIVERSITY (MEDICAL SCHOOL) · PI Anne O'Donnell-Luria, Louise Wilkins-Haug · 1985 to 2026
$12.0MThe Child Heath Research CenterK12HD052896 · NICHD · BOSTON CHILDREN'S HOSPITAL · PI Wendy K Chung · 2007 to 2026
$7.9MSingle-cell epigenomic and cellular plasticityDP2HL151353 · NHLBI · HARVARD UNIVERSITY · PI BUENROSTRO, JASON DANIEL · 2019 to 2019
$2.5MMechanisms of stem cell aging that contribute to clonal outgrowth in head and neck tissuesF32AG071208 · NIA · HARVARD UNIVERSITY · PI KLETZIEN, HEIDI · 2021 to 2023
$205kNHGRI NIH HHS UM1 HG011986NHLBI NIH HHS DP2 HL151353NHLBI NIH HHS P01 HL131477NIA NIH HHS F32 AG071208NICHD NIH HHS K12 HD052896NIGMS NIH HHS T32 GM007748
Abstract
Cis-regulatory elements (CREs) control gene expression and are dynamic in their structure and function, reflecting changes in the composition of diverse effector proteins over time
Indexed as
Regulatory Elements, TranscriptionalRegulatory Sequences, Nucleic AcidAgingAnimalsCell DifferentiationChromatinDeep LearningDNA-Binding ProteinsFemaleGene Expression RegulationHematopoiesisHematopoietic Stem CellsHumansMaleMiceNucleosomesChromatinDNA-Binding ProteinsNucleosomesTranscription Factors
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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.