ArticleBioinformatics (Oxford, England)2021
BART3D: inferring transcriptional regulators associated with differential chromatin interactions from Hi-C data.
Article in Bioinformatics (Oxford, England), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- BARTsc identifies key transcriptional regulators from single-cell omics data.bioRxiv : the preprint server for biology · 2026Article
- Differential analysis of image-based chromatin tracing data with Dory.bioRxiv : the preprint server for biology · 2026Article
- Heritable changes in chromatin contacts associated with transgenerational susceptibility to diet-induced insulin dysregulation and obesity.Nature communications · 2026Article
- BIT: Bayesian Identification of Transcriptional regulators from epigenomics-based query region sets.Nature communications · 2025Article
- A comprehensive review and benchmark of differential analysis tools for Hi-C data.Briefings in bioinformatics · 2025Review
- Genomic clustering tendency of transcription factors reflects phase-separated transcriptional condensates at super-enhancers.Nucleic acids research · 2025Article
- Association Between Activated Loci of HML-2 Primate-Specific Endogenous Retrovirus and Newly Formed Chromatin Contacts in Human Primordial Germ Cell-like Cells.International journal of molecular sciences · 2024Article
- Fob1-dependent condensin recruitment and loop extrusion on yeast chromosome III.PLoS genetics · 2023Article
- Mini-review: Gene regulatory network benefits from three-dimensional chromatin conformation and structural biology.Computational and structural biotechnology journal · 2023Review
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Authors and funding
3 authors.
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Abstract
summaryIdentification of functional transcriptional regulators (TRs) associated with chromatin interactions is an important problem in studies of 3-dimensional genome organization and gene regulation. Direct inference of TR binding has been limited by the resolution of Hi-C data. Here, we present BART3D, a computational method for inferring TRs associated with genome-wide differential chromatin interactions by comparing Hi-C maps from two states, leveraging public ChIP-seq data for human and mouse. We demonstrate that BART3D can detect relevant TRs from dynamic Hi-C profiles with TR perturbation or cell differentiation. BART3D can be a useful tool in 3D genome data analysis and functional genomics research. AVAILABILITY AND IMPLEMENTATION: BART3D is implemented in Python and the source code is available at https://github.com/zanglab/bart3d. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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