ArticleGenome biology2015
Predicting chromatin organization using histone marks.
Article in Genome biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 66 papers.
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Who cites it
66 citing papers in PubMed.
- Origins and consequences of oncogenic 3D chromatin remodelling.Nature reviews. Cancer · 2026Review
- Integrating heterogeneity into topologically associating domain boundary prediction in large genomic context in human.NAR genomics and bioinformatics · 2026Article
- Systematic evaluation of the heterogeneity of topologically associating domain boundaries in a large genomic context in humans.NAR genomics and bioinformatics · 2026Article
- Machine and Deep Learning Methods for Predicting 3D Genome Organization.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Article
- Article
- DeepPHiC: predicting promoter-centered chromatin interactions using a novel deep learning approach.Bioinformatics (Oxford, England) · 2023Article
- Integrative chromatin domain annotation through graph embedding of Hi-C data.Bioinformatics (Oxford, England) · 2023Article
- Accurate prediction of functional states of cis-regulatory modules reveals common epigenetic rules in humans and mice.BMC biology · 2022Article
- Regulation associated modules reflect 3D genome modularity associated with chromatin activity.Nature communications · 2022Article
- Learning representations of chromatin contacts using a recurrent neural network identifies genomic drivers of conformation.Nature communications · 2022Article
- Review
- Comparative 3D genome architecture in vertebrates.BMC biology · 2022Article
- ProbC: joint modeling of epigenome and transcriptome effects in 3D genome.BMC genomics · 2022Article
- HiC1Dmetrics: framework to extract various one-dimensional features from chromosome structure data.Briefings in bioinformatics · 2022Article
- Review
- Computational methods for the prediction of chromatin interaction and organization using sequence and epigenomic profiles.Briefings in bioinformatics · 2021Article
- Epigenomic landscape and 3D genome structure in pediatric high-grade glioma.Science advances · 2021Article
- The Nucleome Data Bank: web-based resources to simulate and analyze the three-dimensional genome.Nucleic acids research · 2021Article
- PredTAD: A machine learning framework that models 3D chromatin organization alterations leading to oncogene dysregulation in breast cancer cell lines.Computational and structural biotechnology journal · 2021Article
6 more citing papers are in PubMed but not listed here.
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4 authors.
Funding
Abstract
Genome-wide mapping of three dimensional chromatin organization is an important yet technically challenging task. To aid experimental effort and to understand the determinants of long-range chromatin interactions, we have developed a computational model integrating Hi-C and histone mark ChIP-seq data to predict two important features of chromatin organization: chromatin interaction hubs and topologically associated domain (TAD) boundaries. Our model accurately and robustly predicts these features across datasets and cell types. Cell-type specific histone mark information is required for prediction of chromatin interaction hubs but not for TAD boundaries. Our predictions provide a useful guide for the exploration of chromatin organization.
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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.