ArticleAlgorithms for molecular biology : AMB2014
Identification of alternative topological domains in chromatin.
Article in Algorithms for molecular biology : AMB, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 136 papers.
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Who cites it
136 citing papers in PubMed.
- Integrating heterogeneity into topologically associating domain boundary prediction in large genomic context in human.NAR genomics and bioinformatics · 2026Article
- TADShop: systematic benchmarking and identification of topologically associating domains.Nature methods · 2026Article
- Formation of topologically associated chromatin domains using quantum annealing.Scientific reports · 2026Article
- The pangenome ofiScience · 2026Article
- A comparative analysis of topological domain callers over RNA-associated interactome.BMC bioinformatics · 2026Article
- Hierarchical Chromatin Rewiring Orchestrates Early Transcriptional Regulation in Mouse Cerebral Cortex Following Focal Ischemia.bioRxiv : the preprint server for biology · 2026Article
- A wavelet-based approach generates quantitative, scale-free and hierarchical descriptions of 3D genome structures and new biological insights.PLoS computational biology · 2026Article
- Analysis of chromatin structure reveals the connection between sQTLs and the splicing of distant genes.Scientific reports · 2025Article
- EmbedTAD Using Graph Embedding and Unsupervised Learning to Identify TADs from High-Resolution Hi-C Data.Communications biology · 2025Article
- Joint analysis of sQTL and Hi-C reveals spatial proximity between sQTLs and target genes in cancer tissues.Scientific reports · 2025Article
- RobusTAD: reference panel based annotation of nested topologically associating domains.Genome biology · 2025Article
- Review
- Machine and Deep Learning Methods for Predicting 3D Genome Organization.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Genome structural dynamics: insights from Gaussian network analysis of Hi-C data.Briefings in functional genomics · 2024Article
- DiffGR: Detecting Differentially Interacting Genomic Regions from Hi-C Contact Maps.Genomics, proteomics & bioinformatics · 2024Article
- Identifying topologically associating domains using differential kernels.PLoS computational biology · 2024Article
- Nucleoporin Elys attaches peripheral chromatin to the nuclear pores in interphase nuclei.Communications biology · 2024Article
- Enhancing Hi-C contact matrices for loop detection with Capricorn: a multiview diffusion model.Bioinformatics (Oxford, England) · 2024Article
- [An identification method of chromatin topological associated domains based on spatial density clustering].Sheng wu yi xue gong cheng xue za zhi = Journal of biomedical engineering = Shengwu yixue gongchengxue zazhi · 2024Article
- A comprehensive benchmarking with interpretation and operational guidance for the hierarchy of topologically associating domains.Nature communications · 2024Article
76 more citing papers are in PubMed but not listed here.
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4 authors.
Funding
Abstract
Chromosome conformation capture experiments have led to the discovery of dense, contiguous, megabase-sized topological domains that are similar across cell types and conserved across species. These domains are strongly correlated with a number of chromatin markers and have since been included in a number of analyses. However, functionally-relevant domains may exist at multiple length scales. We introduce a new and efficient algorithm that is able to capture persistent domains across various resolutions by adjusting a single scale parameter. The ensemble of domains we identify allows us to quantify the degree to which the domain structure is hierarchical as opposed to overlapping, and our analysis reveals a pronounced hierarchical structure in which larger stable domains tend to completely contain smaller domains. The identified novel domains are substantially different from domains reported previously and are highly enriched for insulating factor CTCF binding and histone marks at the boundaries.
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