ArticleBioinformatics (Oxford, England)2016
Identification of hierarchical chromatin domains.
Article in Bioinformatics (Oxford, England), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 92 papers.
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92 citing papers in PubMed, 179 citations in OpenAlex.
- Cross-cell-line conservation-resolved interactions reveal conservation-dependent relationships among CTCF loops.BMC genomics · 2026Article
- RepliSage: a stochastic graph-based framework for 3D chromatin modeling across the cell cycle.Nucleic acids research · 2026Article
- TADShop: systematic benchmarking and identification of topologically associating domains.Nature methods · 2026Article
- A comparative analysis of topological domain callers over RNA-associated interactome.BMC bioinformatics · 2026Article
- The hierarchical folding dynamics of topologically associating domains during early embryo development.BMC biology · 2025Article
- RobusTAD: reference panel based annotation of nested topologically associating domains.Genome biology · 2025Article
- BINDER achieves accurate identification of hierarchical TADs by comprehensively characterizing consensus TAD boundaries.Genome research · 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
- [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
- Article
- Identifying TAD-like domains on single-cell Hi-C data by graph embedding and changepoint detection.Bioinformatics (Oxford, England) · 2024Article
- Computational methods for analysing multiscale 3D genome organization.Nature reviews. Genetics · 2024Review
- The shape of chromatin: insights from computational recognition of geometric patterns in Hi-C data.Briefings in bioinformatics · 2023Review
- Revisiting Assessment of Computational Methods for Hi-C Data Analysis.International journal of molecular sciences · 2023Article
- DeDoc2 Identifies and Characterizes the Hierarchy and Dynamics of Chromatin TAD-Like Domains in the Single Cells.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2023Article
- The 3D genome and its impacts on human health and disease.Life medicine · 2023Review
- HPTAD: A computational method to identify topologically associating domains from HiChIP and PLAC-seq datasets.Computational and structural biotechnology journal · 2023Article
32 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
motivationThe three-dimensional structure of the genome is an important regulator of many cellular processes including differentiation and gene regulation. Recently, technologies such as Hi-C that combine proximity ligation with high-throughput sequencing have revealed domains of self-interacting chromatin, called topologically associating domains (TADs), in many organisms. Current methods for identifying TADs using Hi-C data assume that TADs are non-overlapping, despite evidence for a nested structure in which TADs and sub-TADs form a complex hierarchy.
resultsWe introduce a model for decomposition of contact frequencies into a hierarchy of nested TADs. This model is based on empirical distributions of contact frequencies within TADs, where positions that are far apart have a greater enrichment of contacts than positions that are close together. We find that the increase in contact enrichment with distance is stronger for the inner TAD than for the outer TAD in a TAD/sub-TAD pair. Using this model, we develop the TADtree algorithm for detecting hierarchies of nested TADs. TADtree compares favorably with previous methods, finding TADs with a greater enrichment of chromatin marks such as CTCF at their boundaries. AVAILABILITY AND IMPLEMENTATION: A python implementation of TADtree is available at http://compbio.cs.brown.edu/software/ CONTACT: braphael@cs.brown.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.