ArticleBioinformatics (Oxford, England)2016
Spectral identification of topological 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 42 papers.
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Who cites it
42 citing papers in PubMed.
- 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
- HiCInterpolate: 4D Spatiotemporal Interpolation of Hi-C Data for Genome Architecture Analysis.bioRxiv : the preprint server for biology · 2026Article
- EmbedTAD Using Graph Embedding and Unsupervised Learning to Identify TADs from High-Resolution Hi-C Data.Communications biology · 2025Article
- 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
- Genome structural dynamics: insights from Gaussian network analysis of Hi-C data.Briefings in functional genomics · 2024Article
- A comprehensive benchmarking with interpretation and operational guidance for the hierarchy of topologically associating domains.Nature communications · 2024Article
- Identifying TAD-like domains on single-cell Hi-C data by graph embedding and changepoint detection.Bioinformatics (Oxford, England) · 2024Article
- The shape of chromatin: insights from computational recognition of geometric patterns in Hi-C data.Briefings in bioinformatics · 2023Review
- Deciphering multi-way interactions in the human genome.Nature communications · 2022Article
- Rearrangement of T Cell genome architecture regulates GVHD.iScience · 2022Article
- Hodge theory-based biomolecular data analysis.Scientific reports · 2022Article
- A comparison of topologically associating domain callers over mammals at high resolution.BMC bioinformatics · 2022Article
- TADreg: a versatile regression framework for TAD identification, differential analysis and rearranged 3D genome prediction.BMC bioinformatics · 2022Article
- CASPIAN: A method to identify chromatin topological associated domains based on spatial density cluster.Computational and structural biotechnology journal · 2022Article
- Article
- 4DNvestigator: time series genomic data analysis toolbox.Nucleus (Austin, Tex.) · 2021Article
- SBTD: A Novel Method for Detecting Topological Associated Domains from Hi-C Data.Interdisciplinary sciences, computational life sciences · 2021Article
- SpecHap: a diploid phasing algorithm based on spectral graph theory.Nucleic acids research · 2021Article
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3 authors.
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Abstract
motivationTopological domains have been proposed as the backbone of interphase chromosome structure. They are regions of high local contact frequency separated by sharp boundaries. Genes within a domain often have correlated transcription. In this paper, we present a computational efficient spectral algorithm to identify topological domains from chromosome conformation data (Hi-C data). We consider the genome as a weighted graph with vertices defined by loci on a chromosome and the edge weights given by interaction frequency between two loci. Laplacian-based graph segmentation is then applied iteratively to obtain the domains at the given compactness level. Comparison with algorithms in the literature shows the advantage of the proposed strategy.
resultsAn efficient algorithm is presented to identify topological domains from the Hi-C matrix. AVAILABILITY AND IMPLEMENTATION: The Matlab source code and illustrative examples are available at http://bionetworks.ccmb.med.umich.edu/ CONTACT: : indikar@med.umich.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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