ArticleNucleic acids research2019
MSTD: an efficient method for detecting multi-scale topological domains from symmetric and asymmetric 3D genomic maps.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- TADShop: systematic benchmarking and identification of topologically associating domains.Nature methods · 2026Article
- BandHiC: a memory-efficient and user-friendly Python package for organizing and analyzing Hi-C matrices down to sub-kilobase resolution.BMC genomics · 2026Article
- A comparative analysis of topological domain callers over RNA-associated interactome.BMC bioinformatics · 2026Article
- HyperDeepTAD: a topologically associated domains detection method based on multiway chromatin interaction data and deep learning.BMC genomics · 2026Article
- Deciphering chromatin domain, domain community and chromunity for 3D genome maps with Mactop.Communications biology · 2025Article
- BINDER achieves accurate identification of hierarchical TADs by comprehensively characterizing consensus TAD boundaries.Genome research · 2025Article
- deepTAD: an approach for identifying topologically associated domains based on convolutional neural network and transformer model.Briefings in bioinformatics · 2025Article
- Uncovering topologically associating domains from three-dimensional genome maps with TADGATE.Nucleic acids research · 2025Article
- Topology entropy: Enhancing graph partitioning for TAD identification and single-cell clustering.Computational and structural biotechnology journal · 2025Article
- The shape of chromatin: insights from computational recognition of geometric patterns in Hi-C data.Briefings in bioinformatics · 2023Review
- scHi-CSim: a flexible simulator that generates high-fidelity single-cell Hi-C data for benchmarking.Journal of molecular cell biology · 2023Article
- Deciphering Hierarchical Chromatin Domains and Preference of Genomic Position Forming Boundaries in Single Mouse Embryonic Stem Cells.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2023Article
- A comparison of topologically associating domain callers over mammals at high resolution.BMC bioinformatics · 2022Article
- Mapping nucleosome and chromatin architectures: A survey of computational methods.Computational and structural biotechnology journal · 2022Review
- Joint reconstruction of cis-regulatory interaction networks across multiple tissues using single-cell chromatin accessibility data.Briefings in bioinformatics · 2021Article
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3 authors.
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Abstract
The chromosome conformation capture (3C) technique and its variants have been employed to reveal the existence of a hierarchy of structures in three-dimensional (3D) chromosomal architecture, including compartments, topologically associating domains (TADs), sub-TADs and chromatin loops. However, existing methods for domain detection were only designed based on symmetric Hi-C maps, ignoring long-range interaction structures between domains. To this end, we proposed a generic and efficient method to identify multi-scale topological domains (MSTD), including cis- and trans-interacting regions, from a variety of 3D genomic datasets. We first applied MSTD to detect promoter-anchored interaction domains (PADs) from promoter capture Hi-C datasets across 17 primary blood cell types. The boundaries of PADs are significantly enriched with one or the combination of multiple epigenetic factors. Moreover, PADs between functionally similar cell types are significantly conserved in terms of domain regions and expression states. Cell type-specific PADs involve in distinct cell type-specific activities and regulatory events by dynamic interactions within them. We also employed MSTD to define multi-scale domains from typical symmetric Hi-C datasets and illustrated its distinct superiority to the-state-of-art methods in terms of accuracy, flexibility and efficiency.
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