ArticleGenome biology2021
SuperTAD: robust detection of hierarchical topologically associated domains with optimized structural information.
Article in Genome biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Overcoming Artificial Structures in Resolution-Enhanced Hi-C Data by Signal Decomposition and Multi-Scale Attention.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- A wavelet-based approach generates quantitative, scale-free and hierarchical descriptions of 3D genome structures and new biological insights.PLoS computational biology · 2026Article
- stTrace: detecting spatial-temporal domains from spatial transcriptome to trace developmental path.Briefings in bioinformatics · 2025Article
- RobusTAD: reference panel based annotation of nested topologically associating domains.Genome biology · 2025Article
- deepTAD: an approach for identifying topologically associated domains based on convolutional neural network and transformer model.Briefings in bioinformatics · 2025Article
- Topology entropy: Enhancing graph partitioning for TAD identification and single-cell clustering.Computational and structural biotechnology journal · 2025Article
- 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
- Three-Dimensional Gene Regulation Network in Glioblastoma Ferroptosis.International journal of molecular sciences · 2023Article
- The shape of chromatin: insights from computational recognition of geometric patterns in Hi-C data.Briefings in bioinformatics · 2023Review
- Mapping the semi-nested community structure of 3D chromosome contact networks.PLoS computational biology · 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
- Incorporating cell hierarchy to decipher the functional diversity of single cells.Nucleic acids research · 2023Article
- Detecting TAD-like domains from RNA-associated interactions.Nucleic acids research · 2022Article
- TADfit is a multivariate linear regression model for profiling hierarchical chromatin domains on replicate Hi-C data.Communications biology · 2022Article
- SuperTAD: robust detection of hierarchical topologically associated domains with optimized structural information.Genome biology · 2021Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Topologically associating domains (TADs) are the organizational units of chromosome structures. TADs can contain TADs, thus forming a hierarchy. TAD hierarchies can be inferred from Hi-C data through coding trees. However, the current method for computing coding trees is not optimal. In this paper, we propose optimal algorithms for this computation. In comparison with seven state-of-art methods using two public datasets, from GM12878 and IMR90 cells, SuperTAD shows a significant enrichment of structural proteins around detected boundaries and histone modifications within TADs and displays a high consistency between various resolutions of identical Hi-C matrices.
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