ArticleNucleic acids research2017
A critical assessment of topologically associating domain prediction tools.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 77 papers.
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Who cites it
77 citing papers in PubMed.
- Systematic evaluation of the heterogeneity of topologically associating domain boundaries in a large genomic context in humans.NAR genomics and bioinformatics · 2026Article
- A comparative analysis of topological domain callers over RNA-associated interactome.BMC bioinformatics · 2026Article
- A wavelet-based approach generates quantitative, scale-free and hierarchical descriptions of 3D genome structures and new biological insights.PLoS computational biology · 2026Article
- Deciphering chromatin domain, domain community and chromunity for 3D genome maps with Mactop.Communications biology · 2025Article
- RobusTAD: reference panel based annotation of nested topologically associating domains.Genome biology · 2025Article
- A comprehensive review and benchmark of differential analysis tools for Hi-C data.Briefings in bioinformatics · 2025Review
- HTAD: a human-in-the-loop framework for supervised chromatin domain detection.Genome biology · 2024Article
- Disorganized chromatin hierarchy and stem cell aging in a male patient of atypical laminopathy-based progeria mandibuloacral dysplasia type A.Nature communications · 2024Article
- Identifying topologically associating domains using differential kernels.PLoS computational biology · 2024Article
- Enhancing Hi-C contact matrices for loop detection with Capricorn: a multiview diffusion model.Bioinformatics (Oxford, England) · 2024Article
- Identifying TAD-like domains on single-cell Hi-C data by graph embedding and changepoint detection.Bioinformatics (Oxford, England) · 2024Article
- Formamide denaturation of double-stranded DNA for fluorescence in situ hybridization (FISH) distorts nanoscale chromatin structure.PloS one · 2024Article
- 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
- The 3D chromatin landscape of rhabdomyosarcoma.NAR cancer · 2023Article
- Pattern recognition of topologically associating domains using deep learning.BMC bioinformatics · 2022Article
- Reference panel guided topological structure annotation of Hi-C data.Nature communications · 2022Article
- Mode and Tempo of 3D Genome Evolution in Drosophila.Molecular biology and evolution · 2022Article
- KSHV Topologically Associating Domains in Latent and Reactivated Viral Chromatin.Journal of virology · 2022Article
- TADfit is a multivariate linear regression model for profiling hierarchical chromatin domains on replicate Hi-C data.Communications biology · 2022Article
17 more citing papers are in PubMed but not listed here.
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2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Topologically associating domains (TADs) have been proposed to be the basic unit of chromosome folding and have been shown to play key roles in genome organization and gene regulation. Several different tools are available for TAD prediction, but their properties have never been thoroughly assessed. In this manuscript, we compare the output of seven different TAD prediction tools on two published Hi-C data sets. TAD predictions varied greatly between tools in number, size distribution and other biological properties. Assessed against a manual annotation of TADs, individual TAD boundary predictions were found to be quite reliable, but their assembly into complete TAD structures was much less so. In addition, many tools were sensitive to sequencing depth and resolution of the interaction frequency matrix. This manuscript provides users and designers of TAD prediction tools with information that will help guide the choice of tools and the interpretation of their predictions.
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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.