ArticleAlgorithms for molecular biology : AMB2019
Semi-nonparametric modeling of topological domain formation from epigenetic data.
Article in Algorithms for molecular biology : AMB, 2019. 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.
- Integrating heterogeneity into topologically associating domain boundary prediction in large genomic context in human.NAR genomics and bioinformatics · 2026Article
- Enhancing tumor T cell antigen prediction by integrating deep protein representations.BMC bioinformatics · 2026Article
- A comparative analysis of topological domain callers over RNA-associated interactome.BMC bioinformatics · 2026Article
- Analysis of chromatin structure reveals the connection between sQTLs and the splicing of distant genes.Scientific reports · 2025Article
- Analysis of long-range contacts across cell types outlines a core sequence determinant of 3D genome organization.NAR genomics and bioinformatics · 2025Article
- Joint analysis of sQTL and Hi-C reveals spatial proximity between sQTLs and target genes in cancer tissues.Scientific reports · 2025Article
- Machine and Deep Learning Methods for Predicting 3D Genome Organization.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Article
- Learning representations of chromatin contacts using a recurrent neural network identifies genomic drivers of conformation.Nature communications · 2022Article
- ProbC: joint modeling of epigenome and transcriptome effects in 3D genome.BMC genomics · 2022Article
- preciseTAD: a transfer learning framework for 3D domain boundary prediction at base-pair resolution.Bioinformatics (Oxford, England) · 2022Article
- Review
- Computational methods for the prediction of chromatin interaction and organization using sequence and epigenomic profiles.Briefings in bioinformatics · 2021Article
- Article
- A computational method to predict topologically associating domain boundaries combining histone Marks and sequence information.BMC genomics · 2019Article
- Deconvolution of Ensemble Chromatin Interaction Data Reveals the Latent Mixing Structures in Cell Subpopulations.Journal of computational biology : a journal of computational molecular cell biology · 2016Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
backgroundHi-C experiments capturing the 3D genome architecture have led to the discovery of topologically-associated domains (TADs) that form an important part of the 3D genome organization and appear to play a role in gene regulation and other functions. Several histone modifications have been independently associated with TAD formation, but their combinatorial effects on domain formation remain poorly understood at a global scale.
resultsWe propose a convex semi-nonparametric approach called
conclusionsOur approach,
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Registered trials
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