ArticleFrontiers in genetics2020
TADCompare: An R Package for Differential and Temporal Analysis of Topologically Associated Domains.
Article in Frontiers in genetics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
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50 citing papers in PubMed.
- Genome reorganisation and expansion shape 3D genome architecture and define a distinct regulatory landscape in coleoid cephalopods.Nature communications · 2026Article
- Identification of differential topologically associating domains from low sequencing depth and pseudobulk chromatin contact maps.Genome research · 2026Article
- 3D chromatin organisation contributes to the regulatory logic in differentiating lymphatic endothelium.EMBO reports · 2026Article
- hicream: A flexible framework to identify significantly different regions in Hi-C data.Bioinformatics (Oxford, England) · 2026Article
- MECP2 mutations disrupt pluripotent stem cell fate through remodeling of the three-dimensional genome.Cell death & disease · 2026Article
- esBAF and INO80C fine-tune subcompartments and differentially regulate enhancer-promoter interactions.Genetics · 2026Article
- Topologically associating domains define the 3D genome architecture of mouse totipotent-like stem cells.The Journal of biological chemistry · 2026Article
- Image-based epigenetic profiling with deep learning and high-speed super-resolution microscopy.Epigenetics & chromatin · 2026Article
- SMCHD1 loss re-wires MYOD1 enhancer nexuses and chromatin accessibility landscapes in muscle cells.bioRxiv : the preprint server for biology · 2026Article
- Coordinated gene expression within sustained STAT3-associated chromatin conformations contributes to hepatocellular carcinoma progression.Cancer communications (London, England) · 2025Article
- The Association Between DNA Methylation and Three-Dimensional Genome During Whole Genome Doubling inPlants (Basel, Switzerland) · 2025Article
- esBAF and INO80C fine-tune subcompartments and differentially regulate enhancer-promoter interactions.bioRxiv : the preprint server for biology · 2025Article
- Mechanism of parent-of-origin effects revealed by multi-omic data in euro-chinese hybrid pigs.Nature communications · 2025Article
- SMCHD1 maintains heterochromatin, genome compartments and epigenome landscape in human myoblasts.Nature communications · 2025Article
- Article
- Examining the dynamics of three-dimensional genome organization with multitask matrix factorization.Genome research · 2025Article
- Rewiring of SINE-MIR enhancer topology and Esrrb modulation in expanded and naive pluripotency.Genome biology · 2025Article
- Hi-C profiling in tissues reveals 3D chromatin-regulated breast tumor heterogeneity informing a looping-mediated therapeutic avenue.Cell reports · 2025Article
- Tensor-FLAMINGO unravels the complexity of single-cell spatial architectures of genomes at high-resolution.Nature communications · 2025Article
- Comparing chromatin contact maps at scale: methods and insights.Nature methods · 2025Article
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2 authors.
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Abstract
Recent research using chromatin conformation capture technologies, such as Hi-C, has demonstrated the importance of topologically associated domains (TADs) and smaller chromatin loops, collectively referred hereafter as "interacting domains." Many such domains change during development or disease, and exhibit cell- and condition-specific differences. Quantification of the dynamic behavior of interacting domains will help to better understand genome regulation. Methods for comparing interacting domains between cells and conditions are highly limited. We developed TADCompare, a method for differential analysis of boundaries of interacting domains between two or more Hi-C datasets. TADCompare is based on a spectral clustering-derived measure called the eigenvector gap, which enables a loci-by-loci comparison of boundary differences. Using this measure, we introduce methods for identifying differential and consensus boundaries of interacting domains and tracking boundary changes over time. We further propose a novel framework for the systematic classification of boundary changes. Colocalization- and gene enrichment analysis of different types of boundary changes demonstrated distinct biological functionality associated with them. TADCompare is available on https://github.com/dozmorovlab/TADCompare and Bioconductor (submitted).
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