ArticleNature communications2022
dcHiC detects differential compartments across multiple Hi-C datasets.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 papers.
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Who cites it
63 citing papers in PubMed, 77 citations in OpenAlex.
- A cross-species single-cell kidney epigenome atlas reveals epithelial-dominant aging-like states in disease.Nature aging · 2026Article
- hicream: A flexible framework to identify significantly different regions in Hi-C data.Bioinformatics (Oxford, England) · 2026Article
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- Neuronal activity-driven 3D chromatin dynamics in cortical pyramidal neurons depend on SATB2.Nucleic acids research · 2026Article
- Pig Matrix: a matched multiomics 3D regulatory genomics database for evolutionary and comparative analyses in pigs.Molecular biology and evolution · 2026Article
- A 3D genome atlas of human tonsil and the role of loop extrusion in B cell somatic hypermutation.Science (New York, N.Y.) · 2026Article
- Dose-dependent sensitivity of human three-dimensional chromatin to a heart disease-linked transcription factor.Science (New York, N.Y.) · 2026Article
- Multi-Omics Insights Into the Mechanisms of Early Muscle Fiber Difference and Transformation Between Lean-Type and Chinese Indigenous Pigs.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- ATF4 and CHOP coordinate endoplasmic reticulum stress-responsive gene programs through enhancer activation and chromatin looping.Nucleic acids research · 2026Article
- Inhibition of TGM2 enhances cisplatin sensitivity in MSH2-deficient bladder cancer.Cell death discovery · 2026Article
- Jointly-hic: joint decomposition of contact frequency maps captures salient features of genome architecture across tissues and development.Genome biology · 2026Article
- Kilobase-scale compartments enabled by CRUSH reveal regulatory programs across cell types, single-cells, and ancient mammoths.bioRxiv : the preprint server for biology · 2026Article
- HaploC-tools reveal haplotype-specific chromosome conformation and chromatin states.Nature communications · 2026Article
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- Chromatin dynamics identifies 78 genes at loci associated with elevated intraocular pressure and primary open-angle glaucoma.bioRxiv : the preprint server for biology · 2026Article
- A Multimodal Single-Cell Epigenomic and 3D Genome Atlas of the Human Basal Ganglia.bioRxiv : the preprint server for biology · 2026Article
- Repeat expansions inbioRxiv : the preprint server for biology · 2026Article
- A Single-Cell and Spatial 3D Multi-omic Atlas of Developing Human Basal Ganglia and Inhibitory Neurons.bioRxiv : the preprint server for biology · 2026Article
3 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
The compartmental organization of mammalian genomes and its changes play important roles in distinct biological processes. Here, we introduce dcHiC, which utilizes a multivariate distance measure to identify significant changes in compartmentalization among multiple contact maps. Evaluating dcHiC on four collections of bulk and single-cell contact maps from in vitro mouse neural differentiation (n = 3), mouse hematopoiesis (n = 10), human LCLs (n = 20) and post-natal mouse brain development (n = 3 stages), we show its effectiveness and sensitivity in detecting biologically relevant changes, including those orthogonally validated. dcHiC reported regions with dynamically regulated genes associated with cell identity, along with correlated changes in chromatin states, subcompartments, replication timing and lamin association. With its efficient implementation, dcHiC enables high-resolution compartment analysis as well as standalone browser visualization, differential interaction identification and time-series clustering. dcHiC is an essential addition to the Hi-C analysis toolbox for the ever-growing number of bulk and single-cell contact maps. Available at: https://github.com/ay-lab/dcHiC .
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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.