ArticlePLoS computational biology2020
Capturing cell type-specific chromatin compartment patterns by applying topic modeling to single-cell Hi-C data.
Article in PLoS computational biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 74 papers.
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Who cites it
74 citing papers in PubMed.
- ssJSD: A Fusion of Sparsity and Spatial Information for HiC Single-Cell Clustering.bioRxiv : the preprint server for biology · 2026Article
- Hi-Cformer enables multiscale chromatin contact map modeling for single-cell Hi-C data analysis.Science advances · 2026Article
- Robust and generalizable CNV detection for single-cell sequencing assays.Nucleic acids research · 2026Article
- MINTsC learns multi-way chromatin interactions from single cell high throughput chromatin conformation data.Nature communications · 2026Article
- Systematic clustering alignment and feature characterization for single-cell omics using ACE-OF-Clust.bioRxiv : the preprint server for biology · 2026Article
- Simultaneous modeling of chromatin conformation changes from multiple single-cell interaction maps with ChromMovie.Genome research · 2026Article
- Highly efficient chromatin conformation capture with post-enrichment in single cells by HiChew.Genome biology · 2026Article
- szKendall: spatial-structural-zero-aware dissimilarity measures for subtype discovery using single cell Hi-C data.Nature communications · 2026Article
- MINTsC learns multi-way chromatin interactions from single cell high throughput chromatin conformation data.bioRxiv : the preprint server for biology · 2026Article
- scDIAGRAM: detecting chromatin compartments from individual single-cell Hi-C matrix without imputation or reference features.Briefings in bioinformatics · 2026Article
- Harmonizing single-cell 3D genome data with STARK and scNucleome.Genome biology · 2026Article
- A wavelet-based approach generates quantitative, scale-free and hierarchical descriptions of 3D genome structures and new biological insights.PLoS computational biology · 2026Article
- Generating three-dimensional genome structures with a variational quantum algorithm.Briefings in bioinformatics · 2025Article
- Comprehensive noise reduction in single-cell data with the RECODE platform.Cell reports methods · 2025Article
- A comprehensive benchmark of single-cell Hi-C embedding tools.Nature communications · 2025Article
- Navigating the 3D genome at single-cell resolution: techniques, computation, and mechanistic landscapes.Briefings in bioinformatics · 2025Review
- scHiCcompare: An R Package for Differential Analysis of Single-cell Hi-C Data.Journal of molecular biology · 2025Article
- ChromMovie: A Molecular Dynamics Approach for Simultaneous Modeling of Chromatin Conformation Changes from Multiple Single-Cell Hi-C Maps.bioRxiv : the preprint server for biology · 2025Article
- DeepExDC interprets genomic compartmentalization changes in single-cell Hi-C data.Briefings in bioinformatics · 2025Article
- Tensor-FLAMINGO unravels the complexity of single-cell spatial architectures of genomes at high-resolution.Nature communications · 2025Article
14 more citing papers are in PubMed but not listed here.
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12 authors.
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Abstract
Single-cell Hi-C (scHi-C) interrogates genome-wide chromatin interaction in individual cells, allowing us to gain insights into 3D genome organization. However, the extremely sparse nature of scHi-C data poses a significant barrier to analysis, limiting our ability to tease out hidden biological information. In this work, we approach this problem by applying topic modeling to scHi-C data. Topic modeling is well-suited for discovering latent topics in a collection of discrete data. For our analysis, we generate nine different single-cell combinatorial indexed Hi-C (sci-Hi-C) libraries from five human cell lines (GM12878, H1Esc, HFF, IMR90, and HAP1), consisting over 19,000 cells. We demonstrate that topic modeling is able to successfully capture cell type differences from sci-Hi-C data in the form of "chromatin topics." We further show enrichment of particular compartment structures associated with locus pairs in these topics.
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