ArticleNature genetics2022
DeepLoop robustly maps chromatin interactions from sparse allele-resolved or single-cell Hi-C data at kilobase resolution.
Article in Nature genetics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers, 2 of them syntheses that pooled it.
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Who cites it
50 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Cross-platform Hi-C meta-analysis identifies functional insulators that actively block enhancer-promoter interactions.Nature communications · 2026Pooled it
- Extended genome-wide association study employing the African genome resources panel identifies novel susceptibility loci for Alzheimer's disease in individuals of African ancestry.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2024Pooled it
- Identification of Genome-Wide Chromatin Structural Aberration in Cancer by Hi-C Analysis.Methods in molecular biology (Clifton, N.J.) · 2027Article
- Identification of differential topologically associating domains from low sequencing depth and pseudobulk chromatin contact maps.Genome research · 2026Article
- Hi-Cformer enables multiscale chromatin contact map modeling for single-cell Hi-C data analysis.Science advances · 2026Article
- HiC2Self: Self-supervised denoising for bulk and single-cell Hi-C contact maps.Science advances · 2026Article
- Article
- Rapid reduction in global chromatin loop size after acute STAG2 reconstitution in human cancer cells.bioRxiv : the preprint server for biology · 2026Article
- Targeting Mettl8-Tcf1 axis promotes CD8+ TPEX differentiation and antitumor immunity.The Journal of experimental medicine · 2026Article
- Parallel analysis of replication timing, gene expression, and copy number with PARTAGE.Genome research · 2026Article
- NanoLoop: A Deep Learning Framework Leveraging Nanopore Sequencing for Chromatin Loop Prediction.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Genetic correlation analysis of Alzheimer's disease and stroke implicates PHLPP1 as a shared locus in individuals of African ancestry.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2026Article
- Enhanced Hi-C Capture Analysis reveals complex regulatory architecture at thebioRxiv : the preprint server for biology · 2026Article
- iceDP: identifying inter-chromatin engagement via density peaks clustering algorithm.Briefings in bioinformatics · 2026Article
- CNNKSCEC: a deep learning-based framework for chromatin loop prediction with multi-source feature integration.Frontiers in genetics · 2026Article
- Local genetic correlation analysis of Alzheimer's disease and stroke implicatesmedRxiv : the preprint server for health sciences · 2025Article
- Genomic signatures of subterranean lifestyle and ecological adaptation in Myospalax.BMC biology · 2025Article
- A comprehensive benchmark of single-cell Hi-C embedding tools.Nature communications · 2025Article
- Article
- PARTAGE: Parallel analysis of replication timing and gene expression.bioRxiv : the preprint server for biology · 2025Article
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Authors and funding
14 authors.
Funding
Abstract
Mapping chromatin loops from noisy Hi-C heatmaps remains a major challenge. Here we present DeepLoop, which performs rigorous bias correction followed by deep-learning-based signal enhancement for robust chromatin interaction mapping from low-depth Hi-C data. DeepLoop enables loop-resolution, single-cell Hi-C analysis. It also achieves a cross-platform convergence between different Hi-C protocols and micrococcal nuclease (micro-C). DeepLoop allowed us to map the genetic and epigenetic determinants of allele-specific chromatin interactions in the human genome. We nominate new loci with allele-specific interactions governed by imprinting or allelic DNA methylation. We also discovered that, in the inactivated X chromosome (X
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