ArticleNature communications2021
Chromatin-accessibility estimation from single-cell ATAC-seq data with scOpen.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 73 papers.
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Who cites it
73 citing papers in PubMed.
- Decoding epithelial-mesenchymal transitions with multi-omics.Nature reviews. Genetics · 2026Review
- Scalable joint non-negative matrix factorization for paired single cell gene expression and chromatin accessibility data.NAR genomics and bioinformatics · 2026Article
- Deep Learning for Deciphering the Plant Cis-Regulatory Code.Plants (Basel, Switzerland) · 2026Review
- Article
- Predicting gene-specific regulation with transcriptomic and epigenetic single-cell data.Bioinformatics (Oxford, England) · 2026Article
- BART-spatial unravels biologically significant transcriptional regulators from spatial omics data.bioRxiv : the preprint server for biology · 2026Article
- PAIR: Reconstructing Single-Cell Open-Chromatin Landscapes for Transcription Factor Regulome Mapping.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Shared multicellular injury programs of acute and chronic kidney disease enable mechanistic patient stratification.medRxiv : the preprint server for health sciences · 2026Article
- iAODE for benchmarking and continuum modeling of single-cell chromatin accessibility.Communications biology · 2026Article
- A hitchhiker's guide to single-cell epigenomics: Methods and applications for cancer research.International journal of cancer · 2026Review
- Multimodal-based analysis of single-cell ATAC-seq data enables highly accurate delineation of clinically relevant tumor cell subpopulations.Genome medicine · 2026Article
- Human-scATAC-Corpus: a comprehensive database of scATAC-seq data.Nucleic acids research · 2026Article
- Recent advances in methodologies of epigenomics.Epigenomics · 2026Review
- Nanoparticles in the Treatment of Renal Fibrosis.International journal of nanomedicine · 2026Review
- Live monitoring uncovers divergent epigenetic remodeling during osteogenic and adipogenic differentiation of mesenchymal stem cells.Frontiers in cell and developmental biology · 2026Article
- Computational Analyses and Challenges of Single-cell ATAC-seq.Genomics, proteomics & bioinformatics · 2025Review
- A computational framework to dissect imputation strategies for single-cell histone modification data.NAR genomics and bioinformatics · 2025Article
- EpiAgent: foundation model for single-cell epigenomics.Nature methods · 2025Article
- Video - Visual Integration of Drosophila Enhancer Organization: A tool for integrating and visualizing chromatin accessibility, in vivo transcription factor binding and motif occurrence in tissue-specific differentially expressed genes.bioRxiv : the preprint server for biology · 2025Article
- A hierarchical, count-based model highlights challenges in scATAC-seq data analysis and points to opportunities to extract finer-resolution information.Genome biology · 2025Article
13 more citing papers are in PubMed but not listed here.
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A major drawback of single-cell ATAC-seq (scATAC-seq) is its sparsity, i.e., open chromatin regions with no reads due to loss of DNA material during the scATAC-seq protocol. Here, we propose scOpen, a computational method based on regularized non-negative matrix factorization for imputing and quantifying the open chromatin status of regulatory regions from sparse scATAC-seq experiments. We show that scOpen improves crucial downstream analysis steps of scATAC-seq data as clustering, visualization, cis-regulatory DNA interactions, and delineation of regulatory features. We demonstrate the power of scOpen to dissect regulatory changes in the development of fibrosis in the kidney. This identifies a role of Runx1 and target genes by promoting fibroblast to myofibroblast differentiation driving kidney fibrosis.
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