ArticleNature methods2019
cisTopic: cis-regulatory topic modeling on single-cell ATAC-seq data.
Article in Nature methods, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 270 papers, 2 of them syntheses that pooled it.
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Who cites it
270 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Genetic variation in cis-regulatory domains suggests cell type-specific regulatory mechanisms in immunity.Communications biology · 2023Pooled it
- Guidelines for bioinformatics of single-cell sequencing data analysis in Alzheimer's disease: review, recommendation, implementation and application.Molecular neurodegeneration · 2022Pooled it
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- Decoding epithelial-mesenchymal transitions with multi-omics.Nature reviews. Genetics · 2026Review
- Atlas of cell types and regulatory elements underlying human facial diversity.Nature genetics · 2026Article
- Flow Orchestrated Regulatory Genomics Engine (FORGE): A Configurable Nextflow Pipeline for End-to-End snMultiome Analysis.bioRxiv : the preprint server for biology · 2026Article
- Single-cell multimodal profiling of pan-cancer cell lines uncovers gene regulatory principles underlying intrinsic cell states and environmental features.Nature communications · 2026Article
- High-resolution reconstruction of cell-type-specific transcriptional regulatory processes from bulk sequencing samples.Nature biotechnology · 2026Article
- Single-cell multi-omic atlas and morphogen screening informs midbrain and hindbrain organoid engineering.Nature neuroscience · 2026Article
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- Inferring cell-specific gene regulatory networks based on causal graph embedding.Cell reports methods · 2026Article
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- SpaDC enables sequence-based integrative analysis and regulatory inference of spatial chromatin accessibility data.Communications biology · 2026Article
- Single-cell multimodal profiling of pan-cancer cell lines uncovers gene regulatory principles underlying intrinsic cell states and environmental features.bioRxiv : the preprint server for biology · 2026Article
- Multimodal atlas of human atherosclerosis links granular vascular cell states to coronary artery disease risk.medRxiv : the preprint server for health sciences · 2026Article
- Lifestyle intervention is associated with attenuation of ER stress/inflammation and enhancement of naive immune cell identity in older adults with metabolic disease.bioRxiv : the preprint server for biology · 2026Article
- Hybrid Encoding and Adaptive Guidance for Enhanced Single-Cell Multi-omics Clustering.Interdisciplinary sciences, computational life sciences · 2026Article
- Systematic clustering alignment and feature characterization for single-cell omics using ACE-OF-Clust.bioRxiv : the preprint server for biology · 2026Article
- CRAK-Velo: chromatin accessibility kinetics integration improves RNA velocity estimation.Genome biology · 2026Article
- Cross-modality representation and multi-sample integration of spatially resolved omics data.Briefings in bioinformatics · 2026Article
210 more citing papers are in PubMed but not listed here.
Corrections and comments
- Commented on byStein Aerts.2019
Authors and funding
9 authors.
Funding
Abstract
We present cisTopic, a probabilistic framework used to simultaneously discover coaccessible enhancers and stable cell states from sparse single-cell epigenomics data ( http://github.com/aertslab/cistopic ). Using a compendium of single-cell ATAC-seq datasets from differentiating hematopoietic cells, brain and transcription factor perturbations, we demonstrate that topic modeling can be exploited for robust identification of cell types, enhancers and relevant transcription factors. cisTopic provides insight into the mechanisms underlying regulatory heterogeneity in cell populations.
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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.