ArticleeLife2019
Identifying gene expression programs of cell-type identity and cellular activity with single-cell RNA-Seq.
Article in eLife, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 366 papers, 1 of them a synthesis that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
366 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- Donor-aware integrative single-cell analysis distinguishes consistent memory B-cell programmes from donor-sensitive state boundaries in untreated rheumatoid arthritis.Functional & integrative genomics · 2026Article
- Clonal lineage tracing and parallel multiomics profiling reveal transcriptional heterogeneity induced by ARID1A deficiency.Science advances · 2026Article
- PRISM-GEP: Viewing single-cell expression through the lens of topic modeling.Bioinformatics (Oxford, England) · 2026Article
- Computational approaches for multimodal lineage tracing.Nature reviews. Genetics · 2026Review
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- Unicellular and Multicellular Modes of Selection Impose Distinct Constraints on Cellular Phenotype Evolution.bioRxiv : the preprint server for biology · 2026Article
- Systematic CRISPRi perturbation of 1,408 autism risk genes maps multilevel transcriptional convergence in human cortical neurons.bioRxiv : the preprint server for biology · 2026Article
- Brain Architecture of Punishment Learning.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2026Article
- Scalable joint non-negative matrix factorization for paired single cell gene expression and chromatin accessibility data.NAR genomics and bioinformatics · 2026Article
- Epigenetic modulation of stromal cell states underpins pathological tissue niches in Crohn's disease.Nature immunology · 2026Article
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- KSTITCH links cellular morphology and gene expression in spatial transcriptomics.bioRxiv : the preprint server for biology · 2026Article
- The critical role of the endogenous immune compartment after CAR T cell therapy in recurrent GBM.Cell · 2026Article
- scENature communications · 2026Article
306 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
Abstract
Identifying gene expression programs underlying both cell-type identity and cellular activities (e.g. life-cycle processes, responses to environmental cues) is crucial for understanding the organization of cells and tissues. Although single-cell RNA-Seq (scRNA-Seq) can quantify transcripts in individual cells, each cell's expression profile may be a mixture of both types of programs, making them difficult to disentangle. Here, we benchmark and enhance the use of matrix factorization to solve this problem. We show with simulations that a method we call consensus non-negative matrix factorization (cNMF) accurately infers identity and activity programs, including their relative contributions in each cell. To illustrate the insights this approach enables, we apply it to published brain organoid and visual cortex scRNA-Seq datasets; cNMF refines cell types and identifies both expected (e.g. cell cycle and hypoxia) and novel activity programs, including programs that may underlie a neurosecretory phenotype and synaptogenesis.
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Registered trials
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.