ArticleNature methods2017
SCENIC: single-cell regulatory network inference and clustering.
Article in Nature methods, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4,048 papers.
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Who cites it
4,048 citing papers in PubMed.
- Integrated single-cell multi-omics characterization reveals lipid-associated macrophage-mediated immunosuppression in neoadjuvant immunotherapy of hepatocellular carcinoma.Nature communications · 2026Trial
- Inferring Gene Regulatory Networks in Stem Cells: Methods and Applications.Methods in molecular biology (Clifton, N.J.) · 2027Review
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- Base editing rescues a hereditary motor neuron disease in mouse and patient-derived iPSC organoid models.Molecular therapy. Advances · 2026Article
- Integrated bioinformatics analysis uncovers TNFSF10 as a key panoptosis-related gene in diabetic tubular injury.Renal failure · 2026Article
- Progressive suppression of regulated cell death defines terminal macrophage states in liver cirrhosis.Annals of medicine · 2026Article
- Integrating network medicine and foundation models reveals cell-type-specific regulatory alterations in Alzheimer's disease.NAR genomics and bioinformatics · 2026Article
- Age-associated differences in XBB.1.5 trivalent booster vaccine-induced adaptive responses revealed by single-cell RNA sequencing.Emerging microbes & infections · 2026Article
- Transcriptomic trajectory of hepatocyte ballooning reveals a lipotoxic point of no return and initiates oncogenic regulatory rewiring in MASLD.Biochemistry and biophysics reports · 2026Article
- Cross species single-nucleus characterization of mammillary body.Cell insight · 2026Article
- Single nucleus multiomics reveals an early inflammatory response to high-fat diet in mouse islets.Life science alliance · 2026Article
- Glial Dysfunction and Memory Impairments in a Model of Pediatric Obstructive Sleep Apnea.Glia · 2026Article
- NeuroMetBench: patient-aware evidence bounds for transcript-derived metabolic representations across cancer proteogenomic contexts.Functional & integrative genomics · 2026Article
- Apolipoprotein A1 attenuates epirubicin-induced cardiotoxicity with GPX4-linked ferroptosis-defense modulation.Apoptosis : an international journal on programmed cell death · 2026Article
- A systematic transcriptomic atlas and predictive framework for metabolite-driven T cell state transitions.iScience · 2026Article
- Macrophage- or neutrophil-expressed UPP1 drives tumor growth and immune suppression in the tumor microenvironment.Science advances · 2026Article
- Single-cell gene regulatory networks characterize colonic stem and immune cell homeostasis iniScience · 2026Article
- IRF7 signalling in tanycytes controls brain-body-immune response across the ovarian cycle.Nature metabolism · 2026Article
- Sexual dimorphism in epidermal stem cell dynamics.Nature · 2026Article
- Drug Repurposing for Treating NCOR-Related Intellectual Disability.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
3,988 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
14 authors.
Funding
Abstract
We present SCENIC, a computational method for simultaneous gene regulatory network reconstruction and cell-state identification from single-cell RNA-seq data (http://scenic.aertslab.org). On a compendium of single-cell data from tumors and brain, we demonstrate that cis-regulatory analysis can be exploited to guide the identification of transcription factors and cell states. SCENIC provides critical biological insights into the mechanisms driving cellular heterogeneity.
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