ArticleNature methods2023
SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks.
Article in Nature methods, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 501 papers.
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501 citing papers in PubMed.
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- Upadacitinib Restrains the Pathogenic Fitness of CD4Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- A transcription factor regulatory atlas for activity inference and perturbation prediction.Nucleic acids research · 2026Article
- Explainable machine learning and multimodal single cell analysis link NR4A2 to CD8Journal, genetic engineering & biotechnology · 2026Article
- Single-Cell Transcriptome of Anaplastic Thyroid Cancer Reveals Immunosuppressive Tumor Microenvironment Remodeling.Cancer medicine · 2026Article
- Epigenetic modulation of stromal cell states underpins pathological tissue niches in Crohn's disease.Nature immunology · 2026Article
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10 authors.
Funding
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Abstract
Joint profiling of chromatin accessibility and gene expression in individual cells provides an opportunity to decipher enhancer-driven gene regulatory networks (GRNs). Here we present a method for the inference of enhancer-driven GRNs, called SCENIC+. SCENIC+ predicts genomic enhancers along with candidate upstream transcription factors (TFs) and links these enhancers to candidate target genes. To improve both recall and precision of TF identification, we curated and clustered a motif collection with more than 30,000 motifs. We benchmarked SCENIC+ on diverse datasets from different species, including human peripheral blood mononuclear cells, ENCODE cell lines, melanoma cell states and Drosophila retinal development. Next, we exploit SCENIC+ predictions to study conserved TFs, enhancers and GRNs between human and mouse cell types in the cerebral cortex. Finally, we use SCENIC+ to study the dynamics of gene regulation along differentiation trajectories and the effect of TF perturbations on cell state. SCENIC+ is available at scenicplus.readthedocs.io .
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