ArticleNature methods2020
NicheNet: modeling intercellular communication by linking ligands to target genes.
Article in Nature methods, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1,352 papers.
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Who cites it
1,352 citing papers in PubMed.
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- Single-cell transcriptomics reveals transcriptional reprogramming and microenvironmental remodeling in ectopic ACTH/CRH-secreting pheochromocytomas.Journal of translational medicine · 2026Article
- Decoding epithelial-mesenchymal transitions with multi-omics.Nature reviews. Genetics · 2026Review
- Reconstructing signaling histories of single cells via perturbation screens and transfer learning.Nature methods · 2026Article
- Single-Cell Mapping Identifies Aging-Associated Neutrophil Remodeling Across Multiple Organs.Aging cell · 2026Article
- Multi-stromal organoid co-culture modelling reveals epithelial-fibroblast heterogeneity in pancreatic cancer and pancreatitis.Nature cell biology · 2026Article
- Spatial and single-cell transcriptomics landscape of adenomyosis.Journal of advanced research · 2026Article
- Physiological Aging and Cardiovascular Disease Distinctly Remodel the Human Cardiac Lymphatic Endothelium.bioRxiv : the preprint server for biology · 2026Article
- Single-cell immune repertoire atlas maps coordinated circulating adaptive immune states in inflammatory bowel disease.bioRxiv : the preprint server for biology · 2026Article
1,292 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Computational methods that model how gene expression of a cell is influenced by interacting cells are lacking. We present NicheNet (https://github.com/saeyslab/nichenetr), a method that predicts ligand-target links between interacting cells by combining their expression data with prior knowledge on signaling and gene regulatory networks. We applied NicheNet to tumor and immune cell microenvironment data and demonstrate that NicheNet can infer active ligands and their gene regulatory effects on interacting cells.
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