ArticleBioinformatics (Oxford, England)2024
ICELLNET v2: a versatile method for cell-cell communication analysis from human transcriptomic data.
Article in Bioinformatics (Oxford, England), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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8 citing papers in PubMed.
- Aberrant CD4bioRxiv : the preprint server for biology · 2026Article
- connectomeDB2025: a rigorously curated, multi-species resource of experimentally supported ligand-receptor interactions.Nucleic acids research · 2026Article
- Interrogation of glioma immune microenvironment identifies a non-canonical role for microglial Galectin-9 in tumor cell adhesion and phagocytosis.Frontiers in immunology · 2026Article
- Intercellular communication from myotubes to fibroblasts is differentially impacted by mineralocorticoid receptor signaling and muscular dystrophy.Cell communication and signaling : CCS · 2025Article
- A role for fibroblast and mural cell subsets in a nerve ligation model of neuropathic pain?Brain, behavior, and immunity · 2025Article
- An amphiregulin reporter mouse enables transcriptional and clonal expansion analysis of reparative lung Tregs.JCI insight · 2025Article
- Advances and challenges in cell-cell communication inference: a comprehensive review of tools, resources, and future directions.Briefings in bioinformatics · 2025Review
- Myeloid cells coordinately induce glioma cell-intrinsic and cell-extrinsic pathways for chemoresistance via GP130 signaling.Cell reports. Medicine · 2024Article
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2 authors.
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Abstract
summarySeveral methods have been developed in the past years to infer cell-cell communication networks from transcriptomic data based on ligand and receptor expression. Among them, ICELLNET is one of the few approaches to consider the multiple subunits of ligands and receptors complexes to infer and quantify cell communication. In here, we present a major update of ICELLNET. As compared to its original implementation, we (i) drastically expanded the ICELLNET ligand-receptor database from 380 to 1669 biologically curated interactions, (ii) integrated important families of communication molecules involved in immune crosstalk, cell adhesion, and Wnt pathway, (iii) optimized ICELLNET framework for single-cell RNA sequencing data analyses, (iv) provided new visualizations of cell-cell communication results to facilitate prioritization and biological interpretation. This update will broaden the use of ICELLNET by the scientific community in different biological fields. AVAILABILITY AND IMPLEMENTATION: ICELLNET package is implemented in R. Source code, documentation and tutorials are available on GitHub (https://github.com/soumelis-lab/ICELLNET).
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