ReviewNature protocols2025
CellPhoneDB v5: inferring cell-cell communication from single-cell multiomics data.
Review in Nature protocols, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 120 papers, 1 of them a synthesis that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
120 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Cross-expression meta-analysis of mouse brain slices reveals coordinated gene expression across spatially adjacent cells.Genome biology · 2025Pooled it
- Single-cell analysis of skin and blood reveals systemic immune responses to ultraviolet B and their impairment in MS.Journal of neuroinflammation · 2026Trial
- High-Risk Rhabdomyosarcomas Feature a Convergent Cell State.Cancer research · 2026Article
- Machine learning and computational approaches to model therapeutic response and resistance in diffuse midline glioma.Journal of neuro-oncology · 2026Review
- Spatial transcriptomics identifies a suppressive, T-cell-excluded tumor microenvironment in extramedullary myeloma.Blood advances · 2026Article
- IGF2-associated tumor cells and APOE-positive macrophages define an imatinib resistance-associated niche in gastrointestinal stromal tumors.Gastric cancer : official journal of the International Gastric Cancer Association and the Japanese Gastric Cancer Association · 2026Article
- Upadacitinib Restrains the Pathogenic Fitness of CD4Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Next-generation kidney tissue analysis - spatial omics and digital pathology.Nature reviews. Nephrology · 2026Review
- Hidden causal inference delineates dynamic lncRNA regulation in autism spectrum disorder.Briefings in bioinformatics · 2026Article
- Decoding cell-cell communication in spatial transcriptomics: mechanistic insights, modeling constraints, and analytical caveats.Briefings in bioinformatics · 2026Review
- Mapping ovarian cellular and molecular landscape across the lifespan of women: a scoping review.Human reproduction update · 2026Article
- Fusion-driven oncogenic programs shape the immune landscape in translocation renal cell carcinoma.Nature communications · 2026Article
- Article
- Application and Single-Cell Regulation Mechanism of Engineered EVs Combined With 4D-Printed Hydrogel for Infected Burn Repair.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- A dual pronged approach to cancer immune exclusion: tumor-derived LAIR-1 simultaneously drives fibrosis and blocks immune recruitment in glioma.Research square · 2026Article
- Mapping and engineering the human cell-cell interactome.Nature biotechnology · 2026Review
- Multi-regional Organoid Biobank Reveals FAK-ACSL1-Driven Doxorubicin-Resistance and Predictive Biomarkers in Breast Cancer.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Tumor evolution: signaling pathways, molecular mechanisms and therapeutic targets.Signal transduction and targeted therapy · 2026Review
- Single-Cell Transcriptome Profiles of Foxl1-Lineage Cells Along the Intestinal Crypt-Villus Axis.Cellular and molecular gastroenterology and hepatology · 2026Article
- Mutation-specific dynamics of dedifferentiation trajectories and tumor-stromal interactions in thyroid cancer.Molecular cancer · 2026Article
60 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
10 authors.
Funding
Abstract
Cell-cell communication is essential for tissue development, function and regeneration. The revolution of single-cell genomics technologies offers an unprecedented opportunity to uncover how cells communicate in vivo within their tissue niches and how disruption of these niches can lead to diseases and developmental abnormalities. CellPhoneDB is a bioinformatics toolkit designed to infer cell-cell communication by combining a curated repository of bona fide ligand-receptor interactions with methods to integrate these interactions with single-cell genomics data. Here we present a protocol for the latest version of CellPhoneDB (v5), offering several new features. First, the repository has been expanded by one-third with the addition of new interactions, including ~1,000 interactions mediated by nonpeptidic ligands such as steroidogenic hormones, neurotransmitters and small G-protein-coupled receptor (GPCR)-binding ligands. Second, we outline a new way of using the database that allows users to tailor queries to their experimental designs. Third, the update incorporates novel strategies to prioritize specific cell-cell interactions, leveraging information from other modalities such as tissue microenvironments derived from spatial transcriptomics technologies or transcription factor activities derived from a single-cell assay for transposase accessible chromatin assays. Finally, we describe the new CellPhoneDBViz module to interactively visualize and share results. Altogether, CellPhoneDB v5 enhances the precision of cell-cell communication inference, offering new insights into tissue biology in physiological microenvironments. This protocol typically takes ~15 min and requires basic knowledge of python.
Indexed as
Identifiers
40133495What Socratic holds
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 Socratic graph.