ReviewNature protocols2025
Unraveling cell-cell communication with NicheNet by inferring active ligands from transcriptomics 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 24 papers.
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.
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Who cites it
24 citing papers in PubMed.
- Conserved Metastatic Cell States and Spatial Immune Microenvironment Remodeling Define Pancreatic Cancer Liver Metastases.bioRxiv : the preprint server for biology · 2026Article
- Integrated Transcriptomic Analysis Identifies a Candidate INHBA/Activin A-Associated Macrophage-MuSC Communication Axis in Human Skeletal Muscle Ageing.International journal of molecular sciences · 2026Article
- Article
- APOEScience advances · 2026Article
- Local and circulating cytotoxic CD4medRxiv : the preprint server for health sciences · 2026Article
- Single-Cell Omics Advances in Understanding Tissue Development and Complex Trait Formation in Sheep and Goats.Animals : an open access journal from MDPI · 2026Review
- Targeting the HMGB1-IL32 pathway to alleviate T cell exhaustion in epithelial ovarian cancer.GeroScience · 2026Article
- Quantitative coupling of clonal CNV evolution and spatially restricted malignant states identifies MFGE8 as a candidate late-state-associated target in breast cancer.Journal of translational medicine · 2026Article
- iS2C2: a cointelligent platform for mechanistic discovery of disease cellular crosstalk.Signal transduction and targeted therapy · 2026Article
- CX3CL1/CX3CR1 axis dysregulation contributes to epileptogenic mechanisms in focal cortical dysplasia.Acta neuropathologica communications · 2026Article
- Artificial intelligence-assisted spatial omics-based biomimetic nanoplatform for intelligent and precise intervention in the immunosuppressive core region of ovarian cancer.NPJ precision oncology · 2026Review
- Multimodal bioinformatic analyses of genome-scale expression beyond gene-centric differential expression.Briefings in bioinformatics · 2026Review
- Predictive modeling of molecular activity underlying physical cell-cell interactions.Cell reports methods · 2026Article
- Divergent phenotypic and functional roles of human T follicular helper cells from infancy to adulthood.bioRxiv : the preprint server for biology · 2026Article
- Spatial omics at the forefront: emerging technologies, analytical innovations, and clinical applications.Cancer cell · 2026Review
- Deciphering immune-inflammatory dysregulation in the endometriotic microenvironment: insights from single-cell omics and artificial intelligence.Frontiers in immunology · 2026Review
- Cell-state transitions and microenvironmental remodeling in thyroid cancer progression revealed by single-cell and spatial transcriptomics.Frontiers in immunology · 2026Review
- Multilayer network approaches to omics data integration in digital twins for cancer research.Frontiers in systems biology · 2026Review
- Injured proximal tubule-driven paracrine signaling promotes lipid-associated macrophage expansion and chondroitin sulfate biosynthesis via PPARG/TCF12 in diabetic kidney disease.Frontiers in immunology · 2026Article
- Single-cell transcriptome delineating asymmetric dynamics of CD4Frontiers in immunology · 2026Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Ligand-receptor interactions constitute a fundamental mechanism of cell-cell communication and signaling. NicheNet is a well-established computational tool that infers ligand-receptor interactions that potentially regulate gene expression changes in receiver cell populations. Whereas the original publication delves into the algorithm and validation, this paper describes a best practices workflow cultivated over four years of experience and user feedback. Starting from the input single-cell expression matrix, we describe a 'sender-agnostic' approach that considers ligands from the entire microenvironment and a 'sender-focused' approach that considers ligands only from cell populations of interest. As output, users will obtain a list of prioritized ligands and their potential target genes, along with multiple visualizations. We include further developments made in NicheNet v2, in which we have updated the data sources and implemented a downstream procedure for prioritizing cell type-specific ligand-receptor pairs. Although a standard NicheNet analysis takes <10 min to run, users often invest additional time in making decisions about the approach and parameters that best suit their biological question. This paper serves to aid in this decision-making process by describing the most appropriate workflow for common experimental designs like case-control and cell-differentiation studies. Finally, in addition to the step-by-step description of the code, we also provide wrapper functions that enable the analysis to be run in one line of code, thus tailoring the workflow to users at all levels of computational proficiency.
Indexed as
Identifiers
40038548What OpenQuestion 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 OpenQuestion graph.