ArticleNature communications2022
Comparison of methods and resources for cell-cell communication inference from single-cell RNA-Seq data.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 420 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
420 citing papers in PubMed.
- Checkpoint immunotherapy is associated with preferential activation of tumor antigen-specific CD4Blood neoplasia · 2025Trial
- Spatial transcriptomics unveils the in situ cellular and molecular hallmarks of the lung in fatal COVID-19.Nature communications · 2026Article
- Engineered Microvascular Model of the Blood-Brain-Tumor Barrier Reveals Endothelial Remodeling in Diffuse Midline Glioma.Advanced healthcare materials · 2026Article
- Barrier immune memory is programmed by intestinal epithelial cell presentation of cytosol-delivered bacterial antigens.Nature immunology · 2026Article
- A transcriptional signature of resting mast cells is associated with improved disease outcome in HRGenes and immunity · 2026Article
- Senescent Cell Heterogeneity: Tissue-Dependent Signatures and Age Dynamics Revealed by Human scRNA-Seq Data.International journal of molecular sciences · 2026Article
- Explainable Artificial Intelligence and Gene-Network Analysis Prioritise a TREM2/LGALS3/GPNMB Scar-Associated Macrophage Programme in Human Liver Cirrhosis.International journal of molecular sciences · 2026Article
- A transcription factor regulatory atlas for activity inference and perturbation prediction.Nucleic acids research · 2026Article
- scFlowReport: A Reproducible Workflow for Comparative Downstream Biological Analysis of Single-Cell RNA-seq Data.Biomolecules · 2026Article
- Coordinated Immune Activation Following KRAS Inhibition in Syngeneic Models Reveals Molecular Pathways that Potentiate and Limit Antitumor Immunity.Cancer immunology research · 2026Article
- Single-cell and single-nucleus transcriptomics of the dorsal root ganglion in neuropathic pain: cell-state remodeling and translational prospects.Journal of translational medicine · 2026Review
- scGSI: Graph-guided self-supervised integration of paired single-cell multi-omics.PLoS computational biology · 2026Article
- Spatial cell-cell communication inference based on cell-spot-ligand-receptor heterogeneous graphs.PLoS computational biology · 2026Article
- Decoding cell-cell communication in spatial transcriptomics: mechanistic insights, modeling constraints, and analytical caveats.Briefings in bioinformatics · 2026Review
- Coordinated inflammatory macrophage and vascular smooth muscle cell remodeling signatures in human atherosclerosis: An integrative single-cell and bulk transcriptomic analysis.Journal of cell communication and signaling · 2026Article
- Ten quick tips for spatial transcriptomics analysis.PLoS computational biology · 2026Review
- Clonotypic characterization defines B-cell drivers of clonal expansion and intratumor heterogeneity in IgM monoclonal gammopathies.HemaSphere · 2026Article
- Plasticity of human microglia and brain perivascular macrophages in aging and Alzheimer's disease.Nature genetics · 2026Article
- Advances in Poultry RNA-Omics Research: Technologies, RNA Information Layers, and Applications in Complex Traits.Animals : an open access journal from MDPI · 2026Review
- Peripheral Nerve Injury Induces an Interferon-Responsive State Centered on Satellite Glial Cells in the DRG That Sustains Neuropathic Pain Through STAT1 and CXCL10 Signaling.Brain sciences · 2026Article
360 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
13 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The growing availability of single-cell data, especially transcriptomics, has sparked an increased interest in the inference of cell-cell communication. Many computational tools were developed for this purpose. Each of them consists of a resource of intercellular interactions prior knowledge and a method to predict potential cell-cell communication events. Yet the impact of the choice of resource and method on the resulting predictions is largely unknown. To shed light on this, we systematically compare 16 cell-cell communication inference resources and 7 methods, plus the consensus between the methods' predictions. Among the resources, we find few unique interactions, a varying degree of overlap, and an uneven coverage of specific pathways and tissue-enriched proteins. We then examine all possible combinations of methods and resources and show that both strongly influence the predicted intercellular interactions. Finally, we assess the agreement of cell-cell communication methods with spatial colocalisation, cytokine activities, and receptor protein abundance and find that predictions are generally coherent with those data modalities. To facilitate the use of the methods and resources described in this work, we provide LIANA, a LIgand-receptor ANalysis frAmework as an open-source interface to all the resources and methods.
Indexed as
Identifiers
What 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.