ReviewBriefings in bioinformatics2025
Advances and challenges in cell-cell communication inference: a comprehensive review of tools, resources, and future directions.
Review in Briefings in bioinformatics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Unveiling the role of spatial transcriptomics in the analysis of the tumor immune microenvironment (Review).International journal of molecular medicine · 2026Review
- Mapping ovarian cellular and molecular landscape across the lifespan of women: a scoping review.Human reproduction update · 2026Article
- Decoding cell-cell communication in spatial transcriptomics: mechanistic insights, modeling constraints, and analytical caveats.Briefings in bioinformatics · 2026Review
- Decoding cytarabine-induced damage in the prepubertal testis: A multi-omics atlas of ecosystem and inheritance.iScience · 2026Article
- Leveraging Single-Cell and Spatial Transcriptomics in Gut Nutrition and Mucosal Immunology.The Journal of nutrition · 2026Article
- Computational analysis in spatial transcriptomics: methods and perspectives.Briefings in bioinformatics · 2026Review
- A historical journey of metabolite-protein interaction discovery: from data harmonization to AI-driven prediction.Briefings in bioinformatics · 2026Review
- Unraveling cell-cell communication through spatial transcriptomics: a review of computational methods.Briefings in bioinformatics · 2026Review
- A transcriptomic-driven segmentation and cell simulation framework for high-resolution spatial transcriptomics and cell-cell communication.bioRxiv : the preprint server for biology · 2026Article
- Tracing cell communication programs across conditions at single cell resolution with CCC-RISE.bioRxiv : the preprint server for biology · 2026Article
- Benchmarking tools for deciphering cellular crosstalk in spatially-resolved transcriptomics.Genome biology · 2026Article
- Single-Cell and Spatial Omics: Methods and Applications.MedComm · 2026Review
- Causal modeling reveals cell-cell communication dynamics in the tumor microenvironment during anti-PD-1 therapy in breast cancer patients.Briefings in bioinformatics · 2026Article
- GALA: a unified landmark-free framework for coarse-to-fine spatial alignment across resolutions and modalities in spatial transcriptomics.Briefings in bioinformatics · 2026Article
- Tensor-cell2cell v2 unravels coordinated dynamics of protein- and metabolite-mediated cell-cell communication.Bioinformatics (Oxford, England) · 2026Article
- connectomeDB2025: a rigorously curated, multi-species resource of experimentally supported ligand-receptor interactions.Nucleic acids research · 2026Article
- Integrated multi-omics and single-cell transcriptomic analysis reveals shared molecular mechanisms and cell-cell communication signatures in gout and metabolic syndrome.Frontiers in medicine · 2026Article
- Mapping safety in space: the emerging role of spatial transcriptomics in safe drug development.Frontiers in toxicology · 2026Review
- Cell-state transitions and microenvironmental remodeling in thyroid cancer progression revealed by single-cell and spatial transcriptomics.Frontiers in immunology · 2026Review
- Single-Cell RNA-Seq Reveals a Glycolysis-Biased EMT State in Keloid Keratinocytes That Amplifies the Pro-Inflammatory and Fibrotic Microenvironment.Journal of inflammation research · 2026Article
Corrections and comments
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Authors and funding
12 authors.
Funding
Abstract
Recent advancements in high-resolution and high-throughput sequencing technologies have significantly enhanced the study of cell-cell communication inference using single-cell and spatial transcriptomics data. Over the past 6 years, this growing interest has led to the development of more than 100 bioinformatics tools and nearly 50 resources, primarily in the form of ligand-receptor databases. These tools vary widely in their requirements, scoring approaches, ability to infer inter- and/or intra-cellular communication, assumptions, and limitations. Similarly, cell-cell communication resources differ in many aspects, mainly in the number of annotated interactions, species coverage, and their focus on inter-cellular signaling or both inter- and intra-cellular communication. This abundance and diversity create challenges in identifying compatible and suitable tools and resources to meet specific user needs. In this collaborative effort, we aim to provide a comprehensive report on the current state of cell-cell communication analysis derived from single-cell or spatial transcriptomics data. The report reviews existing methods and resources, addressing all relevant aspects from the user's perspective. It also explores current limitations, pitfalls, and unresolved issues in cell-cell communication inference, offering an aggregated analysis of the existing literature on the topic. Furthermore, we highlight potential future directions in the field and consolidate the collected knowledge into CCC-Catalog (https://sysbiobig.gitlab.io/ccc-catalog), a centralized web platform designed to serve as a hub for bioinformaticians and researchers interested in cell-cell communication inference.
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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.