ArticleBioinformatics (Oxford, England)2021
Cellinker: a platform of ligand-receptor interactions for intercellular communication analysis.
Article in Bioinformatics (Oxford, England), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 papers.
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Who cites it
63 citing papers in PubMed, 96 citations in OpenAlex.
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- Distinct immunometabolic signatures in peripheral blood mononuclear cells are linked to systemic inflammation in type 2 diabetes and diabetic kidney disease.Molecular biomedicine · 2026Article
- Tracing cell communication programs across conditions at single cell resolution with CCC-RISE.bioRxiv : the preprint server for biology · 2026Article
- A Multiscale Computational Architecture to Study Signaling Dynamics at Cell-Cell Interfaces.bioRxiv : the preprint server for biology · 2026Article
- Charting the circulating proteome in ME/CFS using cross-system profiling to uncover mechanistic insights.Cell reports. Medicine · 2026Article
- Integrated molecular, immunoinformatic, and structural analysis reveals emerging antigenic divergence of Foot-and-mouth disease virus serotype O during the 2022-2023 outbreaks in Indonesia.Veterinary world · 2026Article
- CCCdb: a comprehensive manually curated database for cell-cell communication in human and mouse.Nucleic acids research · 2026Article
- The Role of Metabolites in Cell-Cell Communication: A Review of Databases and Computational Tools.Cells · 2025Review
- Multidimensional tumor-blood profiling uncovers systemic lymphocyte-monocyte imbalance in pituitary neuroendocrine tumors.Signal transduction and targeted therapy · 2025Article
- MetaLigand provides a prior-knowledge-guided framework for predicting non-peptide ligand mediated cell-cell communication.Cell reports methods · 2025Article
- Cell Type Specific Inference of Perturbations in Synaptic Communication with MultiNeuronChat.bioRxiv : the preprint server for biology · 2025Article
- CELLetter: leveraging large language model and dual-stream network to identify context-specific ligand-receptor interactions for cell-cell communication analysis.Briefings in bioinformatics · 2025Article
- Connectome-constrained ligand-receptor interaction analysis for understanding brain network communication.Nature communications · 2025Article
- Hybrid hydrogel-extracellular matrix scaffolds identify biochemical and mechanical signatures of cardiac ageing.Nature materials · 2025Article
- CausalCCC: a web server to explore intracellular causal pathways enabling cell-cell communication.Nucleic acids research · 2025Article
- New Insights and Implications of Cell-Cell Interactions in Developmental Biology.International journal of molecular sciences · 2025Review
- A single-cell atlas of spatial and temporal gene expression in the mouse cranial neural plate.eLife · 2025Article
- Mathematically mapping the network of cells in the tumor microenvironment.Cell reports methods · 2025Article
3 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
11 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationLigand-receptor (L-R) interactions mediate cell adhesion, recognition and communication and play essential roles in physiological and pathological signaling. With the rapid development of single-cell RNA sequencing (scRNA-seq) technologies, systematically decoding the intercellular communication network involving L-R interactions has become a focus of research. Therefore, construction of a comprehensive, high-confidence and well-organized resource to retrieve L-R interactions in order to study the functional effects of cell-cell communications would be of great value.
resultsIn this study, we developed Cellinker, a manually curated resource of literature-supported L-R interactions that play roles in cell-cell communication. We aimed to provide a useful platform for studies on cell-cell communication mediated by L-R interactions. The current version of Cellinker documents over 3,700 human and 3,200 mouse L-R protein-protein interactions (PPIs) and embeds a practical and convenient webserver with which researchers can decode intercellular communications based on scRNA-seq data. And over 400 endogenous small molecule (sMOL) related L-R interactions were collected as well. Moreover, to help with research on coronavirus (CoV) infection, Cellinker collects information on 16 L-R PPIs involved in CoV-human interactions (including 12 L-R PPIs involved in SARS-CoV-2 infection). In summary, Cellinker provides a user-friendly interface for querying, browsing and visualizing L-R interactions as well as a practical and convenient web tool for inferring intercellular communications based on scRNA-seq data. We believe this platform could promote intercellular communication research and accelerate the development of related algorithms for scRNA-seq studies. AVAILABILITY: Cellinker is available at http://www.rna-society.org/cellinker/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.