ArticleNucleic acids research2023
Inferring ligand-receptor cellular networks from bulk and spatial transcriptomic datasets with BulkSignalR.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers, 2 of them syntheses that pooled it.
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Who cites it
34 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Conserved hepatic RNA signatures across multiple cohorts reveal novel mechanistic clues for advanced fibrosis in human MASLD.Hepatology communications · 2026Pooled it
- Dynamic Remodeling of Oocyte-Granulosa Cell Communication During Bovine Folliculogenesis Revealed by Transcriptomic Meta-Analyses.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2026Pooled it
- Sex-specific molecular signatures in persistent pain after whiplash injury: an exploratory analysis.Pain reports · 2026Article
- Characterizing the SASP-Dependent Paracrine Spreading of Senescence Between Human Brain Cell Types.Aging cell · 2026Article
- Computational analysis in spatial transcriptomics: methods and perspectives.Briefings in bioinformatics · 2026Review
- Unraveling cell-cell communication through spatial transcriptomics: a review of computational methods.Briefings in bioinformatics · 2026Review
- Addressing multiple facets of ligand-receptor network inference including single-cell proteomics.Nucleic acids research · 2026Article
- Inter-organ communication shapes human metabolic tissue states and resolves anti-diabetic drug response modes in a six-tissue microphysiological system.bioRxiv : the preprint server for biology · 2026Article
- Integrated DNA and RNA profiling refines prognostic stratification independent of therapeutic actionability in cholangiocarcinoma.BMC cancer · 2026Article
- The renal response to FGF23 shifts from phosphaturia toward inflammation in kidney disease.Journal of cell communication and signaling · 2026Article
- Post-Transcriptional Modification Integration for Ligand-Receptor Cellular Network Inference.Molecular & cellular proteomics : MCP · 2026Article
- Characterizing the SASP-Dependent Paracrine Spreading of Senescence Between Human Brain Cell Types.bioRxiv : the preprint server for biology · 2026Article
- Distinct Interferon and Intracellular Signaling Signatures in Systemic Lupus Erythematosus and Dermatomyositis by Integrative Transcriptomic and Proteomic Analysis.ACR open rheumatology · 2026Article
- Data driven network inference and longitudinal transcriptomics unveil dynamic regulation in Chronic Lymphocytic Leukaemia models.NPJ systems biology and applications · 2026Article
- Pathogenomic analysis reveals clinically relevant epithelial-mesenchymal plasticity in esophageal squamous cell carcinoma.Theranostics · 2026Article
- Tumor lactate metabolism shapes immune suppression and therapeutic resistance revealed by integrative multi-omics and digital pathology.Frontiers in immunology · 2026Article
- RICH1 enhances pro-inflammatory TAM infiltration in breast cancer via promoting TRIM21-mediated ubiquitination of RhoA and inhibiting STAT3 phosphorylation.NPJ precision oncology · 2025Article
- Spatial Transcriptomics Reveals Distinct Architectures but Shared Vulnerabilities in Primary and Metastatic Liver Tumors.Cancers · 2025Article
- stClinic dissects clinically relevant niches by integrating spatial multi-slice multi-omics data in dynamic graphs.Nature communications · 2025Article
- An algorithmic perspective on deciphering cell-cell interactions with spatial omics data.Briefings in bioinformatics · 2025Review
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
The study of cellular networks mediated by ligand-receptor interactions has attracted much attention recently owing to single-cell omics. However, rich collections of bulk data accompanied with clinical information exists and continue to be generated with no equivalent in single-cell so far. In parallel, spatial transcriptomic (ST) analyses represent a revolutionary tool in biology. A large number of ST projects rely on multicellular resolution, for instance the Visium™ platform, where several cells are analyzed at each location, thus producing localized bulk data. Here, we describe BulkSignalR, a R package to infer ligand-receptor networks from bulk data. BulkSignalR integrates ligand-receptor interactions with downstream pathways to estimate statistical significance. A range of visualization methods complement the statistics, including functions dedicated to spatial data. We demonstrate BulkSignalR relevance using different datasets, including new Visium liver metastasis ST data, with experimental validation of protein colocalization. A comparison with other ST packages shows the significantly higher quality of BulkSignalR inferences. BulkSignalR can be applied to any species thanks to its built-in generic ortholog mapping functionality.
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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.