ArticleNucleic acids research2020
SingleCellSignalR: inference of intercellular networks from single-cell transcriptomics.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 292 papers, 1 of them a synthesis that pooled it.
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Who cites it
292 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Deep learning in single-cell and spatial transcriptomics data analysis: advances and challenges from a data science perspective.Briefings in bioinformatics · 2025Pooled it
- PlantCCC prioritizes context-specific candidate ligand-receptor communication patterns in plant spatial transcriptomics.Plant molecular biology · 2026Article
- A transcription factor regulatory atlas for activity inference and perturbation prediction.Nucleic acids research · 2026Article
- Decoding cell-cell communication in spatial transcriptomics: mechanistic insights, modeling constraints, and analytical caveats.Briefings in bioinformatics · 2026Review
- Early immune dysregulation iniScience · 2026Article
- The critical role of the endogenous immune compartment after CAR T cell therapy in recurrent GBM.Cell · 2026Article
- T Cell-Macrophage Interactions Influence Chemotherapeutic Response in Ovarian Cancer Patients.International journal of molecular sciences · 2026Article
- A single-cell atlas of porcine hematopoietic development.Nature communications · 2026Article
- Addressing multiple facets of ligand-receptor network inference including single-cell proteomics.Nucleic acids research · 2026Article
- Spatial transcriptomic atlas of aggressive osteosarcomas reveals shared immune landscape and targetable surface markers.Nature communications · 2026Article
- Identifying condition-related cell-cell communication events using supervised tensor analysis.American journal of human genetics · 2026Article
- Article
- Spatial co-expression and cell-cell communication inference from spatially resolved transcriptomics with CONCISE.bioRxiv : the preprint server for biology · 2026Article
- CAGNet: a structure-aware clustering-alternated graph network for cell-cell interaction inference in spatial transcriptomics.BMC bioinformatics · 2026Article
- Single-Cell Transcriptomic Profiling Reveals Immunometabolic Reprogramming and Cell-Cell Communication in the Tumor Microenvironment of Human Hepatocellular Carcinoma.International journal of molecular sciences · 2026Article
- TREM2 restrains myeloid inflammasome activation to protect against photoreceptor degeneration.Journal of neuroinflammation · 2026Article
- CytoSignal detects locations and dynamics of ligand-receptor signaling at cellular resolution from spatial transcriptomic data.Nature genetics · 2026Article
- Targeting the HMGB1-IL32 pathway to alleviate T cell exhaustion in epithelial ovarian cancer.GeroScience · 2026Article
- Identifying potential ligand-receptor interactions by integrating LSTM network and the attention mechanism for cell-cell communication prediction.Journal of translational medicine · 2026Article
- NOD2 activation reprograms infiltrating inflammatory monocytes in the Zika virus infected CNS to maintain neural correlates of learning and memory.bioRxiv : the preprint server for biology · 2026Article
232 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Single-cell transcriptomics offers unprecedented opportunities to infer the ligand-receptor (LR) interactions underlying cellular networks. We introduce a new, curated LR database and a novel regularized score to perform such inferences. For the first time, we try to assess the confidence in predicted LR interactions and show that our regularized score outperforms other scoring schemes while controlling false positives. SingleCellSignalR is implemented as an open-access R package accessible to entry-level users and available from https://github.com/SCA-IRCM. Analysis results come in a variety of tabular and graphical formats. For instance, we provide a unique network view integrating all the intercellular interactions, and a function relating receptors to expressed intracellular pathways. A detailed comparison of related tools is conducted. Among various examples, we demonstrate SingleCellSignalR on mouse epidermis data and discover an oriented communication structure from external to basal layers.
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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.