ArticleNucleic acids research2021
CellCall: integrating paired ligand-receptor and transcription factor activities for cell-cell communication.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 178 papers, 1 of them a synthesis that pooled it.
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Who cites it
178 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
- Integrated single-cell multi-omics characterization reveals lipid-associated macrophage-mediated immunosuppression in neoadjuvant immunotherapy of hepatocellular carcinoma.Nature communications · 2026Trial
- A transcription factor regulatory atlas for activity inference and perturbation prediction.Nucleic acids research · 2026Article
- Hidden causal inference delineates dynamic lncRNA regulation in autism spectrum disorder.Briefings in bioinformatics · 2026Article
- Integrated Genomic and Proteomic Analysis Reveals T-B Lymphocyte Signatures in the MYCN Driven "Immune Desert" of Specific Neuroblastoma Subtypes.CNS neuroscience & therapeutics · 2026Article
- Decoding cell-cell communication in spatial transcriptomics: mechanistic insights, modeling constraints, and analytical caveats.Briefings in bioinformatics · 2026Review
- Integrative pan-cancer and COAD-focused multi-omics analysis of non-histone acetylation substrate-related transcriptional landscapes.NPJ precision oncology · 2026Article
- Single-cell transcriptomic atlas-guided NRG3-ERBB4 axis enhances the efficacy of chemo-immunotherapy during induction phase in high-risk neuroblastoma.Molecular therapy : the journal of the American Society of Gene Therapy · 2026Article
- Single-cell transcriptomics reveals the prognostic and immune infiltration significance of FOLFOX-bevacizumab treatment and lysine crotonylation characteristics in colon cancer.Journal of gastrointestinal oncology · 2026Article
- Article
- Robust identification of cell-cell communication heterogeneity in single cells.bioRxiv : the preprint server for biology · 2026Article
- Meningioma microenvironment harbors a rich immune landscape that evolves with biological state.Neuro-oncology · 2026Article
- Meis1-driven suppression of MIF/CD74 signaling promotes M2 macrophage polarization and protects against inflammatory damage in experimental acute lung injury.Cell biology and toxicology · 2026Article
- Heterogeneity of lymphoid cells in PBMCs in the acute phase of SFTS: Single-cell transcriptome profiling.Journal of biomedical research · 2026Article
- Single-cell-based identification of drug synergy with immunotherapy via tumor microenvironment remodeling.Journal for immunotherapy of cancer · 2026Article
- Senescent epithelial cells remodel the tumor microenvironment and drive early LUAD progression: a multiomics risk model and single-cell analysis.Cellular and molecular life sciences : CMLS · 2026Article
- Multimodal bioinformatic analyses of genome-scale expression beyond gene-centric differential expression.Briefings in bioinformatics · 2026Review
- Spatial transcriptomics and single-cell analyses reveal the role of the cisplatin-resistant gene panel in NSCLC progression and the tumor microenvironment, identifying LOXL2 as a potential therapeutic target.Cancer cell international · 2026Article
- Integrative machine learning identifies a TEAD4-driven endothelial program shaping drug sensitivity and microvascular invasion in HCC.Journal of translational medicine · 2026Article
- Bridging cancer cell-intrinsic driver genes and -extrinsic cell-cell communication with Driver2Comm.PLoS computational biology · 2026Article
118 more citing papers are in PubMed but not listed here.
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Authors and funding
14 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
With the dramatic development of single-cell RNA sequencing (scRNA-seq) technologies, the systematic decoding of cell-cell communication has received great research interest. To date, several in-silico methods have been developed, but most of them lack the ability to predict the communication pathways connecting the insides and outsides of cells. Here, we developed CellCall, a toolkit to infer inter- and intracellular communication pathways by integrating paired ligand-receptor and transcription factor (TF) activity. Moreover, CellCall uses an embedded pathway activity analysis method to identify the significantly activated pathways involved in intercellular crosstalk between certain cell types. Additionally, CellCall offers a rich suite of visualization options (Circos plot, Sankey plot, bubble plot, ridge plot, etc.) to present the analysis results. Case studies on scRNA-seq datasets of human testicular cells and the tumor immune microenvironment demonstrated the reliable and unique functionality of CellCall in intercellular communication analysis and internal TF activity exploration, which were further validated experimentally. Comparative analysis of CellCall and other tools indicated that CellCall was more accurate and offered more functions. In summary, CellCall provides a sophisticated and practical tool allowing researchers to decipher intercellular communication and related internal regulatory signals based on scRNA-seq data. CellCall is freely available at https://github.com/ShellyCoder/cellcall.
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