ArticleScience advances2021
CytoTalk: De novo construction of signal transduction networks using single-cell transcriptomic data.
Article in Science advances, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 93 papers, 1 of them a synthesis that pooled it.
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Who cites it
93 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
- Network Model to Predict Age-Related Transcriptional Reprogramming.Aging cell · 2026Article
- PCIPG: A comprehensive framework for protein complex identification based on a probabilistic graphical model.PLoS computational biology · 2026Article
- Addressing multiple facets of ligand-receptor network inference including single-cell proteomics.Nucleic acids research · 2026Article
- Identifying condition-related cell-cell communication events using supervised tensor analysis.American journal of human genetics · 2026Article
- Spatial co-expression and cell-cell communication inference from spatially resolved transcriptomics with CONCISE.bioRxiv : the preprint server for biology · 2026Article
- Review
- Identifying potential ligand-receptor interactions by integrating LSTM network and the attention mechanism for cell-cell communication prediction.Journal of translational medicine · 2026Article
- Robust identification of cell-cell communication heterogeneity in single cells.bioRxiv : the preprint server for biology · 2026Article
- Differential cell signaling testing for cell-cell communication inference from single-cell data by dominoSignal.Bioinformatics (Oxford, England) · 2026Article
- Bridging cancer cell-intrinsic driver genes and -extrinsic cell-cell communication with Driver2Comm.PLoS computational biology · 2026Article
- Uncovering the molecular logic of cortical wiring between neuronal subtypes across development through ligand-receptor inference.Nature communications · 2026Article
- Decrypting cancer's spatial code: from single cells to tissue niches.Molecular oncology · 2025Review
- CellPhoneDB v5: inferring cell-cell communication from single-cell multiomics data.Nature protocols · 2025Review
- 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
- Cell-cell interactions as predictive and prognostic markers for drug responses in cancer.Genome medicine · 2025Review
- Uncovering Cellular Interactome Drivers of Immune Checkpoint Inhibitor Response in Advanced Melanoma Patients.Cellular and molecular bioengineering · 2025Article
- Hi-C3: a statistical inference-based model for reconstructing higher-order cell-cell communication networks.Briefings in bioinformatics · 2025Article
- Using R, Seurat, and CellChat to Analyze a Single-Cell Transcriptomics Dataset of Mouse Skin Wound Healing.Journal of visualized experiments : JoVE · 2025Article
- Systematic analysis of cellular cross-talk reveals a role for SEMA6D-TREM2 regulating microglial function in Alzheimer's disease.Science translational medicine · 2025Article
33 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Single-cell technology enables study of signal transduction in a complex tissue at unprecedented resolution. We describe CytoTalk for de novo construction of cell type-specific signaling networks using single-cell transcriptomic data. Using an integrated intracellular and intercellular gene network as the input, CytoTalk identifies candidate pathways using the prize-collecting Steiner forest algorithm. Using high-throughput spatial transcriptomic data and single-cell RNA sequencing data with receptor gene perturbation, we demonstrate that CytoTalk has substantial improvement over existing algorithms. To better understand plasticity of signaling networks across tissues and developmental stages, we perform a comparative analysis of signaling networks between macrophages and endothelial cells across human adult and fetal tissues. Our analysis reveals an overall increased plasticity of signaling networks across adult tissues and specific network nodes that contribute to increased plasticity. CytoTalk enables de novo construction of signal transduction pathways and facilitates comparative analysis of these pathways across tissues and conditions.
Identifiers
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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.