ArticleNature genetics2026
CytoSignal detects locations and dynamics of ligand-receptor signaling at cellular resolution from spatial transcriptomic data.
Article in Nature genetics, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers, 1 of them a synthesis that pooled it.
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Who cites it
15 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Cross-expression meta-analysis of mouse brain slices reveals coordinated gene expression across spatially adjacent cells.Genome biology · 2025Pooled it
- Unveiling the role of spatial transcriptomics in the analysis of the tumor immune microenvironment (Review).International journal of molecular medicine · 2026Review
- A dual pronged approach to cancer immune exclusion: tumor-derived LAIR-1 simultaneously drives fibrosis and blocks immune recruitment in glioma.Research square · 2026Article
- Single-cell spatial mapping of human kidney development implicates the microenvironment in guiding cell fate decisions.Nature genetics · 2026Article
- Mediators of cell fate decisions in human fetal kidney development identified using spatial transcriptomics.Nature genetics · 2026Article
- CytoSignal detects locations and dynamics of ligand-receptor signaling at cellular resolution from spatial transcriptomic data.Nature genetics · 2026Article
- Multimodal spatial-omics reveal co-evolution of alveolar progenitors and proinflammatory niches in progression of lung precursor lesions.Cancer cell · 2026Article
- Spatial omics at the forefront: emerging technologies, analytical innovations, and clinical applications.Cancer cell · 2026Review
- Inferring spatial single-cell-level interactions through interpreting cell state and niche correlations learned by self-supervised graph transformer.Nature machine intelligence · 2026Article
- spVelo: RNA velocity inference for multi-batch spatial transcriptomics data.Genome biology · 2025Article
- CellNEST reveals cell-cell relay networks using attention mechanisms on spatial transcriptomics.Nature methods · 2025Article
- Dissecting multilayer cell-cell communications with signaling feedback loops from spatial transcriptomics data.Genome research · 2025Article
- Cross-expression meta-analysis of 695 brain samples reveals coordinated gene expression across spatially adjacent cells.bioRxiv : the preprint server for biology · 2025Article
- Techniques and analytic workflow for spatial transcriptomics and its application to allergy and inflammation.The Journal of allergy and clinical immunology · 2025Review
- Cell signaling characterization for spatial transcriptomics (ST) data using network analysis.Complex networks & their applications. International Conference on Complex Networks and Their Applications · 2025Article
Corrections and comments
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Authors and funding
14 authors.
Funding
Abstract
Cells communicate through ligand-receptor (LR) signaling interactions, but identifying when and where these interactions are active remains challenging. We developed CytoSignal to infer the locations and dynamics of cell-cell communication at cellular resolution from spatial transcriptomic data. Here we show that our cellular resolution, spatially resolved signaling scores enable several important analyses-identifying spatial gradients in signaling strength, quantifying the locations of contact-dependent and diffusible interactions, detecting signaling-associated genes and identifying differential signaling across multisample data. Additionally, we can predict the temporal dynamics of a signaling interaction at each spatial location. We experimentally validate our results in situ by proximity ligation assay, confirming that CytoSignal predicts the locations of LR interactions more accurately than previous approaches. This study addresses the field's current need for a robust and scalable tool to detect cell-cell signaling interactions and their dynamics at cellular resolution from spatial transcriptomic data.
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