ArticleNature methods2023
Screening cell-cell communication in spatial transcriptomics via collective optimal transport.
Article in Nature methods, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 327 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
327 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
- Characterizing intra- and intertumor heterogeneity in ovarian high-grade serous carcinoma subtypes using single-cell and spatial transcriptomics.Genome research · 2026Article
- Atlas of cell types and regulatory elements underlying human facial diversity.Nature genetics · 2026Article
- Spatial and Single-Cell Multi-Omics Analyses of T-Cell Subsets and Interactions in Melanoma Lymph Node Metastasis.Experimental dermatology · 2026Review
- Machine learning and computational approaches to model therapeutic response and resistance in diffuse midline glioma.Journal of neuro-oncology · 2026Review
- A meta-interaction basis for cell-cell communication in tissues.bioRxiv : the preprint server for biology · 2026Article
- Multi-omic analysis of jaw-bone periosteum identifies the role of macrophage-derived SPP1 in CtskBone research · 2026Article
- Semi-metric optimal transport enables robust spatial multi-omics integration.Research square · 2026Article
- Advancing the Deciphering of Host-Microbe Crosstalk with Spatial Omics: A Mini-Review.Current microbiology · 2026Review
- PlantCCC prioritizes context-specific candidate ligand-receptor communication patterns in plant spatial transcriptomics.Plant molecular biology · 2026Article
- Morphogen-guided neocortical organoids with anteroposterior areal identity.Cell stem cell · 2026Article
- T cell-derived CCL5 drives macrophage immunometabolic remodeling in chronic prostatitis via the CCR5-ERK-PKM2/HIF-1α axis.Redox biology · 2026Article
- Data-driven identification of cell subtypes for single-cell transcriptomic data with Subtypist.Briefings in bioinformatics · 2026Article
- Decoding cell-cell communication in spatial transcriptomics: mechanistic insights, modeling constraints, and analytical caveats.Briefings in bioinformatics · 2026Review
- A multiperspective evaluation framework of spatial transcriptomics clustering methods.NAR genomics and bioinformatics · 2026Article
- Spatially guided in vivo single-cell functional genomics of postnatal heart.Nature cardiovascular research · 2026Article
- Spatial cell-cell communication inference based on cell-spot-ligand-receptor heterogeneous graphs.PLoS computational biology · 2026Article
- Multi-omics-driven precision medicine.iMeta · 2026Review
- Spatially organized regulated cell death-immune coupling in solid tumors: integrating spatial omics with actionable regulated cell death biology.Molecular cancer · 2026Review
267 more citing papers are in PubMed but not listed here.
Corrections and comments
- Commented on by
Authors and funding
8 authors.
Funding
Abstract
Spatial transcriptomic technologies and spatially annotated single-cell RNA sequencing datasets provide unprecedented opportunities to dissect cell-cell communication (CCC). However, incorporation of the spatial information and complex biochemical processes required in the reconstruction of CCC remains a major challenge. Here, we present COMMOT (COMMunication analysis by Optimal Transport) to infer CCC in spatial transcriptomics, which accounts for the competition between different ligand and receptor species as well as spatial distances between cells. A collective optimal transport method is developed to handle complex molecular interactions and spatial constraints. Furthermore, we introduce downstream analysis tools to infer spatial signaling directionality and genes regulated by signaling using machine learning models. We apply COMMOT to simulation data and eight spatial datasets acquired with five different technologies to show its effectiveness and robustness in identifying spatial CCC in data with varying spatial resolutions and gene coverages. Finally, COMMOT identifies new CCCs during skin morphogenesis in a case study of human epidermal development.
Indexed as
Identifiers
What OpenQuestion holds
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.