ArticleCell genomics2023
Revealing spatial multimodal heterogeneity in tissues with SpaTrio.
Article in Cell genomics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed.
- STAT3D as a new image-tailored Xenium-based spatial transcriptomics tool for accurately dissecting the tumor microenvironment.Nucleic acids research · 2026Article
- Histopathology-centered computational evolution of spatial omics: integration, mapping, and foundation models.Briefings in bioinformatics · 2026Review
- MultiSP deciphers tissue structure and multicellular communication from spatial multi-omics data.Cell genomics · 2026Article
- SpatialCOC: an integrative framework for spatial continuous mapping and cross-omics correction in spatial multi-omics data.Nature communications · 2026Article
- SMIntegration: A web tool for comprehensive spatial metabolomics and transcriptomics integrated analysis and visualization.GigaScience · 2026Article
- Cell-type deconvolution methods for spatial transcriptomics.Nature reviews. Genetics · 2025Review
- Polyomino reconstructs spatial transcriptomic profiles with single-cell resolution via a region-allocation method.Genome research · 2025Article
- Spatial integration of multi-omics single-cell data with SIMO.Nature communications · 2025Article
- Mesoscale heterogeneity is a critical determinant for spiral pattern formation in developing social amoeba.Scientific reports · 2025Article
- Single-cell genomics and spatial transcriptomics in islet transplantation for diabetes treatment: advancing towards personalized therapies.Frontiers in immunology · 2025Review
- Unraveling the spatial and signaling dynamics and splicing kinetics of immune infiltration in osteoarthritis synovium.Frontiers in immunology · 2025Article
- Deconvolution of spatial transcriptomics data via graph contrastive learning and partial least square regression.Briefings in bioinformatics · 2024Article
- Complete spatially resolved gene expression is not necessary for identifying spatial domains.Cell genomics · 2024Article
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13 authors.
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Abstract
Capturing and depicting the multimodal tissue information of tissues at the spatial scale remains a significant challenge owing to technical limitations in single-cell multi-omics and spatial transcriptomics sequencing. Here, we developed a computational method called SpaTrio that can build spatial multi-omics data by integrating these two datasets through probabilistic alignment and enabling further analysis of gene regulation and cellular interactions. We benchmarked SpaTrio using simulation datasets and demonstrated its accuracy and robustness. Next, we evaluated SpaTrio on biological datasets and showed that it could detect topological patterns of cells and modalities. SpaTrio has also been applied to multiple sets of actual data to uncover spatially multimodal heterogeneity, understand the spatiotemporal regulation of gene expression, and resolve multimodal communication among cells. Our data demonstrated that SpaTrio could accurately map single cells and reconstruct the spatial distribution of various biomolecules, providing valuable multimodal insights into spatial biology.
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