ArticleGenome medicine2025
STopover captures spatial colocalization and interaction in the tumor microenvironment using topological analysis in spatial transcriptomics data.
Article in Genome medicine, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- MSIDAT: an automated platform for improved metabolite annotation in mass spectrometry imaging via mass shift evaluation and customized databases.Analytical and bioanalytical chemistry · 2026Article
- Mutation-specific dynamics of dedifferentiation trajectories and tumor-stromal interactions in thyroid cancer.Molecular cancer · 2026Article
- Interpretable and scalable spatial gene set activity analysis with GESSO uncovers functional tissue architecture.bioRxiv : the preprint server for biology · 2026Article
- SpaNiche: spatial niche analysis to explore colocalization patterns and cellular interactions in spatial transcriptomics data.Genome biology · 2026Article
- Dual-mode action of scalable, high-quality engineered stem cell-derived SIRPα-extracellular vesicles for treating acute liver failure.Nature communications · 2025Article
- Mapping TAM-tumor crosstalk in glioma via ligand-receptor multi-omics: mechanisms of immune evasion.Frontiers in immunology · 2025Review
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Authors and funding
6 authors.
Funding
Abstract
Unraveling the spatial configuration of the tumor microenvironment (TME) is crucial for elucidating tumor-immune interactions based on immuno-oncology. We present STopover, a novel approach utilizing spatially resolved transcriptomics (SRT) data and topological analysis to investigate the TME. By gradually lowering the feature threshold, connected components (CCs) are extracted based on spatial distance and persistence, with Jaccard indices quantifying their spatial overlap, and transcriptomic profiles are permutated to assess statistical significance. Applied to lung and breast cancer SRT, STopover revealed immune and stromal cell infiltration patterns, predicted key cell-cell communication, and identified relevant regions, shedding light on cancer pathophysiology (URL: https://github.com/bsungwoo/STopover ).
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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 Socratic graph.