Deciphering the gene-centric spatial dynamics across tissue and time with GeneSPOT.

GeneSPOT resolves tissue structures and quantifies spatial reorganization of gene programs across conditions, including embryonic development and aging, even when gene expression changes little.

• Why it matters: Spatial omics can map molecular organization in tissues, but most tools emphasize cell states and differential expression, leaving relational spatial dynamics across contexts underexplored.
• What they did: GeneSPOT uses gene-centric optimal transport to characterize spatial relationships among genes and measure how those relationships shift across biological conditions, including paired and unpaired spatial multi-omics.
• The result: Across diverse applications, it integrates multi-omics, reveals spatial convergence during embryonic development, and detects aging-linked spatial reorganization among genes whose expression does not change significantly with age.

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