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Here we introduce SpatialQuery, a framework that can both identify cellular motifs, i.e. recurrent multicellular co-localization patterns, and perform molecular analyses focused on the motifs. It uncovers genes modulated by spatial contexts through differential expression analysis, and detects coordinated expression changes through covariation analysis. SpatialQuery can identify functional tissue units, and goes beyond pairwise analyses to characterize multicellular interactions. Applications to both spatial transcriptomics and proteomics data uncover cross-germ-layer signaling in gut tube patterning, disease-specific fibrotic and immunosuppressive niches in kidney and colon, and regional determinants of motif-associated transcriptional programs in a mouse brain atlas. SpatialQuery is available as a Python package, and we demonstrate how its light computational footprint enables integration into web-based cell atlas portals for interactive visualization and exploration.\n                <\/jats:p>","DOI":"10.64898\/2026.04.22.720136","type":"posted-content","created":{"date-parts":[[2026,4,25]],"date-time":"2026-04-25T00:30:27Z","timestamp":1777077027000},"source":"Crossref","is-referenced-by-count":0,"title":["SpatialQuery: scalable discovery and molecular characterization of multicellular motifs from spatial omics data"],"prefix":"10.64898","author":[{"given":"Shaokun","family":"An","sequence":"first","affiliation":[{"name":"Gene Lay Institute of Immunology and Inflammation, Brigham and Women\u2019s Hospital, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mark","family":"Keller","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0327-8297","authenticated-orcid":false,"given":"Nils","family":"Gehlenborg","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Martin","family":"Hemberg","sequence":"additional","affiliation":[{"name":"Gene Lay Institute of Immunology and Inflammation, Brigham and Women\u2019s Hospital, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"54368","reference":[{"key":"2026050419550852000_2026.04.22.720136v3.1","doi-asserted-by":"publisher","DOI":"10.1038\/s41576-022-00515-3"},{"key":"2026050419550852000_2026.04.22.720136v3.2","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-022-01409-2"},{"key":"2026050419550852000_2026.04.22.720136v3.3","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1038\/s43018-025-01107-w","article-title":"Cellular neighborhoods in cancer","volume":"7","year":"2026","journal-title":"Nat. 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