{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,13]],"date-time":"2026-07-13T16:04:30Z","timestamp":1783958670332,"version":"3.55.0"},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2026,6,29]],"date-time":"2026-06-29T00:00:00Z","timestamp":1782691200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62472195"],"award-info":[{"award-number":["62472195"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62076109"],"award-info":[{"award-number":["62076109"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007847","name":"Natural Science Foundation of Jilin Province","doi-asserted-by":"publisher","award":["20260102302JC"],"award-info":[{"award-number":["20260102302JC"]}],"id":[{"id":"10.13039\/100007847","id-type":"DOI","asserted-by":"publisher"}]},{"name":"the Backbone Talent Program","award":["A2025004"],"award-info":[{"award-number":["A2025004"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,7,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Spatial multi-omics technologies jointly profile transcriptomes, proteins and chromatin accessibility in situ, enabling integrative analysis of tissue organization across molecular layers. However, most existing graph-based integration methods rely on independently constructed modality-specific k-nearest-neighbor graphs. When auxiliary modalities are sparse or noisy, these graphs can become topologically discordant, propagate spurious edges, weaken cross-modal alignment, and reduce spatial domain resolution.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We present Anchored RNA for Integrated Spatial Embedding (ARISE), an RNA expression anchored framework for spatial multi-omics integration. ARISE defines a shared-edge topology by intersecting RNA feature-similarity and spatial-proximity graphs, encodes auxiliary modalities on this common scaffold, and integrates them through inside-out hierarchical fusion. We further show theoretically that graph intersection minimizes false-positive edges within a broad class of k-of-r graph fusion rules, providing a principled basis for topology anchoring. Across various spatial multi-omics benchmarks spanning simulated and real datasets in bi-modal and tri-modal settings, ARISE improves spatial domain identification, cross-modal consistency, and preservation of tissue structure relative to existing methods. Furthermore, the learned representation supports biologically meaningful downstream analyses, including marker-based domain annotation, pathway enrichment, and cis-regulatory inference, indicating that ARISE yields a robust and interpretable framework for spatial multi-omics integration.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The source code is available at https:\/\/github.com\/XiangxiangWang-code\/ARISE. The archived version used in this study is available at https:\/\/doi.org\/10.6084\/m9.figshare.32686137.v2.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btag465","type":"journal-article","created":{"date-parts":[[2026,6,25]],"date-time":"2026-06-25T11:46:07Z","timestamp":1782387967000},"source":"Crossref","is-referenced-by-count":0,"title":["ARISE: RNA-anchored shared-edge topology and hierarchical fusion for spatial multi-omics integration"],"prefix":"10.1093","volume":"42","author":[{"given":"Xiangxiang","family":"Wang","sequence":"first","affiliation":[{"name":"School of Artificial Intelligence, Jilin University , Changchun 130012,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanchi","family":"Su","sequence":"additional","affiliation":[{"name":"School of Information Science and Technology, Northeast Normal University , Changchun 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