{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,5]],"date-time":"2026-09-05T01:12:31Z","timestamp":1788570751699,"version":"build-2803163510"},"reference-count":37,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2026,8,24]],"date-time":"2026-08-24T00:00:00Z","timestamp":1787529600000},"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 Youth","doi-asserted-by":"crossref","award":["62402071"],"award-info":[{"award-number":["62402071"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100012226","name":"Fundamental Research Funds for the Central Universities","doi-asserted-by":"publisher","award":["2024IAIS-QN020"],"award-info":[{"award-number":["2024IAIS-QN020"]}],"id":[{"id":"10.13039\/501100012226","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,8,31]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Integrating spatial multi-omics data is crucial for decoding tissue function, yet existing methods struggle with noise and cross-modal alignment.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We introduce SpaAlign, a novel two-stage framework for the robust integration of multiple omics and histological data. At its core, a contrastive learning stage creates a unified semantic space, followed by a self-supervised clustering stage that enforces structural coherence. Our evaluations demonstrate its effectiveness in accurately delineating the capsule-cortex-medulla architecture in human lymph nodes and precisely identifying germinal centers in human tonsil data, outperforming baseline methods.<\/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\/VitaIntelli-CQU\/SpaAlign. The source code is archived at https:\/\/doi.org\/10.5281\/zenodo.20250508.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btag629","type":"journal-article","created":{"date-parts":[[2026,8,22]],"date-time":"2026-08-22T11:42:13Z","timestamp":1787398933000},"source":"Crossref","is-referenced-by-count":0,"title":["Unified representation learning for spatial multi-omics"],"prefix":"10.1093","volume":"42","author":[{"ORCID":"https:\/\/orcid.org\/0009-0001-6872-3147","authenticated-orcid":false,"given":"Haoxuan","family":"Li","sequence":"first","affiliation":[{"name":"Chongqing University School of Big Data and Software Engineering, , Chongqing, 401331,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-2187-899X","authenticated-orcid":false,"given":"Sijie","family":"Wan","sequence":"additional","affiliation":[{"name":"Chongqing University School of Big Data and Software Engineering, , Chongqing, 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