{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,7]],"date-time":"2026-07-07T15:11:10Z","timestamp":1783437070235,"version":"3.54.6"},"reference-count":47,"publisher":"Oxford University Press (OUP)","issue":"13","license":[{"start":{"date-parts":[[2022,5,26]],"date-time":"2022-05-26T00:00:00Z","timestamp":1653523200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"NSFC","doi-asserted-by":"publisher","award":["61806159"],"award-info":[{"award-number":["61806159"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"NSFC","doi-asserted-by":"publisher","award":["61902301"],"award-info":[{"award-number":["61902301"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Xi\u2019an Municipal Science and Technology Program","award":["2020KJRC0027"],"award-info":[{"award-number":["2020KJRC0027"]}]},{"name":"Doctoral Scientific Research Foundation of Xi\u2019an Polytechnic University","award":["BS202108"],"award-info":[{"award-number":["BS202108"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,6,27]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>Cancer is a heterogeneous group of diseases. Cancer subtyping is a crucial and critical step to diagnosis, prognosis and treatment. Since high-throughput sequencing technologies provide an unprecedented opportunity to rapidly collect multi-omics data for the same individuals, an urgent need in current is how to effectively represent and integrate these multi-omics data to achieve clinically meaningful cancer subtyping.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We propose a novel deep learning model, called Deep Structure Integrative Representation (DSIR), for cancer subtypes dentification by integrating representation and clustering multi-omics data. DSIR simultaneously captures the global structures in sparse subspace and local structures in manifold subspace from multi-omics data and constructs a consensus similarity matrix by utilizing deep neural networks. Extensive tests are performed in 12 different cancers on three levels of omics data from The Cancer Genome Atlas. The results demonstrate that DSIR obtains more significant performances than the state-of-the-art integrative methods.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>https:\/\/github.com\/Polytech-bioinf\/Deep-structure-integrative-representation.git<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac345","type":"journal-article","created":{"date-parts":[[2022,5,31]],"date-time":"2022-05-31T18:59:22Z","timestamp":1654023562000},"page":"3337-3342","source":"Crossref","is-referenced-by-count":18,"title":["Deep structure integrative representation of multi-omics data for cancer subtyping"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6200-8727","authenticated-orcid":false,"given":"Bo","family":"Yang","sequence":"first","affiliation":[{"name":"School of Computer Science, Xi\u2019an Polytechnic University , Xi\u2019an, 710048, China"},{"name":"Donnelly Centre for Cellular and Biomolecular Research, University of Toronto , Toronto, ON M5S 3E1, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yan","family":"Yang","sequence":"additional","affiliation":[{"name":"School of Computer Science, Xi\u2019an Polytechnic University , Xi\u2019an, 710048, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xueping","family":"Su","sequence":"additional","affiliation":[{"name":"School of Electronics and Information, Xi\u2019an Polytechnic University , Xi\u2019an 710048, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,5,26]]},"reference":[{"key":"2023041408093183300_","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41467-021-22336-4","article-title":"Ferroptosis response segregates small cell lung cancer (SCLC) neuroendocrine subtypes","volume":"12","author":"Bebber","year":"2021","journal-title":"Nat. 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