{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,17]],"date-time":"2026-07-17T12:20:37Z","timestamp":1784290837740,"version":"3.55.0"},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"22-23","license":[{"start":{"date-parts":[[2020,12,1]],"date-time":"2020-12-01T00:00:00Z","timestamp":1606780800000},"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\/501100012166","name":"National Key R&D Program of China","doi-asserted-by":"crossref","award":["2019YFC1711000"],"award-info":[{"award-number":["2019YFC1711000"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Key R&D Program of Jiangsu Province","award":["BE2020694"],"award-info":[{"award-number":["BE2020694"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["81973145"],"award-info":[{"award-number":["81973145"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Stratification of cancer patients into distinct molecular subgroups based on multi-omics data is an important issue in the context of precision medicine. Here, we present MOVICS, an R package for multi-omics integration and visualization in cancer subtyping. MOVICS provides a unified interface for 10 state-of-the-art multi-omics integrative clustering algorithms, and incorporates the most commonly used downstream analyses in cancer subtyping researches, including characterization and comparison of identified subtypes from multiple perspectives, and verification of subtypes in external cohort using two model-free approaches for multiclass prediction. MOVICS also creates feature rich customizable visualizations with minimal effort. By analysing two published breast cancer cohort, we signifies that MOVICS can serve a wide range of users and assist cancer therapy by moving away from the \u2018one-size-fits-all\u2019 approach to patient care.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>MOVICS package and online tutorial are freely available at https:\/\/github.com\/xlucpu\/MOVICS.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa1018","type":"journal-article","created":{"date-parts":[[2020,11,24]],"date-time":"2020-11-24T21:43:35Z","timestamp":1606254215000},"page":"5539-5541","source":"Crossref","is-referenced-by-count":201,"title":["<i>MOVICS<\/i>\n                    : an R package for multi-omics integration and visualization in cancer subtyping"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2417-6548","authenticated-orcid":false,"given":"Xiaofan","family":"Lu","sequence":"first","affiliation":[{"name":"State Key Laboratory of Natural Medicines, Research Center of Biostatistics and Computational Pharmacy, China Pharmaceutical University , Nanjing 210009, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jialin","family":"Meng","sequence":"additional","affiliation":[{"name":"Department of Urology, The First Affiliated Hospital of Anhui Medical University, Institute of Urology & Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University , Hefei, Anhui 230022, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yujie","family":"Zhou","sequence":"additional","affiliation":[{"name":"Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University , Shanghai 200001, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liyun","family":"Jiang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Natural Medicines, Research Center of Biostatistics and Computational Pharmacy, China Pharmaceutical University , Nanjing 210009, China"},{"name":"Department of Biostatistics, The University of Texas MD Anderson Cancer Center , Houston, TX 77030, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3347-5021","authenticated-orcid":false,"given":"Fangrong","family":"Yan","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Natural Medicines, Research Center of Biostatistics and Computational Pharmacy, China Pharmaceutical University , Nanjing 210009, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2020,12,14]]},"reference":[{"key":"2023062707100770500_btaa1018-B1","doi-asserted-by":"crossref","first-page":"e0176278","DOI":"10.1371\/journal.pone.0176278","article-title":"Integrative clustering of multi-level \u2018omic data based on non-negative matrix factorization algorithm","volume":"12","author":"Chalise","year":"2017","journal-title":"PLoS One"},{"key":"2023062707100770500_btaa1018-B2","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1093\/annonc\/mdy495","article-title":"Development of tumor mutation burden as an immunotherapy biomarker: utility for the oncology clinic","volume":"30","author":"Chan","year":"2019","journal-title":"Ann. Oncol"},{"key":"2023062707100770500_btaa1018-B3","doi-asserted-by":"crossref","first-page":"eaaf8399","DOI":"10.1126\/science.aaf8399","article-title":"Tumor aneuploidy correlates with markers of immune evasion and with reduced response to immunotherapy","volume":"355","author":"Davoli","year":"2017","journal-title":"Science"},{"key":"2023062707100770500_btaa1018-B4","doi-asserted-by":"crossref","first-page":"966","DOI":"10.3389\/fgene.2019.00966","article-title":"CEPICS: a comparison and evaluation platform for integration methods in cancer subtyping","volume":"10","author":"Duan","year":"2019","journal-title":"Front. Genet"},{"key":"2023062707100770500_btaa1018-B5","doi-asserted-by":"crossref","first-page":"R47","DOI":"10.1186\/gb-2014-15-3-r47","article-title":"Clinical drug response can be predicted using baseline gene expression levels and in vitro drug sensitivity in cell lines","volume":"15","author":"Geeleher","year":"2014","journal-title":"Genome Biol"},{"key":"2023062707100770500_btaa1018-B6","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1186\/1471-2105-14-7","article-title":"GSVA: gene set variation analysis for microarray and RNA-seq data","volume":"14","author":"H\u00e4nzelmann","year":"2013","journal-title":"BMC Bioinformatics"},{"key":"2023062707100770500_btaa1018-B7","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1111\/1467-9868.00293","article-title":"Estimating the number of data clusters via the Gap statistic","volume":"63","author":"Hastie","year":"2001","journal-title":"J. R. Stat. Soc. B"},{"key":"2023062707100770500_btaa1018-B8","doi-asserted-by":"crossref","first-page":"e15543","DOI":"10.1371\/journal.pone.0015543","article-title":"Nearest template prediction: a single-sample-based flexible class prediction with confidence assessment","volume":"5","author":"Hoshida","year":"2010","journal-title":"PLoS One"},{"key":"2023062707100770500_btaa1018-B9","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1093\/biostatistics\/kxj029","article-title":"Are clusters found in one dataset present in another dataset?","volume":"8","author":"Kapp","year":"2007","journal-title":"Biostatistics"},{"key":"2023062707100770500_btaa1018-B10","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol"},{"key":"2023062707100770500_btaa1018-B11","first-page":"2011","article-title":"Clustering and variable selection evaluation of 13 unsupervised methods for multi-omics data integration","volume":"21","author":"Pierre-Jean","year":"2020","journal-title":"Bioinformatics"},{"key":"2023062707100770500_btaa1018-B12","doi-asserted-by":"crossref","first-page":"10546","DOI":"10.1093\/nar\/gky889","article-title":"Multi-omic and multi-view clustering algorithms: review and cancer benchmark","volume":"46","author":"Rappoport","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2023062707100770500_btaa1018-B13","doi-asserted-by":"crossref","first-page":"e47","DOI":"10.1093\/nar\/gkv007","article-title":"limma powers differential expression analyses for RNA-sequencing and microarray studies","volume":"43","author":"Ritchie","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023062707100770500_btaa1018-B14","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","article-title":"edgeR: a Bioconductor package for differential expression analysis of digital gene expression data","volume":"26","author":"Robinson","year":"2010","journal-title":"Bioinformatics"},{"key":"2023062707100770500_btaa1018-B15","first-page":"583","article-title":"Cluster ensembles\u2014a knowledge reuse framework for combining multiple partitions","volume":"3","author":"Strehl","year":"2002","journal-title":"J. Mach. Learn. Res"},{"key":"2023062707100770500_btaa1018-B16","doi-asserted-by":"crossref","first-page":"6567","DOI":"10.1073\/pnas.082099299","article-title":"Diagnosis of multiple cancer types by shrunken centroids of gene expression","volume":"99","author":"Tibshirani","year":"2002","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023062707100770500_btaa1018-B17","doi-asserted-by":"crossref","first-page":"3131","DOI":"10.1093\/bioinformatics\/btx378","article-title":"CancerSubtypes: an R\/Bioconductor package for molecular cancer subtype identification, validation, and visualization","volume":"33","author":"Xu","year":"2017","journal-title":"Bioinformatics"},{"key":"2023062707100770500_btaa1018-B18","doi-asserted-by":"crossref","first-page":"284","DOI":"10.1089\/omi.2011.0118","article-title":"clusterProfiler: an R package for comparing biological themes among gene clusters","volume":"16","author":"Yu","year":"2012","journal-title":"OMICS"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btaa1018\/35058513\/btaa1018.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/22-23\/5539\/50716167\/btaa1018.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/22-23\/5539\/50716167\/btaa1018.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,27]],"date-time":"2023-06-27T03:42:00Z","timestamp":1687837320000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/36\/22-23\/5539\/6033582"}},"subtitle":[],"editor":[{"given":"Pier Luigi","family":"Martelli","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2020,12,1]]},"references-count":18,"journal-issue":{"issue":"22-23","published-print":{"date-parts":[[2021,4,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btaa1018","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2020.09.15.297820","asserted-by":"object"}]},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2020,12,1]]},"published":{"date-parts":[[2020,12,1]]}}}