{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,21]],"date-time":"2026-01-21T07:56:58Z","timestamp":1768982218170,"version":"3.49.0"},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2021,9,29]],"date-time":"2021-09-29T00:00:00Z","timestamp":1632873600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"National Agency of Scientific and Technological Promotion","award":["PICT-2018-01403"],"award-info":[{"award-number":["PICT-2018-01403"]}]},{"name":"Universidad Abierta Interamericana (UAI) and Universidad Nacional de La Plata"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Large-scale cancer genome projects have generated genomic, transcriptomic, epigenomic and clinicopathological data from thousands of samples in almost every human tumor site. Although most omics data and their associated resources are publicly available, its full integration and interpretation to dissect the sources of gene expression modulation require specialized knowledge and software.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We present Multiomix, an interactive cloud-based platform that allows biologists to identify genetic and epigenetic events associated with the transcriptional modulation of cancer-related genes through the analysis of multi-omics data available on public functional genomic databases or user-uploaded datasets. Multiomix consists of an integrated set of functions, pipelines and a graphical user interface that allows retrieval, aggregation, analysis and visualization of different omics data sources. After the user provides the data to be analyzed, Multiomix identifies all significant correlations between mRNAs and non-mRNA genomics features (e.g. miRNA, DNA methylation and CNV) across the genome, the predicted sequence-based interactions (e.g. miRNA\u2013mRNA) and their associated prognostic values.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Multiomix is available at https:\/\/www.multiomix.org. The source code is freely available at https:\/\/github.com\/omics-datascience\/multiomix.<\/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\/btab678","type":"journal-article","created":{"date-parts":[[2021,9,23]],"date-time":"2021-09-23T21:42:43Z","timestamp":1632433363000},"page":"866-868","source":"Crossref","is-referenced-by-count":4,"title":["Multiomix: a cloud-based platform to infer cancer genomic and epigenomic events associated with gene expression modulation"],"prefix":"10.1093","volume":"38","author":[{"given":"Genaro","family":"Camele","sequence":"first","affiliation":[{"name":"Instituto de Investigaci\u00f3n en Inform\u00e1tica (LIDI), Facultad de Inform\u00e1tica, Universidad Nacional de La Plata , La Plata B1900, Argentina"}]},{"given":"Sebastian","family":"Menazzi","sequence":"additional","affiliation":[{"name":"Centro de Altos Estudios en Tecnolog\u00eda Inform\u00e1tica (CAETI), Facultad de Tecnolog\u00eda Inform\u00e1tica, Universidad Abierta Interamericana , Caba C1270AAH, Argentina"}]},{"given":"Hern\u00e1n","family":"Chanfreau","sequence":"additional","affiliation":[{"name":"Centro de Altos Estudios en Tecnolog\u00eda Inform\u00e1tica (CAETI), Facultad de Tecnolog\u00eda Inform\u00e1tica, Universidad Abierta Interamericana , Caba C1270AAH, Argentina"}]},{"given":"Agustin","family":"Marraco","sequence":"additional","affiliation":[{"name":"Centro de Altos Estudios en Tecnolog\u00eda Inform\u00e1tica (CAETI), Facultad de Tecnolog\u00eda Inform\u00e1tica, Universidad Abierta Interamericana , Caba C1270AAH, Argentina"}]},{"given":"Waldo","family":"Hasperu\u00e9","sequence":"additional","affiliation":[{"name":"Instituto de Investigaci\u00f3n en Inform\u00e1tica (LIDI), Facultad de Inform\u00e1tica, Universidad Nacional de La Plata , La Plata B1900, Argentina"}]},{"given":"Matias D","family":"Butti","sequence":"additional","affiliation":[{"name":"Centro de Altos Estudios en Tecnolog\u00eda Inform\u00e1tica (CAETI), Facultad de Tecnolog\u00eda Inform\u00e1tica, Universidad Abierta Interamericana , Caba C1270AAH, Argentina"},{"name":"Centro de Investigaciones Inmunol\u00f3gicas B\u00e1sicas y Aplicadas (CINIBA), Facultad de Ciencias M\u00e9dicas, Universidad Nacional de La Plata , La Plata B1900, Argentina"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9206-2369","authenticated-orcid":false,"given":"Martin C","family":"Abba","sequence":"additional","affiliation":[{"name":"Centro de Investigaciones Inmunol\u00f3gicas B\u00e1sicas y Aplicadas (CINIBA), Facultad de Ciencias M\u00e9dicas, Universidad Nacional de La Plata , La Plata B1900, Argentina"}]}],"member":"286","published-online":{"date-parts":[[2021,9,29]]},"reference":[{"key":"2023020108480715300_btab678-B1","doi-asserted-by":"crossref","first-page":"3980","DOI":"10.1158\/0008-5472.CAN-15-0506","article-title":"A molecular portrait of high-grade ductal carcinoma in situ","volume":"75","author":"Abba","year":"2015","journal-title":"Cancer Res"},{"key":"2023020108480715300_btab678-B2","doi-asserted-by":"crossref","first-page":"W537","DOI":"10.1093\/nar\/gky379","article-title":"The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update","volume":"46","author":"Afgan","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2023020108480715300_btab678-B3","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41467-020-14605-5","article-title":"Transcriptional effects of copy number alterations in a large set of human cancers","volume":"11","author":"Bhattacharya","year":"2020","journal-title":"Nat. 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