{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,15]],"date-time":"2026-06-15T20:22:45Z","timestamp":1781554965381,"version":"3.54.5"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2026,1,20]],"date-time":"2026-01-20T00:00:00Z","timestamp":1768867200000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"NCI Research Project Grant","award":["P01CA25084"],"award-info":[{"award-number":["P01CA25084"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,2,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Integrative Module Analysis for Multi-omics Data (iModMix) is a biology-agnostic framework that enables the discovery of novel associations across any type of quantitative abundance data, including but not limited to transcriptomics, proteomics, and metabolomics. Instead of relying on pathway annotations or prior biological knowledge, iModMix constructs data-driven modules using graphical lasso to estimate sparse networks from omics features. These modules are summarized into eigenfeatures and correlated across datasets for horizontal integration, while preserving the distinct feature sets and interpretability of each omics type. iModMix operates directly on matrices containing expression or abundances for a wide range of features, including but not limited to genes, proteins, and metabolites. Because it does not rely on annotations (e.g., KEGG identifiers), it can seamlessly incorporate both identified and unidentified metabolites, addressing a key limitation of many existing metabolomics tools. iModMix is available as a user-friendly R Shiny application requiring no programming expertise (https:\/\/imodmix.moffitt.org), and as a Bioconductor R package for advanced users (https:\/\/bioconductor.org\/packages\/release\/bioc\/html\/iModMix.html). The tool includes several public and in-house datasets to illustrate its utility in identifying novel multi-omics relationships in diverse biological contexts.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>iModMix is freely available from Bioconductor (https:\/\/bioconductor.org\/packages\/release\/bioc\/html\/iModMix.html), and the example dataset package (iModMixData) is also available from Bioconductor (https:\/\/bioconductor.org\/packages\/release\/ data\/experiment\/html\/iModMixData.html). The R package source code and Docker are available from GitHub: https:\/\/github.com\/biodatalab\/iModMix. Shiny application can be accessed at: https:\/\/imodmix.moffitt.org.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btag030","type":"journal-article","created":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T12:49:07Z","timestamp":1768481347000},"source":"Crossref","is-referenced-by-count":1,"title":["<i>iModMix:<\/i>\n                    integrative module analysis for multi-omics data"],"prefix":"10.1093","volume":"42","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7320-618X","authenticated-orcid":false,"given":"Isis","family":"Narv\u00e1ez-Bandera","sequence":"first","affiliation":[{"name":"Moffitt Cancer Center Department of Biostatistics and Bioinformatics, , Tampa, FL 33612,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4090-4680","authenticated-orcid":false,"given":"Ashley","family":"Lui","sequence":"additional","affiliation":[{"name":"Moffitt Cancer Center Department of Molecular Oncology, , Tampa, FL 33612,","place":["United States"]},{"name":"Moffitt Cancer Center Cancer Biology and Evolution Program, , Tampa, FL 33612,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yonatan Ayalew","family":"Mekonnen","sequence":"additional","affiliation":[{"name":"Moffitt Cancer Center Department of Molecular Oncology, , Tampa, FL 33612,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vanessa","family":"Rubio","sequence":"additional","affiliation":[{"name":"Moffitt Cancer Center Department of Molecular Oncology, , Tampa, FL 33612,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Augustine","family":"Takyi","sequence":"additional","affiliation":[{"name":"University of Utah Huntsman Cancer Institute, , Salt Lake City, UT 84112,","place":["United States"]},{"name":"University of Utah Department of Nutrition and Integrative Physiology, , Salt Lake City, UT 84112,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Noah","family":"Sulman","sequence":"additional","affiliation":[{"name":"University of South Florida Health Informatics Institute, , Tampa, FL 33612,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christopher","family":"Wilson","sequence":"additional","affiliation":[{"name":"Moffitt Cancer Center Department of Biostatistics and Bioinformatics, , Tampa, FL 33612,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hayley D","family":"Ackerman","sequence":"additional","affiliation":[{"name":"Moffitt Cancer Center Department of Molecular Oncology, , Tampa, FL 33612,","place":["United States"]},{"name":"Moffitt Cancer Center Cancer Biology and Evolution Program, , Tampa, FL 33612,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Oscar E","family":"Ospina","sequence":"additional","affiliation":[{"name":"Moffitt Cancer Center Department of Biostatistics and Bioinformatics, , Tampa, FL 33612,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guillermo","family":"Gonzalez-Calderon","sequence":"additional","affiliation":[{"name":"Moffitt Cancer Center Department of Biostatistics and Bioinformatics, , Tampa, FL 33612,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elsa R","family":"Flores","sequence":"additional","affiliation":[{"name":"Moffitt Cancer Center Department of Molecular Oncology, , Tampa, FL 33612,","place":["United States"]},{"name":"Moffitt Cancer Center Cancer Biology and Evolution Program, , Tampa, FL 33612,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9874-3555","authenticated-orcid":false,"given":"Qian","family":"Li","sequence":"additional","affiliation":[{"name":"St. Jude Children\u2019s Research Hospital Department of Biostatistics, , Memphis, TN 38105,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ann","family":"Chen","sequence":"additional","affiliation":[{"name":"Children\u2019s Mercy Research Institute Division of Health Services and Outcome Research, , Kansas City, MO 64108,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brooke L","family":"Fridley","sequence":"additional","affiliation":[{"name":"Children\u2019s Mercy Research Institute Division of Health Services and Outcome Research, , Kansas City, MO 64108,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0882-308X","authenticated-orcid":false,"given":"Paul A","family":"Stewart","sequence":"additional","affiliation":[{"name":"University of Utah Huntsman Cancer Institute, , Salt Lake City, UT 84112,","place":["United States"]},{"name":"University of Utah Department of Nutrition and Integrative Physiology, , Salt Lake City, UT 84112,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,1,19]]},"reference":[{"key":"2026022206564972200_btag030-B1","doi-asserted-by":"publisher","first-page":"1029","DOI":"10.1038\/s42255-023-00817-8","article-title":"A multimodal atlas of tumour metabolism reveals the architecture of gene-metabolite covariation","volume":"5","author":"Benedetti","year":"2023","journal-title":"Nat Metab"},{"key":"2026022206564972200_btag030-B2","doi-asserted-by":"publisher","first-page":"4164","DOI":"10.1073\/pnas.0308531101","article-title":"Metagenes and molecular pattern discovery using matrix factorization","volume":"101","author":"Brunet","year":"2004","journal-title":"Proc Natl Acad Sci USA"},{"key":"2026022206564972200_btag030-B3","doi-asserted-by":"publisher","first-page":"e0176278","DOI":"10.1371\/journal.pone.0176278","article-title":"Integrative clustering of multi-level 'omic data based on non-negative matrix factorization algorithm","volume":"12","author":"Chalise","year":"2017","journal-title":"PLoS One"},{"key":"2026022206564972200_btag030-B4","doi-asserted-by":"publisher","first-page":"432","DOI":"10.1093\/biostatistics\/kxm045","article-title":"Sparse inverse covariance estimation with the graphical lasso","volume":"9","author":"Friedman","year":"2008","journal-title":"Biostatistics"},{"key":"2026022206564972200_btag030-B5","doi-asserted-by":"publisher","DOI":"10.3390\/metabo11030184","article-title":"Approaches to integrating metabolomics and multi-omics data: a primer","volume":"11","author":"Jendoubi","year":"2021","journal-title":"Metabolites"},{"key":"2026022206564972200_btag030-B6","doi-asserted-by":"publisher","first-page":"W90","DOI":"10.1093\/nar\/gkw377","article-title":"Enrichr: a comprehensive gene set enrichment analysis web server 2016 update","volume":"44","author":"Kuleshov","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2026022206564972200_btag030-B7","doi-asserted-by":"publisher","first-page":"559","DOI":"10.1186\/1471-2105-9-559","article-title":"WGCNA: an R package for weighted correlation network analysis","volume":"9","author":"Langfelder","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"2026022206564972200_btag030-B8","doi-asserted-by":"publisher","first-page":"719","DOI":"10.1093\/bioinformatics\/btm563","article-title":"Defining clusters from a hierarchical cluster tree: the dynamic tree cut package for R","volume":"24","author":"Langfelder","year":"2008","journal-title":"Bioinformatics"},{"key":"2026022206564972200_btag030-B9","doi-asserted-by":"publisher","first-page":"770","DOI":"10.1038\/nmeth.3940","article-title":"Revealing disease-associated pathways by network integration of untargeted metabolomics","volume":"13","author":"Pirhaji","year":"2016","journal-title":"Nat Methods"},{"key":"2026022206564972200_btag030-B10","doi-asserted-by":"publisher","first-page":"4245","DOI":"10.1073\/pnas.1208949110","article-title":"Pattern discovery and cancer gene identification in integrated cancer genomic data\u2014PubMed","volume":"110","author":"Qianxing","year":"2013","journal-title":"Proc Natl Acad Sci USA"},{"key":"2026022206564972200_btag030-B11","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-8-22","article-title":"Gene network interconnectedness and the generalized topological overlap measure","volume":"8","author":"Yip","year":"2007","journal-title":"BMC Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btag030\/66464647\/btag030.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/42\/2\/btag030\/66464647\/btag030.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/42\/2\/btag030\/66464647\/btag030.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,2,22]],"date-time":"2026-02-22T11:56:58Z","timestamp":1771761418000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btag030\/8430290"}},"subtitle":[],"editor":[{"given":"Pier Luigi","family":"Martelli","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,1,19]]},"references-count":11,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2026,2,3]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btag030","relation":{},"ISSN":["1367-4811"],"issn-type":[{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,2]]},"published":{"date-parts":[[2026,1,19]]},"article-number":"btag030"}}