{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,15]],"date-time":"2026-05-15T05:26:22Z","timestamp":1778822782943,"version":"3.51.4"},"reference-count":60,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2024,8,10]],"date-time":"2024-08-10T00:00:00Z","timestamp":1723248000000},"content-version":"vor","delay-in-days":16,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Greater Bay Area Institute of Precision Medicine","award":["I0007"],"award-info":[{"award-number":["I0007"]}]},{"DOI":"10.13039\/501100012456","name":"National Social Science Foundation","doi-asserted-by":"publisher","award":["32370639"],"award-info":[{"award-number":["32370639"]}],"id":[{"id":"10.13039\/501100012456","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003453","name":"Natural Science Foundation of Guangdong Province","doi-asserted-by":"publisher","award":["2024A1515012116"],"award-info":[{"award-number":["2024A1515012116"]}],"id":[{"id":"10.13039\/501100003453","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100022821","name":"Shanghai Key Laboratory of Psychotic Disorders","doi-asserted-by":"publisher","award":["21-K01"],"award-info":[{"award-number":["21-K01"]}],"id":[{"id":"10.13039\/100022821","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Hector II Foundation"},{"name":"German Federal Ministry of Education and Research","award":["01EK2101B"],"award-info":[{"award-number":["01EK2101B"]}]},{"name":"German Center for Mental Health"},{"name":"Buchholz-Fachinformationsdienst GmbH"},{"DOI":"10.13039\/501100003554","name":"Lundbeck Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003554","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,7,25]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Navigating the complex landscape of high-dimensional omics data with machine learning models presents a significant challenge. The integration of biological domain knowledge into these models has shown promise in creating more meaningful stratifications of predictor variables, leading to algorithms that are both more accurate and generalizable. However, the wider availability of machine learning tools capable of incorporating such biological knowledge remains limited. Addressing this gap, we introduce BioM2, a novel R package designed for biologically informed multistage machine learning. BioM2 uniquely leverages biological information to effectively stratify and aggregate high-dimensional biological data in the context of machine learning. Demonstrating its utility with genome-wide DNA methylation and transcriptome-wide gene expression data, BioM2 has shown to enhance predictive performance, surpassing traditional machine learning models that operate without the integration of biological knowledge. A key feature of BioM2 is its ability to rank predictor variables within biological categories, specifically Gene Ontology pathways. This functionality not only aids in the interpretability of the results but also enables a subsequent modular network analysis of these variables, shedding light on the intricate systems-level biology underpinning the predictive outcome. We have proposed a biologically informed multistage machine learning framework termed BioM2 for phenotype prediction based on omics data. BioM2 has been incorporated into the BioM2 CRAN package (https:\/\/cran.r-project.org\/web\/packages\/BioM2\/index.html).<\/jats:p>","DOI":"10.1093\/bib\/bbae384","type":"journal-article","created":{"date-parts":[[2024,8,10]],"date-time":"2024-08-10T15:09:05Z","timestamp":1723302545000},"source":"Crossref","is-referenced-by-count":8,"title":["<i>BioM2<\/i>: biologically informed multi-stage machine learning for phenotype prediction using omics data"],"prefix":"10.1093","volume":"25","author":[{"given":"Shunjie","family":"Zhang","sequence":"first","affiliation":[{"name":"School of Biology and Biological Engineering, South China University of Technology , Guangzhou , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pan","family":"Li","sequence":"additional","affiliation":[{"name":"Center for Intelligent Medicine , Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, , No. 6, 2nd Nanjiang Road, Nansha District, 511462 Guangzhou , China"},{"name":"Fudan University , Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, , No. 6, 2nd Nanjiang Road, Nansha District, 511462 Guangzhou , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shenghan","family":"Wang","sequence":"additional","affiliation":[{"name":"Center for Intelligent Medicine , Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, , No. 6, 2nd Nanjiang Road, Nansha District, 511462 Guangzhou , China"},{"name":"Fudan University , Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, , No. 6, 2nd Nanjiang Road, Nansha District, 511462 Guangzhou , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jijun","family":"Zhu","sequence":"additional","affiliation":[{"name":"Center for Intelligent Medicine , Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, , No. 6, 2nd Nanjiang Road, Nansha District, 511462 Guangzhou , China"},{"name":"Fudan University , Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, , No. 6, 2nd Nanjiang Road, Nansha District, 511462 Guangzhou , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhongting","family":"Huang","sequence":"additional","affiliation":[{"name":"Center for Intelligent Medicine , Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, , No. 6, 2nd Nanjiang Road, Nansha District, 511462 Guangzhou , China"},{"name":"Fudan University , Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, , No. 6, 2nd Nanjiang Road, Nansha District, 511462 Guangzhou , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fuqiang","family":"Cai","sequence":"additional","affiliation":[{"name":"School of Biology and Biological Engineering, South China University of Technology , Guangzhou , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sebastian","family":"Freidel","sequence":"additional","affiliation":[{"name":"Hector Institute for Artificial Intelligence in Psychiatry , Central Institute of Mental Health, Medical Faculty Mannheim, , M7, Mannheim 68161 , Germany"},{"name":"Heidelberg University , Central Institute of Mental Health, Medical Faculty Mannheim, , M7, Mannheim 68161 , Germany"},{"name":"Department of Psychiatry and Psychotherapy , Central Institute of Mental Health, Medical Faculty Mannheim, , J5, Mannheim 68159 , Germany"},{"name":"Heidelberg University , Central Institute of Mental Health, Medical Faculty Mannheim, , J5, Mannheim 68159 , Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fei","family":"Ling","sequence":"additional","affiliation":[{"name":"School of Biology and Biological Engineering, South China University of Technology , Guangzhou , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0261-5063","authenticated-orcid":false,"given":"Emanuel","family":"Schwarz","sequence":"additional","affiliation":[{"name":"Hector Institute for Artificial Intelligence in Psychiatry , Central Institute of Mental Health, Medical Faculty Mannheim, , M7, Mannheim 68161 , Germany"},{"name":"Heidelberg University , Central Institute of Mental Health, Medical Faculty Mannheim, , M7, Mannheim 68161 , Germany"},{"name":"Department of Psychiatry and Psychotherapy , Central Institute of Mental Health, Medical Faculty Mannheim, , J5, Mannheim 68159 , Germany"},{"name":"Heidelberg University , Central Institute of Mental Health, Medical Faculty Mannheim, , J5, Mannheim 68159 , Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2057-9019","authenticated-orcid":false,"given":"Junfang","family":"Chen","sequence":"additional","affiliation":[{"name":"Center for Intelligent Medicine , Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, , No. 6, 2nd Nanjiang Road, Nansha District, 511462 Guangzhou , China"},{"name":"Fudan University , Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, , No. 6, 2nd Nanjiang Road, Nansha District, 511462 Guangzhou , China"},{"name":"Center for Evolutionary Biology , School of Life Sciences, Fudan University, Shanghai , China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2024,8,10]]},"reference":[{"key":"2024081014142742300_ref1","doi-asserted-by":"crossref","first-page":"947","DOI":"10.1016\/j.tcb.2022.04.008","article-title":"Technological and 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