{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:37Z","timestamp":1772138077235,"version":"3.50.1"},"reference-count":30,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2025,8,29]],"date-time":"2025-08-29T00:00:00Z","timestamp":1756425600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"China Scholarship Council \u2013 University of Melbourne PhD Scholarship"},{"DOI":"10.13039\/501100000925","name":"National Health and Medical Research Council","doi-asserted-by":"publisher","award":["GNT2025648"],"award-info":[{"award-number":["GNT2025648"]}],"id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Integrating the knockoff framework with any variable-selection method delivers stringent false discovery rate (FDR) control without recourse to p-values, offering a powerful alternative for differential expression analysis of high-throughput omics datasets. However, existing knockoff generators rely on restrictive modelling assumptions or coarse approximations that often inflate the FDR when applied to real-world data.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We introduce Partial Least Squares Knockoff (PLSKO), an efficient, assumption-free generator that remains robust across diverse omics platforms. Our extensive simulations show that PLSKO is the only method to maintain FDR control with sufficient power in complex non-linear settings. Our semi-simulation studies drawn from RNA-seq, proteomics, metabolomics, and microbiome experiments confirm PLSKO generates valid knockoff variables. In pre-eclampsia multi-omics case studies, we combine PLSKO with Aggregation Knockoff to address the randomness of knockoffs and improve power, and demonstrate the method\u2019s ability to recover biologically meaningful features.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Our proposed algorithm is available on Github (https:\/\/github.com\/guannan-yang\/PLSKO) and Zenodo (https:\/\/doi.org\/10.5281\/zenodo.16879594)<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf475","type":"journal-article","created":{"date-parts":[[2025,8,27]],"date-time":"2025-08-27T11:41:11Z","timestamp":1756294871000},"source":"Crossref","is-referenced-by-count":0,"title":["PLSKO: a robust knockoff generator to control false discovery rate in omics variable selection"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9134-5551","authenticated-orcid":false,"given":"Guannan","family":"Yang","sequence":"first","affiliation":[{"name":"Melbourne Integrative Genomics, School of Mathematics and Statistics, The University of Melbourne , Parkville, VIC 3010,","place":["Australia"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2440-6665","authenticated-orcid":false,"given":"Ellen","family":"Menkhorst","sequence":"additional","affiliation":[{"name":"Department of Obstetrics and Gynaecology, The University of Melbourne , Parkville, VIC 3010,","place":["Australia"]},{"name":"Gynaecology Research Centre, Royal Women\u2019s Hospital , Parkville, VIC 3010,","place":["Australia"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1425-950X","authenticated-orcid":false,"given":"Evdokia","family":"Dimitriadis","sequence":"additional","affiliation":[{"name":"Department of Obstetrics and Gynaecology, The University of Melbourne , Parkville, VIC 3010,","place":["Australia"]},{"name":"Gynaecology Research Centre, Royal Women\u2019s Hospital , Parkville, VIC 3010,","place":["Australia"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3923-1116","authenticated-orcid":false,"given":"Kim-Anh","family":"L\u00ea Cao","sequence":"additional","affiliation":[{"name":"Melbourne Integrative Genomics, School of Mathematics and Statistics, The University of Melbourne , Parkville, VIC 3010,","place":["Australia"]}]}],"member":"286","published-online":{"date-parts":[[2025,8,29]]},"reference":[{"key":"2025091923394856600_btaf475-B1","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1111\/1468-0262.00273","article-title":"Determining the number of factors in approximate factor models","volume":"70","author":"Bai","year":"2002","journal-title":"Econometrica"},{"key":"2025091923394856600_btaf475-B2","doi-asserted-by":"crossref","first-page":"670","DOI":"10.1902\/jop.2007.060362","article-title":"Evidence of periopathogenic 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