{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,6]],"date-time":"2026-04-06T14:39:08Z","timestamp":1775486348148,"version":"3.50.1"},"reference-count":51,"publisher":"Oxford University Press (OUP)","issue":"21","license":[{"start":{"date-parts":[[2019,4,9]],"date-time":"2019-04-09T00:00:00Z","timestamp":1554768000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"United States National Science Foundation Collaborative Research","award":["DBI-1458515"],"award-info":[{"award-number":["DBI-1458515"]}]},{"name":"Green Super Rice for the Resource Poor Africa and Asia Phase III"},{"name":"International Rice Research Institute","award":["A-2015-50"],"award-info":[{"award-number":["A-2015-50"]}]},{"name":"International Rice Research Institute","award":["DRPC2015-49"],"award-info":[{"award-number":["DRPC2015-49"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>Genomic scanning approaches that detect one locus at a time are subject to many problems in genome-wide association studies and quantitative trait locus mapping. The problems include large matrix inversion, over-conservativeness for tests after Bonferroni correction and difficulty in evaluation of the total genetic contribution to a trait\u2019s variance. Targeting these problems, we take a further step and investigate a multiple locus model that detects all markers simultaneously in a single model.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We developed a sparse Bayesian learning (SBL) method for quantitative trait locus mapping and genome-wide association studies. This new method adopts a coordinate descent algorithm to estimate parameters (marker effects) by updating one parameter at a time conditional on current values of all other parameters. It uses an L2 type of penalty that allows the method to handle extremely large sample sizes (&amp;gt;100\u2009000). Simulation studies show that SBL often has higher statistical powers and the simulated true loci are often detected with extremely small P-values, indicating that SBL is insensitive to stringent thresholds in significance testing.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>An R package (sbl) is available on the comprehensive R archive network (CRAN) and https:\/\/github.com\/MeiyueComputBio\/sbl\/tree\/master\/R%20packge.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz244","type":"journal-article","created":{"date-parts":[[2019,4,6]],"date-time":"2019-04-06T03:42:54Z","timestamp":1554522174000},"page":"4327-4335","source":"Crossref","is-referenced-by-count":5,"title":["A coordinate descent approach for sparse Bayesian learning in high dimensional QTL mapping and genome-wide association studies"],"prefix":"10.1093","volume":"35","author":[{"given":"Meiyue","family":"Wang","sequence":"first","affiliation":[{"name":"Department of Botany and Plant Sciences, University of California , Riverside, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shizhong","family":"Xu","sequence":"additional","affiliation":[{"name":"Department of Botany and Plant Sciences, University of California , Riverside, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,4,9]]},"reference":[{"key":"2023062712472422400_btz244-B1","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the false discovery rate: a practical and powerful approach to multiple testing","volume":"57","author":"Benjamini","year":"1995","journal-title":"J. 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