{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,9]],"date-time":"2026-01-09T20:57:10Z","timestamp":1767992230473,"version":"3.49.0"},"reference-count":49,"publisher":"Oxford University Press (OUP)","issue":"6","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Phosphorylation is the most important post-translational modification in eukaryotes. Although many computational phosphorylation site prediction tools exist for mammals, and a few were created specifically for Arabidopsis thaliana, none are currently available for other plants.<\/jats:p>\n               <jats:p>Results: In this article, we propose a novel random forest-based method called PHOSFER (PHOsphorylation Site FindER) for applying phosphorylation data from other organisms to enhance the accuracy of predictions in a target organism. As a test case, PHOSFER is applied to phosphorylation sites in soybean, and we show that it more accurately predicts soybean sites than both the existing Arabidopsis-specific predictors, and a simpler machine-learning scheme that uses only known phosphorylation sites and non-phosphorylation sites from soybean. In addition to soybean, PHOSFER will be extended to other organisms in the near future.<\/jats:p>\n               <jats:p>Availability: PHOSFER is available via a web interface at http:\/\/saphire.usask.ca.<\/jats:p>\n               <jats:p>Contact: \u00a0brett.trost@usask.ca<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt031","type":"journal-article","created":{"date-parts":[[2013,1,23]],"date-time":"2013-01-23T05:48:54Z","timestamp":1358920134000},"page":"686-694","source":"Crossref","is-referenced-by-count":42,"title":["Computational phosphorylation site prediction in plants using random forests and organism-specific instance weights"],"prefix":"10.1093","volume":"29","author":[{"given":"Brett","family":"Trost","sequence":"first","affiliation":[{"name":"Department of Computer Science, University of Saskatchewan, Saskatoon, SK S7N 5C9, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anthony","family":"Kusalik","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Saskatchewan, Saskatoon, SK S7N 5C9, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2013,1,22]]},"reference":[{"key":"2023012810285645600_btt031-B1","doi-asserted-by":"crossref","first-page":"D115","DOI":"10.1093\/nar\/gkh131","article-title":"UniProt: the Universal Protein knowledgebase","volume":"32","author":"Apweiler","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2023012810285645600_btt031-B2","doi-asserted-by":"crossref","first-page":"273","DOI":"10.1186\/1471-2105-11-273","article-title":"Machine learning approach to predict protein phosphorylation sites by incorporating evolutionary information","volume":"11","author":"Biswas","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2023012810285645600_btt031-B3","doi-asserted-by":"crossref","first-page":"1351","DOI":"10.1006\/jmbi.1999.3310","article-title":"Sequence and structure-based prediction of eukaryotic protein phosphorylation sites","volume":"294","author":"Blom","year":"1999","journal-title":"J. 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