{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,25]],"date-time":"2026-02-25T12:26:28Z","timestamp":1772022388899,"version":"3.50.1"},"reference-count":24,"publisher":"Oxford University Press (OUP)","issue":"22","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2007,11,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: Most computational methodologies for miRNA:mRNA target gene prediction use the seed segment of the miRNA and require cross-species sequence conservation in this region of the mRNA target. Methods that do not rely on conservation generate numbers of predictions, which are too large to validate. We describe a target prediction method (NBmiRTar) that does not require sequence conservation, using instead, machine learning by a na\u00efve Bayes classifier. It generates a model from sequence and miRNA:mRNA duplex information from validated targets and artificially generated negative examples. Both the \u2018seed\u2019 and \u2018out-seed\u2019 segments of the miRNA:mRNA duplex are used for target identification.<\/jats:p><jats:p>Results: The application of machine-learning techniques to the features we have used is a useful and general approach for microRNA target gene prediction. Our technique produces fewer false positive predictions and fewer target candidates to be tested. It exhibits higher sensitivity and specificity than algorithms that rely on conserved genomic regions to decrease false positive predictions.<\/jats:p><jats:p>Availability: The NBmiRTar program is available at http:\/\/wotan.wistar.upenn.edu\/NBmiRTar\/<\/jats:p><jats:p>Contact: \u00a0yousef@wistar.org<\/jats:p><jats:p>Supplementary information: \u00a0http:\/\/wotan.wistar.upenn.edu\/NBmiRTar\/<\/jats:p>","DOI":"10.1093\/bioinformatics\/btm484","type":"journal-article","created":{"date-parts":[[2007,10,10]],"date-time":"2007-10-10T00:24:37Z","timestamp":1191975877000},"page":"2987-2992","source":"Crossref","is-referenced-by-count":125,"title":["Na\u00efve Bayes for microRNA target predictions\u2014machine learning for microRNA targets"],"prefix":"10.1093","volume":"23","author":[{"given":"Malik","family":"Yousef","sequence":"first","affiliation":[{"name":"The Wistar Institute, Philadelphia, PA 19104, USA"}]},{"given":"Segun","family":"Jung","sequence":"additional","affiliation":[{"name":"The Wistar Institute, Philadelphia, PA 19104, USA"}]},{"given":"Andrew V.","family":"Kossenkov","sequence":"additional","affiliation":[{"name":"The Wistar Institute, Philadelphia, PA 19104, USA"}]},{"given":"Louise C.","family":"Showe","sequence":"additional","affiliation":[{"name":"The Wistar Institute, Philadelphia, PA 19104, USA"}]},{"given":"Michael K.","family":"Showe","sequence":"additional","affiliation":[{"name":"The Wistar Institute, Philadelphia, PA 19104, USA"}]}],"member":"286","published-online":{"date-parts":[[2007,10,8]]},"reference":[{"key":"2023041208261343200_","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1016\/S0092-8674(04)00045-5","article-title":"MicroRNAs: genomics, biogenesis, mechanism, and function","volume":"116","author":"Bartel","year":"2004","journal-title":"Cell"},{"key":"2023041208261343200_","doi-asserted-by":"crossref","first-page":"e85","DOI":"10.1371\/journal.pbio.0030085","article-title":"Principles of microRNA-target recognition","volume":"3","author":"Brennecke","year":"2005","journal-title":"PLoS Biol."},{"key":"2023041208261343200_","doi-asserted-by":"crossref","first-page":"1288","DOI":"10.1101\/gad.1310605","article-title":"The developmental miRNA profiles of zebrafish as determined by small RNA cloning","volume":"19","author":"Chen","year":"2005","journal-title":"Genes Dev."},{"key":"2023041208261343200_","doi-asserted-by":"crossref","first-page":"R1","DOI":"10.1186\/gb-2003-5-1-r1","article-title":"MicroRNA targets in Drosophila","volume":"5","author":"Enright","year":"2003","journal-title":"Genome Biol."},{"key":"2023041208261343200_","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1016\/j.molcel.2007.06.017","article-title":"MicroRNA targeting specificity in mammals: determinants beyond seed pairing","volume":"27","author":"Grimson","year":"2007","journal-title":"Mol. 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