{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,7]],"date-time":"2026-02-07T04:03:46Z","timestamp":1770437026242,"version":"3.49.0"},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"2","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Small RNA sequencing and degradome sequencing (also known as parallel analysis of RNA ends) have provided rich information on the microRNA (miRNA) and its cleaved mRNA targets on a genome-wide scale in plants, but no computational tools have been developed to effectively and conveniently deconvolute the miRNA\u2013target interaction (MTI).<\/jats:p>\n               <jats:p>Results: A freely available package, MTide, was developed by combining modified miRDeep2 and CleaveLand4 with some other useful scripts to explore MTI in a comprehensive way. By searching for targets of a complete miRNAs, we can facilitate large-scale identification of miRNA targets, allowing us to discover regulatory interaction networks.<\/jats:p>\n               <jats:p>Availability and implementation: \u00a0http:\/\/bis.zju.edu.cn\/MTide<\/jats:p>\n               <jats:p>Contact: \u00a0mchen@zju.edu.cn<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu633","type":"journal-article","created":{"date-parts":[[2014,9,26]],"date-time":"2014-09-26T00:20:55Z","timestamp":1411690855000},"page":"290-291","source":"Crossref","is-referenced-by-count":73,"title":["MTide: an integrated tool for the identification of miRNA\u2013target interaction in plants"],"prefix":"10.1093","volume":"31","author":[{"given":"Zhao","family":"Zhang","sequence":"first","affiliation":[{"name":"1 Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China and 2 Department of Control Science and Engineering, Zhejiang University, Hangzhou 310058, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Li","family":"Jiang","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China and 2 Department of Control Science and Engineering, Zhejiang University, Hangzhou 310058, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jingjing","family":"Wang","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China and 2 Department of Control Science and Engineering, Zhejiang University, Hangzhou 310058, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peizhen","family":"Gu","sequence":"additional","affiliation":[{"name":"1 Department 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