{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,7]],"date-time":"2026-02-07T07:43:17Z","timestamp":1770450197545,"version":"3.49.0"},"reference-count":33,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2017,11,9]],"date-time":"2017-11-09T00:00:00Z","timestamp":1510185600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/100007225","name":"Ministry of Science and Technology","doi-asserted-by":"publisher","award":["MOST 105-2311-B-006 -004-MY3"],"award-info":[{"award-number":["MOST 105-2311-B-006 -004-MY3"]}],"id":[{"id":"10.13039\/100007225","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007225","name":"Ministry of Science and Technology","doi-asserted-by":"publisher","award":["MOST 104-2313-B-006-002"],"award-info":[{"award-number":["MOST 104-2313-B-006-002"]}],"id":[{"id":"10.13039\/100007225","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001869","name":"Academia Sinica","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001869","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>MicroRNAs (miRNAs) are endogenous non-coding small RNAs (of about 22 nucleotides), which play an important role in the post-transcriptional regulation of gene expression via either mRNA cleavage or translation inhibition. Several machine learning-based approaches have been developed to identify novel miRNAs from next generation sequencing (NGS) data. Typically, precursor\/genomic sequences are required as references for most methods. However, the non-availability of genomic sequences is often a limitation in miRNA discovery in non-model plants. A systematic approach to determine novel miRNAs without reference sequences is thus necessary.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>In this study, an effective method was developed to identify miRNAs from non-model plants based only on NGS datasets. The miRNA prediction model was trained with several duplex structure-related features of mature miRNAs and their passenger strands using a support vector machine algorithm. The accuracy of the independent test reached 96.61% and 93.04% for dicots (Arabidopsis) and monocots (rice), respectively. Furthermore, true small RNA sequencing data from orchids was tested in this study. Twenty-one predicted orchid miRNAs were selected and experimentally validated. Significantly, 18 of them were confirmed in the qRT-PCR experiment. This novel approach was also compiled as a user-friendly program called microRPM (miRNA Prediction Model).<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>This resource is freely available at http:\/\/microRPM.itps.ncku.edu.tw.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx725","type":"journal-article","created":{"date-parts":[[2017,11,8]],"date-time":"2017-11-08T12:12:53Z","timestamp":1510143173000},"page":"1108-1115","source":"Crossref","is-referenced-by-count":25,"title":["microRPM: a microRNA prediction model based only on plant small RNA sequencing data"],"prefix":"10.1093","volume":"34","author":[{"given":"Kuan-Chieh","family":"Tseng","sequence":"first","affiliation":[{"name":"College of Biosciences and Biotechnology, Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yi-Fan","family":"Chiang-Hsieh","sequence":"additional","affiliation":[{"name":"College of Biosciences and Biotechnology, Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hsuan","family":"Pai","sequence":"additional","affiliation":[{"name":"Institute of Plant and Microbial Biology, Academia Sinica, NanKang, Taipei, Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chi-Nga","family":"Chow","sequence":"additional","affiliation":[{"name":"College of Biosciences and Biotechnology, Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shu-Chuan","family":"Lee","sequence":"additional","affiliation":[{"name":"Institute of Plant and Microbial Biology, Academia Sinica, NanKang, Taipei, Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Han-Qin","family":"Zheng","sequence":"additional","affiliation":[{"name":"College of Biosciences and Biotechnology, Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Po-Li","family":"Kuo","sequence":"additional","affiliation":[{"name":"College of Biosciences and Biotechnology, Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Guan-Zhen","family":"Li","sequence":"additional","affiliation":[{"name":"College of Biosciences and Biotechnology, Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yu-Cheng","family":"Hung","sequence":"additional","affiliation":[{"name":"College of Biosciences and Biotechnology, Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Na-Sheng","family":"Lin","sequence":"additional","affiliation":[{"name":"Institute of Plant and Microbial Biology, Academia Sinica, NanKang, Taipei, Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wen-Chi","family":"Chang","sequence":"additional","affiliation":[{"name":"College of Biosciences and Biotechnology, Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2017,11,9]]},"reference":[{"key":"2023012712563420200_btx725-B1","doi-asserted-by":"crossref","first-page":"D991","DOI":"10.1093\/nar\/gks1193","article-title":"NCBI GEO: archive for functional genomics data sets\u2013update","volume":"41","author":"Barrett","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2023012712563420200_btx725-B2","doi-asserted-by":"crossref","first-page":"D226","DOI":"10.1093\/nar\/gks1005","article-title":"Rfam 11.0: 10 years of RNA families","volume":"41","author":"Burge","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2023012712563420200_btx725-B3","first-page":"27.","article-title":"LIBSVM: a library for support vector machines","volume":"2","author":"Chang","year":"2011","journal-title":"ACM Trans. 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