{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2022,4,1]],"date-time":"2022-04-01T01:26:31Z","timestamp":1648776391133},"reference-count":29,"publisher":"World Scientific Pub Co Pte Lt","issue":"05","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Bioinform. Comput. Biol."],"published-print":{"date-parts":[[2016,10]]},"abstract":"<jats:p> RNA-seq, the next generation sequencing platform, enables researchers to explore deep into the transcriptome of organisms, such as identifying functional non-coding RNAs (ncRNAs), and quantify their expressions on tissues. The functions of ncRNAs are mostly related to their secondary structures. Thus by exploring the clustering in terms of structural profiles of the corresponding read-segments would be essential and this fuels in our motivation behind this research. In this manuscript we proposed PR2S2Clust, Patched RNA-seq Read Segments\u2019 Structure-oriented Clustering, which is an analysis platform to extract features to prepare the secondary structure profiles of the RNA-seq read segments. It provides a strategy to employ the profiles to annotate the segments into ncRNA classes using several clustering strategies. The system considers seven pairwise structural distance metrics by considering short-read mappings onto each structure, which we term as the \u201cpatched structure\u201d while clustering the segments. In this regard, we show applications of both classical and ensemble clusterings of the partitional and hierarchical variations. Extensive real-world experiments over three publicly available RNA-seq datasets and a comparative analysis over four competitive systems confirm the effectiveness and superiority of the proposed system. The source codes and dataset of PR2S2Clust are available at the http:\/\/biomecis.uta.edu\/~ashis\/res\/PR2S2Clust-suppl\/ . <\/jats:p>","DOI":"10.1142\/s021972001650027x","type":"journal-article","created":{"date-parts":[[2016,7,26]],"date-time":"2016-07-26T00:09:42Z","timestamp":1469491782000},"page":"1650027","source":"Crossref","is-referenced-by-count":2,"title":["PR2S2Clust: Patched RNA-seq read segments\u2019 structure-oriented clustering"],"prefix":"10.1142","volume":"14","author":[{"given":"Ashis Kumer","family":"Biswas","sequence":"first","affiliation":[{"name":"Department of Computer Science and Engineering, The University of Texas at Arlington, Texas 76019, USA"}]},{"given":"Jean X.","family":"Gao","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Engineering, The University of Texas at Arlington, Texas 76019, USA"}]}],"member":"219","published-online":{"date-parts":[[2016,11,3]]},"reference":[{"key":"S021972001650027XBIB001","doi-asserted-by":"publisher","DOI":"10.1038\/nrg2484"},{"key":"S021972001650027XBIB002","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp120"},{"key":"S021972001650027XBIB003","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp419"},{"key":"S021972001650027XBIB004","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btr598"},{"key":"S021972001650027XBIB005","doi-asserted-by":"publisher","DOI":"10.3389\/fgene.2013.00133"},{"key":"S021972001650027XBIB006","doi-asserted-by":"publisher","DOI":"10.1016\/j.sbi.2006.05.010"},{"key":"S021972001650027XBIB007","doi-asserted-by":"publisher","DOI":"10.1038\/nbt1144"},{"key":"S021972001650027XBIB008","doi-asserted-by":"publisher","DOI":"10.1093\/hmg\/ddl046"},{"key":"S021972001650027XBIB009","doi-asserted-by":"publisher","DOI":"10.1016\/S0092-8674(04)00045-5"},{"key":"S021972001650027XBIB010","doi-asserted-by":"publisher","DOI":"10.1038\/nsmb729"},{"key":"S021972001650027XBIB011","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/16.7.583"},{"key":"S021972001650027XBIB012","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0409169102"},{"key":"S021972001650027XBIB013","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.0030065"},{"key":"S021972001650027XBIB014","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.0030193"},{"key":"S021972001650027XBIB015","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bts224"},{"key":"S021972001650027XBIB016","doi-asserted-by":"publisher","DOI":"10.1109\/TPAMI.2005.113"},{"key":"S021972001650027XBIB017","first-page":"583","volume":"3","author":"Strehl A","year":"2003","journal-title":"J Mach Learn Res"},{"key":"S021972001650027XBIB018","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp419"},{"key":"S021972001650027XBIB019","doi-asserted-by":"publisher","DOI":"10.1007\/BF01908075"},{"key":"S021972001650027XBIB020","doi-asserted-by":"publisher","DOI":"10.1101\/gr.7179508"},{"key":"S021972001650027XBIB021","doi-asserted-by":"publisher","DOI":"10.1101\/gr.106849.110"},{"key":"S021972001650027XBIB022","doi-asserted-by":"publisher","DOI":"10.1007\/BF00818163"},{"key":"S021972001650027XBIB023","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkp367"},{"key":"S021972001650027XBIB025","doi-asserted-by":"publisher","DOI":"10.1109\/TIT.1976.1055501"},{"key":"S021972001650027XBIB026","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btg295"},{"key":"S021972001650027XBIB028","doi-asserted-by":"publisher","DOI":"10.1007\/s10878-012-9505-8"},{"key":"S021972001650027XBIB029","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-642-38067-9_27"},{"key":"S021972001650027XBIB032","doi-asserted-by":"publisher","DOI":"10.1261\/rna.029041.111"},{"key":"S021972001650027XBIB033","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gki473"}],"container-title":["Journal of Bioinformatics and Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.worldscientific.com\/doi\/pdf\/10.1142\/S021972001650027X","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,8,7]],"date-time":"2019-08-07T12:14:42Z","timestamp":1565180082000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.worldscientific.com\/doi\/abs\/10.1142\/S021972001650027X"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,10]]},"references-count":29,"journal-issue":{"issue":"05","published-online":{"date-parts":[[2016,11,3]]},"published-print":{"date-parts":[[2016,10]]}},"alternative-id":["10.1142\/S021972001650027X"],"URL":"https:\/\/doi.org\/10.1142\/s021972001650027x","relation":{},"ISSN":["0219-7200","1757-6334"],"issn-type":[{"value":"0219-7200","type":"print"},{"value":"1757-6334","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,10]]}}}