{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,8]],"date-time":"2026-01-08T02:48:11Z","timestamp":1767840491012,"version":"3.49.0"},"reference-count":34,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2018,4,25]],"date-time":"2018-04-25T00:00:00Z","timestamp":1524614400000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100004612","name":"Funda\u00e7\u00e3o Arauc\u00e1ria","doi-asserted-by":"publisher","award":["019\/2015"],"award-info":[{"award-number":["019\/2015"]}],"id":[{"id":"10.13039\/501100004612","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,3,25]]},"DOI":"10.1093\/bib\/bby034","type":"journal-article","created":{"date-parts":[[2018,4,4]],"date-time":"2018-04-04T15:11:07Z","timestamp":1522854667000},"page":"682-689","source":"Crossref","is-referenced-by-count":58,"title":["Pattern recognition analysis on long noncoding RNAs: a tool for prediction in plants"],"prefix":"10.1093","volume":"20","author":[{"given":"Tatianne da Costa","family":"Negri","sequence":"first","affiliation":[{"name":"Department of Computer Science, Bioinformatics Graduate Program (PPGBIOINFO), Federal University of Technology - Paran\u00e1, UTFPR, Campus Corn\u00e9lio, Proc\u00f3pio, Brazil and Informatics and Knowledge Management Graduate Program, Universidade Nove de Julho, S\u00e3o Paulo, Brazil"}]},{"given":"Wonder Alexandre Luz","family":"Alves","sequence":"additional","affiliation":[{"name":"Informatics and Knowledge Management Graduate Program, Universidade Nove de Julho, S\u00e3o Paulo, Brazil"}]},{"given":"Pedro Henrique","family":"Bugatti","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Bioinformatics Graduate Program (PPGBIOINFO), Federal University of Technology - Paran\u00e1, UTFPR, Campus Corn\u00e9lio, Proc\u00f3pio, Brazil"}]},{"given":"Priscila Tiemi Maeda","family":"Saito","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Bioinformatics Graduate Program (PPGBIOINFO), Federal University of Technology - Paran\u00e1, UTFPR, Campus Corn\u00e9lio, Proc\u00f3pio, Brazil"}]},{"given":"Douglas Silva","family":"Domingues","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Bioinformatics Graduate Program (PPGBIOINFO), Federal University of Technology - Paran\u00e1, UTFPR, Campus Corn\u00e9lio, Proc\u00f3pio, Brazil and Department of Botany, Institute of Biosciences, S\u00e3o Paulo State University, UNESP, Rio Claro, SP, Brazil"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8887-0582","authenticated-orcid":false,"given":"Alexandre Rossi","family":"Paschoal","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Bioinformatics Graduate Program (PPGBIOINFO), Federal University of Technology - Paran\u00e1, UTFPR, Campus Corn\u00e9lio, Proc\u00f3pio, Brazil"}]}],"member":"286","published-online":{"date-parts":[[2018,4,24]]},"reference":[{"key":"2019061808001793000_bby034-B1","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1146\/annurev-biochem-051410-092902","article-title":"Genome regulation by long noncoding RNAs","volume":"81","author":"Rinn","year":"2012","journal-title":"Annu Rev Biochem"},{"issue":"3","key":"2019061808001793000_bby034-B2","doi-asserted-by":"crossref","first-page":"651","DOI":"10.1534\/genetics.112.146704","article-title":"Long noncoding RNAs: past, present, and future","volume":"193","author":"Kung","year":"2013","journal-title":"Genetics"},{"issue":"3","key":"2019061808001793000_bby034-B3","doi-asserted-by":"crossref","first-page":"300","DOI":"10.1038\/nsmb.2480","article-title":"Structure and function of long noncoding RNAs in epigenetic regulation","volume":"20","author":"Mercer","year":"2013","journal-title":"Nat Struct Mol Biol"},{"issue":"1","key":"2019061808001793000_bby034-B4","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1186\/s12870-017-0984-8","article-title":"Systematic comparison of lncRNAs with protein coding mRNAs in population expression and their response to environmental change","volume":"17","author":"Xu","year":"2017","journal-title":"BMC Plant Biol"},{"issue":"2","key":"2019061808001793000_bby034-B5","doi-asserted-by":"crossref","first-page":"R40","DOI":"10.1186\/gb-2014-15-2-r40","article-title":"Genome-wide discovery and characterization of maize long non-coding RNAs","volume":"15","author":"Li","year":"2014","journal-title":"Genome Biol"},{"issue":"12","key":"2019061808001793000_bby034-B6","doi-asserted-by":"crossref","first-page":"512","DOI":"10.1186\/s13059-014-0512-1","article-title":"Genome-wide screening and functional analysis identify a large number of long noncoding RNAs involved in the sexual reproduction of rice","volume":"15","author":"Zhang","year":"2014","journal-title":"Genome Biol"},{"issue":"6","key":"2019061808001793000_bby034-B7","doi-asserted-by":"crossref","first-page":"e0156723","DOI":"10.1371\/journal.pone.0156723","article-title":"Genome-wide analysis of long noncoding RNAs and their responses to drought stress in cotton (Gossypium hirsutum L.)","volume":"11","author":"Lu","year":"2016","journal-title":"PLoS One"},{"issue":"8","key":"2019061808001793000_bby034-B8","doi-asserted-by":"crossref","first-page":"1033","DOI":"10.1038\/ng2079","article-title":"Target mimicry provides a new mechanism for regulation of microRNA activity","volume":"39","author":"Franco-Zorrilla","year":"2007","journal-title":"Nat Genet"},{"issue":"1","key":"2019061808001793000_bby034-B9","doi-asserted-by":"crossref","first-page":"176","DOI":"10.3390\/genes3010176","article-title":"Molecular functions of long non-coding RNAs in plants","volume":"3","author":"Zhu","year":"2012","journal-title":"Genes"},{"issue":"1","key":"2019061808001793000_bby034-B10","doi-asserted-by":"crossref","first-page":"655","DOI":"10.1186\/s12864-016-2929-2","article-title":"Systematic characterization of novel lncRNAs responding to phosphate starvation in Arabidopsis thaliana","volume":"17","author":"Yuan","year":"2016","journal-title":"BMC Genomics"},{"issue":"7274","key":"2019061808001793000_bby034-B11","doi-asserted-by":"crossref","first-page":"799","DOI":"10.1038\/nature08618","article-title":"Cold-induced silencing by long antisense transcripts of an Arabidopsis Polycomb target","volume":"462","author":"Swiezewski","year":"2009","journal-title":"Nature"},{"issue":"6-7","key":"2019061808001793000_bby034-B12","doi-asserted-by":"crossref","first-page":"685","DOI":"10.1007\/s10577-013-9392-6","article-title":"Epigenetic regulation by long noncoding RNAs in plants","volume":"21","author":"Heo","year":"2013","journal-title":"Chromosome Res"},{"issue":"4","key":"2019061808001793000_bby034-B13","doi-asserted-by":"crossref","first-page":"474","DOI":"10.1261\/rna.049965.115","article-title":"RNA World research-still evolving","volume":"21","author":"Cech","year":"2015","journal-title":"RNA"},{"issue":"22","key":"2019061808001793000_bby034-B14","doi-asserted-by":"crossref","first-page":"e183","DOI":"10.1093\/nar\/gkx866","article-title":"PLncPRO for prediction of long non-coding RNAs (lncRNAs) in plants and its application for discovery of abiotic stress-responsive lncRNAs in rice and chickpea","volume":"45","author":"Singh","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2019061808001793000_bby034-B15","doi-asserted-by":"crossref","first-page":"W345","DOI":"10.1093\/nar\/gkm391","article-title":"CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine","volume":"35(suppl_2)","author":"Kong","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"2019061808001793000_bby034-B16","doi-asserted-by":"crossref","first-page":"W12","DOI":"10.1093\/nar\/gkx428","article-title":"CPC2: a fast and accurate coding potential calculator based on sequence intrinsic features","volume":"45","author":"Kang","year":"2017","journal-title":"Nucleic Acids Res"},{"issue":"D1","key":"2019061808001793000_bby034-B17","doi-asserted-by":"crossref","first-page":"D982","DOI":"10.1093\/nar\/gku1162","article-title":"PNRD: a plant non-coding RNA database","volume":"43","author":"Yi","year":"2015","journal-title":"Nucleic Acids Res"},{"issue":"2","key":"2019061808001793000_bby034-B18","doi-asserted-by":"crossref","first-page":"404","DOI":"10.1111\/tpj.13018","article-title":"Analysis of non-coding transcriptome in rice and maize uncovers roles of conserved lncRNAs associated with agriculture traits","volume":"84","author":"Wang","year":"2015","journal-title":"Plant J"},{"issue":"1","key":"2019061808001793000_bby034-B19","doi-asserted-by":"crossref","first-page":"34109","DOI":"10.1038\/srep34109","article-title":"Genome-wide long non-coding RNA screening, identification and characterization in a model microorganism Chlamydomonas reinhardtii","volume":"6","author":"Li","year":"2016","journal-title":"Sci Rep"},{"issue":"7","key":"2019061808001793000_bby034-B20","doi-asserted-by":"crossref","first-page":"e0158784","DOI":"10.1371\/journal.pone.0158784","article-title":"Genome wide identification and functional prediction of long non-coding RNAs responsive to sclerotinia sclerotiorum infection in Brassica napus","volume":"11","author":"Joshi","year":"2016","journal-title":"PLoS One"},{"issue":"6","key":"2019061808001793000_bby034-B21","doi-asserted-by":"crossref","first-page":"e74","DOI":"10.1093\/nar\/gkt006","article-title":"CPAT: coding-potential assessment tool using an alignment-free logistic regression model","volume":"41","author":"Wang","year":"2013","journal-title":"Nucleic Acids Res"},{"issue":"2","key":"2019061808001793000_bby034-B22","doi-asserted-by":"crossref","first-page":"328","DOI":"10.1016\/j.gene.2015.07.069","article-title":"PLNlncRbase: a resource for experimentally identified lncRNAs in plants","volume":"573","author":"Xuan","year":"2015","journal-title":"Gene"},{"issue":"D1","key":"2019061808001793000_bby034-B23","doi-asserted-by":"crossref","first-page":"D1161","DOI":"10.1093\/nar\/gkv1215","article-title":"GREENC: a Wiki-based database of plant lncRNAs","volume":"44","author":"Paytuvi Gallart","year":"2016","journal-title":"Nucleic Acids Res"},{"issue":"D1","key":"2019061808001793000_bby034-B24","doi-asserted-by":"crossref","first-page":"D1178","DOI":"10.1093\/nar\/gkr944","article-title":"Phytozome: a comparative platform for green plant genomics","volume":"40","author":"Goodstein","year":"2012","journal-title":"Nucleic Acids Res"},{"issue":"13","key":"2019061808001793000_bby034-B25","doi-asserted-by":"crossref","first-page":"1658","DOI":"10.1093\/bioinformatics\/btl158","article-title":"Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences","volume":"22","author":"Li","year":"2006","journal-title":"Bioinformatics"},{"issue":"1","key":"2019061808001793000_bby034-B26","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1186\/1748-7188-6-26","article-title":"ViennaRNA Package 2.0","volume":"6","author":"Lorenz","year":"2011","journal-title":"Algorithms Mol Biol"},{"issue":"1","key":"2019061808001793000_bby034-B27","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1145\/1656274.1656278","article-title":"The WEKA data mining software: an update","volume":"11","author":"Hall","year":"2009","journal-title":"SIGKDD Explor"},{"issue":"1-2","key":"2019061808001793000_bby034-B28","doi-asserted-by":"crossref","first-page":"273","DOI":"10.1016\/S0004-3702(97)00043-X","article-title":"Wrappers for feature subset selection","volume":"97","author":"Kohavi","year":"1997","journal-title":"Artif Intell"},{"key":"2019061808001793000_bby034-B29","volume-title":"Data Mining: Practical Machine Learning Tools and Techniques","author":"Witten","year":"2011"},{"key":"2019061808001793000_bby034-B30","volume-title":"Pattern Classification","author":"Duda","year":"1973"},{"issue":"4","key":"2019061808001793000_bby034-B31","doi-asserted-by":"crossref","first-page":"1663","DOI":"10.1007\/s00438-016-1210-3","article-title":"Genome-wide identification and characterization of novel lncRNAs in Populus under nitrogen deficiency","volume":"291","author":"Chen","year":"2016","journal-title":"Mol Genet Genomics"},{"issue":"4","key":"2019061808001793000_bby034-B32","doi-asserted-by":"crossref","first-page":"1181","DOI":"10.1111\/nph.13429","article-title":"Long noncoding RNAs and their proposed functions in fibre development of cotton (Gossypium spp.)","volume":"207","author":"Wang","year":"2015","journal-title":"New Phytol"},{"issue":"1","key":"2019061808001793000_bby034-B33","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1007\/s00425-014-2168-1","article-title":"Genome-wide identification of novel long non-coding RNAs in Populus tomentosa tension wood, opposite wood and normal wood xylem by RNA-seq","volume":"241","author":"Chen","year":"2015","journal-title":"Planta"},{"issue":"1","key":"2019061808001793000_bby034-B34","doi-asserted-by":"crossref","first-page":"11252.","DOI":"10.1038\/s41598-017-11206-z","article-title":"Long noncoding RNAs in the model species Brachypodium distachyon","volume":"7","author":"Quattro","year":"2017","journal-title":"Sci Rep"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bib\/article-pdf\/20\/2\/682\/28834078\/bby034.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,6,18]],"date-time":"2019-06-18T08:02:59Z","timestamp":1560844979000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/20\/2\/682\/4985385"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,4,24]]},"references-count":34,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2018,4,24]]},"published-print":{"date-parts":[[2019,3,25]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bby034","relation":{},"ISSN":["1477-4054"],"issn-type":[{"value":"1477-4054","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2019,3]]},"published":{"date-parts":[[2018,4,24]]}}}