{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,24]],"date-time":"2026-01-24T07:46:49Z","timestamp":1769240809691,"version":"3.49.0"},"reference-count":19,"publisher":"Oxford University Press (OUP)","issue":"22","license":[{"start":{"date-parts":[[2016,8,4]],"date-time":"2016-08-04T00:00:00Z","timestamp":1470268800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Basic Research Program of China","doi-asserted-by":"crossref","award":["2015CB150200"],"award-info":[{"award-number":["2015CB150200"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001809","name":"National Science Foundation of China","doi-asserted-by":"crossref","award":["91435111"],"award-info":[{"award-number":["91435111"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,11,15]]},"abstract":"<jats:p>Motivation: Recent studies reveal an important role of non-coding circular RNA (circRNA) in the control of cellular processes. Because of differences in the organization of plant and mammal genomes, the sensitivity and accuracy of circRNA prediction programs using algorithms developed for animals and humans perform poorly for plants.<\/jats:p>\n               <jats:p>Results: A circRNA prediction software for plants (termed PcircRNA_finder) was developed that is more sensitive in detecting circRNAs than other frequently used programs (such as find_circ and CIRCexplorer), Based on analysis of simulated and real rRNA-\/RNAase R RNA-Seq data from Arabidopsis thaliana and rice PcircRNA_finder provides a more comprehensive sensitive, precise prediction method for plants circRNAs.<\/jats:p>\n               <jats:p>Availability and Implementation: \u00a0http:\/\/ibi.zju.edu.cn\/bioinplant\/tools\/manual.htm.<\/jats:p>\n               <jats:p>Contact: \u00a0fanlj@zju.edu.cn<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw496","type":"journal-article","created":{"date-parts":[[2016,8,5]],"date-time":"2016-08-05T01:54:16Z","timestamp":1470362056000},"page":"3528-3529","source":"Crossref","is-referenced-by-count":64,"title":["PcircRNA_finder: a software for circRNA prediction in plants"],"prefix":"10.1093","volume":"32","author":[{"given":"Li","family":"Chen","sequence":"first","affiliation":[{"name":"1Institute of Crop Sciences & Institute of Bioinformatics"}]},{"given":"Yongyi","family":"Yu","sequence":"additional","affiliation":[{"name":"1Institute of Crop Sciences & Institute of Bioinformatics"}]},{"given":"Xinchen","family":"Zhang","sequence":"additional","affiliation":[{"name":"1Institute of Crop Sciences & Institute of Bioinformatics"}]},{"given":"Chen","family":"Liu","sequence":"additional","affiliation":[{"name":"1Institute of Crop Sciences & Institute of Bioinformatics"}]},{"given":"Chuyu","family":"Ye","sequence":"additional","affiliation":[{"name":"1Institute of Crop Sciences & Institute of Bioinformatics"}]},{"given":"Longjiang","family":"Fan","sequence":"additional","affiliation":[{"name":"1Institute of Crop Sciences & Institute of Bioinformatics"},{"name":"2Research Center of Air Pollution and Health, Zhejiang University, Hangzhou 310058, China"}]}],"member":"286","published-online":{"date-parts":[[2016,8,4]]},"reference":[{"key":"2023020114081834800_btw496-B1","doi-asserted-by":"crossref","first-page":"e29","DOI":"10.1093\/nar\/gkv1013","article-title":"NCLscan: accurate identification of non-co-linear transcripts (fusion, trans-splicing and circular RNA) with a good balance between sensitivity and precision","volume":"44","author":"Chuang","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2023020114081834800_btw496-B2","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-seq aligner","volume":"29","author":"Dobin","year":"2013","journal-title":"Bioinformatics"},{"key":"2023020114081834800_btw496-B3","doi-asserted-by":"crossref","first-page":"384","DOI":"10.1038\/nature11993","article-title":"Natural RNA circles function as efficient microRNA sponges","volume":"495","author":"Hansen","year":"2013","journal-title":"Nature"},{"key":"2023020114081834800_btw496-B4","doi-asserted-by":"crossref","first-page":"R34","DOI":"10.1186\/gb-2014-15-2-r34","article-title":"A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection","volume":"15","author":"Hoffmann","year":"2014","journal-title":"Genome Biol"},{"key":"2023020114081834800_btw496-B5","doi-asserted-by":"crossref","first-page":"453","DOI":"10.1038\/nbt.2890","article-title":"Detecting and characterizing circular RNAs","volume":"32","author":"Jeck","year":"2014","journal-title":"Nat. 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