{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,8]],"date-time":"2026-01-08T02:13:29Z","timestamp":1767838409234,"version":"3.49.0"},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"20","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Pseudouridine (\u03a8), catalyzed by pseudouridine synthase (PUS), is the most abundant RNA modification and has important cellular functions. Developing an algorithm to identify \u03a8 sites is an important work. And it is better if the algorithm could assign which PUS modifies the \u03a8 sites. Here, we developed PPUS (http:\/\/lyh.pkmu.cn\/ppus\/), the first web server to predict PUS-specific \u03a8 sites. PPUS employed support vector machine as the classifier and used nucleotides around \u03a8 sites as the features. Currently, PPUS could accurately predict new \u03a8 sites for PUS1, PUS4 and PUS7 in yeast and PUS4 in human. PPUS is well designed and friendly to user.<\/jats:p>\n               <jats:p>Availability and Implementation: Our web server is available freely for non-commercial purposes at: http:\/\/lyh.pkmu.cn\/ppus\/<\/jats:p>\n               <jats:p>Contact: liyanhui@bjmu.edu.cn or cuiqinghua@hsc.pku.edu.cn<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv366","type":"journal-article","created":{"date-parts":[[2015,6,16]],"date-time":"2015-06-16T00:30:31Z","timestamp":1434414631000},"page":"3362-3364","source":"Crossref","is-referenced-by-count":76,"title":["PPUS: a web server to predict PUS-specific pseudouridine sites"],"prefix":"10.1093","volume":"31","author":[{"given":"Yan-Hui","family":"Li","sequence":"first","affiliation":[{"name":"1 Institute of Cardiovascular Sciences, Peking University Health Science Center,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gaigai","family":"Zhang","sequence":"additional","affiliation":[{"name":"2 Department of Geriatrics and Gerontology, Beijing Huaxin Hospital, the First Affiliated Hospital of Tsinghua University and"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qinghua","family":"Cui","sequence":"additional","affiliation":[{"name":"3 Department of Biomedical Informatics, Peking University Health Science Center, Beijing, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2015,6,14]]},"reference":[{"key":"2023020202322779700_btv366-B1","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1038\/nature13802","article-title":"Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells","volume":"515","author":"Carlile","year":"2014","journal-title":"Nature"},{"key":"2023020202322779700_btv366-B2","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1145\/1961189.1961199","article-title":"LIBSVM: a library for support vector machines","volume":"2","author":"Chang","year":"2011","journal-title":"ACM Trans. Intell. Syst. Technol."},{"key":"2023020202322779700_btv366-B3","doi-asserted-by":"crossref","first-page":"675","DOI":"10.1111\/ped.12217","article-title":"Pathophysiology and genetic mutations in congenital sideroblastic anemia","volume":"55","author":"Fujiwara","year":"2013","journal-title":"Pediatr. Int."},{"key":"2023020202322779700_btv366-B4","doi-asserted-by":"crossref","first-page":"210","DOI":"10.1016\/j.tibs.2013.01.002","article-title":"RNA pseudouridylation: new insights into an old modification","volume":"38","author":"Ge","year":"2013","journal-title":"Trends Biochem. Sci."},{"key":"2023020202322779700_btv366-B5","first-page":"4884","article-title":"An essential yeast protein, CBF5p, binds in\u00a0vitro to centromeres and microtubules","volume":"13","author":"Jiang","year":"1993","journal-title":"Mol. Cell. Biol."},{"key":"2023020202322779700_btv366-B6","doi-asserted-by":"crossref","first-page":"1018","DOI":"10.1109\/72.788642","article-title":"Moderating the outputs of support vector machine classifiers","volume":"10","author":"Kwok","year":"1999","journal-title":"IEEE Trans. Neural. Netw."},{"key":"2023020202322779700_btv366-B7","doi-asserted-by":"crossref","first-page":"700","DOI":"10.1016\/j.mad.2010.10.001","article-title":"Systematic analysis and prediction of longevity genes in Caenorhabditis elegans","volume":"131","author":"Li","year":"2010","journal-title":"Mech. Ageing Dev."},{"key":"2023020202322779700_btv366-B8","doi-asserted-by":"crossref","first-page":"e106691","DOI":"10.1371\/journal.pone.0106691","article-title":"iDNA-Prot|dis: identifying DNA-binding proteins by incorporating amino acid distance-pairs and reduced alphabet profile into the general pseudo amino acid composition","volume":"9","author":"Liu","year":"2014","journal-title":"PLoS One"},{"key":"2023020202322779700_btv366-B9","doi-asserted-by":"crossref","first-page":"S3","DOI":"10.1186\/1471-2105-15-S16-S3","article-title":"Using distances between Top-n-gram and residue pairs for protein remote homology detection","volume":"15","author":"Liu","year":"2014","journal-title":"BMC Bioinformatics"},{"key":"2023020202322779700_btv366-B10","doi-asserted-by":"crossref","first-page":"e0121501","DOI":"10.1371\/journal.pone.0121501","article-title":"Identification of real microRNA precursors with a pseudo structure status composition approach","volume":"10","author":"Liu","year":"2015","journal-title":"PLoS One"},{"key":"2023020202322779700_btv366-B11","doi-asserted-by":"crossref","first-page":"e110799","DOI":"10.1371\/journal.pone.0110799","article-title":"Transcriptome-wide mapping of pseudouridines: pseudouridine synthases modify specific mRNAs in S","volume":"9","author":"Lovejoy","year":"2014","journal-title":"PLoS One"},{"key":"2023020202322779700_btv366-B12","doi-asserted-by":"crossref","first-page":"326","DOI":"10.1186\/1471-2105-15-326","article-title":"Prediction of uridine modifications in tRNA sequences","volume":"15","author":"Panwar","year":"2014","journal-title":"BMC Bioinformatics"},{"key":"2023020202322779700_btv366-B13","doi-asserted-by":"crossref","first-page":"148","DOI":"10.1016\/j.cell.2014.08.028","article-title":"Transcriptome-wide mapping reveals widespread dynamic-regulated pseudouridylation of ncRNA and mRNA","volume":"159","author":"Schwartz","year":"2014","journal-title":"Cell"},{"key":"2023020202322779700_btv366-B14","doi-asserted-by":"crossref","first-page":"7461","DOI":"10.1128\/MCB.19.11.7461","article-title":"Point mutations in yeast CBF5 can abolish in\u00a0vivo pseudouridylation of rRNA","volume":"19","author":"Zebarjadian","year":"1999","journal-title":"Mol. Cell. Biol."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/20\/3362\/49035446\/bioinformatics_31_20_3362.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/20\/3362\/49035446\/bioinformatics_31_20_3362.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T03:51:25Z","timestamp":1675309885000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/31\/20\/3362\/195840"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,6,14]]},"references-count":14,"journal-issue":{"issue":"20","published-print":{"date-parts":[[2015,10,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btv366","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2015,10,15]]},"published":{"date-parts":[[2015,6,14]]}}}