{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,8]],"date-time":"2026-05-08T07:53:23Z","timestamp":1778226803274,"version":"3.51.4"},"reference-count":42,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2021,7,5]],"date-time":"2021-07-05T00:00:00Z","timestamp":1625443200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Doherty Institute at the University of Melbourne"},{"name":"NHMRC career development fellowship","award":["APP1103384"],"award-info":[{"award-number":["APP1103384"]}]},{"name":"NHMRC-EU project","award":["GNT1195743"],"award-info":[{"award-number":["GNT1195743"]}]},{"name":"National Health and Medical Research Council of Australia","award":["APP1127948"],"award-info":[{"award-number":["APP1127948"]}]},{"name":"National Health and Medical Research Council of Australia","award":["APP1144652"],"award-info":[{"award-number":["APP1144652"]}]},{"DOI":"10.13039\/501100000923","name":"Australian Research Council","doi-asserted-by":"publisher","award":["LP110200333"],"award-info":[{"award-number":["LP110200333"]}],"id":[{"id":"10.13039\/501100000923","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000923","name":"Australian Research Council","doi-asserted-by":"publisher","award":["DP120104460"],"award-info":[{"award-number":["DP120104460"]}],"id":[{"id":"10.13039\/501100000923","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01 AI111965"],"award-info":[{"award-number":["R01 AI111965"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,11,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Pseudouridine is a ubiquitous RNA modification type present in eukaryotes and prokaryotes, which plays a vital role in various biological processes. Almost all kinds of RNAs are subject to this modification. However, it remains a great challenge to identify pseudouridine sites via experimental approaches, requiring expensive and time-consuming experimental research. Therefore, computational approaches that can be used to perform accurate in silico identification of pseudouridine sites from the large amount of RNA sequence data are highly desirable and can aid in the functional elucidation of this critical modification. Here, we propose a new computational approach, termed Porpoise, to accurately identify pseudouridine sites from RNA sequence data. Porpoise builds upon a comprehensive evaluation of 18 frequently used feature encoding schemes based on the selection of four types of features, including binary features, pseudo k-tuple composition, nucleotide chemical property and position-specific trinucleotide propensity based on single-strand (PSTNPss). The selected features are fed into the stacked ensemble learning framework to enable the construction of an effective stacked model. Both cross-validation tests on the benchmark dataset and independent tests show that Porpoise achieves superior predictive performance than several state-of-the-art approaches. The application of model interpretation tools demonstrates the importance of PSTNPs for the performance of the trained models. This new method is anticipated to facilitate community-wide efforts to identify putative pseudouridine sites and formulate novel testable biological hypothesis.<\/jats:p>","DOI":"10.1093\/bib\/bbab245","type":"journal-article","created":{"date-parts":[[2021,6,8]],"date-time":"2021-06-08T19:21:23Z","timestamp":1623180083000},"source":"Crossref","is-referenced-by-count":47,"title":["Porpoise: a new approach for accurate prediction of RNA pseudouridine sites"],"prefix":"10.1093","volume":"22","author":[{"given":"Fuyi","family":"Li","sequence":"first","affiliation":[{"name":"Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, the University of Melbourne, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xudong","family":"Guo","sequence":"additional","affiliation":[{"name":"Ningxia University, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peipei","family":"Jin","sequence":"additional","affiliation":[{"name":"Department of Clinical Laboratory of Ruijin Hospital, affiliated with Shanghai Jiao Tong University School of Medicine, Shanghai, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jinxiang","family":"Chen","sequence":"additional","affiliation":[{"name":"Northwest A&F University, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dongxu","family":"Xiang","sequence":"additional","affiliation":[{"name":"Faculty of Engineering and Information Technology, The University of Melbourne, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jiangning","family":"Song","sequence":"additional","affiliation":[{"name":"Monash Biomedicine Discovery Institute, Monash University, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lachlan J M","family":"Coin","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology at the University of Melbourne, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2021,7,5]]},"reference":[{"key":"2021110815080481400_ref1","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":"2021110815080481400_ref2","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1080\/152165400410182","article-title":"Pseudouridine in RNA: what, where, how, and why","volume":"49","author":"Charette","year":"2000","journal-title":"IUBMB Life"},{"key":"2021110815080481400_ref3","doi-asserted-by":"crossref","first-page":"1121","DOI":"10.1080\/07391102.1998.10509006","article-title":"An RNA model system for investigation of 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