{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,3]],"date-time":"2026-06-03T01:13:56Z","timestamp":1780449236125,"version":"3.54.1"},"reference-count":75,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2023,5,8]],"date-time":"2023-05-08T00:00:00Z","timestamp":1683504000000},"content-version":"vor","delay-in-days":7,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Scientific Foundation of China","doi-asserted-by":"crossref","award":["62202388"],"award-info":[{"award-number":["62202388"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2022YFF1000104"],"award-info":[{"award-number":["2022YFF1000104"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Qin Chuangyuan Innovation and Entrepreneurship Talent Project","award":["QCYRCXM-2022-230"],"award-info":[{"award-number":["QCYRCXM-2022-230"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,5,19]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>A-to-I editing is the most prevalent RNA editing event, which refers to the change of adenosine (A) bases to inosine (I) bases in double-stranded RNAs. Several studies have revealed that A-to-I editing can regulate cellular processes and is associated with various human diseases. Therefore, accurate identification of A-to-I editing sites is crucial for understanding RNA-level (i.e. transcriptional) modifications and their potential roles in molecular functions. To date, various computational approaches for A-to-I editing site identification have been developed; however, their performance is still unsatisfactory and needs further improvement. In this study, we developed a novel stacked-ensemble learning model, ATTIC (A-To-I ediTing predICtor), to accurately identify A-to-I editing sites across three species, including Homo sapiens, Mus musculus and Drosophila melanogaster. We first comprehensively evaluated 37 RNA sequence-derived features combined with 14 popular machine learning algorithms. Then, we selected the optimal base models to build a series of stacked ensemble models. The final ATTIC framework was developed based on the optimal models improved by the feature selection strategy for specific species. Extensive cross-validation and independent tests illustrate that ATTIC outperforms state-of-the-art tools for predicting A-to-I editing sites. We also developed a web server for ATTIC, which is publicly available at http:\/\/web.unimelb-bioinfortools.cloud.edu.au\/ATTIC\/. We anticipate that ATTIC can be utilized as a useful tool to accelerate the identification of A-to-I RNA editing events and help characterize their roles in post-transcriptional regulation.<\/jats:p>","DOI":"10.1093\/bib\/bbad170","type":"journal-article","created":{"date-parts":[[2023,5,8]],"date-time":"2023-05-08T03:02:00Z","timestamp":1683514920000},"source":"Crossref","is-referenced-by-count":24,"title":["ATTIC is an integrated approach for predicting A-to-I RNA editing sites in three species"],"prefix":"10.1093","volume":"24","author":[{"given":"Ruyi","family":"Chen","sequence":"first","affiliation":[{"name":"College of Information Engineering, Northwest A&F University , Shaanxi 712100 , China"},{"name":"The Peter Doherty Institute for Infection and Immunity, The University of Melbourne , VIC 3000 , Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fuyi","family":"Li","sequence":"additional","affiliation":[{"name":"College of Information Engineering, Northwest A&F University , Shaanxi 712100 , China"},{"name":"The Peter Doherty Institute for Infection and Immunity, The University of Melbourne , VIC 3000 , Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xudong","family":"Guo","sequence":"additional","affiliation":[{"name":"College of Information Engineering, Northwest A&F University , Shaanxi 712100 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yue","family":"Bi","sequence":"additional","affiliation":[{"name":"Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University , VIC 3800 , Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chen","family":"Li","sequence":"additional","affiliation":[{"name":"Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University , VIC 3800 , Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shirui","family":"Pan","sequence":"additional","affiliation":[{"name":"School of Information and Communication Technology, Griffith University , QLD 4222 , Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lachlan J M","family":"Coin","sequence":"additional","affiliation":[{"name":"The Peter Doherty Institute for Infection and Immunity, The University of Melbourne , VIC 3000 , Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiangning","family":"Song","sequence":"additional","affiliation":[{"name":"Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University , VIC 3800 , Australia"},{"name":"Monash Data Futures Institute, Monash University , VIC 3800 , Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2023,5,6]]},"reference":[{"key":"2023101110501590300_ref1","doi-asserted-by":"crossref","first-page":"493","DOI":"10.3109\/10409238.2012.714350","article-title":"A-to-I editing of protein coding and noncoding RNAs","volume":"47","author":"Mallela","year":"2012","journal-title":"Crit Rev Biochem Mol Biol"},{"key":"2023101110501590300_ref2","doi-asserted-by":"crossref","first-page":"5235","DOI":"10.1021\/bi300419r","article-title":"Evolutionary origin of RNA editing","volume":"51","author":"Gray","year":"2012","journal-title":"Biochemistry"},{"key":"2023101110501590300_ref3","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1146\/annurev-biochem-060208-105251","article-title":"Functions and regulation of RNA editing by ADAR deaminases","volume":"79","author":"Nishikura","year":"2010","journal-title":"Annu Rev 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