{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,31]],"date-time":"2026-01-31T00:47:21Z","timestamp":1769820441742,"version":"3.49.0"},"reference-count":103,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2022,10,4]],"date-time":"2022-10-04T00:00:00Z","timestamp":1664841600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["81872798"],"award-info":[{"award-number":["81872798"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["U1909208"],"award-info":[{"award-number":["U1909208"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004731","name":"Natural Science Foundation of Zhejiang Province","doi-asserted-by":"publisher","award":["LR21H300001"],"award-info":[{"award-number":["LR21H300001"]}],"id":[{"id":"10.13039\/501100004731","id-type":"DOI","asserted-by":"publisher"}]},{"name":"National High-Level Talents Special Support Plan of China"},{"name":"Fundamental Research Fund for Central Universities","award":["2018QNA7023"],"award-info":[{"award-number":["2018QNA7023"]}]},{"name":"Key Research and Development Program of Zhejiang Province","award":["2020C03010"],"award-info":[{"award-number":["2020C03010"]}]},{"name":"Westlake Laboratory of Life Sciences and Biomedicine"},{"name":"Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare"},{"name":"Information Technology Center of Zhejiang University"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,11,19]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>In recent years, many studies have illustrated the significant role that non-coding RNA (ncRNA) plays in biological activities, in which lncRNA, miRNA and especially their interactions have been proved to affect many biological processes. Some in silico methods have been proposed and applied to identify novel lncRNA\u2013miRNA interactions (LMIs), but there are still imperfections in their RNA representation and information extraction approaches, which imply there is still room for further improving their performances. Meanwhile, only a few of them are accessible at present, which limits their practical applications. The construction of a new tool for LMI prediction is thus imperative for the better understanding of their relevant biological mechanisms. This study proposed a novel method, ncRNAInter, for LMI prediction. A comprehensive strategy for RNA representation and an optimized deep learning algorithm of graph neural network were utilized in this study. ncRNAInter was robust and showed better performance of 26.7% higher Matthews correlation coefficient than existing reputable methods for human LMI prediction. In addition, ncRNAInter proved its universal applicability in dealing with LMIs from various species and successfully identified novel LMIs associated with various diseases, which further verified its effectiveness and usability. All source code and datasets are freely available at https:\/\/github.com\/idrblab\/ncRNAInter.<\/jats:p>","DOI":"10.1093\/bib\/bbac411","type":"journal-article","created":{"date-parts":[[2022,10,5]],"date-time":"2022-10-05T18:49:23Z","timestamp":1664995763000},"source":"Crossref","is-referenced-by-count":32,"title":["ncRNAInter: a novel strategy based on graph neural network to discover interactions between lncRNA and miRNA"],"prefix":"10.1093","volume":"23","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4728-7702","authenticated-orcid":false,"given":"Hanyu","family":"Zhang","sequence":"first","affiliation":[{"name":"College of Pharmaceutical Sciences, Zhejiang University , Hangzhou 310058, China"},{"name":"Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare , Hangzhou 330110, China"}]},{"given":"Yunxia","family":"Wang","sequence":"additional","affiliation":[{"name":"College of Pharmaceutical Sciences, Zhejiang University , Hangzhou 310058, China"}]},{"given":"Ziqi","family":"Pan","sequence":"additional","affiliation":[{"name":"College of Pharmaceutical Sciences, Zhejiang University , Hangzhou 310058, China"}]},{"given":"Xiuna","family":"Sun","sequence":"additional","affiliation":[{"name":"College of Pharmaceutical Sciences, Zhejiang University , Hangzhou 310058, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7619-2975","authenticated-orcid":false,"given":"Minjie","family":"Mou","sequence":"additional","affiliation":[{"name":"College of Pharmaceutical Sciences, Zhejiang University , Hangzhou 310058, China"}]},{"given":"Bing","family":"Zhang","sequence":"additional","affiliation":[{"name":"Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare , Hangzhou 330110, China"}]},{"given":"Zhaorong","family":"Li","sequence":"additional","affiliation":[{"name":"Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare , Hangzhou 330110, China"}]},{"given":"Honglin","family":"Li","sequence":"additional","affiliation":[{"name":"School of Computer Science and Technology, East China Normal University , Shanghai 200062, China"},{"name":"Shanghai Key Laboratory of New Drug Design, East China University of Science and Technology , Shanghai 200237, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8069-0053","authenticated-orcid":false,"given":"Feng","family":"Zhu","sequence":"additional","affiliation":[{"name":"College of Pharmaceutical Sciences, Zhejiang University , Hangzhou 310058, China"},{"name":"Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare , Hangzhou 330110, China"}]}],"member":"286","published-online":{"date-parts":[[2022,10,4]]},"reference":[{"key":"2022112111112609100_ref1","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1038\/nrd.2016.246","article-title":"MicroRNA therapeutics: towards a new era for the management of cancer and other diseases","volume":"16","author":"Rupaimoole","year":"2017","journal-title":"Nat Rev Drug Discov"},{"key":"2022112111112609100_ref2","doi-asserted-by":"crossref","first-page":"D140","DOI":"10.1093\/nar\/gky1051","article-title":"LncRNA2Target v2.0: a comprehensive database for target genes of lncRNAs in human and mouse","volume":"47","author":"Cheng","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2022112111112609100_ref3","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1016\/j.cell.2014.03.008","article-title":"The noncoding RNA revolution-trashing old rules to forge new 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