{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,19]],"date-time":"2026-03-19T21:40:56Z","timestamp":1773956456990,"version":"3.50.1"},"reference-count":50,"publisher":"Oxford University Press (OUP)","issue":"22","license":[{"start":{"date-parts":[[2018,5,29]],"date-time":"2018-05-29T00:00:00Z","timestamp":1527552000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"National Key Research and Development Program of China","award":["2017YFC1200205"],"award-info":[{"award-number":["2017YFC1200205"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31671366"],"award-info":[{"award-number":["31671366"]}],"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":["91231119"],"award-info":[{"award-number":["91231119"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Special Research Project of \u2018Clinical Medicine\u2009+\u2009X\u2019"},{"DOI":"10.13039\/501100007937","name":"Peking University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100007937","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,11,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>To characterize long non-coding RNAs (lncRNAs), both identifying and functionally annotating them are essential to be addressed. Moreover, a comprehensive construction for lncRNA annotation is desired to facilitate the research in the field.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We present LncADeep, a novel lncRNA identification and functional annotation tool. For lncRNA identification, LncADeep integrates intrinsic and homology features into a deep belief network and constructs models targeting both full- and partial-length transcripts. For functional annotation, LncADeep predicts a lncRNA\u2019s interacting proteins based on deep neural networks, using both sequence and structure information. Furthermore, LncADeep integrates KEGG and Reactome pathway enrichment analysis and functional module detection with the predicted interacting proteins, and provides the enriched pathways and functional modules as functional annotations for lncRNAs. Test results show that LncADeep outperforms state-of-the-art tools, both for lncRNA identification and lncRNA\u2013protein interaction prediction, and then presents a functional interpretation. We expect that LncADeep can contribute to identifying and annotating novel lncRNAs.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>LncADeep is freely available for academic use at http:\/\/cqb.pku.edu.cn\/ZhuLab\/lncadeep\/ and https:\/\/github.com\/cyang235\/LncADeep\/.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty428","type":"journal-article","created":{"date-parts":[[2018,5,23]],"date-time":"2018-05-23T19:16:35Z","timestamp":1527102995000},"page":"3825-3834","source":"Crossref","is-referenced-by-count":133,"title":["LncADeep: an<i>ab initio<\/i>lncRNA identification and functional annotation tool based on deep learning"],"prefix":"10.1093","volume":"34","author":[{"given":"Cheng","family":"Yang","sequence":"first","affiliation":[{"name":"Department of Biomedical Engineering, College of Engineering, and Centre for Quantitative Biology, Peking University, Beijing, China"},{"name":"Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA"}]},{"given":"Longshu","family":"Yang","sequence":"additional","affiliation":[{"name":"Department of Biomedical Engineering, College of Engineering, and Centre for Quantitative Biology, Peking University, Beijing, China"}]},{"given":"Man","family":"Zhou","sequence":"additional","affiliation":[{"name":"Department of Biomedical Engineering, College of Engineering, and Centre for Quantitative Biology, Peking University, Beijing, China"}]},{"given":"Haoling","family":"Xie","sequence":"additional","affiliation":[{"name":"Department of Biomedical Engineering, College of Engineering, and Centre for Quantitative Biology, Peking University, Beijing, China"},{"name":"Peking University-Tsinghua University-National Institute of Biological Sciences (PTN) Joint PhD Program and College of Life Sciences, Peking University, Beijing, China"}]},{"given":"Chengjiu","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Biomedical Engineering, College of Engineering, and Centre for Quantitative Biology, Peking University, Beijing, China"}]},{"given":"May D","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA"}]},{"given":"Huaiqiu","family":"Zhu","sequence":"additional","affiliation":[{"name":"Department of Biomedical Engineering, College of Engineering, and Centre for Quantitative Biology, Peking University, Beijing, China"},{"name":"Peking University-Tsinghua University-National Institute of Biological Sciences (PTN) Joint PhD Program and College of Life Sciences, Peking University, Beijing, China"}]}],"member":"286","published-online":{"date-parts":[[2018,5,29]]},"reference":[{"key":"2023012712350556500_bty428-B1","doi-asserted-by":"crossref","first-page":"3897","DOI":"10.1093\/bioinformatics\/btv480","article-title":"LncRNA-id: long non-coding RNA identification using balanced random forests","volume":"31","author":"Achawanantakun","year":"2015","journal-title":"Bioinformatics"},{"key":"2023012712350556500_bty428-B2","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.jtbi.2016.04.025","article-title":"rpiCOOL: a tool for in silico RNA\u2013protein interaction detection using random forest","volume":"402","author":"Akbaripour-Elahabad","year":"2016","journal-title":"J. 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