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A variety of powerful computational methods have been developed to predict such valuable interactions. However, all these methods rely heavily on the \u2018digitalization\u2019 (also known as \u2018encoding\u2019) of RNA-associated interacting pairs into a computer-recognizable descriptor. In other words, it is urgently needed to have a powerful tool that can not only represent each interacting partner but also integrate both partners into a computer-recognizable interaction. Herein, RNAincoder (deep learning-based encoder for RNA-associated interactions) was therefore proposed to (a) provide a comprehensive collection of RNA encoding features, (b) realize the representation of any RNA-associated interaction based on a well-established deep learning-based embedding strategy\u00a0and (c) enable large-scale scanning of all possible feature combinations to identify the one of optimal performance in RNA-associated interaction prediction. The effectiveness of RNAincoder was extensively validated by case studies on benchmark datasets. All in all, RNAincoder is distinguished for its capability in providing a more accurate representation of RNA-associated interactions, which makes it an indispensable complement to other available tools. RNAincoder can be accessed at https:\/\/idrblab.org\/rnaincoder\/<\/jats:p>","DOI":"10.1093\/nar\/gkad404","type":"journal-article","created":{"date-parts":[[2023,5,11]],"date-time":"2023-05-11T15:51:03Z","timestamp":1683820263000},"page":"W509-W519","source":"Crossref","is-referenced-by-count":42,"title":["RNAincoder: a deep learning-based encoder for RNA and RNA-associated interaction"],"prefix":"10.1093","volume":"51","author":[{"given":"Yunxia","family":"Wang","sequence":"first","affiliation":[{"name":"College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University , Hangzhou \u00a0310058, China"}]},{"given":"Zhen","family":"Chen","sequence":"additional","affiliation":[{"name":"College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University , Hangzhou \u00a0310058, China"}]},{"given":"Ziqi","family":"Pan","sequence":"additional","affiliation":[{"name":"College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University , Hangzhou \u00a0310058, China"}]},{"given":"Shijie","family":"Huang","sequence":"additional","affiliation":[{"name":"College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University , Hangzhou \u00a0310058, China"}]},{"given":"Jin","family":"Liu","sequence":"additional","affiliation":[{"name":"College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University , Hangzhou \u00a0310058, China"}]},{"given":"Weiqi","family":"Xia","sequence":"additional","affiliation":[{"name":"College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University , Hangzhou \u00a0310058, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7818-7915","authenticated-orcid":false,"given":"Hongning","family":"Zhang","sequence":"additional","affiliation":[{"name":"College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University , Hangzhou \u00a0310058, China"}]},{"given":"Mingyue","family":"Zheng","sequence":"additional","affiliation":[{"name":"Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai \u00a0201203, China"}]},{"given":"Honglin","family":"Li","sequence":"additional","affiliation":[{"name":"College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University , Hangzhou \u00a0310058, China"},{"name":"School of Pharmacy, East China University of Science and Technology , Shanghai \u00a0200237, China"}]},{"given":"Tingjun","family":"Hou","sequence":"additional","affiliation":[{"name":"College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University , Hangzhou \u00a0310058, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8069-0053","authenticated-orcid":false,"given":"Feng","family":"Zhu","sequence":"additional","affiliation":[{"name":"College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University , Hangzhou \u00a0310058, China"},{"name":"Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare , Hangzhou \u00a0330110, China"},{"name":"Westlake Laboratory of Life Sciences and Biomedicine , Hangzhou , Zhejiang , China"}]}],"member":"286","published-online":{"date-parts":[[2023,5,11]]},"reference":[{"key":"2023070505011990500_B1","doi-asserted-by":"crossref","first-page":"475","DOI":"10.1038\/s41580-020-0243-y","article-title":"The expanding regulatory mechanisms and cellular functions of circular RNAs","volume":"21","author":"Chen","year":"2020","journal-title":"Nat. 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