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A task-specific encoding algorithm for RNAs and RNA-associated interactions based on convolutional autoencoder

文献类型：期刊论文

作者Wang, Yunxia5; Pan, Ziqi5; Mou, Minjie5; Xia, Weiqi5; Zhang, Hongning5; Zhang, Hanyu5; Liu, Jin5; Zheng, Lingyan4,5; Luo, Yongchao5; Zheng, Hanqi5
刊名NUCLEIC ACIDS RESEARCH
出版日期2023-10-27
页码14
ISSN号0305-1048
DOI10.1093/nar/gkad929
通讯作者Zhu, Feng(zhufeng@zju.edu.cn)
英文摘要RNAs play essential roles in diverse physiological and pathological processes by interacting with other molecules (RNA/protein/compound), and various computational methods are available for identifying these interactions. However, the encoding features provided by existing methods are limited and the existing tools does not offer an effective way to integrate the interacting partners. In this study, a task-specific encoding algorithm for RNAs and RNA-associated interactions was therefore developed. This new algorithm was unique in (a) realizing comprehensive RNA feature encoding by introducing a great many of novel features and (b) enabling task-specific integration of interacting partners using convolutional autoencoder-directed feature embedding. Compared with existing methods/tools, this novel algorithm demonstrated superior performances in diverse benchmark testing studies. This algorithm together with its source code could be readily accessed by all user at: https://idrblab.org/corain/ and https://github.com/idrblab/corain/. Graphical Abstract
WOS关键词WEB SERVER ; SEQUENCE ; MIRNA ; PROTEINS ; DATABASE
资助项目National Natural Science Foundation of China[82373790] ; National Natural Science Foundation of China[22220102001] ; National Natural Science Foundation of China[U1909208] ; National Natural Science Foundation of China[81872798] ; Natural Science Foundation of Zhejiang Province[LR21H300001] ; Leading Talent of the 'Ten Thousand Plan' - National High-Level Talents Special Supports Plan of China ; National Key R & D Program of China[2022YFC3400501] ; Key R & D Program of Zhejiang Province[2020C03010] ; Double Top-Class 'Universities Projects[181201*194232101] ; Fundamental Research Funds for Central University[2018QNA7023] ; Alibaba-Zhejiang University Joint Research Center Future Digital Healthcare ; Westlake Laboratory (Westlake Laboratory of Life Science Biomedicine) ; Alibaba Cloud ; Information Technology Center of Zhejiang University
WOS研究方向Biochemistry & Molecular Biology
语种英语
WOS记录号WOS:001091349100001
出版者OXFORD UNIV PRESS
源URL[http://119.78.100.183/handle/2S10ELR8/307545]  
专题新药研究国家重点实验室
通讯作者Zhu, Feng
作者单位1.Westlake Lab Life Sci & Biomed, Hangzhou, Zhejiang, Peoples R China
2.Zhejiang Univ, Polytech Inst, Sch Med, Hangzhou 310058, Peoples R China
3.Chinese Acad Sci, Shanghai Inst Mat Med, Drug Discovery & Design Ctr, State Key Lab Drug Res, Shanghai 201203, Peoples R China
4.Zhejiang Univ, Innovat Inst Artificial Intelligence Med, Alibaba ZJU Joint Res Ctr Future Digital Healthcar, Hangzhou 330110, Peoples R China
5.Zhejiang Univ, Affiliated Hosp 2, Coll Pharmaceut Sci, Sch Med,Polytech Inst, Hangzhou 310058, Peoples R China
推荐引用方式
GB/T 7714		 Wang, Yunxia,Pan, Ziqi,Mou, Minjie,et al. A task-specific encoding algorithm for RNAs and RNA-associated interactions based on convolutional autoencoder[J]. NUCLEIC ACIDS RESEARCH,2023:14.
APA Wang, Yunxia.,Pan, Ziqi.,Mou, Minjie.,Xia, Weiqi.,Zhang, Hongning.,...&Zhu, Feng.(2023).A task-specific encoding algorithm for RNAs and RNA-associated interactions based on convolutional autoencoder.NUCLEIC ACIDS RESEARCH,14.
MLA Wang, Yunxia,et al."A task-specific encoding algorithm for RNAs and RNA-associated interactions based on convolutional autoencoder".NUCLEIC ACIDS RESEARCH (2023):14.

入库方式： OAI收割

来源：上海药物研究所

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