Journal article

PASSION: an ensemble neural network approach for identifying the binding sites of RBPs on circRNAs

Cangzhi Jia, Yue Bi, Jinxiang Chen, Andre Leier, Fuyi Li, Jiangning Song

Bioinformatics | OXFORD UNIV PRESS | Published : 2020

Abstract

MOTIVATION: Different from traditional linear RNAs (containing 5' and 3' ends), circular RNAs (circRNAs) are a special type of RNAs that have a closed ring structure. Accumulating evidence has indicated that circRNAs can directly bind proteins and participate in a myriad of different biological processes. RESULTS: For identifying the interaction of circRNAs with 37 different types of circRNA-binding proteins (RBPs), we develop an ensemble neural network, termed PASSION, which is based on the concatenated artificial neural network (ANN) and hybrid deep neural network frameworks. Specifically, the input of the ANN is the optimal feature subset for each RBP, which has been selected from six typ..

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University of Melbourne Researchers

Grants

Awarded by Fundamental Research Funds for the Central Universities


Awarded by National Natural Science Foundation of Liaoning Province


Awarded by National Health and Medical Research Council of Australia (NHMRC)


Awarded by Australian Research Council (ARC)


Funding Acknowledgements

C.J.'s work was supported by Fundamental Research Funds for the Central Universities [3132019175 and 3132019323], the National Natural Science Foundation of Liaoning Province [20180550307], J.S. and F.L.'s work was supported by the National Health and Medical Research Council of Australia (NHMRC) [1144652 and 1127948], the Australian Research Council (ARC) [LP110200333 and DP120104460] and a Major Inter-Disciplinary Research (IDR) project awarded by Monash University. A.L.'s work was supported in part by the Informatics Institute, UAB School of Medicine.