Xiaoyong Pan, Yi Fang, and et al.,
RBPsuite 2.0: an updated RNA-protein binding site prediction suite with high coverage on species and proteins based on deep learning
BMC Biology (In press 2025). [View website]

Xiaoyong Pan, Yi Fang, XianFeng Li, Yang Yang, and Hong-Bin Shen
RBPsuite: RNA-protein binding sites prediction suite based on deep learning.
BMC Genomics, 2020, 21:884. [View article]

Hehe Wu, Xiaoyong Pan*, Yang Yang, and Hong-Bin Shen*
Recognizing binding sites of poorly characterized RNA-binding proteins on circular RNAs using attention Siamese network.
Briefings in Bioinformatics, 2021, 22: bbab279. [View article]

Kaiming Zhang#, Xiaoyong Pan#, Yang Yang, and Hong-Bin Shen
CRIP: predicting circRNA-RBP interaction sites using a codon-based encoding and hybrid deep neural networks.
RNA, 2019, 25(12):1604-1615. [View article]

Xiaoyong Pan, Peter Rijnbeek, Junchi Yan and Hong-Bin Shen
Prediction of RNA-protein sequence and structure binding preferences using deep convolutional and recurrent neural networks.
BMC Genomics, 2018, 19: 511. [View article]

Xiaoyong Pan and Hong-Bin Shen
Predicting RNA-protein binding sites and motifs through combining local and global deep convolutional neural networks.
Bioinformatics, 2018, 34: 3427-3436.  [View article]