A Novel Computational Method for MiRNA-Disease Association Prediction. - Zhichao Jiang; Zhen Shen 003; Wenzheng Bao (ICIC (1), 2017)

SPYSMDA: SPY Strategy-Based MiRNA-Disease Association Prediction. - Zhichao Jiang; Zhen Shen 003; Wenzheng Bao (ICIC (2), 2017)

CMFHMDA: Collaborative Matrix Factorization for Human Microbe-Disease Association Prediction. - Zhen Shen 003; Zhichao Jiang; Wenzheng Bao (ICIC (2), 2017)

miRNA-Disease Association Prediction with Collaborative Matrix Factorization. - Zhen Shen 003; You-Hua Zhang; Kyungsook Han; Asoke K. Nandi; Barry Honig; De-Shuang Huang (Complex., 2017)

Capsule Network for Predicting RNA-Protein Binding Preferences Using Hybrid Feature. - Zhen Shen 003; Su-Ping Deng; De-Shuang Huang (IEEE ACM Trans. Comput. Biol. Bioinform., 2020)

RNA-Protein Binding Sites Prediction via Multi Scale Convolutional Gated Recurrent Unit Networks. - Zhen Shen 003; Su-Ping Deng; De-Shuang Huang (IEEE ACM Trans. Comput. Biol. Bioinform., 2020)

Deep Convolution Recurrent Neural Network for Predicting RNA-Protein Binding Preference in mRNA UTR Region. - Zhen Shen 003; YanLing Shao; Lin Yuan 001 (ICIC (3), 2021)

Joint Association Analysis Method to Predict Genes Related to Liver Cancer. - Lin Yuan 001; Zhen Shen 003 (ICIC (3), 2021)

A survey on deep learning in DNA/RNA motif mining. - Ying He; Zhen Shen 003; Qinhu Zhang; Siguo Wang; De-Shuang Huang (Briefings Bioinform., 2021)

A machine learning framework that integrates multi-omics data predicts cancer-related LncRNAs. - Lin Yuan 001; Jing Zhao; Tao Sun; Zhen Shen 003 (BMC Bioinform., 2021)

Predicting in-vitro Transcription Factor Binding Sites Using DNA Sequence + Shape. - Qinhu Zhang; Zhen Shen 003; De-Shuang Huang (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

Bio-ATT-CNN: A Novel Method for Identification of Glioblastoma. - Jinling Lai; Zhen Shen 003; Lin Yuan 001 (ICIC (2), 2022)

A Deep Learning Model for RNA-Protein Binding Preference Prediction Based on Hierarchical LSTM and Attention Network. - Zhen Shen 003; Qinhu Zhang; Kyungsook Han; De-Shuang Huang (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

An Improved Method for CFNet Identifying Glioma Cells. - Lin Yuan 001; Jinling Lai; Zhen Shen 003; Wendong Yu; Hongwei Wei; Ling Zhao; Zhijie Xu; Xingang Wang; Yushui Geng (ICIC (3), 2023)

Identification of CircRNA-Disease Associations from the Integration of Multi-dimensional Bioinformatics with Graph Auto-encoder and Attention Fusion Model. - Lin Yuan 001; Jiawang Zhao; Zhen Shen 003; Wendong Yu; Hongwei Wei; Shengguo Sun; Xingang Wang; Yushui Geng (ICIC (3), 2023)

iCircDA-NEAE: Accelerated attribute network embedding and dynamic convolutional autoencoder for circRNA-disease associations prediction. - Lin Yuan 001; Jiawang Zhao; Zhen Shen 003; Qinhu Zhang; Yushui Geng; Chun-Hou Zheng 001; De-Shuang Huang (PLoS Comput. Biol., 2023)

scMGATGRN: a multiview graph attention network-based method for inferring gene regulatory networks from single-cell transcriptomic data. - Lin Yuan 001; Ling Zhao; Yufeng Jiang; Zhen Shen 003; Qinhu Zhang; Ming Zhang; Chun-Hou Zheng 001; De-Shuang Huang (Briefings Bioinform., 2024)

Identification of ferroptosis-related lncRNAs for predicting prognosis and immunotherapy response in non-small cell lung cancer. - Lin Yuan 001; Shengguo Sun; Qinhu Zhang; Hai-Tao Li; Zhen Shen 003; Chunyu Hu 001; Xiaogang Zhao; Lan Ye; Chun-Hou Zheng 001; De-Shuang Huang (Future Gener. Comput. Syst., 2024)

iCRBP-LKHA: Large convolutional kernel and hybrid channel-spatial attention for identifying circRNA-RBP interaction sites. - Lin Yuan 001; Ling Zhao; Jinling Lai; Yufeng Jiang; Qinhu Zhang; Zhen Shen 003; Chun-Hou Zheng 001; De-Shuang Huang (PLoS Comput. Biol., 2024)

A Remote Sensing Target Detection Model Based on Lightweight Feature Enhancement and Feature Refinement Extraction. - Dongen Guo; Zhuoke Zhou; Fengshuo Guo; Chaoxin Jia; Xiaohong Huang; Jiangfan Feng; Zhen Shen 003 (IEEE J. Sel. Top. Appl. Earth Obs. Remote. Sens., 2024)

A brief survey of deep learning-based models for CircRNA-protein binding sites prediction. - Zhen Shen 003; Lin Yuan 001; Wenzheng Bao; Siguo Wang; Qinhu Zhang; De-Shuang Huang (Neurocomputing, 2025)