A Label-Embedding Online Nonnegative Matrix Factorization Algorithm. - Zhibo Guo; Ying Zhang 053 (IEEE Access, 2019)

Online object tracking by sparse and structural model. - Zhibo Guo; Kejun Lin; Jian Huang; Ying Zhang 053; Zhengda Cui (Clust. Comput., 2019)

A Neural Network Model Compression Approach Based on Deep Feature Map Transfer. - Zhibo Guo; Xin Yao; Yixuan Xu; Ying Zhang 053; Linghao Wang (IEEE Access, 2020)

Leveraging the attention mechanism to improve the identification of DNA N6-methyladenine sites. - Ying Zhang 053; Yan Liu 038; Jian Xu 009; Xiaoyu Wang 016; Xinxin Peng; Jiangning Song; Dong-Jun Yu (Briefings Bioinform., 2021)

Improving protein fold recognition using triplet network and ensemble deep learning. - Yan Liu 038; Ke Han; Yi-Heng Zhu 001; Ying Zhang 053; Long-Chen Shen; Jiangning Song; Dong-Jun Yu (Briefings Bioinform., 2021)

Prediction of disease-associated nsSNPs by integrating multi-scale ResNet models with deep feature fusion. - Fang Ge; Ying Zhang 053; Jian Xu 009; Muhammad Arif 012; Jiangning Song; Dong-Jun Yu (Briefings Bioinform., 2022)

Prediction of Multiple Types of RNA Modifications via Biological Language Model. - Ying Zhang 053; Fang Ge; Fuyi Li; Xibei Yang; Jiangning Song; Dong-Jun Yu (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

SMG: self-supervised masked graph learning for cancer gene identification. - Yan Cui 008; Zhikang Wang; Xiaoyu Wang 016; Yiwen Zhang; Ying Zhang 053; Tong Pan; Zhe Zhang; Shanshan Li; Yuming Guo 001; Tatsuya Akutsu; Jiangning Song (Briefings Bioinform., 2023)

SNN6mA: Improved DNA N6-methyladenine site prediction using Siamese network-based feature embedding. - Xuan Yu; Jun Hu; Ying Zhang 053 (Comput. Biol. Medicine, 2023)

Interpretable prediction models for widespread m6A RNA modification across cell lines and tissues. - Ying Zhang 053; Zhikang Wang; Yiwen Zhang; Shanshan Li; Yuming Guo 001; Jiangning Song; Dong-Jun Yu (Bioinform., 2023)

BLAM6A-Merge: Leveraging Attention Mechanisms and Feature Fusion Strategies to Improve the Identification of RNA N6-Methyladenosine Sites. - Yunpeng Xia; Ying Zhang 053; Dian Liu; Yi-Heng Zhu 001; Zhikang Wang; Jiangning Song; Dong-Jun Yu (IEEE ACM Trans. Comput. Biol. Bioinform., 2024)

SCREEN: A Graph-based Contrastive Learning Tool to Infer Catalytic Residues and Assess Enzyme Mutations. - Tong Pan; Yue Bi; Xiaoyu Wang 016; Ying Zhang 053; Geoffrey I. Webb; Robin B. Gasser; Lukasz A. Kurgan; Jiangning Song (Genom. Proteom. Bioinform., 2025)

Dual-Branch Contrastive Network with Deep Separable Convolution for Enhanced 6mA Site Identification. - Youwei Sun; Zhifei Wang; Ying Zhang 053; Jiangning Song; Dong-Jun Yu (J. Chem. Inf. Model., 2025)

Identifying Protein-Nucleotide Binding Residues via Grouped Multi-task Learning and Pre-trained Protein Language Models. - Jiashun Wu; Yan Liu 038; Ying Zhang 053; Xiaoyu Wang 016; He Yan; Yiheng Zhu 001; Jiangning Song; Dong-Jun Yu (J. Chem. Inf. Model., 2025)

MutPNI: A Unified Model Architecture for Accurately Predicting the Effects of Mutations on Protein-Nucleic Acid Interactions. - Zihao Yan; Fang Ge; Ying Zhang 053; He Yan; Yan Liu; Yi-Heng Zhu; Jiangning Song; Dong-Jun Yu (J. Chem. Inf. Model., 2025)