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 008; Yuming Guo 001; Tatsuya Akutsu; Jiangning Song (Briefings Bioinform., 2023)

MULGA, a unified multi-view graph autoencoder-based approach for identifying drug-protein interaction and drug repositioning. - Jiani Ma; Chen Li 021; Yiwen Zhang; Zhikang Wang; Shanshan Li 008; Yuming Guo 001; Lin Zhang 015; Hui Liu 024; Xin Gao 001; Jiangning Song (Bioinform., 2023)

Surformer: An interpretable pattern-perceptive survival transformer for cancer survival prediction from histopathology whole slide images. - Zhikang Wang; Qian Gao; Xiaoping Yi; Xinyu Zhang 017; Yiwen Zhang; Daokun Zhang; Pietro Liò; Chris Bain; Richard Bassed; Shanshan Li 008; Yuming Guo 001; Seiya Imoto; et al. (Comput. Methods Programs Biomed., 2023)

Interpretable prediction models for widespread m6A RNA modification across cell lines and tissues. - Ying Zhang 053; Zhikang Wang; Yiwen Zhang; Shanshan Li 008; Yuming Guo 001; Jiangning Song; Dong-Jun Yu (Bioinform., 2023)

GraphormerDTI: A graph transformer-based approach for drug-target interaction prediction. - Mengmeng Gao; Daokun Zhang; Yi Chen; Yiwen Zhang; Zhikang Wang; Xiaoyu Wang 016; Shanshan Li 008; Yuming Guo 001; Geoffrey I. Webb; Anh T. N. Nguyen; Lauren T. May; Jiangning Song (Comput. Biol. Medicine, 2024)

Deep learning approaches for non-coding genetic variant effect prediction: current progress and future prospects. - Xiaoyu Wang 016; Fuyi Li; Yiwen Zhang; Seiya Imoto; Hsin-Hui Shen; Shanshan Li 008; Yuming Guo 001; Jian Yang 005; Jiangning Song (Briefings Bioinform., 2024)

MLSNet: a deep learning model for predicting transcription factor binding sites. - Yuchuan Zhang; Zhikang Wang; Fang Ge; Xiaoyu Wang 016; Yiwen Zhang; Shanshan Li 008; Yuming Guo 001; Jiangning Song; Dong-Jun Yu (Briefings Bioinform., 2024)

Structure-Directed Pan-Specific T-Cell Receptor-Peptide-Major Histocompatibility Complex Interaction Prediction. - Letao Gao; Yumeng Zhang; Fang Ge; Shanshan Li 008; Yuming Guo 001; Jiangning Song; Dong-Jun Yu (J. Chem. Inf. Model., 2025)

Integrating Graph Convolutional Networks for Missing Gene Expression Imputation. - Ying Zhang 053; Hong-Jin Yu; Zihao Yan; Tong Pan; Yiwen Zhang; Yan Liu 038; Shanshan Li 008; Yuming Guo 001; Jiangning Song; Dong-Jun Yu (IEEE Trans. Comput. Biol. Bioinform., 2025)

Multimodal geometric learning for antimicrobial peptide identification by leveraging alphafold2-predicted structures and surface features. - Zehua Sun; Jing Xu 008; Yumeng Zhang; Yiwen Zhang; Zhikang Wang; Xiaoyu Wang 016; Shanshan Li 008; Yuming Guo 001; Hsin Hui Shen; Jiangning Song (Briefings Bioinform., 2025)