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)

Positive-unlabeled learning in bioinformatics and computational biology: a brief review. - Fuyi Li; Shuangyu Dong; André Leier; Meiya Han; Xudong Guo; Jing Xu; Xiaoyu Wang 016; Shirui Pan; Cangzhi Jia; Yang Zhang 010; Geoffrey I. Webb; Lachlan J. M. Coin; et al. (Briefings Bioinform., 2022)

RBP-TSTL is a two-stage transfer learning framework for genome-scale prediction of RNA-binding proteins. - Xinxin Peng; Xiaoyu Wang 016; Yuming Guo 001; Zongyuan Ge; Fuyi Li; Xin Gao 001; Jiangning Song (Briefings Bioinform., 2022)

ASPIRER: a new computational approach for identifying non-classical secreted proteins based on deep learning. - Xiaoyu Wang 016; Fuyi Li; Jing Xu; Jia Rong; Geoffrey I. Webb; Zongyuan Ge; Jian Li 052; Jiangning Song (Briefings Bioinform., 2022)

PreAcrs: a machine learning framework for identifying anti-CRISPR proteins. - Lin Zhu; Xiaoyu Wang 016; Fuyi Li; Jiangning Song (BMC Bioinform., 2022)

Multiplex-detection Based Multiple Instance Learning Network for Whole Slide Image Classification. - Zhikang Wang; Yue Bi; Tong Pan; Xiaoyu Wang 016; Chris Bain; Richard Bassed; Seiya Imoto; Jianhua Yao 001; Jiangning Song (CoRR, 2022)

Targeting tumor heterogeneity: multiplex-detection-based multiple instance learning for whole slide image classification. - Zhikang Wang; Yue Bi; Tong Pan; Xiaoyu Wang 016; Chris Bain; Richard Bassed; Seiya Imoto; Jianhua Yao 001; Roger J. Daly; Jiangning Song (Bioinform., 2023)

TIMER is a Siamese neural network-based framework for identifying both general and species-specific bacterial promoters. - Yan Zhu 006; Fuyi Li; Xudong Guo; Xiaoyu Wang 016; Lachlan J. M. Coin; Geoffrey I. Webb; Jiangning Song; Cangzhi Jia (Briefings 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)

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; Yuming Guo 001; Jian Yang; Jiangning Song (Briefings Bioinform., 2024)

MORE: a multi-omics data-driven hypergraph integration network for biomedical data classification and biomarker identification. - Yuhan Wang; Zhikang Wang; Xuan Yu; Xiaoyu Wang 016; Jiangning Song; Dong-Jun Yu; Fang Ge (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; Yuming Guo 001; Jiangning Song; Dong-Jun Yu (Briefings Bioinform., 2024)

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; Yuming Guo 001; Geoffrey I. Webb; Anh T. N. Nguyen; Lauren T. May; Jiangning Song (Comput. Biol. Medicine, 2024)

PmxPred: A data-driven approach for the identification of active polymyxin analogues against gram-negative bacteria. - Xiaoyu Wang 016; Nitin Patil; Fuyi Li; Zhikang Wang; Haolan Zhan; Daniel Schmidt; Philip Thompson; Yuming Guo 001; Cornelia B. Landersdorfer; Hsin-Hui Shen; Anton Y. Peleg; Jian Li 052; et al. (Comput. Biol. Medicine, 2024)

CoPRA: Bridging Cross-domain Pretrained Sequence Models with Complex Structures for Protein-RNA Binding Affinity Prediction. - Rong Han; Xiaohong Liu 007; Tong Pan; Jing Xu; Xiaoyu Wang 016; Wuyang Lan; Zhenyu Li; Zixuan Wang; Jiangning Song; Guangyu Wang; Ting Chen 006 (AAAI, 2025)

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

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)

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)