Yanyi Chu, Yan Zhang, Qiankun Wang, Lingfeng Zhang, Xuhong Wang, Yanjing Wang, Dennis Russell Salahub, Qin Xu, Jianmin Wang, Xue Jiang, Yi Xiong*, Dong-Qing Wei*. A transformer-based model to predict peptide-HLA class I binding and optimize mutated peptides for vaccine design. Nature Machine Intelligence.  2022; 4:300–311. (ESI高被引论文)

Junwei Chen, Bowen Zhao, Shenggeng Lin, Heqi Sun, Xueying Mao, Meng Wang, Yanyi Chu, Liang Hong, Dong-Qing Wei, Min Li*, Yi Xiong*. TEPCAM: prediction of T cell receptor-epitope binding specificity via interpretable deep learning. Protein Science. 2024; 33(1):e4841.

Heqi Sun, Jianmin Wang*, Hongyan Wu, Shenggeng Lin, Junwei Chen, Jinghua Wei, Shuai Lv, Yi Xiong*, Dong-Qing Wei*. A multimodal deep learning framework for predicting PPI-modulator interactions. Journal of Chemical Information and Modeling. 2023;63:7363−7372.

Shenggeng Lin, Weizhi Chen, Gengwang Chen, Songchi Zhou, Dong-Qing Wei*, Yi Xiong*. MDDI-SCL: predicting multi-type drug-drug interactions via supervised contrastive learning. Journal of Cheminformatics. 2022;14:81.

Yanyi Chu, Aman Chandra Kaushik, Xiangeng Wang, Wei Wang, Yufang Zhang, Xiaoqi Shan, Dennis Russell Salahub, Yi Xiong*, Dong-Qing Wei*. DTI-CDF: a cascade deep forest model towards the prediction of drug-target interactions based on hybrid features. Briefings in Bioinformatics. 2021;22(1):451–462. (ESI高被引论文)