UniDL4BioPep: a universal deep learning architecture for binary classification in peptide bioactivity. - Zhenjiao Du; Xingjian Ding; Yixiang Xu; Yonghui Li (Briefings Bioinform., 2023)

FusionESP: Improved Enzyme-Substrate Pair Prediction by Fusing Protein and Chemical Knowledge. - Zhenjiao Du; Weimin Fu; Xiaolong Guo; Doina Caragea; Yonghui Li (J. Chem. Inf. Model., 2025)

pLM4CPPs: Protein Language Model-Based Predictor for Cell Penetrating Peptides. - Nandan Kumar; Zhenjiao Du; Yonghui Li (J. Chem. Inf. Model., 2025)