Structural and dynamic basis of substrate permissiveness in hydroxycinnamoyltransferase (HCT). - Ying-Chih Chiang; Olesya Levsh; Chun Kei Lam; Jing-Ke Weng; Yi Wang 100 (PLoS Comput. Biol., 2018)

On the force field optimisation of β-lactam cores using the force field Toolkit. - Qiyang Wu; Tianyang Huang; Songyan Xia; Frank Otto; Tzong-Yi Lee; Hsien-Da Huang; Ying-Chih Chiang (J. Comput. Aided Mol. Des., 2022)

miRTarBase update 2022: an informative resource for experimentally validated miRNA-target interactions. - Hsi-Yuan Huang; Yang-Chi-Dung Lin; Shi-Dong Cui; Yixian Huang; Yun Tang; Jia-Tong Xu; Jiayang Bao; Yulin Li; Jia Wen; Hua-Li Zuo; Weijuan Wang; Jing Li; et al. (Nucleic Acids Res., 2022)

dbAMP 2.0: updated resource for antimicrobial peptides with an enhanced scanning method for genomic and proteomic data. - Jhih-Hua Jhong; Lantian Yao; Yuxuan Pang; Zhongyan Li; Chia-Ru Chung; Rulan Wang; Shangfu Li; Wenshuo Li; Mengqi Luo; Renfei Ma; Yuqi Huang; Xiaoning Zhu; et al. (Nucleic Acids Res., 2022)

A risk assessment framework for multidrug-resistant Staphylococcus aureus using machine learning and mass spectrometry technology. - Zhuo Wang; Yuxuan Pang; Chia-Ru Chung; Hsin-Yao Wang; Haiyan Cui; Ying-Chih Chiang; Jorng-Tzong Horng; Jang-Jih Lu; Tzong-Yi Lee (Briefings Bioinform., 2023)

Predicting Anti-inflammatory Peptides by Ensemble Machine Learning and Deep Learning. - Jiahui Guan; Lantian Yao; Chia-Ru Chung; Peilin Xie; Yilun Zhang; Junyang Deng; Ying-Chih Chiang; Tzong-Yi Lee (J. Chem. Inf. Model., 2023)

A two-stage computational framework for identifying antiviral peptides and their functional types based on contrastive learning and multi-feature fusion strategy. - Jiahui Guan; Lantian Yao; Peilin Xie; Chia-Ru Chung; Yixian Huang; Ying-Chih Chiang; Tzong-Yi Lee (Briefings Bioinform., 2024)

ACP-CapsPred: an explainable computational framework for identification and functional prediction of anticancer peptides based on capsule network. - Lantian Yao; Peilin Xie; Jiahui Guan; Chia-Ru Chung; Wenyang Zhang; Junyang Deng; Yixian Huang; Ying-Chih Chiang; Tzong-Yi Lee (Briefings Bioinform., 2024)

CapsEnhancer: An Effective Computational Framework for Identifying Enhancers Based on Chaos Game Representation and Capsule Network. - Lantian Yao; Peilin Xie; Jiahui Guan; Chia-Ru Chung; Yixian Huang; Yuxuan Pang; Huacong Wu; Ying-Chih Chiang; Tzong-Yi Lee (J. Chem. Inf. Model., 2024)

Graph-RPI: predicting RNA-protein interactions via graph autoencoder and self-supervised learning strategies. - Jiahui Guan; Lantian Yao; Peilin Xie; Zhihao Zhao; Dian Meng; Tzong-Yi Lee; Junwen Wang; Ying-Chih Chiang (Briefings Bioinform., 2025)

StackDILI: Enhancing Drug-Induced Liver Injury Prediction through Stacking Strategy with Effective Molecular Representations. - Jiahui Guan; Danhong Dong; Peilin Xie; Zhihao Zhao; Yilin Guo; Tzong-Yi Lee; Lantian Yao; Ying-Chih Chiang (J. Chem. Inf. Model., 2025)

StackPIP: An Effective Computational Framework for Accurate and Balanced Identification of Proinflammatory Peptides. - Lantian Yao; Feng Wang; Peilin Xie; Jiahui Guan; Zhihao Zhao; Xuxin He; Xingchen Liu; Ying-Chih Chiang; Tzong-Yi Lee (J. Chem. Inf. Model., 2025)