AVPIden: a new scheme for identification and functional prediction of antiviral peptides based on machine learning approaches. - Yuxuan Pang; Lantian Yao; Jhih-Hua Jhong; Zhuo Wang; Tzong-Yi Lee (Briefings Bioinform., 2021)

CircNet 2.0: an updated database for exploring circular RNA regulatory networks in cancers. - Yigang Chen 001; Lantian Yao; Yun Tang; Jhih-Hua Jhong; Jingting Wan; Jingyue Chang; Shi-Dong Cui; Yijun Luo; Xiao-Xuan Cai; Wenshuo Li; Qi Chen; Hsi-Yuan Huang; et al. (Nucleic Acids Res., 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)

dbPTM in 2022: an updated database for exploring regulatory networks and functional associations of protein post-translational modifications. - Zhongyan Li; Shangfu Li; Mengqi Luo; Jhih-Hua Jhong; Wenshuo Li; Lantian Yao; Yuxuan Pang; Zhuo Wang; Rulan Wang; Renfei Ma; Jinhan Yu; Yuqi Huang; et al. (Nucleic Acids Res., 2022)

Integrating transformer and imbalanced multi-label learning to identify antimicrobial peptides and their functional activities. - Yuxuan Pang; Lantian Yao; Jingyi Xu; Zhuo Wang; Tzong-Yi Lee (Bioinform., 2022)

KinasePhos 3.0: Redesign and Expansion of the Prediction on Kinase-specific Phosphorylation Sites. - Renfei Ma; Shangfu Li; Wenshuo Li; Lantian Yao; Hsien-Da Huang; Tzong-Yi Lee (Genom. Proteom. Bioinform., 2023)

Extraction of microRNA-target interaction sentences from biomedical literature by deep learning approach. - Mengqi Luo; Shangfu Li; Yuxuan Pang; Lantian Yao; Renfei Ma; Hsi-Yuan Huang; Hsien-Da Huang; 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)