Multi-omics profiling reveals microRNA-mediated insulin signaling networks. - Yang-Chi-Dung Lin; Hsi-Yuan Huang; Sirjana Shrestha; Chih-Hung Chou; Yen-Hua Chen; Chi-Ru Chen; Hsiao-Chin Hong; Jing Li; Yi-An Chang; Men-Yee Chiew; Ya-Rong Huang; Siang-Jyun Tu; et al. (BMC Bioinform., 2020)

miRTarBase 2020: updates to the experimentally validated microRNA?target interaction database. - Hsi-Yuan Huang; Yang-Chi-Dung Lin; Jing Li; Kai-Yao Huang; Sirjana Shrestha; Hsiao-Chin Hong; Yun Tang; Yigang Chen 001; Chen-Nan Jin; Yuan Yu; Jia-Tong Xu; Yue-Ming Li; et al. (Nucleic Acids Res., 2020)

MethHC 2.0: information repository of DNA methylation and gene expression in human cancer. - Hsi-Yuan Huang; Jing Li; Yun Tang; Yixian Huang; Yigang Chen 001; Yue-Yang Xie; Zhe-Yuan Zhou; Xin-Yi Chen; Si-Yuan Ding; Meng-Fan Luo; Chen-Nan Jin; Le-Shan Zhao; et al. (Nucleic Acids Res., 2021)

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)

Quantitative model for genome-wide cyclic AMP receptor protein binding site identification and characteristic analysis. - Yigang Chen 001; Yang-Chi-Dung Lin; Yijun Luo; Xiao-Xuan Cai; Peng Qiu; Shi-Dong Cui; Zhe Wang; Hsi-Yuan Huang; Hsien-Da Huang (Briefings Bioinform., 2023)

DeepDrugmiR: a two-stage deep learning method for inferring small molecules' regulatory effects on microRNA expression. - Yixian Huang; Huacong Wu; Ying Cai; Danhong Dong; Sicong Yu; Yigang Chen 001; Zihao Zhu; Yang-Chi-Dung Lin; Hsien-Da Huang; Hsi-Yuan Huang (BCB, 2024)

DrugRepoBank: a comprehensive database and discovery platform for accelerating drug repositioning. - Yixian Huang; Danhong Dong; Wenyang Zhang; Ruiting Wang; Yang-Chi-Dung Lin; Hua-Li Zuo; Hsi-Yuan Huang; Hsien-Da Huang (Database J. Biol. Databases Curation, 2024)

SCOPE-DTI: Semi-Inductive Dataset Construction and Framework Optimization for Practical Usability Enhancement in Deep Learning-Based Drug Target Interaction Prediction. - Yigang Chen 001; Xiang Ji; Ziyue Zhang; Yuming Zhou; Yang-Chi-Dung Lin; Hsi-Yuan Huang; Tao Zhang; Yi Lai; Ke Chen; Chang Su; Xingqiao Lin; Zihao Zhu; et al. (CoRR, 2025)