ViTa: prediction of host microRNAs targets on viruses. - Paul Wei-Che Hsu; Li-Zen Lin; Sheng-Da Hsu; Justin Bo-Kai Hsu; Hsien-Da Huang (Nucleic Acids Res., 2007)

Incorporating support vector machine for identifying protein tyrosine sulfation sites. - Wen-Chi Chang; Tzong-Yi Lee; Dray-Ming Shien; Justin Bo-Kai Hsu; Jorng-Tzong Horng; Po-Chiang Hsu; Ting-Yuan Wang; Hsien-Da Huang; Rong-Long Pan (J. Comput. Chem., 2009)

Incorporating structural characteristics for identification of protein methylation sites. - Dray-Ming Shien; Tzong-Yi Lee; Wen-Chi Chang; Justin Bo-Kai Hsu; Jorng-Tzong Horng; Po-Chiang Hsu; Ting-Yuan Wang; Hsien-Da Huang (J. Comput. Chem., 2009)

N-Ace: Using solvent accessibility and physicochemical properties to identify protein N-acetylation sites. - Tzong-Yi Lee; Justin Bo-Kai Hsu; Feng-Mao Lin; Wen-Chi Chang; Po-Chiang Hsu; Hsien-Da Huang (J. Comput. Chem., 2010)

miRTar: an integrated system for identifying miRNA-target interactions in Human. - Justin Bo-Kai Hsu; Chih-Min Chiu; Sheng-Da Hsu; Wei-Yun Huang; Chia-Hung Chien; Tzong-Yi Lee; Hsien-Da Huang (BMC Bioinform., 2011)

RegPhos: a system to explore the protein kinase-substrate phosphorylation network in humans. - Tzong-Yi Lee; Justin Bo-Kai Hsu; Wen-Chi Chang; Hsien-Da Huang (Nucleic Acids Res., 2011)

GPMiner: an integrated system for mining combinatorial cis-regulatory elements in mammalian gene group. - Tzong-Yi Lee; Wen-Chi Chang; Justin Bo-Kai Hsu; Tzu-Hao Chang; Dray-Ming Shien (BMC Genom., 2012)

An enhanced computational platform for investigating the roles of regulatory RNA and for identifying functional RNA motifs. - Tzu-Hao Chang; Hsi-Yuan Huang; Justin Bo-Kai Hsu; Shun-Long Weng; Jorng-Tzong Horng; Hsien-Da Huang (BMC Bioinform., 2013)

Incorporating significant amino acid pairs and protein domains to predict RNA splicing-related proteins with functional roles. - Justin Bo-Kai Hsu; Kai-Yao Huang; Julia Tzu-Ya Weng; Chien-Hsun Huang; Tzong-Yi Lee (J. Comput. Aided Mol. Des., 2014)

MDD-carb: a combinatorial model for the identification of protein carbonylation sites with substrate motifs. - Hui-Ju Kao; Shun-Long Weng; Kai-Yao Huang; Fergie Joanda Kaunang; Justin Bo-Kai Hsu; Chien-Hsun Huang; Tzong-Yi Lee (BMC Syst. Biol., 2017)

Investigation and identification of functional post-translational modification sites associated with drug binding and protein-protein interactions. - Min-Gang Su; Julia Tzu-Ya Weng; Justin Bo-Kai Hsu; Kai-Yao Huang; Yu-Hsiang Chi; Tzong-Yi Lee (BMC Syst. Biol., 2017)

Characterization and identification of lysine glutarylation based on intrinsic interdependence between positions in the substrate sites. - Kai-Yao Huang; Hui-Ju Kao; Justin Bo-Kai Hsu; Shun-Long Weng; Tzong-Yi Lee (BMC Bioinform., 2019)

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)