Characterization and identification of protein O-GlcNAcylation sites with substrate specificity. - Hsin-Yi Wu; Cheng-Tsung Lu; Hui-Ju Kao; Yi-Ju Chen; Yu-Ju Chen; Tzong-Yi Lee (BMC Bioinform., 2014)

topPTM: a new module of dbPTM for identifying functional post-translational modifications in transmembrane proteins. - Min-Gang Su; Kai-Yao Huang; Cheng-Tsung Lu; Hui-Ju Kao; Ya-Han Chang; Tzong-Yi Lee (Nucleic Acids Res., 2014)

A two-layered machine learning method to identify protein O-GlcNAcylation sites with O-GlcNAc transferase substrate motifs. - Hui-Ju Kao; Chien-Hsun Huang; Neil Arvin Bretaña; Cheng-Tsung Lu; Kai-Yao Huang; Shun-Long Weng; Tzong-Yi Lee (BMC Bioinform., 2015)

UbiSite: incorporating two-layered machine learning method with substrate motifs to predict ubiquitin-conjugation site on lysines. - Chien-Hsun Huang; Min-Gang Su; Hui-Ju Kao; Jhih-Hua Jhong; Shun-Long Weng; Tzong-Yi Lee (BMC Syst. Biol., 2016)

dbPTM 2016: 10-year anniversary of a resource for post-translational modification of proteins. - Kai-Yao Huang; Min-Gang Su; Hui-Ju Kao; Yun-Chung Hsieh; Jhih-Hua Jhong; Kuang-Hao Cheng; Hsien-Da Huang; Tzong-Yi Lee (Nucleic Acids Res., 2016)

Investigation and identification of protein carbonylation sites based on position-specific amino acid composition and physicochemical features. - Shun-Long Weng; Kai-Yao Huang; Fergie Joanda Kaunang; Chien-Hsun Huang; Hui-Ju Kao; Tzu-Hao Chang; Hsin-Yao Wang; Jang-Jih Lu; Tzong-Yi Lee (BMC Bioinform., 2017)

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)

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 2019: exploring disease association and cross-talk of post-translational modifications. - Kai-Yao Huang; Tzong-Yi Lee; Hui-Ju Kao; Chen-Tse Ma; Chao-Chun Lee; Tsai-Hsuan Lin; Wen-Chi Chang; Hsien-Da Huang (Nucleic Acids Res., 2019)

iDPGK: characterization and identification of lysine phosphoglycerylation sites based on sequence-based features. - Kai-Yao Huang; Fang-Yu Hung; Hui-Ju Kao; Hui-Hsuan Lau; Shun-Long Weng (BMC Bioinform., 2020)

SuccSite: Incorporating Amino Acid Composition and Informative k-spaced Amino Acid Pairs to Identify Protein Succinylation Sites. - Hui-Ju Kao; Van-Nui Nguyen; Kai-Yao Huang; Wen-Chi Chang; Tzong-Yi Lee (Genom. Proteom. Bioinform., 2020)

iDVIP: identification and characterization of viral integrase inhibitory peptides. - Kai-Yao Huang; Hui-Ju Kao; Tzu-Hsiang Weng; Chia-Hung Chen; Shun-Long Weng (Briefings Bioinform., 2022)