Investigation and identification of protein γ-glutamyl carboxylation sites. - Tzong-Yi Lee; Cheng-Tsung Lu; Shu-An Chen; Neil Arvin Bretaña; Tzu-Hsiu Cheng; Min-Gang Su; Kai-Yao Huang (BMC Bioinform., 2011)

ViralPhos: incorporating a recursively statistical method to predict phosphorylation sites on virus proteins. - Kai-Yao Huang; Cheng-Tsung Lu; Neil Arvin Bretaña; Tzong-Yi Lee; Tzu-Hao Chang (BMC Bioinform., 2013)

dbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications. - Cheng-Tsung Lu; Kai-Yao Huang; Min-Gang Su; Tzong-Yi Lee; Neil Arvin Bretaña; Wen-Chi Chang; Yi-Ju Chen; Yu-Ju Chen; Hsien-Da Huang (Nucleic Acids Res., 2013)

RegPhos 2.0: an updated resource to explore protein kinase-substrate phosphorylation networks in mammals. - Kai-Yao Huang; Hsin-Yi Wu; Yi-Ju Chen; Cheng-Tsung Lu; Min-Gang Su; Yun-Chung Hsieh; Chih-Ming Tsai; Kuo-I Lin; Hsien-Da Huang; Tzong-Yi Lee; Yu-Ju Chen (Database J. Biol. Databases Curation, 2014)

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)

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)

An interpretable rule-based diagnostic classification of diabetic nephropathy among type 2 diabetes patients. - Guan-Mau Huang; Kai-Yao Huang; Tzong-Yi Lee; Julia Weng (BMC Bioinform., 2015)

ViralmiR: a support-vector-machine-based method for predicting viral microRNA precursors. - Kai-Yao Huang; Tzong-Yi Lee; Yu-Chuan Teng; Tzu-Hao Chang (BMC Bioinform., 2015)

Characterization and identification of ubiquitin conjugation sites with E3 ligase recognition specificities. - Van-Nui Nguyen; Kai-Yao Huang; Chien-Hsun Huang; Tzu-Hao Chang; Neil Arvin Bretaña; K. Robert Lai; Julia Weng; Tzong-Yi Lee (BMC Bioinform., 2015)

dbSNO 2.0: a resource for exploring structural environment, functional and disease association and regulatory network of protein S-nitrosylation. - Yi-Ju Chen; Cheng-Tsung Lu; Min-Gang Su; Kai-Yao Huang; Wei-Chieh Ching; Hsiao-Hsiang Yang; Yen-Chen Liao; Yu-Ju Chen; Tzong-Yi Lee (Nucleic Acids Res., 2015)

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)

UbiNet: an online resource for exploring the functional associations and regulatory networks of protein ubiquitylation. - Van-Nui Nguyen; Kai-Yao Huang; Julia Tzu-Ya Weng; K. Robert Lai; Tzong-Yi Lee (Database J. Biol. Databases Curation, 2016)

Gene expression profiling identifies candidate biomarkers for active and latent tuberculosis. - Shih-Wei Lee; Lawrence Shih-Hsin Wu; Guan-Mau Huang; Kai-Yao Huang; Tzong-Yi Lee; Julia Tzu-Ya Weng (BMC Bioinform., 2016)

A new scheme to discover functional associations and regulatory networks of E3 ubiquitin ligases. - Kai-Yao Huang; Julia Tzu-Ya Weng; Tzong-Yi Lee; Shun-Long Weng (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)

Identification of natural antimicrobial peptides from bacteria through metagenomic and metatranscriptomic analysis of high-throughput transcriptome data of Taiwanese oolong teas. - Kai-Yao Huang; Tzu-Hao Chang; Jhih-Hua Jhong; Yu-Hsiang Chi; Wen-Chi Li; Chien-Lung Chan; K. Robert Lai; Tzong-Yi Lee (BMC Syst. Biol., 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)

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)

A New Scheme to Characterize and Identify Protein Ubiquitination Sites. - Van-Nui Nguyen; Kai-Yao Huang; Chien-Hsun Huang; K. Robert Lai; Tzong-Yi Lee (IEEE ACM Trans. Comput. Biol. Bioinform., 2017)

Genome-wide discovery of viral microRNAs based on phylogenetic analysis and structural evolution of various human papillomavirus subtypes. - Shun-Long Weng; Kai-Yao Huang; Julia Tzu-Ya Weng; Fang-Yu Hung; Tzu-Hao Chang; Tzong-Yi Lee (Briefings Bioinform., 2018)

Machine Learning-Based Method for Obesity Risk Evaluation Using Single-Nucleotide Polymorphisms Derived from Next-Generation Sequencing. - Hsin-Yao Wang; Shih-Cheng Chang; Wan-Ying Lin; Chun-Hsien Chen; Szu-Hsien Chiang; Kai-Yao Huang; Bo-Yu Chu; Jang-Jih Lu; Tzong-Yi Lee (J. Comput. Biol., 2018)

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)

dbAMP: an integrated resource for exploring antimicrobial peptides with functional activities and physicochemical properties on transcriptome and proteome data. - Jhih-Hua Jhong; Yu-Hsiang Chi; Wen-Chi Li; Tsai-Hsuan Lin; Kai-Yao Huang; Tzong-Yi Lee (Nucleic Acids Res., 2019)

Rapid classification of group B Streptococcus serotypes based on matrix-assisted laser desorption ionization-time of flight mass spectrometry and machine learning techniques. - Hsin-Yao Wang; Wen-Chi Li; Kai-Yao Huang; Chia-Ru Chung; Jorng-Tzong Horng; Jen-Fu Hsu; Jang-Jih Lu; Tzong-Yi Lee (BMC Bioinform., 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)

Incorporating deep learning and multi-omics autoencoding for analysis of lung adenocarcinoma prognostication. - Tzong-Yi Lee; Kai-Yao Huang; Cheng-Hsiang Chuang; Cheng-Yang Lee; Tzu-Hao Chang (Comput. Biol. Chem., 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)

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)

UbiNet 2.0: a verified, classified, annotated and updated database of E3 ubiquitin ligase-substrate interactions. - Zhongyan Li; Siyu Chen; Jhih-Hua Jhong; Yuxuan Pang; Kai-Yao Huang; Shangfu Li; Tzong-Yi Lee (Database J. Biol. Databases Curation, 2021)

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)