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Journal Articles
- 2022
[j32]Kai-Yao Huang
, Hui-Ju Kao, Tzu-Hsiang Weng, Chia-Hung Chen, Shun-Long Weng:
iDVIP: identification and characterization of viral integrase inhibitory peptides. Briefings Bioinform. 23(6) (2022)- 2021
- [j31]Zhongyan Li, Siyu Chen, Jhih-Hua Jhong, Yuxuan Pang, Kai-Yao Huang, Shangfu Li, Tzong-Yi Lee:
UbiNet 2.0: a verified, classified, annotated and updated database of E3 ubiquitin ligase-substrate interactions. Database J. Biol. Databases Curation 2021 (2021) - 2020
- [j30]Kai-Yao Huang, Fang-Yu Hung, Hui-Ju Kao, Hui-Hsuan Lau, Shun-Long Weng:
iDPGK: characterization and identification of lysine phosphoglycerylation sites based on sequence-based features. BMC Bioinform. 21-S(1): 568 (2020) - [j29]Tzong-Yi Lee, Kai-Yao Huang, Cheng-Hsiang Chuang, Cheng-Yang Lee, Tzu-Hao Chang:
Incorporating deep learning and multi-omics autoencoding for analysis of lung adenocarcinoma prognostication. Comput. Biol. Chem. 87: 107277 (2020) - [j28]Hui-Ju Kao, Van-Nui Nguyen, Kai-Yao Huang, Wen-Chi Chang, Tzong-Yi Lee:
SuccSite: Incorporating Amino Acid Composition and Informative k-spaced Amino Acid Pairs to Identify Protein Succinylation Sites. Genom. Proteom. Bioinform. 18(2): 208-219 (2020) - [j27]Hsi-Yuan Huang, Yang-Chi-Dung Lin, Jing Li, Kai-Yao Huang, Sirjana Shrestha, Hsiao-Chin Hong, Yun Tang, Yi-Gang Chen, Chen-Nan Jin, Yuan Yu, Jia-Tong Xu, Yue-Ming Li, Xiao-Xuan Cai, Zhen-Yu Zhou, Xiao-Hang Chen, Yuan-Yuan Pei, Liang Hu, Jin-Jiang Su, Shi-Dong Cui, Fei Wang, Yue-Yang Xie, Si-Yuan Ding, Meng-Fan Luo, Chih-Hung Chou, Nai-Wen Chang, Kai-Wen Chen, Yu-Hsiang Cheng, Xin-Hong Wan, Wen-Lian Hsu, Tzong-Yi Lee, Feng-Xiang Wei, Hsien-Da Huang:
miRTarBase 2020: updates to the experimentally validated microRNA?target interaction database. Nucleic Acids Res. 48(Database-Issue): D148-D154 (2020) - 2019
- [j26]Kai-Yao Huang, Hui-Ju Kao, Justin Bo-Kai Hsu, Shun-Long Weng, Tzong-Yi Lee:
Characterization and identification of lysine glutarylation based on intrinsic interdependence between positions in the substrate sites. BMC Bioinform. 19-S(13): 13-25 (2019) - [j25]Hsin-Yao Wang, Wen-Chi Li, Kai-Yao Huang, Chia-Ru Chung, Jorng-Tzong Horng, Jen-Fu Hsu, Jang-Jih Lu, Tzong-Yi Lee:
Rapid classification of group B Streptococcus serotypes based on matrix-assisted laser desorption ionization-time of flight mass spectrometry and machine learning techniques. BMC Bioinform. 20-S(19): 703 (2019) - [j24]Jhih-Hua Jhong, Yu-Hsiang Chi, Wen-Chi Li, Tsai-Hsuan Lin, Kai-Yao Huang, Tzong-Yi Lee:
dbAMP: an integrated resource for exploring antimicrobial peptides with functional activities and physicochemical properties on transcriptome and proteome data. Nucleic Acids Res. 47(Database-Issue): D285-D297 (2019) - [j23]Kai-Yao Huang, Tzong-Yi Lee, Hui-Ju Kao, Chen-Tse Ma, Chao-Chun Lee, Tsai-Hsuan Lin, Wen-Chi Chang, Hsien-Da Huang:
dbPTM in 2019: exploring disease association and cross-talk of post-translational modifications. Nucleic Acids Res. 47(Database-Issue): D298-D308 (2019) - 2018
- [j22]Shun-Long Weng, Kai-Yao Huang, Julia Tzu-Ya Weng, Fang-Yu Hung, Tzu-Hao Chang, Tzong-Yi Lee:
Genome-wide discovery of viral microRNAs based on phylogenetic analysis and structural evolution of various human papillomavirus subtypes. Briefings Bioinform. 19(6): 1102-1114 (2018) - [j21]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:
Machine Learning-Based Method for Obesity Risk Evaluation Using Single-Nucleotide Polymorphisms Derived from Next-Generation Sequencing. J. Comput. Biol. 25(12): 1347-1360 (2018) - 2017
- [j20]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:
Investigation and identification of protein carbonylation sites based on position-specific amino acid composition and physicochemical features. BMC Bioinform. 18(S-3): 125-141 (2017) - [j19]Kai-Yao Huang, Tzu-Hao Chang, Jhih-Hua Jhong, Yu-Hsiang Chi, Wen-Chi Li, Chien-Lung Chan, K. Robert Lai, Tzong-Yi Lee:
Identification of natural antimicrobial peptides from bacteria through metagenomic and metatranscriptomic analysis of high-throughput transcriptome data of Taiwanese oolong teas. BMC Syst. Biol. 11(S-7): 29-44 (2017) - [j18]Min-Gang Su, Julia Tzu-Ya Weng, Justin Bo-Kai Hsu, Kai-Yao Huang, Yu-Hsiang Chi, Tzong-Yi Lee:
Investigation and identification of functional post-translational modification sites associated with drug binding and protein-protein interactions. BMC Syst. Biol. 11(S-7): 69-80 (2017) - [j17]Hui-Ju Kao, Shun-Long Weng, Kai-Yao Huang, Fergie Joanda Kaunang, Justin Bo-Kai Hsu, Chien-Hsun Huang, Tzong-Yi Lee:
MDD-carb: a combinatorial model for the identification of protein carbonylation sites with substrate motifs. BMC Syst. Biol. 11(S-7): 127-140 (2017) - [j16]Van-Nui Nguyen, Kai-Yao Huang, Chien-Hsun Huang, K. Robert Lai, Tzong-Yi Lee:
A New Scheme to Characterize and Identify Protein Ubiquitination Sites. IEEE ACM Trans. Comput. Biol. Bioinform. 14(2): 393-403 (2017) - 2016
- [j15]Van-Nui Nguyen, Kai-Yao Huang, Julia Tzu-Ya Weng, K. Robert Lai, Tzong-Yi Lee:
UbiNet: an online resource for exploring the functional associations and regulatory networks of protein ubiquitylation. Database J. Biol. Databases Curation 2016 (2016) - [j14]Shih-Wei Lee, Lawrence Shih-Hsin Wu, Guan-Mau Huang, Kai-Yao Huang, Tzong-Yi Lee, Julia Tzu-Ya Weng:
Gene expression profiling identifies candidate biomarkers for active and latent tuberculosis. BMC Bioinform. 17(S-1): 3 (2016) - [j13]Kai-Yao Huang, Julia Tzu-Ya Weng, Tzong-Yi Lee, Shun-Long Weng:
A new scheme to discover functional associations and regulatory networks of E3 ubiquitin ligases. BMC Syst. Biol. 10(S-1): 3 (2016) - [j12]Kai-Yao Huang, Min-Gang Su, Hui-Ju Kao, Yun-Chung Hsieh, Jhih-Hua Jhong, Kuang-Hao Cheng, Hsien-Da Huang, Tzong-Yi Lee:
dbPTM 2016: 10-year anniversary of a resource for post-translational modification of proteins. Nucleic Acids Res. 44(Database-Issue): 435-446 (2016) - 2015
- [j11]Van-Nui Nguyen, Kai-Yao Huang, Chien-Hsun Huang, Tzu-Hao Chang, Neil Arvin Bretaña, K. Robert Lai, Julia Weng, Tzong-Yi Lee:
Characterization and identification of ubiquitin conjugation sites with E3 ligase recognition specificities. BMC Bioinform. 16(S-1): S1 (2015) - [j10]Guan-Mau Huang, Kai-Yao Huang, Tzong-Yi Lee, Julia Weng:
An interpretable rule-based diagnostic classification of diabetic nephropathy among type 2 diabetes patients. BMC Bioinform. 16(S-1): S5 (2015) - [j9]Kai-Yao Huang, Tzong-Yi Lee, Yu-Chuan Teng, Tzu-Hao Chang:
ViralmiR: a support-vector-machine-based method for predicting viral microRNA precursors. BMC Bioinform. 16(S-1): S9 (2015) - [j8]Hui-Ju Kao, Chien-Hsun Huang, Neil Arvin Bretaña, Cheng-Tsung Lu, Kai-Yao Huang, Shun-Long Weng, Tzong-Yi Lee:
A two-layered machine learning method to identify protein O-GlcNAcylation sites with O-GlcNAc transferase substrate motifs. BMC Bioinform. 16(S18): S10 (2015) - [j7]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:
dbSNO 2.0: a resource for exploring structural environment, functional and disease association and regulatory network of protein S-nitrosylation. Nucleic Acids Res. 43(Database-Issue): 503-511 (2015) - 2014
- [j6]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:
RegPhos 2.0: an updated resource to explore protein kinase-substrate phosphorylation networks in mammals. Database J. Biol. Databases Curation 2014 (2014) - [j5]Justin Bo-Kai Hsu, Kai-Yao Huang, Julia Tzu-Ya Weng, Chien-Hsun Huang, Tzong-Yi Lee:
Incorporating significant amino acid pairs and protein domains to predict RNA splicing-related proteins with functional roles. J. Comput. Aided Mol. Des. 28(1): 49-60 (2014) - [j4]Min-Gang Su, Kai-Yao Huang, Cheng-Tsung Lu, Hui-Ju Kao, Ya-Han Chang, Tzong-Yi Lee:
topPTM: a new module of dbPTM for identifying functional post-translational modifications in transmembrane proteins. Nucleic Acids Res. 42(Database-Issue): 537-545 (2014) - 2013
- [j3]Kai-Yao Huang, Cheng-Tsung Lu, Neil Arvin Bretaña, Tzong-Yi Lee, Tzu-Hao Chang:
ViralPhos: incorporating a recursively statistical method to predict phosphorylation sites on virus proteins. BMC Bioinform. 14(S-16): S10 (2013) - [j2]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:
dbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications. Nucleic Acids Res. 41(Database-Issue): 295-305 (2013) - 2011
- [j1]Tzong-Yi Lee, Cheng-Tsung Lu, Shu-An Chen, Neil Arvin Bretaña, Tzu-Hsiu Cheng, Min-Gang Su, Kai-Yao Huang:
Investigation and identification of protein γ-glutamyl carboxylation sites. BMC Bioinform. 12(S-13): S10 (2011)
Coauthor Index
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