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2020 – today

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2024
[j78]
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Lantian Yao, Peilin Xie, Jiahui Guan, Chia-Ru Chung, Yixian Huang, Yuxuan Pang, Huacong Wu, Ying-Chih Chiang, Tzong-Yi Lee:
CapsEnhancer: An Effective Computational Framework for Identifying Enhancers Based on Chaos Game Representation and Capsule Network. J. Chem. Inf. Model. 64(14): 5725-5736 (2024)
2023
[j77]
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Mengqi Luo, Shangfu Li, Yuxuan Pang, Lantian Yao, Renfei Ma, Hsi-Yuan Huang, Hsien-Da Huang, Tzong-Yi Lee:
Extraction of microRNA-target interaction sentences from biomedical literature by deep learning approach. Briefings Bioinform. 24(1) (2023)
[j76]
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Renfei Ma, Shangfu Li, Luca Parisi, Wenshuo Li, Hsien-Da Huang, Tzong-Yi Lee:
Holistic similarity-based prediction of phosphorylation sites for understudied kinases. Briefings Bioinform. 24(2) (2023)
[j75]
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Rulan Wang, Chia-Ru Chung, Hsien-Da Huang, Tzong-Yi Lee:
Identification of species-specific RNA N6-methyladinosine modification sites from RNA sequences. Briefings Bioinform. 24(2) (2023)
[j74]
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Zhuo Wang, Yuxuan Pang, Chia-Ru Chung, Hsin-Yao Wang, Haiyan Cui, Ying-Chih Chiang, Jorng-Tzong Horng, Jang-Jih Lu, Tzong-Yi Lee:
A risk assessment framework for multidrug-resistant Staphylococcus aureus using machine learning and mass spectrometry technology. Briefings Bioinform. 24(6) (2023)
[j73]
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Renfei Ma, Shangfu Li, Wenshuo Li, Lantian Yao, Hsien-Da Huang, Tzong-Yi Lee:
KinasePhos 3.0: Redesign and Expansion of the Prediction on Kinase-specific Phosphorylation Sites. Genom. Proteom. Bioinform. 21(1): 228-241 (2023)
[j72]
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Jiahui Guan, Lantian Yao, Chia-Ru Chung, Peilin Xie, Yilun Zhang, Junyang Deng, Ying-Chih Chiang, Tzong-Yi Lee:
Predicting Anti-inflammatory Peptides by Ensemble Machine Learning and Deep Learning. J. Chem. Inf. Model. 63(24): 7886-7898 (2023)
2022
[j71]
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Yuxuan Pang, Lantian Yao, Jingyi Xu, Zhuo Wang, Tzong-Yi Lee:
Integrating transformer and imbalanced multi-label learning to identify antimicrobial peptides and their functional activities. Bioinform. 38(24): 5368-5374 (2022)
[j70]
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Qiyang Wu, Tianyang Huang, Songyan Xia, Frank Otto, Tzong-Yi Lee, Hsien-Da Huang, Ying-Chih Chiang:
On the force field optimisation of β-lactam cores using the force field Toolkit. J. Comput. Aided Mol. Des. 36(7): 537-547 (2022)
[j69]
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  - journals/nar/ChenYTJWCCLCLCH22
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Yigang Chen, Lantian Yao, Yun Tang, Jhih-Hua Jhong, Jingting Wan, Jingyue Chang, Shi-Dong Cui, Yijun Luo, Xiao-Xuan Cai, Wenshuo Li, Qi Chen, Hsi-Yuan Huang, Zhuo Wang, Weiming Chen, Tzu-Hao Chang, Feng-Xiang Wei, Tzong-Yi Lee, Hsien-Da Huang:
CircNet 2.0: an updated database for exploring circular RNA regulatory networks in cancers. Nucleic Acids Res. 50(D1): 93-101 (2022)
[j68]
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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, Jie Ni, Yini Ruan, Liping Li, Yidan Chen, Yue-Yang Xie, Zihao Zhu, Xiao-Xuan Cai, Xin-Yi Chen, Lantian Yao, Yigang Chen, Yijun Luo, Shupeng Luxu, Mengqi Luo, Chih-Min Chiu, Kun Ma, Lizhe Zhu, Gui-Juan Cheng, Chen Bai, Ying-Chih Chiang, Liping Wang, Feng-Xiang Wei, Tzong-Yi Lee, Hsien-Da Huang:
miRTarBase update 2022: an informative resource for experimentally validated miRNA-target interactions. Nucleic Acids Res. 50(D1): 222-230 (2022)
[j67]
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Jhih-Hua Jhong, Lantian Yao, Yuxuan Pang, Zhongyan Li, Chia-Ru Chung, Rulan Wang, Shangfu Li, Wenshuo Li, Mengqi Luo, Renfei Ma, Yuqi Huang, Xiaoning Zhu, Jiahong Zhang, Hexiang Feng, Qifan Cheng, Chunxuan Wang, Kun Xi, Li-Ching Wu, Tzu-Hao Chang, Jorng-Tzong Horng, Lizhe Zhu, Ying-Chih Chiang, Zhuo Wang, Tzong-Yi Lee:
dbAMP 2.0: updated resource for antimicrobial peptides with an enhanced scanning method for genomic and proteomic data. Nucleic Acids Res. 50(D1): 460-470 (2022)
[j66]
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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, Xiaoning Zhu, Qifan Cheng, Hexiang Feng, Jiahong Zhang, Chunxuan Wang, Justin Bo-Kai Hsu, Wen-Chi Chang, Feng-Xiang Wei, Hsien-Da Huang, Tzong-Yi Lee:
dbPTM in 2022: an updated database for exploring regulatory networks and functional associations of protein post-translational modifications. Nucleic Acids Res. 50(D1): 471-479 (2022)
2021
[j65]
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Yuxuan Pang, Zhuo Wang, Jhih-Hua Jhong, Tzong-Yi Lee:
Identifying anti-coronavirus peptides by incorporating different negative datasets and imbalanced learning strategies. Briefings Bioinform. 22(2): 1085-1095 (2021)
[j64]
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Hsin-Yao Wang, Chia-Ru Chung, Zhuo Wang, Shangfu Li, Bo-Yu Chu, Jorng-Tzong Horng, Jang-Jih Lu, Tzong-Yi Lee:
A large-scale investigation and identification of methicillin-resistant Staphylococcus aureus based on peaks binning of matrix-assisted laser desorption ionization-time of flight MS spectra. Briefings Bioinform. 22(3) (2021)
[j63]
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Yuxuan Pang, Lantian Yao, Jhih-Hua Jhong, Zhuo Wang, Tzong-Yi Lee:
AVPIden: a new scheme for identification and functional prediction of antiviral peptides based on machine learning approaches. Briefings Bioinform. 22(6) (2021)
[j62]
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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)
[j61]
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Yu Wan, Zhuo Wang, Tzong-Yi Lee:
Incorporating support vector machine with sequential minimal optimization to identify anticancer peptides. BMC Bioinform. 22(1): 286 (2021)
[j60]
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Mengqi Luo, Zhongyan Li, Shangfu Li, Tzong-Yi Lee:
A representation and deep learning model for annotating ubiquitylation sentences stating E3 ligase - substrate interaction. BMC Bioinform. 22(1): 507 (2021)
2020
[j59]
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Chia-Ru Chung, Ting-Rung Kuo, Li-Ching Wu, Tzong-Yi Lee, Jorng-Tzong Horng:
Characterization and identification of antimicrobial peptides with different functional activities. Briefings Bioinform. 21(3): 1098-1114 (2020)
[j58]
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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)
[j57]
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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)
[j56]
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  - journals/nar/HuangLLHSHTCJYX20
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Hsi-Yuan Huang, Yang-Chi-Dung Lin, Jing Li, Kai-Yao Huang, Sirjana Shrestha, Hsiao-Chin Hong, Yun Tang, Yigang 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)

2010 – 2019

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2019
[j55]
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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)
[j54]
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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)
[j53]
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  - journals/nar/ChowLHLTLKZC19
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Chi-Nga Chow, Tzong-Yi Lee, Yu-Cheng Hung, Guan-Zhen Li, Kuan-Chieh Tseng, Ya-Hsin Liu, Po-Li Kuo, Han-Qin Zheng, Wen-Chi Chang:
PlantPAN3.0: a new and updated resource for reconstructing transcriptional regulatory networks from ChIP-seq experiments in plants. Nucleic Acids Res. 47(Database-Issue): D1155-D1163 (2019)
[j52]
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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)
[j51]
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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
[j50]
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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)
[j49]
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Chi-Nga Chow, Yi-Fan Chiang-Hsieh, Chia-Hung Chien, Han-Qin Zheng, Tzong-Yi Lee, Nai-Yun Wu, Kuan-Chieh Tseng, Ping-Fu Hou, Wen-Chi Chang:
Delineation of condition specific Cis- and Trans-acting elements in plant promoters under various Endo- and exogenous stimuli. BMC Genom. 19(S2) (2018)
[j48]
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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
[j47]
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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)
[j46]
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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)
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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)
[j44]
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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)
[j43]
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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
[j42]
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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)
[j41]
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Van-Minh Bui, Cheng-Tsung Lu, Trang-Thi Ho, Tzong-Yi Lee:
MDD-SOH: exploiting maximal dependence decomposition to identify S-sulfenylation sites with substrate motifs. Bioinform. 32(2): 165-172 (2016)
[j40]
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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)
[j39]
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Van-Minh Bui, Shun-Long Weng, Cheng-Tsung Lu, Tzu-Hao Chang, Julia Tzu-Ya Weng, Tzong-Yi Lee:
SOHSite: incorporating evolutionary information and physicochemical properties to identify protein S-sulfenylation sites. BMC Genom. 17(S-1): 9 (2016)
[j38]
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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)
[j37]
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Chien-Hsun Huang, Min-Gang Su, Hui-Ju Kao, Jhih-Hua Jhong, Shun-Long Weng, Tzong-Yi Lee:
UbiSite: incorporating two-layered machine learning method with substrate motifs to predict ubiquitin-conjugation site on lysines. BMC Syst. Biol. 10(S-1): 6 (2016)
[j36]
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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)
[j35]
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Chi-Nga Chow, Han-Qin Zheng, Nai-Yun Wu, Chia-Hung Chien, Hsien-Da Huang, Tzong-Yi Lee, Yi-Fan Chiang-Hsieh, Ping-Fu Hou, Tien-Yi Yang, Wen-Chi Chang:
PlantPAN 2.0: an update of plant promoter analysis navigator for reconstructing transcriptional regulatory networks in plants. Nucleic Acids Res. 44(Database-Issue): 1154-1160 (2016)
2015
[j34]
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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)
[j33]
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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)
[j32]
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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)
[j31]
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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)
[j30]
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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
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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)
[j28]
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Yi-Ju Chen, Cheng-Tsung Lu, Tzong-Yi Lee, Yu-Ju Chen:
dbGSH: a database of S-glutathionylation. Bioinform. 30(16): 2386-2388 (2014)
[j27]
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Hsin-Yi Wu, Cheng-Tsung Lu, Hui-Ju Kao, Yi-Ju Chen, Yu-Ju Chen, Tzong-Yi Lee:
Characterization and identification of protein O-GlcNAcylation sites with substrate specificity. BMC Bioinform. 15(S-16): S1 (2014)
[j26]
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Tzong-Yi Lee, Cheng-Wei Chang, Cheng-Tsung Lu, Tzu-Hsiu Cheng, Tzu-Hao Chang:
Identification and characterization of lysine-methylated sites on histones and non-histone proteins. Comput. Biol. Chem. 50: 11-18 (2014)
[j25]
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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)
[j24]
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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
[j23]
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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)
[j22]
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Min-Gang Su, Tzong-Yi Lee:
Incorporating substrate sequence motifs and spatial amino acid composition to identify kinase-specific phosphorylation sites on protein three-dimensional structures. BMC Bioinform. 14(S-16): S2 (2013)
[j21]
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Tzu-Hao Chang, Li-Ching Wu, Tzong-Yi Lee, Shu-Pin Chen, Hsien-Da Huang, Jorng-Tzong Horng:
EuLoc: a web-server for accurately predict protein subcellular localization in eukaryotes by incorporating various features of sequence segments into the general form of Chou's PseAAC. J. Comput. Aided Mol. Des. 27(1): 91-103 (2013)
[j20]
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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)
2012
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Tzong-Yi Lee, Yi-Ju Chen, Cheng-Tsung Lu, Wei-Chieh Ching, Yu-Chuan Teng, Hsien-Da Huang, Yu-Ju Chen:
dbSNO: a database of cysteine S-nitrosylation. Bioinform. 28(17): 2293-2295 (2012)
[j18]
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Tzong-Yi Lee, Wen-Chi Chang, Justin Bo-Kai Hsu, Tzu-Hao Chang, Dray-Ming Shien:
GPMiner: an integrated system for mining combinatorial cis-regulatory elements in mammalian gene group. BMC Genom. 13(S-1): S3 (2012)
2011
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Tzong-Yi Lee, Zong-Qing Lin, Sheng-Jen Hsieh, Neil Arvin Bretaña, Cheng-Tsung Lu:
Exploiting maximal dependence decomposition to identify conserved motifs from a group of aligned signal sequences. Bioinform. 27(13): 1780-1787 (2011)
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Shu-An Chen, Yu-Yen Ou, Tzong-Yi Lee, M. Michael Gromiha:
Prediction of transporter targets using efficient RBF networks with PSSM profiles and biochemical properties. Bioinform. 27(15): 2062-2067 (2011)
[j15]
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Tzong-Yi Lee, Neil Arvin Bretaña, Cheng-Tsung Lu:
PlantPhos: using Maximal Dependence Decomposition to Identify Plant Phosphorylation Sites with Substrate Site Specificity. BMC Bioinform. 12: 261 (2011)
[j14]
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Justin Bo-Kai Hsu, Chih-Min Chiu, Sheng-Da Hsu, Wei-Yun Huang, Chia-Hung Chien, Tzong-Yi Lee, Hsien-Da Huang:
miRTar: an integrated system for identifying miRNA-target interactions in Human. BMC Bioinform. 12: 300 (2011)
[j13]
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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)
[j12]
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Cheng-Tsung Lu, Shu-An Chen, Neil Arvin Bretaña, Tzu-Hsiu Cheng, Tzong-Yi Lee:
Carboxylator: incorporating solvent-accessible surface area for identifying protein carboxylation sites. J. Comput. Aided Mol. Des. 25(10): 987-995 (2011)
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Tzong-Yi Lee, Justin Bo-Kai Hsu, Wen-Chi Chang, Hsien-Da Huang:
RegPhos: a system to explore the protein kinase-substrate phosphorylation network in humans. Nucleic Acids Res. 39(Database-Issue): 777-787 (2011)
2010
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Shu-An Chen, Tzong-Yi Lee, Yu-Yen Ou:
Incorporating significant amino acid pairs to identify O-linked glycosylation sites on transmembrane proteins and non-transmembrane proteins. BMC Bioinform. 11: 536 (2010)
[j9]
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Tzong-Yi Lee, Justin Bo-Kai Hsu, Feng-Mao Lin, Wen-Chi Chang, Po-Chiang Hsu, Hsien-Da Huang:
N-Ace: Using solvent accessibility and physicochemical properties to identify protein N-acetylation sites. J. Comput. Chem. 31(15): 2759-2771 (2010)

2000 – 2009

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2009
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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:
Incorporating structural characteristics for identification of protein methylation sites. J. Comput. Chem. 30(9): 1532-1543 (2009)
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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:
Incorporating support vector machine for identifying protein tyrosine sulfation sites. J. Comput. Chem. 30(15): 2526-2537 (2009)
2007
[j6]
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Yung-Hao Wong, Tzong-Yi Lee, Han-Kuen Liang, Chia-Mao Huang, Ting-Yuan Wang, Yi-Huan Yang, Chia-Huei Chu, Hsien-Da Huang, Ming-Tat Ko, Jenn-Kang Hwang:
KinasePhos 2.0: a web server for identifying protein kinase-specific phosphorylation sites based on sequences and coupling patterns. Nucleic Acids Res. 35(Web-Server-Issue): 588-594 (2007)
2006
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Tzong-Yi Lee, Jorng-Tzong Horng, Hsueh-Fen Juan, Hsien-Da Huang, Li-Cheng Wu, Meng-Feng Tsai, Hsuan-Cheng Huang:
An agent-based system to discover protein-protein interactions, identify protein complexes and proteins with multiple peptide mass fingerprints. J. Comput. Chem. 27(9): 1020-1032 (2006)
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Tzong-Yi Lee, Hsien-Da Huang, Jui-Hung Hung, Hsi-Yuan Huang, Yuh-Shyong Yang, Tzu-Hao Wang:
dbPTM: an information repository of protein post-translational modification. Nucleic Acids Res. 34(Database-Issue): 622-627 (2006)
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Jui-Hung Hung, Hsien-Da Huang, Tzong-Yi Lee:
ProKware: integrated software for presenting protein structural properties in protein tertiary structures. Nucleic Acids Res. 34(Web-Server-Issue): 89-94 (2006)
2005
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Hsien-Da Huang, Tzong-Yi Lee, Shih-Wei Tzeng, Li-Cheng Wu, Jorng-Tzong Horng, Ann-Ping Tsou, Kuan-Tsae Huang:
Incorporating hidden Markov models for identifying protein kinase-specific phosphorylation sites. J. Comput. Chem. 26(10): 1032-1041 (2005)
[j1]
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Hsien-Da Huang, Tzong-Yi Lee, Shih-Wei Tzeng, Jorng-Tzong Horng:
KinasePhos: a web tool for identifying protein kinase-specific phosphorylation sites. Nucleic Acids Res. 33(Web-Server-Issue): 226-229 (2005)

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