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LEE, Tzong-Yi


Associate Professor

Education Background

PhD (Bioinformatics, National Chiao Tung University, Taiwan)

BS (Computer Science and Information Engineering, National Central University, Taiwan)

Research Field
Bioinformatics, Genomics and Proteomics, Network Biology, Data Mining in Omics Science, Shallow and Deep Learning, Database Design and Software Development.


Dr. Tzong-Yi Lee received the B.S. degree in Computer Science and Information Engineering from National Central University (NCU), Taiwan and the Ph.D. degree in Bioinformatics from National Chiao Tung University (NCTU), Taiwan, in 2002 and 2008, respectively. From 2009 to 2017, Dr. Lee was an Assistant Professor, Associate Professor (2012), and Professor (2015) with the Department of Computer Science and Engineering, Yuan Ze University, Taiwan. Currently he is an Associate Professor in the School of Science and Engineering, The Chinese University of Hong Kong, Shenzhen, China. Dr. Lee’s research interests include bioinformatics, genomics and proteomics, network biology, data mining in Omics science, shallow and deep learning, database design and software development. His research team currently specialize in gene promoters and transcriptional regulations, circular RNA regulation, microbiota and functional analyses, protein post-translational modifications (PTMs), protein kinases and signaling pathway, protein ubiquitylation and E3 ligases regulations, protein glycosylation and glycosyl-structure identification, antimicrobial peptides (AMPs), multidrug-resistant pathogens diagnosis, and drug repurposing. His longer-term research goals are focusing on the integration of Bioinformatics and Omics science to address emerging biological and clinical questions for precision medicine.

Dr. Lee have published over 70 articles in SCI journals, including Nucleic Acids Research, Bioinformatics, Briefings in Bioinformatics, Journal of Proteome Research, DATABASE: The Journal of Biological Databases and Curation, BMC Genomics, PLoS ONE, IEEE/ACM Transactions on Computational Biology and Bioinformatics, etc. His research achievements have awarded him with Yuan Ze University Young Scholar Research Award (2011), Yuan Ze University Outstanding Research Award (2012 and 2016), and the Y. Z. Hsu Outstanding Professor Award (2015). Additionally, he is one of the Editorial Board of Genomics, Proteomics, and Bioinformatics (GPB), Proteomics & Bioinformatics: Current Research, International Journal of Bioinformatics & Biological Systems (IJBBS), and Informatics since 2015.

Academic Publications:

Selected Journal Publications (* corresponding author):

1.    Hui-Ju Kao, Kai-Yao Huang and Tzong-Yi Lee*, 2018, “Exploiting Deep Learning Method to Identify Succinylated Sites on Lysine Residues”, Bioinformatics, accepted.

2.    Hsin-Yao Wang‡, Tzong-Yi Lee‡ (‡ joint first authorship), Yi-Ju Tseng, Tsui-Ping Liu, Kai-Yao Huang, YungTa Chang, Chun-Hsien Chen*, Jang-Jih Lu*, March 2018, "A new scheme for strain typing of methicillin-resistant Staphylococcus aureus on the basis of matrix-assisted laser desorption ionization time-of-flight mass spectrometry by using machine learning approach," PLoS ONE, 13(3): e0194289. 

3.    Kai-Yao Huang, Tzu-Hao Chang, Jhih-Hua Jhong, Yu-Hsiang Chi, Wen-Chi Li, Chien-Lung Chan, K. Robert Lai and Tzong-Yi Lee*, 2017, "Identification of natural antimicrobial peptides from bacteria through metagenomic and metatranscriptomic analysis of high-throughput transcriptome data of Taiwanese oolong teas," BMC Systems Biology, Vol. 11 (Suppl 7):131.

4.    Shun-Long Weng†, Kai-Yao Huang† († joint first authorship), Julia Tzu-Ya Weng, Fang-Yu Hung, Tzu-Hao Chang* and Tzong-Yi Lee*, 2017, “Genome-wide discovery of viral microRNAs based on phylogenetic analysis and structural evolution of various human papillomavirus subtypes,” Briefings in Bioinformatics, 2017 bbx046. doi: 10.1093/bib/bbx046.

5.    Van-Nui Nguyen, Kai-Yao Huang, Chien-Hsun Huang, K. Robert Lai* and Tzong-Yi Lee*, 2017, "A new scheme to characterize and identify protein ubiquitination sites," IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 14(2):393-403.

6.    Kai-Yao Huang, Min-Gang Su, Hui-Ju Kao, Yun-Chung Hsieh, Jhih-Hua Jhong, Kuang-Hao Cheng, Hsien-Da Huang, Tzong-Yi Lee*, 2016, "dbPTM 2016: ten-year anniversary of a resource of post-translational modification of proteins," Nucleic Acids Research 2016 Jan. 4, Vol. 44(D1):D435-D446.

7.    Chi-Nga Chow, Han-Qin Zheng, Nai-Yun Wu, Chia-Hung Chien, Hsien-Da Huang, Tzong-Yi Lee, Yi-Fan Chian-Hsieh, Ping-Fu Hou, Tien-Yi Yang, and Wen-Chi Chang*, 2016, "PlantPAN 2.0: an update of Plant Promoter Analysis Navigator for reconstructing transcriptional regulatory networks in plants," Nucleic Acids Research 2016 Jan. 4; Vol. 44(D1):D1154-D1160.

8.    Van-Nui Nguyen, Kai-Yao Huang, Julia Tzu-Ya Weng, K. Robert Lai* and Tzong-Yi Lee*, 2016, "UbiNet: an online resource for exploring functional associations and regulatory networks of protein ubiquitylation," DATABASE: The Journal of Biological Databases and Curation, 2016 Apr 25;2016. pii: baw054.

9.    Van-Minh Bui, Cheng-Tsung Lu, Thi-Trang Ho, and Tzong-Yi Lee*, 2016, "MDD-SOH: Exploiting maximal dependence decomposition to identify S-sulfenylation sites with substrate motifs" Bioinformatics, 2016 Jan 15, 32(2):165-72.

10.  Yi-Ju Chen, Cheng-Tsung Lu, Min-Gang Su, Kai-Yao Huang, Wei-Chieh Ching, Hsiao-Hsiang Yang, Yen-Chen Liao, Yu-Ju Chen* and Tzong-Yi Lee*, 2015, "dbSNO 2.0: a resource for exploring structural environment, functional and disease associations, and regulatory networks of protein S-nitrosylation" Nucleic Acids Research Vol. 43 (D1): D503-11.

11.  Yi-Ju Chen, Cheng-Tsung Lu, Tzong-Yi Lee* and Yu-Ju Chen*, 2014, "dbGSH: a database of S-Glutathionylation" Bioinformatics, 2014 Aug 15;30(16):2386-8.

12.  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* and Yu-Ju Chen*, 2014, "RegPhos 2.0: an updated resource to explore protein kinase-substrate phosphorylation networks in mammals," DATABASE: The Journal of Biological Databases and Curation, 2014(0): bau034.

13.  Min-Gang Su, Kai-Yao Huang, Cheng-Tsung Lu, Hui-Ju Kao, Ya-Han Chang and Tzong-Yi Lee*, 2014, "topPTM: a new module of dbPTM for identifying functional post-translational modifications in transmembrane proteins," Nucleic Acids Research, Vol. 42 (D1): D537-D545.

14.  Cheng-Tsung Lu, Kai-Yao Huang, Min-Gang Su, Tzong-Yi Lee*, Neil Arvin Bretaña, Wen-Chi Chang, Yi-Ju Chen, Yu-Ju Chen and Hsien-Da Huang*, 2013, "dbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications," Nucleic Acids Research, 41 (D1):D295-305.

15.  Tzong-Yi Lee*, Yi-Ju Chen, Cheng-Tsung Lu, Wei-Chieh Ching, Yu-Chuan Teng, Hsien-Da Huang and Yu-Ju Chen*, 2012, "dbSNO: a database of cysteine S-Nitrosylation," Bioinformatics, 28(17):2293-5.

16.  Tzong-Yi Lee*, Wen-Chi Chang*, Justin BK Hsu, Tzu-Hao Chang and Dray-Ming Shien, 2012, January "GPMiner: an integrated system for mining combinatorial cis-regulatory elements in mammalian gene group," BMC Genomics, 13(Suppl 1):S3.

17.  C.H. Chien, Y.M. Sun, W.C. Chang, P.Y. Chiang-Hsieh, Tzong-Yi Lee, W.C. Tsai, J.T. Horng, A.P. Tsou*, H.D. Huang*, 2011, "Identifying transcriptional start sites of human microRNAs based on high-throughput sequencing data," Nucleic Acids Research, 39(21):9345-9356.

18.  Tzong-Yi Lee*, Zong-Qing Lin, Sheng-Jen Hsieh, Neil Arvin Bretaña, and Cheng-Tsung Lu, 2011, "Exploiting maximal dependence decomposition to identify conserved motifs from a group of aligned signal sequences," Bioinformatics, 27(13): 1780-1787.

19.  Shu-An Chen, Yu-Yen Ou, Tzong-Yi Lee and M. Michael Gromiha*, 2011, June "Prediction of transporter targets using efficient RBF networks with PSSM profiles and biochemical properties," Bioinformatics, 27(15):2062-7.

20.  Tzong-Yi Lee, Justin Bo-Kai Hsu, Wen-Chi Chang, and Hsien-Da Huang* , 2011, "RegPhos: a system to explore the protein kinase-substrate phosphorylation network in humans," Nucleic Acids Research, Vol. 39, D777-D787.

21.  Dray-Ming Shien†, Tzong-Yi Lee† († joint first authorship), Wen-Chi Chang, Justin B.K. Hsu, Jorng-Tzong Horng, Po-Chian Hsu, Ting-Yuan Wang and Hsien-Da Huang*, 2010, "Incorporating Structural Characteristics for Identification of Protein Methylation Sites," Journal of Computational Chemistry, Vol. 30, No. 9, pp.1532-1543.

22.  Tzong-Yi Lee, Justin Bo-Kai Hsu, Feng-Mao Lin, Wen-Chi Chang, Po-Chiang Hsu, and Hsien-Da Huang, 2010, "N-Ace: using solvent accessibility and physicochemical properties to identify protein N-Acetylation sites," Journal of Computational Chemistry, Vol. 31 (15), 2759-2771. (Cover Story)

23.  W.C. Chang†, Tzong-Yi Lee† († joint first authorship), D.M. Shien, J. B.K. Hsu, P.C. Hsu, T.Y. Wang, J.T. Horng, H.D. Huang* and R.L. Pan*, 2009, Nov 30 "Incorporating support vector machine for identifying protein tyrosine sulfation sites," Journal of Computational Chemistry, 2009 Nov 30; 30(15):2526-37.

24.  W.C. Chang, Tzong-Yi Lee, H.D. Huang*, H.Y. Huang, R.L. Pan*, 2008, "PlantPAN: Plant Promoter Analysis Navigator, for identifying combinatorial cis-regulatory elements with distance constraint in plant gene group," BMC Genomics, 9:561.

25.  Y.H. Wong†, Tzong-Yi Lee† († joint first authorship), H.K. Liang, C.M. Huang, Y.H. Yang, C.H. Chu, H.D. Huang* , M.T. Ko, and J.K. Hwang, 2007, "KinasePhos 2.0: a web server for identifying protein kinase-specific phosphorylation sites based on sequences and coupling patterns," Nucleic Acids Research, Vol 35, W588-594.

26.  Tzong-Yi Lee, J.T. Horng, H.F. Juan, H.D. Huang, L.C. Wu, and F.M. Lin, 2006, "An agent-based system to discover protein-protein interactions, identify protein complexes and proteins with multiple peptide mass fingerprints," Journal of Computational Chemistry, Vol. 27, No. 9, 1020-32.

27.  Tzong-Yi Lee, H.D. Huang*, J.H. Hung, Y.S. Yang, and T.H. Wang*, 2006, "dbPTM: An information repository of protein post-translational modification," Nucleic Acids Research, Vol. 34, D622-D627. 

28.  J.H. Hung†, H.D. Huang†,* († joint first authorship), and Tzong-Yi Lee, "ProKware: an integrated software for presenting protein structural properties in protein tertiary structures," Nucleic Acids Research, Vol 34, W89-W94.

29.  H.D. Huang, Tzong-Yi Lee, L.C. Wu, F.M. Lin, J.T. Horng, and A.P. Tsou, 2005, "MultiProtIdent: identifying proteins using database search and protein-protein interactions," Journal of Proteome Research, Vol. 4(3), 690-697.

30.  H.D. Huang*, Tzong-Yi Lee, S.W. Tseng, and J.T. Horng, 2005, "KinasePhos: a web tool for identifying protein kinase-specific phosphorylation sites," Nucleic Acids Research, Vol. 33, W226-229.