李宗夷

Dr. Tzong-Yi Lee


Professor,

Department of Computer Science & Engineering
Graduate Program in Biomedical Informatics
Yuan Ze University

Contact Information 聯絡資訊



  • Office : R3312C , Building #3

  • Laboratory : R1607A , Building #1

  • Phone : 886-3-4638800 ext. 3007


Experience 經歷


  • Professor - 2015/08 ~

Department of Computer Science & Engineering,
Graduate Program in Biomedical Informatics,
Yuan Ze University.

  • Associate Professor - 2012/08 ~ 2015/07

Department of Computer Science & Engineering,
Graduate Program in Biomedical Informatics,
Yuan Ze University.

  • Assistant Professor - 2009/08 ~ 2012/07

Department of Computer Science & Engineering,
Graduate Program in Biomedical Informatics,
Yuan Ze University.

  • System and Network Manager - 2004/08 ~ 2008/07

College of Biological Science and Technology,
National Chiao Tung University.

Education 學歷


  • Ph.D. - 2004/08 ~ 2008/07,

Institute of Bioinformatics, National Chiao Tung University

  • M.D. - 2002/08 ~ 2004/07,

Institute of Computer Science and Information Engineering, National Central University

  • B.S. - 1998/08 ~ 2002/07,

Department of Computer Science and Information Engineering, National Central University

Awards 獲獎紀錄

  • 2016 - 元智大學103學年度研究傑出獎 (Yuan Ze University Outstanding Research Award)
  • 2015 - 科技部104年度特殊優秀人才獎助
  • 2015 - 第十三屆有庠傑出教授獎(新聞連結)
  • 2014 - 科技部103年度百人拓荒研究計畫獎助
  • 2014 - 科技部103年度優秀年輕學者研究計畫獎助(三年期)
  • 2014 - 科技部103年度特殊優秀人才獎助
  • 2013 - 國科會102年度特殊優秀人才獎助
  • 2012 - 元智大學100學年度研究傑出獎 (Yuan Ze University Outstanding Research Award)
  • 2012 - 國科會101年度優秀年輕學者研究計畫獎助(兩年期)
  • 2012 - 國科會101年度特殊優秀人才獎助
  • 2011 - 元智大學100學年度青年學者研究獎 (Yuan Ze University Young Scholar Research Award)
  • 2008 - Research Excellence Award (College of Biological Science and Technology, National Chiao Tung University, Taiwan)
  • 2007 - Research Excellence Award (College of Biological Science and Technology, National Chiao Tung University, Taiwan)
  • 2006 - Research Excellence Award (College of Biological Science and Technology, National Chiao Tung University, Taiwan)

Publications

Journal Papers & Conference Papers

(*Corresponding author)

1. 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 (accepted), (SCI, IF: 9.617; 2/56 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)

2. Shun-Long Weng, Kai-Yao Huang, Fergie Joanda Kaunang, Chien-Hsun Huang, Hui-Ju Kao, Tzu-Hao Chang, Hsin-Yao Wang, Jang-Jih Lu and Tzong-Yi Lee*, 2017, “Investigation and identification of protein carbonylation sites based on position-specific amino acid composition and physicochemical features,” BMC Bioinformatics, Vol. 18 (Suppl 3):16. (SCI, 2015 IF:2.435; 10/56 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)

3. 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. (SCI, 2015 IF:1.609; 26/123 in STATISTICS & PROBABILITY)

4. Van-Nui Nguyen, Thi-Xuan Tran, Hai-Minh Nguyen, Hong-Tan Nguyen and Tzong-Yi Lee*, 2017, “A new schema to identify S-farnesyl cysteine prenylation sites with substrate motifs,” In: Akagi M., Nguyen TT., Vu DT., Phung TN., Huynh VN. (eds) Advances in Information and Communication Technology. ICTA 2016. Advances in Intelligent Systems and Computing, vol 538. Springer, Cham. (EI)

5. 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. (SCI, 2015 IF:9.202; 18/289 in BIOCHEMISTRY & MOLECULAR BIOLOGY)

6. 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. (SCI, 2015 IF:9.202; 18/289 in BIOCHEMISTRY & MOLECULAR BIOLOGY)

7. 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. (SCI, 2015 IF: 2.627; 8/56 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)

8. Van-Minh Bui, Shun-Long Weng, Cheng-Tsung Lu, Tzu-Hao Chang, Julia Tzu-Ya Weng and Tzong-Yi Lee*, 2016, "SOHSite: incorporating evolutionary information and physicochemical properties to identify protein S-sulfenylation sites," BMC Genomics, Vol. 17 (Suppl 1):9. (SCI, 2015 IF:3.867; 32/161 in BIOTECHNOLOGY & APPLIED MICROBIOLOGY)

9. Kai-Yao Huang, Julia Tzu-Ya Weng, Tzong-Yi Lee* and Shun-Long Weng*, 2016, "A new scheme to discover functional associations and regulatory networks of E3 ubiquitin ligases," BMC Systems Biology, Vol. 10 (Suppl 1):3. (SCI, 2015 IF:2.213; 11/56 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)

10. Chien-Hsun Huang, Min-Gang Su, Hui-Ju Kao, Jhih-Hua Jhong, Shun-Long Weng and Tzong-Yi Lee*, 2016, "Incorporating two-layered machine learning method with substrate motifs to predict ubiquitin-conjugation site on lysines," BMC Systems Biology, Vol. 10 (Suppl 1):6. (SCI, 2015 IF:2.213; 11/56 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)

11. Shih-Wei Lee, Lawrence Shih-Hsin Wu, Guan-Mau Huang, Kai-Yao Huang, Tzong-Yi Lee, and Julia Tzu-Ya Weng*, 2016, "Gene expression profiling identifies candidate biomarkers for active and latent tuberculosis," BMC Bioinformatics, Vol. 17 (Suppl 1):3. (SCI, 2015 IF:2.435; 10/56 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)

12. 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. (SCI, 2015 IF: 5.766; 3/56 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)

13. Hui-Ju Kao†, Chien-Hsun Huang† († joint first authorship), Neil Arvin Bretaña, Cheng-Tsung Lu, Kai-Yao Huang, Shun-Long Weng*, and Tzong-Yi Lee*, 2015, "A two-layered machine learning method to identify protein O-GlcNAcylation sites with O-GlcNAc transferase substrate motifs," BMC Bioinformatics, Vol. 16, Suppl 18, S10. (SCI, 2014 IF:2.576; 11/57 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)

14. Yi-Ju Chen, Cheng-Tsung Lu, Kai-Yao Huang, Hsin-Yi Wu, Yu-Ju Chen*, Tzong-Yi Lee*, 2015, "GSHSite: exploiting an iteratively statistical method to identify S-glutathionylation sites with substrate specificity," PLoS ONE, Vol. 10 (4): e0118752. (SCI, 2014 IF:3.234; 8/56 in MULTIDISCIPLINARY SCIENCES)

15. Van-Nui Nguyen, Kai-Yao Huang, Chien-Hsun Huang, Tzu-Hao Chang, Neil Arvin Bretaña, K. Robert Lai, Julia Tzu-Ya Weng* and Tzong-Yi Lee*, "Characterization and Identification of Ubiquitin Conjugation Sites with E3 Ligase Recognition Specificities," BMC Bioinformatics, Vo. 16 (Suppl. 1), S1. (SCI, 2014 IF:2.576; 10/56 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)

16. 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. (SCI, 2014 IF:9.112; 20/289 in BIOCHEMISTRY & MOLECULAR BIOLOGY)

17. Guan-Mau Huang, Kai-Yao Huang, Tzong-Yi Lee, and Tzu-Ya Weng*, "An interpretable rule-based diagnostic classification of diabetic nephropathy among type 2 diabetes patients," BMC Bioinformatics, Vol. 16 (Suppl. 1), S5. (SCI, 2014 IF:2.576; 10/56 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)

18. Kai-Yao Huang†, Tzong-Yi Lee († joint first authorship), Yu-Chuan Teng and Tzu-Hao Chang*, "ViralmiR: a support-vector-machine-based method for predicting viral microRNA precursors," BMC Bioinformatics, Vol. 16 (Suppl. 1), S9. (SCI, 2014 IF:2.576; 10/56 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)

19. Tzu-Ya Weng, Li-Ching Wu, Wen-Chi Chang, Tzu-Hao Chang, Tatsuya Akutsu, and Tzong-Yi Lee*, 2014, "Novel Bioinformatics Approaches for Analysis of High-Throughput Biological Data," BioMed Research International, Vol. 2014, Article ID 814092, 3 pages. (SCI, 2013 IF:2.706; 53/165 in BIOTECHNOLOGY & APPLIED MICROBIOLOGY)

20. Hsin-Yi Wu, Cheng-Tsung Lu, Hui-Ju Kao, Yi-Ju chen, Tzong-Yi Lee* and Yu-Ju Chen*, 2014, "Characterization and identification of protein O-GlcNAcylation sites with substrate specificity," BMC Bioinformatics, Vol. 15 (Suppl 16), S1. (SCI, 2012 IF:3.024; 6/47 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)

21. Yi-Ju Chen, Wei-Chieh Ching, Jinn-Shiun Chen, Tzong-Yi Lee, Cheng-Tsung Lu, Hsiao-Chiao Chou, Pei-Yi Lin, Kay-Hooi Khoo, Jenn-Han Chen and Yu-Ju Chen*, 2014, "Decoding the S-nitrosoproteomic Atlas in Individualized Human Colorectal Cancer Tissues Using a Label-free Quantitation Strategy," Journal of Proteome Research, Vol. 13 (11): 4942-58. (SCI, 2013 IF:5.001; 9/78 in BIOCHEMICAL RESEARCH METHODS)

22. Lawrence Shih-Hsin Wu, Shih-Wei Lee, Kai-Yao Huang, Tzong-Yi Lee, Paul Hsu, and Tzu-Ya Weng, 2014, "Systematic expression profiling analysis identifies specific microRNA-gene interactions that may differentiate between active and latent tuberculosis infection," BioMed Research International, Vol. 2014 (2014), Article ID 895179, 9 pages. (SCI, 2013 IF:2.706; 53/165 in BIOTECHNOLOGY & APPLIED MICROBIOLOGY)

23. 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. (SCI, 2014 IF: 4.981; 5-year IF: 8.136; 3/56 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)

24. Cheng-Tsung Lu†, Tzong-Yi Lee† († joint first authorship), Yu-Ju Chen, and Yi-Ju Chen*, 2014, "An intelligent system for identifying acetylated lysine on histones and non-histone proteins," Journal of Biomedicine and Biotechnology, Vol. 2014, Article ID 528650, 11 pages. (SCI, 2013 IF:2.706; 53/165 in BIOTECHNOLOGY & APPLIED MICROBIOLOGY)

25. Min-Gang Su, Chien-Hsun Huang, Tzong-Yi Lee, Yu-Ju Chen and Hsin-Yi Wu*, 2014, Incorporating amino acids composition and functional domains for identifying bacterial toxin proteins," Journal of Biomedicine and Biotechnology, Vol. 2014, Article ID 972692, 7 pages. (SCI, 2013 IF:2.706; 53/165 in BIOTECHNOLOGY & APPLIED MICROBIOLOGY)

26. 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. (SCI, 2013 IF:4.457; 5/52 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)

27. Tzong-Yi Lee, Cheng-Wei Chang, Cheng-Tzung Lu, Tzu-Hsiu Cheng and Tzu-Hao Chang*, 2014, "Identification and characterization of lysine methylation sites on histones and non-histone proteins," Computational Biology and Chemistry, Vol. 50, June 2014, Pages 11–18. (SCI, 2013 IF:1.595; 32/83 in Biology)

28. Justin Bo-Kai Hsu, Kai-Yao Huang, Tzu-Ya Weng, Chien-Hsun Huang, Tzong-Yi Lee*, 2014, "Incorporating significant amino acid pairs and protein domains to identify RNA splicing related proteins with functional roles," Journal of Computer-Aided Molecular Design, Vol. 28 (1):49-60. (SCI, 2013 IF:2.782; 13/102 in COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS)

29. 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. (SCI, 2013 IF:8.808; 22/291 in BIOCHEMISTRY & MOLECULAR BIOLOGY)

30. Kai-Yao Huang, Cheng-Tsung Lu, Neil Arvin Bretaña, Tzong-Yi Lee* and Tzu-Hao Chang*, 2013, "ViralPhos: incorporating a recursively statistical method to predict phosphorylation sites on virus proteins", BMC Bioinformatics, Vol. 14 (Suppl 12), S10. (SCI, 2012 IF:3.024; 6/47 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)

31. Min-Gang Su, Kai-Yao Huang, Chi-Hua Tung and Tzong-Yi Lee*, 2013, "A new scheme to predict phosphorylation sites on protein structures,"International Journal of Bioscience, Biochemistry and Bioinformatics (IJBBB), Vol. 3, No. 5, 473-478.

32. Cheng-Tsung Lu, Kai-Yao Huang, Neil Arvin Bretaña, Wen-Chi Chang and Tzong-Yi Lee*, 2013, "Exploiting two-layered support vector machine to predict phosphorylation sites on virus proteins," International Journal of Bioscience, Biochemistry and Bioinformatics (IJBBB), Vol. 3, No. 5, 460-465.

33. Min-Gang Su and Tzong-Yi Lee*, 2013, "Incorporating substrate sequence motifs and spatial amino acid composition to identify kinase-specific phosphorylation sites on protein three-dimensional structures", BMC Bioinformatics, Vol. 14 (Suppl 16), S2. (SCI, 2012 IF:3.024; 6/47 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)

34. Tzu-Hao Chang, Li-Ching Wu, Tzong-Yi Lee, Shu-Pin Chen, Hsien-Da Huang* and Jorng-Tzong Horng*, 2013, "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,"Journal of Computer-Aided Molecular Design, 27 (1):91-103. (SCI, 2012 IF:3.172; 11/99 in COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS)

35. 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. (SCI, 2012 IF:8.278; 27/290 in BIOCHEMISTRY & MOLECULAR BIOLOGY)

36. 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. (SCI, 2011 IF:5.468; 1/47 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)

37. Neil Arvin Bretaña, Cheng-Tsung Lu, Chiu-Yun Chiang, Min-Gang Su, Kai-Yao Huang, Tzong-Yi Lee* and Shun-Long Weng, 2012, "Identifying Protein Phosphorylation Sites with Kinase Substrate Specificity on Human Viruses," PLoS ONE, 7(7): e40694. (SCI, 2011 IF:4.092; 12/84 in BIOLOGY)

38. 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. (SCI, 2011 IF: 4.073; 26/157 in BIOTECHNOLOGY & APPLIED MICROBIOLOGY)

39. Cheng-Tsung Lu, Neil Arvin Bretaña, Tzu-Hsiu Cheng, and Tzong-Yi Lee*, 2011, "Carboxylator: incorporating solvent-accessible surface area for identifying protein carboxylation sites," Journal of Computer-Aided Molecular Design, 25(10):987-95. (SCI, 2010 IF:3.374; 4/97 in COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS)

40. Justin Bo-Kai Hsu, Neil Arvin Bretaña, Tzong-Yi Lee* and Hsien-Da Huang*, 2011, "Incorporating evolutionary information and functional domains for identifying RNA splicing factors," PLoS ONE, 6(11): e27567. (SCI, 2010 IF:4.411; 12/85 in BIOLOGY)

41. Tzong-Yi Lee*, Cheng-Tsung Lu, Shu-An Chen, Neil Arvin Bretaña, Tzu-Hsiu Cheng, Min-Gang Su, and Kai-Yao Huang, 2011, "Investigation and identification of protein γ-glutamyl carboxylation sites," BMC Bioinformatics, 12 Suppl 11, S10. (SCI, 2010 IF: 3.028; 4/37 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)

42. 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. (SCI, 2011 IF: 8.026; 26/289 in BIOCHEMISTRY & MOLECULAR BIOLOGY) (Citations: 56)

43. Justin Bo-Kai Hsu, Chih-Min Chiu, Sheng-Da Hsu, Wei-Yun Huang, Chia-Hung Chien, Tzong-Yi Lee and Hsien-Da Huang*, 2011, "miRTar: an integrated system for identifying miRNA-target interactions in Human," BMC Bioinformatics, 12:300. (SCI, 2010 IF: 3.028; 4/37 in MATHEMATICAL & COMPUTATIONAL BIOLOGY) (Citations: 28)

44. Tzong-Yi Lee*, Yi-Ju Chen, Tsung-Cheng Lu, Hsien-Da Huang and Yu-Ju Chen*, 2011, "SNOSite: exploiting maximal dependence decomposition to identify cysteine S-nitrosylation with substrate site specificity," PLoS ONE, 6(7): e21849. (SCI, 2010 IF:4.411; 12/85 in BIOLOGY)

45. Tzong-Yi Lee*, Neil ARVIN Bretana, and Cheng-Tsung Lu, 2011, "PlantPhos: using Maximal Dependence Decomposition to Identify Plant Phosphorylation Sites with Substrate Site Specificity," BMC Bioinformatics, 12:261. (SCI, 2010 IF: 3.028; 4/37 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)

46. 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. (SCI, 2011 IF:5.468; 1/47 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)

47. 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. (SCI, 2011 IF:5.468; 1/47 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)

48. Tzong-Yi Lee*, Shu-An Chen, Hsin-Yi Hung, and Yu-Yen Ou, 2011, "Incorporating distant sequence features and radial basis function network to identify ubiquitin conjugation sites," PLoS ONE, 6(3): e17331. (SCI, 2010 IF:4.411; 12/85 in BIOLOGY)

49. 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. (SCI, 2011 IF: 8.026; 26/289 in BIOCHEMISTRY & MOLECULAR BIOLOGY)

50. Dray-Ming Shien, Tzong-Yi Lee, 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. (SCI, 2010 IF: 4.050; 27/144 in CHEMISTRY, MULTIDISCIPLINARY)

51. Shu-An Chen†, Tzong-Yi Lee<† († joint first authorship), and Yu-Yen Ou*, 2010, "Incorporating significant amino acid pairs to identify O-linked glycosylation sites on transmembrane proteins and non-transmembrane proteins," BMC Bioinformatics, 11:536. (SCI, 2010 IF: 3.028; 4/37 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)

52. 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. (SCI, 2010 IF: 4.050; 27/144 in CHEMISTRY, MULTIDISCIPLINARY) (Cover Story)

53. D.M. Shien†, Tzong-Yi Lee† († joint first authorship), W.C. Chang, J.B.K. Hsu, J.T. Horng, P.C. Hsu, T.Y. Wang and H.D. Huang*, 2009, Jul 15 "Incorporating Structural Characteristics for Identification of Protein Methylation Sites," Journal of Computational Chemistry, Vol. 30, No. 9, pp.1532-1543. (SCI, 2010 IF: 4.050; 27/144 in CHEMISTRY, MULTIDISCIPLINARY) (Citations: 40)

54. 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, . (SCI, 2010 IF: 4.050; 27/144 in CHEMISTRY, MULTIDISCIPLINARY)

55. Tzong-Yi Lee, J.B.K. Hsu, W.C. Chang, T.Y. Wang, P.C. Hsu, and H.D. Huang*, 2009, "A Comprehensive Resource for Integrating and Displaying Protein Post-Translational Modifications," BMC Research Notes, 2(1):111.

56. 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. (SCI, 2010 IF: 4.206; 24/160 in BIOTECHNOLOGY & APPLIED MICROBIOLOGY) (Citations: 116)

57. 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. (SCI, 2010 IF: 7.836; 30/286 in BIOCHEMISTRY & MOLECULAR BIOLOGY) (Citations: 124)

58. 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. (SCI, 2010 IF: 4.050; 27/144 in CHEMISTRY, MULTIDISCIPLINARY)

59. 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. (SCI, 2010 IF: 7.836; 30/286 in BIOCHEMISTRY & MOLECULAR BIOLOGY) (Citations: 93)

60. 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. (SCI, 2010 IF: 7.836; 30/286 in BIOCHEMISTRY & MOLECULAR BIOLOGY)

61. H.D. Huang*, Tzong-Yi Lee, S.W. Tseng, L.C. Wu, J.T. Horng, and A.P. Tsou, 2005, "Incorporating Hidden Markov Model for identifying protein kinase-specific phosphorylation sites," Journal of Computational Chemistry, Vol. 26, pp.1032-1041. (SCI, 2010 IF: 4.050; 27/144 in CHEMISTRY, MULTIDISCIPLINARY) (Citations: 33)

62. 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. (SCI, 2010 IF: 5.460; 9/71 in BIOCHEMICAL RESEARCH METHODS)

63. 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. (SCI, 2010 IF: 7.836; 30/286 in BIOCHEMISTRY & MOLECULAR BIOLOGY) (Citations: 139)

1. Van-Minh Bui, Shun-Long Weng, Cheng-Tsung Lu, Tzu-Hao Chang, Julia Tzu-Ya Weng and Tzong-Yi Lee (Presenter), "SOHSite: incorporating evolutionary information and physicochemical properties to identify protein S-sulfenylation sites," The Fourteenth Asia Pacific Bioinformatics Conference (APBC 2016), 11-13 January 2016, San Francisco Bay Area, United States

2. Kai-Yao Huang (Presenter), Julia Tzu-Ya Weng, Tzong-Yi Lee and Shun-Long Weng, 2016, "A new scheme to discover functional associations and regulatory networks of E3 ubiquitin ligases," The Fourteenth Asia Pacific Bioinformatics Conference (APBC 2016), 11-13 January 2016, San Francisco Bay Area, United States

3. Chien-Hsun Huang, Min-Gang Su (Presenter), Hui-Ju Kao, Jhih-Hua Jhong, Shun-Long Weng and Tzong-Yi Lee, 2016, "Incorporating two-layered machine learning method with substrate motifs to predict ubiquitin-conjugation site on lysines," The Fourteenth Asia Pacific Bioinformatics Conference (APBC 2016), 11-13 January 2016, San Francisco Bay Area, United States

4. Shih-Wei Lee, Lawrence Shih-Hsin Wu, Guan-Mau Huang, Kai-Yao Huang, Tzong-Yi Lee, and Julia Tzu-Ya Weng, 2016, "Gene expression profiling identifies candidate biomarkers for active and latent tuberculosis," The Fourteenth Asia Pacific Bioinformatics Conference (APBC 2016), 11-13 January 2016, San Francisco Bay Area, United States

5. Hui-Ju Kao (Oral speaker), Chien-Hsun Huang, Neil Arvin Bretaña, Cheng-Tsung Lu, Kai-Yao Huang, Shun-Long Weng, and Tzong-Yi Lee "A two-layered machine learning method to identify protein O-GlcNAcylation sites with O-GlcNAc transferase substrate motifs," 14th International Conference on Bioinformatics (GIW/InCoB 2015), 9 - 11 September, Odaiba, Tokyo, Japan

6. Kai-Yao Huang, Tzong-Yi Lee, Pin-Hao Ho and Tzu-Hao Chang, "Computational Identification of Novel Epstein-Barr Virus MicroRNA using RNA-seq data in Nasopharyngeal Carcinoma," The 2015 International Forum – Agriculture, Biology, and Life Science (IFABL 2015), 23-25 June, Sapporo, Japan

7. Hui-Ju Kao (Presenter) and Tzong-Yi Lee, "Characterization and Identification of Protein O-linked Glycosylation Sites based on Glycosyltransferase Substrate Specificities," The Thirteenth Asia Pacific Bioinformatics Conference (APBC 2015), 21-23 January 2015, HsinChu, Taiwan (Best Poster Presentation Award)

8. Van-Nui Nguyen (Oral speaker), Kai-Yao Huang, Chien-Hsun Huang, Tzu-Hao Chang, Neil Arvin Bretaña, K. Robert Lai, Julia Tzu-Ya Weng andTzong-Yi Lee, "Characterization and Identification of Ubiquitin Conjugation Sites with E3 Ligase Recognition Specificities," The Thirteenth Asia Pacific Bioinformatics Conference (APBC 2015), 21-23 January 2015, HsinChu, Taiwan

9. Guan-Mau Huang, Tzong-Yi Lee, Kai-Yao Huang, Shih-Hsin Wu and Tzu-Ya Weng, "An interpretable rule-based diagnostic classification of diabetic nephropathy among type 2 diabetes patients," The Thirteenth Asia Pacific Bioinformatics Conference (APBC 2015), 21-23 January 2015, HsinChu, Taiwan

10. Kai-Yao Huang (Oral speaker), Tzong-Yi Lee, Yu-Chuan Teng and Tzu-Hao Chang, "ViralmiR: identification of viral microRNA precursor based on sequence and structure information," The Thirteenth Asia Pacific Bioinformatics Conference (APBC 2015), 21-23 January 2015, HsinChu, Taiwan

11. Hsin-Yi Wu, Cheng-Tsung Lu (Oral speaker), Hui-Ju Kao, Yi-Ju Chen, Tzong-Yi Lee and Yu-Ju chen, "Characterization and identification of protein O-GlcNAcylation sites with substrate specificity," 13th International Conference on Bioinformatics (InCoB 2014), 31st July - 2nd August, Sydney, New South Wales, Australia

12. Kai-Yao Huang (Oral speaker), Ming-Gang Su, Hui-Ju Kao, Ya-Han Chang, Tzong-Yi Lee, "PhosNet: A Web Tool to Reconstruct the Protein Kinase–substrate Phosphorylattion Network Integrating Protein-protein Interaction and Biological Pathway Data," The 3rd International Congress on Natural Sciences and Engineering (ICNSE 2014), 7 - 9 May, 2014, Koyto, Japan

13. Julia Tzu-Ya Weng, Kai-Yao Huang, Shih-Wei Lee, Lawrence Shih-Hsin Wu, Yi-Cheng Chen and Tzong-Yi Lee, "Systematic Pipeline for the analysis of microRNA-gene interactions in active and latent TB infection," IEEE International Symposium on Bioelectronics and Bioinformatics (IEEE ISBB 2014), April 11-14, Taoyuan, Taiwan

14. Tzong-Yi Lee, Cheng-Tzung Lu, Tzu-Hsiu Cheng and Tzu-Hao Chang (Oral speaker), "Identification and characterization of lysine methylation sites on histones and non-histone proteins," The Twelfth Asia Pacific Bioinformatics Conference (APBC 2014), January 17-19, Shanghai, China

15. Kai-Yao Huang, Cheng-Tsung Lu (Oral speaker), Neil Arvin Bretaña, Tzong-Yi Lee and Tzu-Hao Chang, "ViralPhos: incorporating a recursively statistical method to predict phosphorylation sites on virus proteins" 12th International Conference on Bioinformatics (InCoB 2013), September 20 - 22, Taicang, China

16. Min-Gang Su (Oral speaker) and Tzong-Yi Lee, "Incorporating substrate sequence motifs and spatial amino acid composition to identify kinase-specific phosphorylation sites on protein three-dimensional structures" 12th International Conference on Bioinformatics (InCoB 2013), September 20 - 22, Taicang, China

17. Min-Gang Su, Chi-Hua Tung and Tzong-Yi Lee (Oral speaker), "A new scheme to identify kinase-specific phosphorylation sites on protein three-dimensional structures," 4th Asia Oceania Mass Spectrometry Conference and 10th Taiwan Society for Mass Spectrometry Annual Conference (4th AMOSE and 10th TSMS Annual Conference), July 10-12, 2013, Taipei, Taiwan

18. Wen-Chi Chang, Mou-Yuan Yeh, Tzong-Yi Lee and Ying-Chi Wen, "Characterization and identification of tissue-specific promoters in rice," 10th International Workshop on Computational Systems Biology (WCSB2013), June 10-12, Tampere, Finland

19. Cheng-Tsung Lu (Oral speaker), Kai-Yao Huang, Neil Arvin Bretaña, Wen-Chi Chang and Tzong-Yi Lee (Session Chair), "Exploiting two-layered support vector machine to predict phosphorylation sites on virus proteins," 2nd International Conference on Bioinformatics and Biomedical Science (ICBBS2013), June 8-9, Kuala Lumpur, Malaysia

20. Min-Gang Su (Oral speaker), Kai-Yao Huang, Chi-Hua Tung and Tzong-Yi Lee (Session Chair), "A new scheme to predict phosphorylation sites on protein structures," 2nd International Conference on Bioinformatics and Biomedical Science (ICBBS2013), June 8-9, Kuala Lumpur, Malaysia

21. Kai-Yao Huang (Oral speaker) and Tzong-Yi Lee, "SplicePred: a Novel Resource for Identifying RNA Splicing-related Proteins," The 6th Asian Young Researchers Conference on Computational and Omics Biology (AYRCOB2012), December 20-21, Shenzhen, China

22. Min-Gang Su (Oral speaker) and Tzong-Yi Lee, "topPTM: a Database of Post-translational Modifications on Transmembrane Proteins," The 6th Asian Young Researchers Conference on Computational and Omics Biology (AYRCOB2012), December 20-21, Shenzhen, China

23. Cheng-Tsung Lu (Oral speaker) and Tzong-Yi Lee, "SNONet: Discovery of Protein S-Nitrosylation and Nitric Oxide Signaling Network," The 6th Asian Young Researchers Conference on Computational and Omics Biology (AYRCOB2012), December 20-21, Shenzhen, China

24. Tzong-Yi Lee and Wen-Chi Chang (Oral speaker), "GPMiner: an integrated system for mining combinatorial cis-regulatory elements in mammalian gene group," The Tenth Asia Pacific Bioinformatics Conference (APBC 2012), January 17-19, Melbourne, Australia

25. Tzong-Yi Lee (Oral speaker), Cheng-Tsung Lu, Shu-An Chen, Neil Arvin Bretaña and Tzu-Hsiu Cheng, "Investigation and identification of protein γ-glutamyl carboxylation sites," Asia Pacific Bioinformatics Network's 10th InCoB - 1st ISCB Asia Joint Conference 20111 (InCoB 2011), November 30 - December 2, Kuala Lumpur, Malaysia

26. Tzong-Yi Lee (Oral speaker) and Hsien-Da Huang, "PTM-X: an integrated resource for identifying protein post-translational modifications," 11th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2007), April 21 - 25, San Francisco, USA

Teaching

Course
  • Systems Biology (MSc, Spring semester, 2015)

  • Algorithms (Undergraduate, Spring semester, 2014 ~)

  • Database System Concepts (Undergraduate, Autumn semester, 2013 ~)

  • BioMedical Databases (MSc, Spring semester, 2012 ~)

  • Data Structure (Undergraduate, Spring semester, 2010 ~)

  • Special Topics on Computational Proteomics (MSc, Autumn semester, 2011 ~)

  • Introduction to Bioinformatics (Undergraduate, Autumn semester, 2011 - 2012)

  • Design and Implementation of BioMedical Databases (MSc, Spring semester, 2010 - 2011)

  • Linear Algebra (Undergraduate, Autumn semester, 2009 - 2012)

Invited Talks

Speech
‧ 2016/10/11
"Toward precision medicine based on BiOmics"
National Health Research Institutes, Taiwan.

‧ 2016/09/20
"A platform for microbiota identification and functional analysis (微生物群落與功能性分析平台)"
Food Industry Research and Development Institute, Taiwan.

‧ 2016/08/25
"Big data analytics in genomics, transcriptomics and proteomics"
Development Center for Biotechnology (DCB), Taiwan.

‧ 2016/06/22

"Digging for Meaning in the Big Data of Human Biology"
Institute of Information Science, Academia Sinica, Taiwan.

‧ 2016/06/16
"Toward precision medicine by big data analytics in genomics and proteomics"
School of Pharmacy, Kaohsiung Medical University, Taiwan.

‧ 2016/05/24
"Toward a precision medicine based on big data in genomics and proteomics"
Institute of Biochemistry and Molecular Biology, National Yang Ming University, Taiwan.

‧ 2015/11/12
"Big Data in Personalized Medicine and Healthcare"
Graduate Institute of Biomedical Informatics, Taipei Medical University, Taiwan.

‧ 2015/06/26
"Big Data Analytics for Personalized Medicine"
Department of Medical Informatics, Tzu Chi University, Taiwan.

‧ 2015/05/14
"Big Data in Genomics and Proteomics"
Department of Computer Science and Engineering, National Taiwan Ocean University, Taiwan.

‧ 2015/05/05
"A new scheme to study kinase regulatory networks for time-dependent phosphoproteome data"
Institute of Systems Biology and Bioinformatics, National Central University, Taiwan.

‧ 2014/12/24
"What can Bioinformatics do in Genomics and Proteomics?"
Department of Computer Science and Engineering, Yuan Ze University, Taiwan.

‧ 2014/12/18
"New Schemes to Study Kinase Regulatory Networks"
Graduate Institute of Biomedical Informatics, Taipei Medical University, Taiwan.

‧ 2014/06/05
"Characterization and identification of protein post-translational modifications"
Department of Medical Informatics, Tzu Chi University, Taiwan.

‧ 2014/05/26
"Bioinformatics: Studying Protein Phosphorylation from Informatics to Biology"
Graduate Program in BioMedical Informatics, Yuan Ze University, Taiwan.

‧ 2014/05/15
"The new schemes for characterization and identification of protein post-translational modifications"
Taiwan International Graduate Program (TIGP), Academia Sinica, Taiwan.

‧ 2014/02/20
"A new scheme to identify kinase-specific phosphorylation sites on protein three-dimensional structures"
Systems Biology and Bioinformatics Symposium (SBBS 2014), Taiwan.

‧ 2013/12/16
"Bioinformatics: Studying Protein Phosphorylation from Informatics to Biology"
Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Taiwan.

‧ 2013/12/12
"Application of Bioinformatics in Protein Identification and Functional Analysis"
Graduate Institute of Biomedical Informatics, Taipei Medical University, Taiwan.

‧ 2013/05/30
"Bioinformatics Approaches in Studying Protein Phosphorylation"
Graduate Institute of Biomedical Informatics, Taipei Medical University, Taiwan.

‧ 2012/10/19
"Bioinformatics and Systems Biology in Protein Post-translational Modifications"
Department of Computer Science and Information Engineering, National Cheng-Kung University, Taiwan.

‧ 2012/03/06
"Studying protein phosphorylation from informatics to biology"
Institute of Tropical Plant Science, National Cheng-Kung University, Taiwan.

‧ 2011/10/18
"Computational Proteomics: studying proteomics from informatics to biology"
Chung Hua University, Department of Bioinformatics, Taiwan.

‧ 2010/12/15
"Bioinformatics: from Informatics to Biology"
Department of Computer Science and Information Engineering, National Central University, Taiwan.

‧ 2010/10/12
"Application of statistical method on the identification of protein phosphorylation sites"
Graduate Institute of Statistics, National Central University, Taiwan.

‧ 2009/05/04
"Bioinformatics and Proteomics"
Department of Computer Science and Engineering, Yuan Ze University, Taiwan.

‧ 2009/04/23
"Computational Proteomics"
Institute of Systems Biology and Bioinformatics, National Central University, Taiwan.

‧ 2009/04/20
"Computational Proteomics in Protein Identification, Protein Post-Translational Modification and Protein Networks"
Department of Life Science, National Cheng-Kung University, Taiwan.

Academic Services

Editorial Board Member, Program Committee & Referee
  • 2016 - Editorial Board Member of Informatics
  • 2015 - Editorial Board Member of Genomics, Proteomics & Bioinformatics (GPB)
  • 2015 - Editorial Board Member of International Journal of Bioinformatics & Biological Systems (IJBBS)
  • 2015 - Program Committee, The Fourteenth Asia Pacific Bioinformatics Conference (APBC2016)
  • 2015 - Program Committee, The 2015 Conference on Technologies and Applications of Artificial Intelligence (TAAI2015)
  • 2015 - Program Committee, The 1st International Conference on New Materials, Colloid and Polymer Science (ICNMCPS 2015)
  • 2014 - Program Committee, 2015 International Conference on Platform Technology and Service (PlatCon2015)
  • 2014 - Program Committee, The Thirteenth Asia Pacific Bioinformatics Conference (APBC2015)
  • 2014 - Lead Guest Editor, Special Issue on "Novel bioinformatics approaches for analysis of high-throughput biological data", BioMed Research International (SCI, 2012 IF:2.88)
  • 2014 - Referee for Nucleic Acids Research, PLoS ONE, and BMC Bioinformaics
  • 2013 - Referee for Nucleic Acids Research, Bioinformatics, PLoS ONE, BMC Bioinformaics
  • 2013 - Session Chair, 2nd International Conference on Bioinformatics and Biomedical Science (ICBBS2013)
  • 2012 - Program Committee, The 2012 Conference on Technologies and Applications of Artificial Intelligence (TAAI2012)
  • 2011 - Referee for BMC Genomics and BMC Bioinformatics
  • 2010 - Referee for BMC Bioinformatics
  • 2009 - Program Committee, The 2009 International Conference on Digital Content (ICDC2009)

About BiOmic Laboratory

「計算系統生物學實驗室(Computational Systems Biology Laboratory)」成立於2010年,由 李宗夷 教授 擔任本實驗室之指導教授,本實驗室以培育資訊、生物、統計等跨領域專業人才為宗旨。本實驗室專注於生物資訊與系統生物學相關研究,包含基因調控網路、蛋白質體學與蛋白質轉譯後修飾作用、Metagenomics and Metatranscriptomics、癌症生物標誌與藥物設計、訊息傳遞與代謝路徑等,並結合雲端運算與大數據技術建構高效能及高穩定度之生物資料庫與分析系統。

©2017 BiOmics Lab YZU. All Rights Reserved.

Search