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Name: 鄒文雄
Department: 國立海洋大學 / 生科系大學部課程 [elearning courses]
Research: 計算生物學,生物分子模擬
Office: 綜合二館Rm302A
Self-Introduction

基因體與蛋白質結構模擬實驗室

 分機: 5522 (老師辦公室),  5523 (實驗室)

學歷:交通大學電子物理系學士清華大學生命科學所碩士國防醫學院生命科學所-中央研究院生物醫學所博士

經歷:中央研究院博士後研究員法國科學研究國家中心副研究員台灣基因科技公司經理高雄醫學大學助理教授臺灣海洋大學助理教授副教授教授美國維吉尼亞大學訪問教授

主要研究領域:計算生物學、生物資訊、結構生物學

相關研究領域生物分子電腦模擬、DNA序列分析

工具CPU (中央處理器) + GPU (圖形處理器)

研究計畫簡介

膜蛋白SCF-KIT的異位調節(allosteric regulation)

人類血清白蛋白Human Serum Albumin的異位調節(allosteric regulation)

蛋白質分子動力學模擬的時序分析與機器學習。

基因體與轉錄體分析。

 

實驗室常用技術

C, Python, Perl, Matlab, R, Gromacs, Amber

歡迎想玩數據分析、熱愛尋找自然現象的特殊模式與預測未來的人才加入,本實驗室配有大型計算伺服器主機,提供能力升級契機與未來就業準備!

 

未來產業連結:數據分析產業、資訊產業、製藥產業、生物資訊產業、人工智慧

 

 

Publication
Paper
1. Jing Hou, Heping Zheng*, Wen‐Shyong Tzou, David R. Cooper, Maksymilian Chruszcz, Mahendra D. Chordia, Keehwan Kwon, Marek Grabowski, Wladek Minor*, "Differences in substrate specificity of V. cholerae FabH enzymes suggest new approaches for the development of novel antibiotics and biofuels.," FEBS J. 2018 Aug;285(15):2900-2921, Aug, 2018.
2. Hung KS, Hsiao CC, Pai TW, Hu CH, Tzou WS, Wang WD, Chen YR, "Functional enrichment analysis based on long noncoding RNA associations.," BMC Syst Biol. 2018 Apr 24;12(Suppl 4):45., Apr, 2018.
3. Pei-Xin Lai, Chung-Wein Chen, Shih-Chun Wei, Tzu-Yu Lin, Hong-Jyuan Jian, Irving Po-Jung Lai, Ju-Yi Mao, Pang-Hung Hsu, Han-Jia Lin, Wen-Shyong Tzou, Shiow-Yi Chen, Scott G. Harroun, Jui-Yang Lai, Chih-Ching Huang*, "Ultrastrong Trapping of VEGF by Graphene Oxide: Anti-angiogenesis Application," Biomaterials. 2016 109:12-22., 2016.
4. Chi-Fu Chou, Han-Jia Lin, Chih-Yu Tsai, Tzung-Yi Lin, Hsin-Yu Chung, Chia-Yin Chiang, Chung-Hao Li, Tun-Wen Pai, Chin-Hwa Hu, and Wen-Shyong Tzou*., "Hypoxia-inducible factor 2-alpha participates in the regulation of intersegmental vessels angiogenesis and neuromast deposition.," Journal of Marine Science and Technology, Vol. 24, No. 2, pp. 347-358, 2015.
5. Wen‑Sing Liang, Tsuei‑Yun Fang, Hong‑Ting Lin, Tristan C. Liu, Wen‑Jung Lu, Wen‑Shyong Tzou, Shye‑Jye Tang, Fu‑Pang Lin, Shiu‑Mei Liu, Chorng‑Liang Pan*, "Cloning, expression, and characterization of Pseudomonas vesicularis MA103 β‑1,3‑xylanase in Escherichia coli ClearColi BL21(DE3)," Fish Sci (2015) 81:1135–1143, 2015.
6. Wen-Shyong Tzou*, Ying-Tsang Lo, Tun-Wen Pai, Chin-Hwa Hu, Chung-Hao Li., "Stochastic Simulation of Notch Signaling Reveals Novel Factors that Mediate the Differentiation of Neural Stem Cells," Journal of Computational Biology, 21(7):1-20., 2014.
7. Wen-Shyong Tzou*, Ying Chu, Tzung-Yi Lin, Chin-Hwa Hu, Tun-Wen Pai, Hsin-Fu Liu, Han-Jia Lin, Ildeofonso Cases, Ana Rojas, Mayka Sanchez, Zong-Ye You, Ming-Wei Hsu., "Molecular evolution of multiple-level control of heme biosynthesis pathway in animal kingdom.," PLoS One, 9(1): e86718, 2014., 2014.
8. Xing-Guang Hung, Wen-Chi Tseng, Shiu-Mei Liu, Wen-Shyong Tzou, Tsuei-Yun Fang*, "Characterization of a thermophilic l-arabinose isomerase from Characterization of a thermophilic l-arabinose isomerase from thermoanaerobacterium saccharolyticum NTOU1.," Biochemical Engineering Journal, 83:121–128, 2014.
9. Tzung-Yi Lin, Chi-Fu Chou, Hsin-Yu Chung, Chia-Yin Chiang, Chung-Hao Li,Jen-Leih Wu, Han-Jia Lin, Tun-Wen Pai, Chin-Hwa Hu, Wen-Shyong Tzou*, "Hypoxia-inducible factor 2 alpha is essential for hepatic outgrowth and functions via the regulation of leg1 transcription in the zebrafish embryo.," PLoS One, 9(7): e101980, 2014.
10. Chien-Ming Chen, Yu-Lun Lu, Chi-Pong Sio, Guan-Chung Wu, Wen-Shyong Tzou, Tun-Wen Pai*, "Gene Ontology based housekeeping gene selection for RNA-seq normalization," Methods, 67(3): 354-363, 2014.
11. Chien-Ming Chen, Tun-Wen Pai*, Chia-Sheng Chuang, Jhen-Li Huang, Wen-Shyong Tzou, Chin-Hua Hu, "Identifying significant associations of orthologous simple sequence repeats with gene ontologies," International Journal of Data Mining and Bioinformatics, 9(1):37-51, 2014.
12. C.-T. Chang, H.-Y. Chung, H.-T. Su, H.-P. Tseng, W.-S. Tzou, C.-H. Hu*., "Regulation of zebrafish CYP3A65 transcription by AHR2," Toxicology and Applied Pharmacology, 270(2):174-184, 2013.
13. H.-Y. Chung, C.-T. Chang, H.-W. Young, S. P. Hu, W.-S. Tzou, C.-H. Hu*., "Ethanol inhibits retinal and CNS differentiation due to failure of cell cycle exit via an apoptosis-independent pathway," Neurotoxicology and Teratology, 38:92-103, 2013.
14. Ying-Tsang Lo, Hsin-Wei Wang, Tun-Wen Pai*, Wen-Shoung Tzou, Hui-Huang Hsu, Hao-Teng Chang., "Protein-ligand binding region prediction (PLB-SAVE) based on geometric features and CUDA acceleration," BMC Bioinformatics, 14 Suppl 4:S4, 2013.
15. Wei-Hung Chang, Chi-Ying Lee, Chih-Yu Lin, Wei-Yun Chen, Meng-Chieh Chen, Wen-Shyong Tzou, and Yet-Ran Chen*., "UniQua: A Universal Signal Processor for MS-Based Qualitative and Quantitative Proteomics Applications," Analytical Chemistry, 85(2):890-897, 2013.
16. Fu-Pang Lin*, Hsiu-Yen Ma, Hui-Ju Lin, Shiu-Mei Liu, Wen-Shyong Tzou, "Biochemical characterization of two truncated forms of amylopullulanase from Thermoanaerobacterium saccharolyticum NTOU1 to identify its enzymatically active region," Applied Biochemistry and Biotechnology, 165(3-4):1047-1056, 2011.
17. C.-S. Chuang, T.-W. Pai*, H.-C. Hu, W.-S. Tzou, M.-D.-T. Chang, H.-T. Chang, C.-C. Chen, "Functional pathway mapping analysis for hypoxia-inducible factors," BMC Systems Biology, 5 Suppl 1:S3, 2011.
18. C.-Y. Ko, M.-Y. Tsai, W.-F. Tseng, C.-H. Cheng, C.-R. Huang, J.-S. Wu, H.-Y. Chung, C.-S. Hsieh, C.-K. Sun, S.-P. Hwang, C.-H. Yuh, C.-J. Huang, T.-W. Pai, W.-S. Tzou and C.-H. Hu*., "Integration of CNS survival and differentiation by HIF2α," Cell Death and Differentiation, 18(11):1757–1770, 2011.
19. K.-S. Hung, S.-M. Liu, T.-Y. Fang, W.-S. Tzou, F.-P. Lin, K.-H. Sun and S.-J. Tang*., "Characterization of a salt-tolerant xylanase from Thermoanaerobacterium saccharolyticum NTOU1," Biotechnology Letters, 33(7):1441-1447, 2011.
20. W.-P. Lee and W.-S. Tzou*., "Fast Revelation of the Motif Mode for a Yeast Protein Interaction Network Through Intelligent Agent-Based Distributed Computing," Protein and Peptide Letters, 17(9):1091-1101, 2010.
21. C.-J. Lin, W.-C. Tseng, T.-H. Lin, S.-M. Liu, W.-S. Tzou and T.-Y. Fang*., "Characterization of a Thermophilic l-Rhamnose Isomerase from Thermoanaerobacterium saccharolyticum NTOU1," Journal of Agricultural and Food Chemistry, 58(19):10431–10436, 2010.
22. C.-M. Chen, C.-C. Chen, T.-H. Shih, T.-W. Pai*, H.-C. Hu, and W.-S. Tzou., "Efficient algorithms for identifying orthologous simple sequence repeats of disease genes," Journal of Systems Science and Complexity, 23:906-916, 2010.
23. W.-S. Tzou, W.-P. Lee* and B.-C. Jeng., "Exploiting knowledge ontology and software agents for PPI network analysis," Expert Systems with Applications, 36(10):12605–12612, 2009.
24. W.-P. Lee and W.-S. Tzou*., "Computational methods for discovering gene networks from expression data," Briefings in Bioinformatics, 10(4):408-423, 2009.
25. Tun-Wen Pai*, Chien-Ming Chen, Meng-Chang Hsiao, Ronshan Cheng, Wen-Shyong Tzou, Chin-Hua Hu., "An online conserved SSR discovery through cross-species comparison," Advances and Applications in Bioinformatics and Chemistry, 2:23-35, 2009.
26. Yin HC, Tseng HP, Chung HY, Ko CY, Tzou WS, Buhler DR, Hu CH*, "Influence of TCDD on zebrafish CYP1B1 transcription during development.," Toxicol Sci. 2008 May;103(1):158-68., 2008.
27. Pai TW*, Chang MD, Tzou WS, Su BH, Wu PC, Chang HT, Chou WI., "REMUS: a tool for identification of unique peptide segments as epitopes.," Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W198-201., 2006.
28. Chuang KH, Cheng CM, Roffler SR, Lu YL, Lin SR, Wang JY, Tzou WS, Su YC, Chen BM, Cheng TL*, "Combination cancer therapy by hapten-targeted prodrug-activating enzymes and cytokines.," Bioconjug Chem. 2006 May-Jun;17(3):707-14., 2006.
29. Lee WP, Jeng BC, Pai TW, Tsai CP, Yu CY, Tzou WS*, "Differential evolutionary conservation of motif modes in the yeast protein interaction network.," BMC Genomics. 2006 Apr 25;7:89., 2006.
30. Wang JY, Yeh CS, Tzou WS, Hsieh JS, Chen FM, Lu CY, Yu FJ, Cheng TL, Huang TJ, Lin SR*, "Analysis of progressively overexpressed genes in tumorigenesis of colorectal cancers using cDNA microarray.," Oncol Rep. 2005 Jul;14(1):65-72., 2005.
31. Howng SL, Sy WD, Cheng TS, Lieu AS, Wang C, Tzou WS, Cho CL, Hong YR., "Genomic organization, alternative splicing, and promoter analysis of human dynamin-like protein gene.," Biochem Biophys Res Commun. 2004 Feb 13;314(3):766-72., 2004.
32. Wang JY, Hsieh JS, Chang MY, Huang TJ, Chen FM, Cheng TL, Alexandersen K, Huang YS, Tzou WS, Lin SR*, "Molecular detection of APC, K- ras, and p53 mutations in the serum of colorectal cancer patients as circulating biomarkers.," World J Surg. 2004 Jul;28(7):721-6., 2004.
33. Wang JY, Hsieh JS, Chen CC, Tzou WS, Cheng TL, Chen FM, Huang TJ, Huang YS, Huang SY, Yang T, Lin SR., "Alterations of APC, c-met, and p53 genes in tumor tissue and serum of patients with gastric cancers.," J Surg Res. 2004 Aug;120(2):242-8., 2004.
34. Yeh CS, Chen FM, Wang JY, Cheng TL, Hwang MJ, Tzou WS*, "Directional shape complementarity at the protein-DNA interface.," J Mol Recognit. 2003 Jul-Aug;16(4):213-22., 2003.
35. Yang PK, Tzou WS, Hwang MJ*, "Restraint-driven formation of alpha-helical coiled coils in molecular dynamics simulations.," Biopolymers. 1999 Nov;50(6):667-77., 1999.
36. Tzou WS, Hwang MJ*, "Modeling helix-turn-helix protein-induced DNA bending with knowledge-based distance restraints.," Biophys J. 1999 Sep;77(3):1191-205., 1999.
37. Lee CY, Yang PK, Tzou WS, Hwang MJ*, "Estimates of relative binding free energies for HIV protease inhibitors using different levels of approximations.," Protein Eng. 1998 Jun;11(6):429-37., 1998.
38. Tzou WS, Hwang MJ*, "A model for Fis N-terminus and Fis-invertase recognition.," FEBS Lett. 1997 Jan 13;401(1):1-5., 1997.
39. Yu SM*, Tzou WS, Lo WS, Kuo YH, Lee HT, Wu R., "Regulation of alpha-amylase-encoding gene expression in germinating seeds and cultured cells of rice.," Gene. 1992 Dec 15;122(2):247-53., 1992.