Yo-Cheng (Mark) Chang

Contact Email: markycchang@gmail.com

D.Phil. candidate
Life Sciences Interface Doctoral Training Centre, University of Oxford.

Supervisors:
Prof. Judith P. Armitage, Department of Biochemistry, University of Oxford.
Dr. Antonis Papachristodoulou, Department of Engineering Sciences, University of Oxford.

College supervisor:
Prof. Juton Hein, Department of Statistics, University of Oxford.

Education

• 2005.10-present: Doctoral student, Life Sciences Interface Doctoral Training Centre, University of Oxford, UK.
• 1997.9-1999.6: M.S. in Biomedical Engineering, National Yang Ming University, Taiwan.
• 1993.9-1997.6: B.S. in Biomedical Engineering, Chung-Yuan Christian University, Taiwan.

Work Experience

• 2005.3-2005.9: Project Manager, The Taiwan Biobank Project, Institute for Information Industry, Taiwan.
• 2000.7-2005.1: Associate Researcher, Biomedical Engineering Center, Industrial Technology Research Institute, Taiwan.
  • Department of Nanobiotechnology (2003.1-2005.1)
  • Department of Genomics (2000.7-2003.1)
• 1999.9-2000.6: Research Assistant, Department of Biomedical Engineering, National Yang Ming University, Taiwan.

Teaching Experience

• 2005.2-2005.7: Adjunct Lecturer (Course: Computational biology), Department of Biotechnology, Ming Chuan University, Taiwan.
• 2004.9-2005.1: Adjunct Lecturer (Course: Bioinformatics), Graduate Institute of Life Sciences, Tamkang University, Taiwan.
• 2003.3-2003.6: Instructor (Course: Special topics in bioinformatics), Graduate Program of Bioinformatics, National Yang Ming University, Taiwan.
• 2002.12: Instructor (Course: Microarray data analysis), Tze-Chiang Foundation of Science & Technology, Taiwan.

Projects

• 2007-present: Design and construction of synthetic biological components with robust performance and stability based on the bacterial two-component system, LSI DTC, Oxford.
• 2007-2008: A systematic, algorithmic methodology for model reduction of large-scale biochemical networks, Department of Engineering Science, Oxford.
• 2006: In-vitro transcription and translation in lipid-bilayer vesicles, LSI DTC, Oxford.
• 2006: Photosynthetic-driven ATP synthesis by bacteriorhodopsin and F1Fo ATP synthase co-reconstituted in large unilamellar vesicles, LSI DTC, Oxford.
• 2004-2005: Simulation of the conjugation between mouse IgG antibody and nanoparticle, ITRI, Taiwan.
• 2003-2004: Conservation profiling of functionally coupled gene clusters through multiple genome comparison, NYMU, Taiwan.
• 2003: Whole genome annotation and analysis of Klebsiella pneumoniae, NYMU, Taiwan.
• 2003: Whole genome annotation and analysis of Mycoplasma fermentans M64, NYMU, Taiwan.
• 2002-2003: Integrated protein-protein interaction and microarray database, ITRI, Taiwan.
• 2002: Large-scale analysis of bacterial repeat sequences, NYMU&ITRI, Taiwan.
• 2002: Automated protein classification system based on machine learning methods, ITRI, Taiwan.
• 2001-2002: Whole genome annotation and analysis of Vibrio vulnificus YJ016, NYMU&ITRI, Taiwan.
• 2001-2002: Automated and object-oriented bacteria genome annotation system, ITRI, Taiwan.
• 2000-2001: Automated microarray probe design system, ITRI, Taiwan.

Publications

• Journal:

1. Yo-Cheng Chang and Antonis Papachristodoulou. "A systematic, algorithmic methodology for model reduction of large-scale biochemical networks." (in preparation)
2. Chung-Yung Chen, Keh-Ming Wu, Yo-Cheng Chang, Chuan-Hsiung Chang, Hui-Chi Tsai, Tsai-Lien Liao, Yen-Ming Liu, Hsiang-Ju Chen, Arthur Bo-Ting Shen, Jian-Chiuan Li, Teh-Li Su, Chung-Ping Shao, Chung-Te Lee, Lien-I Hor, and Shih-Feng Tsai. "Comparative genome analysis of an invasive marine pathogen, Vibrio vulnificus." Genome Research 13(12):2577-87, Dec. 2003.

• Conference:

1. Yo-Cheng Chang, George H. Wadhams, Judith P. Armitage, and Antonis Papachristodoulou. "RoSBNet: From Robust Synthetic Biological Parts to Whole Systems: Theoretical, Practical and Ethical Challenges." The 4th International Meeting on Synthetic Biology (Synthetic Biology 4.0), Oct. 2008, Hong Kong, China.
2. Yo-Cheng Chang, Antonis Papachristodoulou, George H. Wadhams, and Judith P. Armitage. "A new design concept for synthetic biological components with desired and robust performance based on bacterial two-component system." ESF-EMBO Symposium on Bacterial Networks 2008 (BacNet'08), Sep. 2008, Sant Feliu de Guixols, Spain.
3. Yo-Cheng Chang and Antonis Papachristodoulou. "A systematic, algorithmic methodology for reducing biochemical network models" The 9th International Conference on Systems Biology (ICSB 2008), Aug. 2008, Gothenburg, Sweden.
4. Yo-Cheng Chang, Simon Ross, Mark Wallace, Richard Berry, and Anthony Watts, "Photosynthetic-driven ATP synthesis by bacteriorhodopsin and F1Fo ATP synthase co-reconstituted in large unilamellar vesicles." EPSRC Life Sciences Interface DTC Conference, July 2006, Oxford, UK.
5. Yo-Cheng Chang and Yuh-Jiuan Lin. "Simulation of the conjugation between mouse IgG antibody and nanoparticle." 2nd ITRI Conference of Computational Nanobiotechnology, Dec. 2004, Hsin-Chu, Taiwan.
6. Hon-Wei Chen, Yo-Cheng Chang, Der-Ming Liou, and Chuan-Hsiung Chang. "Conservation profiling of functionally-coupled gene clusters through multiple genome comparison." 12th International Conference on Intelligent Systems for Molecular Biology (ISMB/ECCB), Jul.-Aug. 2004, Glasgow, UK.
7. Chung-Yung Chen, Keh-Min Wu, Yo-Cheng Chang, Chuan-Hsiung Chang, Wnsi S Hu, and Shih-Feng Tsai. "The complete genome analysis of human respiratory pathogen Mycoplasma fermentans." 2nd NHRI Conference on Bacterial Gene Regulation and Pathegenesis, Apr. 2004, Tao-Yuan, Taiwan.
8. Chao-Chih Pan, Ju-hwa Lin, Jeng-Dau Wu, Yao-Sung Chang, Chun-Ju Chang, Meng-Chorng Tyan, Charng-Yih Leu, Yo-Cheng Chang, Jie-Len Huang, and Chuan-Hsiung Chang. "FeverChip^TM for fever-causing pathogen detection and identification." IBC's 8th Annual Biochip Technology Conference, Oct.-Nov. 2001, San Diego, USA.

Book/Article Translations

• Traditional Chinese translation of the MIT Open CourseWare, OOPS, 2005.
  • Layer 1 translation of "18.417 Introduction to Computational Molecular Biology".
• The Traditional Chinese version of "Developing Bioinformatics Computer Skills", O'Reilly, 2002.
  • Chapter 7, "Sequence Analysis, Pairwise Alignment, and Database Searching".
  • Chapter 8, "Multiple Sequence Alignments, Trees, and Profiles".

Invited Talks

• 2004.9: "Modeling genetic networks of a living cell.", Department of Mathematics, Tamkang University, Taiwan.
• 2004.4: "Principles, applications, and recent research topics of bioinformatics.", Graduate Institute of Life Sciences, Tamkang University, Taiwan.

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