Scholars@Duke

• Background
• 

  Education, Training, and Certifications

  • M.D., University of Colorado School of Medicine 2007
  • Ph.D., University of Colorado at Boulder 2005
• Recognition
• 

  In the News

  • JUN 2, 2016

    Duke Biomanufacturing Technology Licensed by Spinoff Company DMC
• Research
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  Selected Grants

  • Sustainable Biological Production of Energetic Materials  awarded by Office of Naval Research 2016 - 2019
  • Process Intensification for Reduced Commercial CAPEX of Biofuels Production (PRICE CAP) using Dynamic Metabolic Control  awarded by Department of Energy 2016 - 2018
  • EAGER:Dynamic Flux Control Enabled by Synthetic Metabolic Valves  awarded by  National Science Foundation 2014 - 2017
  • Modular Microbial Chasses for the Rapid Scale Up of Living Foundary Molecules  awarded by Defense Advanced Research Projects Agency 2014 - 2016
  • Multi-Site Public Engagement with Science-Synthetic Biology  awarded by Museum of Science 2016
• Publications and Artistic Works
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  Selected Publications

  • Book Sections

    • Lipscomb, TW, Lipscomb, ML, Gill, RT, and Lynch, MD. "Metabolic Engineering of Recombinant E. coli for the Production of 3-Hydroxypropionate." In Engineering Complex Phenotypes in Industrial Strains, 185-120. October 24, 2012.  Full Text

  • Conference Papers

    • Lynch, MD. "A rational microbial design perspective in the design build test era." January 1, 2014.
    • Lynch, MD, Manness, PC, Lipscomb, M, Warnecke, T, and Liao, H. "Novel biological conversion of hydrogen and carbon dioxide directly into biodiesel." December 1, 2011.
    • Lipscomb, ML, Warnecke, T, Hans, L, Maness, LP, and Lynch, MD. "Novel biological conversion of hydrogen and carbon dioxide directly into biodiesel." August 25, 2011.
    • Lynch, MD, Warnecke, T, Singh, A, and Gill, RT. "Genomics tools for elucidating the function of trait conferring genes." December 1, 2005.
    • Warnecke, T, Lynch, MD, and Gill, RT. "Identification of organic acid tolerance genes in E. coli for biorefinery applications." December 1, 2005.

  • Journal Articles

    • Burg, JM, Cooper, CB, Ye, Z, Reed, BR, Moreb, EA, and Lynch, MD. "Large-scale bioprocess competitiveness: the potential of dynamic metabolic control in two-stage fermentations." Current Opinion in Chemical Engineering 14 (November 2016): 121-136.  Full Text
    • Lynch, MD. "Into new territory: improved microbial synthesis through engineering of the essential metabolic network." Current opinion in biotechnology 38 (April 2016): 106-111.  Full Text
    • Boyle, NR, Reynolds, TS, Evans, R, Lynch, M, and Gill, RT. "Recombineering to homogeneity: extension of multiplex recombineering to large-scale genome editing." Biotechnology journal 8, no. 5 (May 2013): 515-522. (Review)  Full Text
    • Garst, A, Lynch, M, Evans, R, and Gill, RT. "Strategies for the multiplex mapping of genes to traits." Microbial cell factories 12 (January 2013): 99-. (Review)  Full Text
    • Warnecke, TE, Lynch, MD, Lipscomb, ML, and Gill, RT. "Identification of a 21 amino acid peptide conferring 3-hydroxypropionic acid stress-tolerance to Escherichia coli." Biotechnology and bioengineering 109, no. 5 (May 2012): 1347-1352.  Full Text
    • Prior, JE, Lynch, MD, and Gill, RT. "Broad-host-range vectors for protein expression across gram negative hosts." Biotechnology and bioengineering 106, no. 2 (June 2010): 326-332.  Full Text
    • Warnecke, TE, Lynch, MD, Karimpour-Fard, A, Lipscomb, ML, Handke, P, Mills, T, Ramey, CJ, Hoang, T, and Gill, RT. "Rapid dissection of a complex phenotype through genomic-scale mapping of fitness altering genes." Metabolic engineering 12, no. 3 (May 2010): 241-250.  Full Text
    • Singh, A, Lynch, MD, and Gill, RT. "Genes restoring redox balance in fermentation-deficient E. coli NZN111." Metabolic engineering 11, no. 6 (November 2009): 347-354.  Full Text
    • Gall, S, Lynch, MD, Sandoval, NR, and Gill, RT. "Parallel mapping of genotypes to phenotypes contributing to overall biological fitness." Metabolic engineering 10, no. 6 (November 2008): 382-393.  Full Text
    • Warnecke, TE, Lynch, MD, Karimpour-Fard, A, Sandoval, N, and Gill, RT. "A genomics approach to improve the analysis and design of strain selections." Metabolic engineering 10, no. 3-4 (May 9, 2008): 154-165.  Full Text
    • Bonomo, J, Lynch, MD, Warnecke, T, Price, JV, and Gill, RT. "Genome-scale analysis of anti-metabolite directed strain engineering." Metabolic engineering 10, no. 2 (March 2008): 109-120.  Full Text
    • Lynch, MD, Warnecke, T, and Gill, RT. "SCALEs: multiscale analysis of library enrichment." Nature methods 4, no. 1 (January 2007): 87-93.  Full Text
    • Lynch, MD, and Gill, RT. "Broad host range vectors for stable genomic library construction." Biotechnology and bioengineering 94, no. 1 (May 2006): 151-158.  Full Text
    • Lynch, MD, Gill, RT, and Stephanopoulos, G. "Mapping phenotypic landscapes using DNA micro-arrays." Metabolic engineering 6, no. 3 (July 2004): 177-185.  Full Text
• Teaching and Mentoring
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  Recent Courses

  • BME 490L: Special Topics in Biomedical Engineering Design (DR) 2017
  • BME 493: Projects in Biomedical Engineering (GE) 2017
  • BME 494: Projects in Biomedical Engineering (GE) 2017
  • BME 590: Special Topics in Biomedical Engineering 2017
  • BME 790L: Advanced Topics with the Lab for Graduate Students in Biomedical Engineering 2017
  • BME 791: Graduate Independent Study 2017
  • EGR 393: Research Projects in Engineering 2016
  • PHYSICS 493: Research Independent Study 2016
  • BME 244L9: Quantitative Physiology with Biostatistical Applications 2015
  • BME 244L: Quantitative Physiology with Biostatistical Applications 2015
  • BME 899: Special Readings in Biomedical Engineering 2015
• Scholarly, Clinical, and Service Activities
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  Outreach and Engaged Scholarship

  • Bass Connections Faculty Team Member. Duke Undergraduate International Genetically Engineered Machine (iGEM) Team. August 2017 - May 2018  2017 - 2018
  • Bass Connections Faculty Team Member. Duke Undergraduate International Genetically Engineered Machine (iGEM) Team. August 2016 - May 2017  2016 - 2017

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