Scholars@Duke

• Background
• 

  Education, Training, & Certifications

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

  Previous Appointments & Affiliations

  • Assistant Professor of Chemistry, Chemistry, Trinity College of Arts & Sciences 2019 - 2022
  • Assistant Professor in the Department of Chemistry, Chemistry, Trinity College of Arts & Sciences 2014 - 2018
  • Assistant Research Professor in the Department of Biomedical Engineering, Biomedical Engineering, Pratt School of Engineering 2013 - 2014
• Recognition
• 

  In the News

  • JUN 2, 2016

    Duke Biomanufacturing Technology Licensed by Spinoff Company DMC

  • NOV 5, 2014

    Pratt School of Engineering

    Michael Lynch: Bending Microbial Metabolisms to Generate New Chemicals
• Research
• 

  Selected Grants

  • University Training Program in Biomolecular and Tissue Engineering awarded by National Institutes of Health 1994 - 2027
  • Automated CRISPR Enabled DNA Synthesis (CEDS) awarded by National Institutes of Health 2022 - 2024
  • Biological Production of Thermal Stabilizers awarded by Oak Ridge National Laboratory 2020 - 2023
  • Sustainable, Low Cost Production of Biosynthetic 1,2,4-Butanetriol and Butanetriol Trinitrate awarded by Naval Air Warfare Center 2021 - 2023
  • Rapid diagnosis and quantification of HIV by direct capture, labelling and detection of individual virions awarded by National Institutes of Health 2019 - 2022
  • Production of a beta-carotene derivatives using Dynamic Metabolic Control awarded by BASF Corporation 2019 - 2021
  • Process Intensification for Reduced Commercial CAPEX of Biofuels Production (PRICE CAP) using Dynamic Metabolic Control awarded by Department of Energy 2016 - 2019
  • A Platform for Next Generation Biologics awarded by North Carolina Biotechnology Center 2018 - 2019
  • Sustainable Biological Production of Energetic Materials awarded by Office of Naval Research 2016 - 2019
  • Dynamic Metabolic Control for the Production of Limonene awarded by DMC Limited 2017 - 2019
  • A High through-put Automated Strain Evaluation Platform for Advanced Renewable Chemicals and Materials awarded by Office of Naval Research 2017 - 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
• 

  External Relationships

  • DMC Biotechnologies
  • Roke Biotechnologies, LLC
• Publications & Artistic Works
• 

  Selected Publications

  • Academic Articles

    • Yang, Tian, Zhixia Ye, and Michael D. Lynch. “"Multiagent" Screening Improves Directed Enzyme Evolution by Identifying Epistatic Mutations.” Acs Synthetic Biology 11, no. 5 (May 4, 2022): 1971–83. https://doi.org/10.1021/acssynbio.2c00136.
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    • Decker, John S., Romel Menacho-Melgar, and Michael D. Lynch. “Integrated autolysis, DNA hydrolysis and precipitation enables an improved bioprocess for Q-Griffithsin, a broad-spectrum antiviral and clinical-stage anti-COVID-19 candidate.” Biochemical Engineering Journal 181 (April 2022): 108403. https://doi.org/10.1016/j.bej.2022.108403.
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    • Moreb, Eirik A., and Michael D. Lynch. “A Meta-Analysis of gRNA Library Screens Enables an Improved Understanding of the Impact of gRNA Folding and Structural Stability on CRISPR-Cas9 Activity.” The Crispr Journal 5, no. 1 (February 2022): 146–54. https://doi.org/10.1089/crispr.2021.0084.
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    • Menacho-Melgar, Romel, and Michael D. Lynch. “Simple Scalable Protein Expression and Extraction Using Two-stage Autoinducible Cell Autolysis and DNA/RNA Autohydrolysis in Escherichia coli.” Bio Protocol 12, no. 2 (January 20, 2022): e4297. https://doi.org/10.21769/bioprotoc.4297.
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    • Menacho-Melgar, Romel, and Michael D. Lynch. “Measuring Oligonucleotide Hydrolysis in Cellular Lysates via Viscosity Measurements.” Bio Protocol 12, no. 2 (January 20, 2022): e4304. https://doi.org/10.21769/bioprotoc.4304.
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    • Hennigan, Jennifer N., and Michael D. Lynch. “The past, present, and future of enzyme-based therapies.” Drug Discovery Today 27, no. 1 (January 2022): 117–33. https://doi.org/10.1016/j.drudis.2021.09.004.
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    • Menacho-Melgar, Romel, Jennifer N. Hennigan, and Michael D. Lynch. “Optimization of phosphate-limited autoinduction broth for two-stage heterologous protein expression in Escherichia coli.” Biotechniques 71, no. 5 (November 2021): 566–72. https://doi.org/10.2144/btn-2021-0055.
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    • Ye, Zhixia, Shuai Li, Jennifer N. Hennigan, Juliana Lebeau, Eirik A. Moreb, Jacob Wolf, and Michael D. Lynch. “Two-stage dynamic deregulation of metabolism improves process robustness & scalability in engineered E. coli.” Metabolic Engineering 68 (September 30, 2021): 106–18. https://doi.org/10.1016/j.ymben.2021.09.009.
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    • Moreb, E. A., and M. D. Lynch. “Genome dependent Cas9/gRNA search time underlies sequence dependent gRNA activity.” Nature Communications 12, no. 1 (August 19, 2021): 5034. https://doi.org/10.1038/s41467-021-25339-3.
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    • Rios, J., J. Lebeau, T. Yang, S. Li, and M. D. Lynch. “A critical review on the progress and challenges to a more sustainable, cost competitive synthesis of adipic acid.” Green Chemistry 23, no. 9 (May 7, 2021): 3172–90. https://doi.org/10.1039/d1gc00638j.
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    • Lynch, Michael D. “The bioprocess TEA calculator: An online technoeconomic analysis tool to evaluate the commercial competitiveness of potential bioprocesses.” Metabolic Engineering 65 (May 2021): 42–51. https://doi.org/10.1016/j.ymben.2021.03.004.
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    • Efromson, John P., Shuai Li, and Michael D. Lynch. “BioSamplr: An open source, low cost automated sampling system for bioreactors.” Hardwarex 9 (April 2021): e00177. https://doi.org/10.1016/j.ohx.2021.e00177.
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    • Li, Shuai, Zhixia Ye, Eirik A. Moreb, Jennifer N. Hennigan, Daniel Baez Castellanos, Tian Yang, and Michael D. Lynch. “Dynamic control over feedback regulatory mechanisms improves NADPH flux and xylitol biosynthesis in engineered E. coli.” Metabolic Engineering 64 (March 2021): 26–40. https://doi.org/10.1016/j.ymben.2021.01.005.
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    • Ye, Zhixia, Eirik A. Moreb, Shuai Li, Juliana Lebeau, Romel Menacho-Melgar, Matthew Munson, and Michael D. Lynch. “Escherichia coli Cas1/2 Endonuclease Complex Modifies Self-Targeting CRISPR/Cascade Spacers Reducing Silencing Guide Stability.” Acs Synthetic Biology 10, no. 1 (January 2021): 29–37. https://doi.org/10.1021/acssynbio.0c00398.
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    • Moreb, Eirik A., Mitchell Hutmacher, and Michael D. Lynch. “CRISPR-Cas "Non-Target" Sites Inhibit On-Target Cutting Rates.” The Crispr Journal 3, no. 6 (December 2020): 550–61. https://doi.org/10.1089/crispr.2020.0065.
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    • Efromson, John, Shuai Li, and Michael Lynch. “BioSamplr: An open source, low cost automated sampling system for bioreactors,” October 25, 2020. https://doi.org/10.1101/2020.10.25.354183.
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    • Menacho-Melgar, Romel, Eirik A. Moreb, John P. Efromson, Tian Yang, Jennifer N. Hennigan, Ruixin Wang, and Michael D. Lynch. “Improved two-stage protein expression and purification via autoinduction of both autolysis and auto DNA/RNA hydrolysis conferred by phage lysozyme and DNA/RNA endonuclease.” Biotechnology and Bioengineering 117, no. 9 (September 2020): 2852–60. https://doi.org/10.1002/bit.27444.
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    • Ye, Zhixia, Shuai Li, Jennifer Hennigan, Juliana Lebeau, Eirik Moreb, Jacob Wolf, and Michael Lynch. “Two-stage Dynamic Deregulation of Metabolism Improves Process Robustness & Scalability in EngineeredE. coli,” August 30, 2020. https://doi.org/10.1101/2020.08.30.274290.
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    • Li, Shuai, Eirik Moreb, Zhixia Ye, Jennifer Hennigan, Daniel Baez Castellanos, Tian Yang, and Michael Lynch. “Dynamic control over feedback regulatory mechanisms improves NADPH fluxes and xylitol biosynthesis in engineered E. coli,” July 27, 2020. https://doi.org/10.1101/2020.07.27.222588.
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    • Ye, Zhixia, Juliana Lebeau, Eirik Moreb, Romel Menacho-Melgar, and Michael Lynch. “TheE. coliCas1/2 endonuclease complex reduces CRISPR/Cascade guide array stability,” July 27, 2020. https://doi.org/10.1101/2020.07.27.223214.
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    • Li, Shuai, Zhixia Ye, Juliana Lebeau, Eirik Moreb, and Michael Lynch. “Dynamic control over feedback regulation identifies pyruvate-ferredoxin oxidoreductase as a central metabolic enzyme in stationary phase E. coli,” July 26, 2020. https://doi.org/10.1101/2020.07.26.219949.
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    • Moreb, Eirik Adim, Zhixia Ye, John P. Efromson, Jennifer N. Hennigan, Romel Menacho-Melgar, and Michael D. Lynch. “Media Robustness and Scalability of Phosphate Regulated Promoters Useful for Two-Stage Autoinduction in E. coli.” Acs Synthetic Biology 9, no. 6 (June 2020): 1483–86. https://doi.org/10.1021/acssynbio.0c00182.
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    • Moreb, Eirik, Zhixia Ye, John Efromson, Jennifer Hennigan, Romel Menacho-Melgar, and Michael Lynch. “Robustness testing and scalability of phosphate regulated promoters useful for two-stage autoinduction in E. coli,” January 26, 2020. https://doi.org/10.1101/2020.01.26.920280.
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    • Decker, John S., Romel Menacho-Melgar, and Michael D. Lynch. “Low-Cost, Large-Scale Production of the Anti-viral Lectin Griffithsin.” Frontiers in Bioengineering and Biotechnology 8 (January 2020): 1020. https://doi.org/10.3389/fbioe.2020.01020.
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    • Lebeau, Juliana, John P. Efromson, and Michael D. Lynch. “A Review of the Biotechnological Production of Methacrylic Acid.” Frontiers in Bioengineering and Biotechnology 8 (January 2020): 207. https://doi.org/10.3389/fbioe.2020.00207.
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    • Menacho-Melgar, Romel, Zhixia Ye, Eirik Moreb, Tian Yang, John Efromson, John Decker, and Michael Lynch. “Improved, scalable, two-stage, autoinduction of recombinant protein expression in E. coli utilizing phosphate depletion,” October 28, 2019. https://doi.org/10.1101/820787.
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    • Menacho-Melgar, Romel, John S. Decker, Jennifer N. Hennigan, and Michael D. Lynch. “A review of lipidation in the development of advanced protein and peptide therapeutics.” Journal of Controlled Release : Official Journal of the Controlled Release Society 295 (February 2019): 1–12. https://doi.org/10.1016/j.jconrel.2018.12.032.
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    • Moreb, Eirik Adim, Benjamin Hoover, Adam Yaseen, Nisakorn Valyasevi, Zoe Roecker, Romel Menacho-Melgar, and Michael D. Lynch. “Managing the SOS Response for Enhanced CRISPR-Cas-Based Recombineering in E. coli through Transient Inhibition of Host RecA Activity.” Acs Synthetic Biology 6, no. 12 (December 2017): 2209–18. https://doi.org/10.1021/acssynbio.7b00174.
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    • Burg, J. M., C. B. Cooper, Z. Ye, B. R. Reed, E. A. Moreb, and M. D. Lynch. “Large-scale bioprocess competitiveness: the potential of dynamic metabolic control in two-stage fermentations.” Current Opinion in Chemical Engineering 14 (November 1, 2016): 121–36. https://doi.org/10.1016/j.coche.2016.09.008.
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    • Lynch, Michael D. “Into new territory: improved microbial synthesis through engineering of the essential metabolic network.” Current Opinion in Biotechnology 38 (April 2016): 106–11. https://doi.org/10.1016/j.copbio.2016.01.009.
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    • Garst, Andrew, Michael Lynch, Ron Evans, and Ryan T. Gill. “Strategies for the multiplex mapping of genes to traits.” Microbial Cell Factories 12 (October 30, 2013): 99. https://doi.org/10.1186/1475-2859-12-99.
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    • Boyle, Nanette R., T Steele Reynolds, Ron Evans, Michael Lynch, and Ryan T. Gill. “Recombineering to homogeneity: extension of multiplex recombineering to large-scale genome editing.” Biotechnology Journal 8, no. 5 (May 2013): 515–22. https://doi.org/10.1002/biot.201200237.
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    • Warnecke, T. E., M. D. Lynch, M. L. Lipscomb, and R. T. Gill. “Identification of a 21 amino acid peptide conferring 3-hydroxypropionic acid stress-tolerance to Escherichia coli.” Biotechnology and Bioengineering 109, no. 5 (May 2012): 1347–52. https://doi.org/10.1002/bit.24398.
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    • Prior, Jamie E., Michael D. Lynch, and Ryan T. Gill. “Broad-host-range vectors for protein expression across gram negative hosts.” Biotechnology and Bioengineering 106, no. 2 (June 2010): 326–32. https://doi.org/10.1002/bit.22695.
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    • Warnecke, T. E., M. D. Lynch, A. Karimpour-Fard, M. L. Lipscomb, P. Handke, T. Mills, C. J. Ramey, T. Hoang, and R. T. Gill. “Rapid dissection of a complex phenotype through genomic-scale mapping of fitness altering genes.” Metabolic Engineering 12, no. 3 (May 2010): 241–50. https://doi.org/10.1016/j.ymben.2009.12.002.
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    • Singh, Amarjeet, Michael D. Lynch, and Ryan T. Gill. “Genes restoring redox balance in fermentation-deficient E. coli NZN111.” Metabolic Engineering 11, no. 6 (November 2009): 347–54. https://doi.org/10.1016/j.ymben.2009.07.002.
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    • Gall, S., M. D. Lynch, N. R. Sandoval, and R. T. Gill. “Parallel mapping of genotypes to phenotypes contributing to overall biological fitness.” Metabolic Engineering 10, no. 6 (November 2008): 382–93. https://doi.org/10.1016/j.ymben.2008.08.003.
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    • Warnecke, T. E., M. D. Lynch, A. Karimpour-Fard, N. Sandoval, and R. T. Gill. “A genomics approach to improve the analysis and design of strain selections.” Metabolic Engineering 10, no. 3–4 (May 9, 2008): 154–65. https://doi.org/10.1016/j.ymben.2008.04.004.
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    • Bonomo, Jeanne, Michael D. Lynch, Tanya Warnecke, James V. Price, and Ryan T. Gill. “Genome-scale analysis of anti-metabolite directed strain engineering.” Metabolic Engineering 10, no. 2 (March 2008): 109–20. https://doi.org/10.1016/j.ymben.2007.10.002.
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    • Lynch, Michael D., Tanya Warnecke, and Ryan T. Gill. “SCALEs: multiscale analysis of library enrichment.” Nature Methods 4, no. 1 (January 2007): 87–93. https://doi.org/10.1038/nmeth946.
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    • Lynch, Michael D., and Ryan T. Gill. “Broad host range vectors for stable genomic library construction.” Biotechnology and Bioengineering 94, no. 1 (May 2006): 151–58. https://doi.org/10.1002/bit.20836.
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    • Lynch, Michael D., Ryan T. Gill, and Gregory Stephanopoulos. “Mapping phenotypic landscapes using DNA micro-arrays.” Metabolic Engineering 6, no. 3 (July 2004): 177–85. https://doi.org/10.1016/j.ymben.2004.01.002.
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    • Hennigan, Jennifer, Phillip Wagner, Chris Burk, John Efromson, Zhixia Ye, Matthew Lipscomb, and Michael Lynch. “A Technoeconomic Evaluation of the Potential of Industrial Biotechnology for the Competitive Production of Commodity and Bulk Chemicals,” n.d. https://doi.org/10.26434/chemrxiv.13238996.v1.
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    • Menacho-Melgar, Romel, Jennifer N. Hennigan, and Michael D. Lynch. “Optimization of Phosphate Limited Autoinduction Broth for 2-Stage Heterologous Protein Expression in E. coli,” n.d. https://doi.org/10.1101/2021.06.08.447502.
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    • Menacho-Melgar, Romel, Tian Yang, and Michael D. Lynch. “Instant Taq: Rapid Autoinducible Expression and Chromatography-free Purification of Taq polymerase,” n.d. https://doi.org/10.1101/2021.09.25.461774.
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    • Moreb, E. A., and M. D. Lynch. “An Analysis of gRNA Sequence Dependent Cleavage Highlights the Importance of Genomic Context on CRISPR-Cas Activity,” n.d. https://doi.org/10.1101/2021.05.06.442929.
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    • Moreb, E. A., and Michael D. Lynch. “A meta-analysis of gRNA library screens enables an improved understanding of the impact of gRNA folding and structural stability on CRISPR-Cas9 activity,” n.d. https://doi.org/10.1101/2021.05.29.446220.
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    • Yang, Tian, Zhixia Ye, and Michael D. Lynch. ““Multi-Agent” Screening Improves the Efficiency of Directed Enzyme Evolution,” n.d. https://doi.org/10.1101/2021.04.06.438652.
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  • Book Sections

    • Lipscomb, T. W., M. L. Lipscomb, R. T. Gill, and M. D. Lynch. “Metabolic Engineering of Recombinant E. coli for the Production of 3-Hydroxypropionate.” In Engineering Complex Phenotypes in Industrial Strains, 185–120, 2012. https://doi.org/10.1002/9781118433034.ch7.
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  • Conference Papers

    • Lynch, M. D. “A rational microbial design perspective in the design build test era.” In Metabolic Engineering X, 505–28, 2014.
    • Lipscomb, Matthew L., Tanya Warnecke Lipscomb, Hans Liao, PinChing Maness, and Michael D. Lynch. “Production of fungible diesel via fatty acid synthesis from hydrogen and carbon dioxide feedstocks.” In Abstracts of Papers of the American Chemical Society, Vol. 243. AMER CHEMICAL SOC, 2012.
       Link to Item
    • Watson, Faith D., Christopher P. Mercogliano, Wendy K. Ribble, Rebecca D. Anderson, Hans H. Liao, Tanya W. Lipscomb, and Michael D. Lynch. “Enzyme engineering of malonyl coA reductase (MCR) to improve 3-hydroxypropionate (3HP) production.” In Abstracts of Papers of the American Chemical Society, Vol. 243. AMER CHEMICAL SOC, 2012.
       Link to Item
    • Lynch, M. D., P. C. Manness, M. Lipscomb, T. Warnecke, and H. Liao. “Novel biological conversion of hydrogen and carbon dioxide directly into biodiesel.” In Acs National Meeting Book of Abstracts, 2011.
    • Lipscomb, M. L., T. Warnecke, L. Hans, L. P. Maness, and M. D. Lynch. “Novel biological conversion of hydrogen and carbon dioxide directly into biodiesel.” In Acs National Meeting Book of Abstracts, 2011.
    • Mercogliano, Christopher P., Hans H. Liao, and Michael D. Lynch. “Enzyme evolution of an alpha-keto decarboxylase.” In Abstracts of Papers of the American Chemical Society, Vol. 241. AMER CHEMICAL SOC, 2011.
       Link to Item
    • Lynch, M. D., T. Warnecke, A. Singh, and R. T. Gill. “Genomics tools for elucidating the function of trait conferring genes.” In Aiche Annual Meeting, Conference Proceedings, 9189, 2005.
    • Warnecke, T., M. D. Lynch, and R. T. Gill. “Identification of organic acid tolerance genes in E. coli for biorefinery applications.” In Aiche Annual Meeting, Conference Proceedings, 8984, 2005.
    • Lynch, M. D., T. Warnecke, and R. T. Gill. “Mixed-library parallel gene trait mapping: A quantitative micro-array technique for the genome-wide identification of trait conferring genes.” In Abstracts of Papers of the American Chemical Society, 229:U202–U202. AMER CHEMICAL SOC, 2005.
       Link to Item
    • Warnecke, T. E., M. D. Lynch, and R. T. Gill. “Post-genomics approach to understanding E. Coli network architecture.” In Abstracts of Papers of the American Chemical Society, 229:U227–U227. AMER CHEMICAL SOC, 2005.
       Link to Item

  • Preprints

    • Li, Shuai, Zhixia Ye, Eirik A. Moreb, Romel Menacho-Melgar, and Michael D. Lynch. “The Development of 2-stage Microfermentation Protocols for High Throughput Cell Factory Evaluations.” Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/2022.02.25.481916.
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• Teaching & Mentoring
• 

  Recent Courses

  • BME 590L: Special Topics with Lab 2022
  • BME 490L: Special Topics in Biomedical Engineering Design (DR) 2021
  • BME 790L: Advanced Topics with the Lab for Graduate Students in Biomedical Engineering 2021
  • BME 490L: Special Topics in Biomedical Engineering Design (DR) 2020
  • BME 590D: Special Topics with Discussion 2020
  • BME 703S: Engineering Management Seminar for Master of Science Students 2020
  • BME 790L: Advanced Topics with the Lab for Graduate Students in Biomedical Engineering 2020
• Scholarly, Clinical, & Service Activities
• 

  Outreach & Engaged Scholarship

  • Bass Connections Faculty Team Leader. Duke Undergraduate International Genetically Engineered Machine. 2018 - 2019  2018 - 2019
  • 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

Some information on this profile has been compiled automatically from Duke databases and external sources. (Our About page explains how this works.) If you see a problem with the information, please write to Scholars@Duke and let us know. We will reply promptly.