Michael D Lynch
Assistant Professor in the Department of Biomedical Engineering
Current Research Interests
Focused on genetically engineering microbes to shut off their growth circuits and turn on new pathways to produce different compounds—improving production of biofuels, pharmacological molecules and industrial chemicals.
Current Appointments & Affiliations
- Assistant Professor in the Department of Biomedical Engineering, Biomedical Engineering, Pratt School of Engineering 2014
- Faculty Fellow in The Energy Initiative, Duke University Energy Initiative, Initiatives 2012
- Associate of the Duke Initiative for Science & Society, Duke Science & Society, Initiatives 2017
Contact Information
- Background
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Education, Training, & Certifications
- M.D., University of Colorado School of Medicine 2007
- Ph.D., University of Colorado - Boulder 2005
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Duke Appointment History
- 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
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In the News
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JUN 2, 2016 -
NOV 5, 2014 Pratt School of Engineering
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- Research
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Selected Grants
- Biological Production of Thermal Stabilizers awarded by Oak Ridge National Laboratory 2020 - 2023
- Rapid diagnosis and quantification of HIV by direct capture, labelling and detection of individual virions awarded by National Institutes of Health 2019 - 2022
- University Training Program in Biomolecular and Tissue Engineering awarded by National Institutes of Health 1994 - 2022
- Production of a beta-carotene derivatives using Dynamic Metabolic Control awarded by BASF Corporation 2019 - 2020
- 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
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External Relationships
- DMC Biotechnologies
- Roke Biotechnologies, LLC
- Publications & Artistic Works
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Selected Publications
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Academic Articles
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Efromson, J. P., S. Li, and M. D. Lynch. “BioSamplr: An open source, low cost automated sampling system for bioreactors (Accepted).” Hardwarex 9 (April 1, 2021). https://doi.org/10.1016/j.ohx.2021.e00177.Full Text
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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 (January 16, 2021): 26–40. https://doi.org/10.1016/j.ymben.2021.01.005.Full Text
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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.Full Text
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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.Full Text
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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.Full Text
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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.Full Text
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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 Engineered E. coli,” August 30, 2020. https://doi.org/10.1101/2020.08.30.274290.Full Text
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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.Full Text
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Ye, Zhixia, Juliana Lebeau, Eirik Moreb, Romel Menacho-Melgar, and Michael Lynch. “The E. coli Cas1/2 endonuclease complex reduces CRISPR/Cascade guide array stability,” July 27, 2020. https://doi.org/10.1101/2020.07.27.223214.Full Text
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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.Full Text
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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.Full Text
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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.Full Text
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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.Full Text
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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.Full Text
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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.Full Text
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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.Full Text
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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.Full Text
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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.Full Text
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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.Full Text
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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.Full Text
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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.Full Text
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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.Full Text
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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.Full Text
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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.Full Text
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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.Full Text
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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.Full Text
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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.Full Text
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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.Full Text
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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.Full Text
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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.Full Text
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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.Full Text
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Book Sections
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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.Full Text
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Conference Papers
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Lynch, M. D. “A rational microbial design perspective in the design build test era.” In Metabolic Engineering X, 505–28, 2014.
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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
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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
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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.
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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.
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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
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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, 2005.
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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, 2005.
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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
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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
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- Teaching & Mentoring
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Recent Courses
- 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
- BME 490L: Special Topics in Biomedical Engineering Design (DR) 2019
- BME 493: Projects in Biomedical Engineering (GE) 2019
- BME 494: Projects in Biomedical Engineering (GE) 2019
- BME 590L: Special Topics with Lab 2019
- BME 790L: Advanced Topics with the Lab for Graduate Students in Biomedical Engineering 2019
- BME 791: Graduate Independent Study 2019
- BME 792: Continuation of Graduate Independent Study 2019
- ISS 293: ISS Research Independent Study 2019
- Scholarly, Clinical, & Service Activities
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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
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