Michael D Lynch | Scholars@Duke

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
Education, Training, & Certifications
- M.D., University of Colorado School of Medicine 2007
- Ph.D., University of Colorado at Boulder 2005
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
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 - 2022
- Process Intensification for Reduced Commercial CAPEX of Biofuels Production (PRICE CAP) using Dynamic Metabolic Control awarded by Department of Energy 2016 - 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 Platform for Next Generation Biologics awarded by North Carolina Biotechnology Center 2018
- 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
Publications & Artistic Works
Selected Publications
- Academic Articles
  - Legione, AR, Amery-Gale, J, Lynch, M, Haynes, L, Gilkerson, JR, Sansom, FM, and Devlin, JM. "Variation in the microbiome of the urogenital tract of Chlamydia-free female koalas (Phascolarctos cinereus) with and without 'wet bottom'." Plos One 13, no. 3 (January 2018): e0194881-null. Full Text
  - Taylor, S, Lynch, M, Terkildsen, M, Stevenson, G, Yates, A, Piro, N, de Araujo, J, and Gray, R. "Utility of fur as a biomarker for persistent organic pollutants in Australian fur seals (Arctocephalus pusillus doriferus)." The Science of the Total Environment 610-611 (January 2018): 1310-1320. Full Text
  - Heil, JR, Lynch, MDJ, Cheng, J, Matysiakiewicz, O, D'Alessio, M, and Charles, TC. "The Completed PacBio Single-Molecule Real-Time Sequence of Methylosinus trichosporium Strain OB3b Reveals the Presence of a Third Large Plasmid." Genome Announcements 5, no. 49 (December 7, 2017). Full Text
  - Moreb, EA, Hoover, B, Yaseen, A, Valyasevi, N, Roecker, Z, Menacho-Melgar, R, and Lynch, MD. "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): 2209-2218. Full Text
  - Lynch, M, McGrath, K, Raj, K, McLaren, P, Payne, K, McCoy, R, and Giger, U. "HEREDITARY FACTOR VII DEFICIENCY IN THE ASIAN ELEPHANT (ELEPHAS MAXIMUS) CAUSED BY A F7 MISSENSE MUTATION." Journal of Wildlife Diseases 53, no. 2 (April 2017): 248-257. Full Text
  - Legione, AR, Patterson, JLS, Whiteley, P, Firestone, SM, Curnick, M, Bodley, K, Lynch, M, Gilkerson, JR, Sansom, FM, and Devlin, JM. "Koala retrovirus genotyping analyses reveal a low prevalence of KoRV-A in Victorian koalas and an association with clinical disease." Journal of Medical Microbiology 66, no. 2 (February 2017): 236-244. Full Text
  - 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
  - Legione, AR, Patterson, JLS, Whiteley, PL, Amery-Gale, J, Lynch, M, Haynes, L, Gilkerson, JR, Polkinghorne, A, Devlin, JM, and Sansom, FM. "Identification of unusual Chlamydia pecorum genotypes in Victorian koalas (Phascolarctos cinereus) and clinical variables associated with infection." Journal of Medical Microbiology 65, no. 5 (May 2016): 420-428. Full Text
  - Legione, AR, Amery-Gale, J, Lynch, M, Haynes, L, Gilkerson, JR, Sansom, FM, and Devlin, JM. "Chlamydia pecorum Infection in Free-ranging Koalas ( Phascolarctos cinereus ) on French Island, Victoria, Australia." Journal of Wildlife Diseases 52, no. 2 (April 2016): 426-429. 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. (Review) Full Text
  - Coetsee, A, Harley, D, Lynch, M, Coulson, G, de Milliano, J, Cooper, M, and Groenewegen, R. "Radio-transmitter attachment methods for monitoring the endangered eastern barred bandicoot (Perameles gunnii)." Australian Mammalogy 38, no. 2 (2016): 221-221. Full Text
  - Patterson, JLS, Lynch, M, Anderson, GA, Noormohammadi, AH, Legione, A, Gilkerson, JR, and Devlin, JM. "The prevalence and clinical significance of Chlamydia infection in island and mainland populations of Victorian koalas (Phascolarctos cinereus)." Journal of wildlife diseases 51, no. 2 (April 2015): 309-317. Full Text
  - Fanson, KV, Lynch, M, Vogelnest, L, Miller, G, and Keeley, T. "Response to long-distance relocation in Asian elephants (Elephas maximus): monitoring adrenocortical activity via serum, urine, and feces." European Journal of Wildlife Research 59, no. 5 (October 2013): 655-664. 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
  - Ramos, P, Lynch, M, Hu, M, Arnould, JPY, Norman, R, and Beveridge, I. "Morphometric and molecular characterization of the species of Uncinaria Frölich, 1789 (Nematoda) parasitic in the Australian fur seal Arctocephalus pusillus doriferus (Schreber), with notes on hookworms in three other pinniped hosts." Systematic Parasitology 85, no. 1 (May 2013): 65-78. 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. (Letter) Full Text
  - Lynch, M, Kirkwood, R, Gray, R, Robson, D, Burton, G, Jones, L, Sinclair, R, and Arnould, JPY. "Characterization and causal investigations of an alopecia syndrome in Australian fur seals ( Arctocephalus pusillus doriferus )." Journal of Mammalogy 93, no. 2 (April 30, 2012): 504-513. Full Text
  - Lynch, M, Taylor, TK, Duignan, PJ, Swingler, J, Marenda, M, Arnould, JPY, and Kirkwood, R. "Mycoplasmas in Australian fur seals (Arctocephalus pusillus doriferus): identification and association with abortion." Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc 23, no. 6 (November 2011): 1123-1130. Full Text
  - Lynch, M, Nielsen, O, Duignan, PJ, Kirkwood, R, Hoskins, A, and Arnould, JPY. "Serologic survey for potential pathogens and assessment of disease risk in Australian fur seals." Journal of wildlife diseases 47, no. 3 (July 2011): 555-565. Full Text
  - Lynch, M, Kirkwood, R, Mitchell, A, Duignan, P, and Arnould, JPY. "Prevalence and significance of an alopecia syndrome in Australian fur seals ( Arctocephalus pusillus doriferus )." Journal of Mammalogy 92, no. 2 (April 15, 2011): 342-351. Full Text
  - Lynch, M, Duignan, PJ, Taylor, T, Nielsen, O, Kirkwood, R, Gibbens, J, and Arnould, JPY. "Epizootiology of Brucella infection in Australian fur seals." Journal of Wildlife Diseases 47, no. 2 (April 2011): 352-363. 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
  - Spence, M, Newell, JA, Lynch, M, Lee, TJ, Demetrio, J, and Mattson, C. "A Comparative Analysis of Techniques Used to Estimate the Mean Recoil Compressive Strength of High Performance Polymers." High Performance Polymers 16, no. 3 (September 2004): 381-390. 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. (Review) Full Text
  - Newell, JA, Kurzeja, T, Spence, M, and Lynch, M. "Analysis of Recoil Compressive Failure in High Performance Polymers Using Two and Four Parameter Weibull Models." High Performance Polymers 14, no. 4 (December 2002): 425-434. Full Text
  - Kirkwood, R, Gales, N, Lynch, M, and Dann, P. "Satellite tracker deployments on adult, male Australian fur seals Arctocephalus pusillus doriferus: Methods and preliminary results." Australian Mammalogy 24, no. 1 (January 1, 2002): 73-83.
- Book Sections
  - Lynch, M, and Bodley, K. "Phocid Seals." In Zoo Animal and Wildlife Immobilization and Anesthesia: Second Edition, 647-659. September 15, 2014. Full Text
  - 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
  - Lynch, M, and Bodley, K. "Phocid Seals." In Zoo Animal and Wildlife Immobilization and Anesthesia, 459-468. April 14, 2008. Full Text
- Conference Papers
  - Kennedy, P, Duffy, N, Horgan, S, and Lynch, M. "Chemical Process Safety Education: Joint Industry-Academic venture." January 1, 2015.
  - Lynch, MD. "A rational microbial design perspective in the design build test era." January 1, 2014.
  - Lipscomb, ML, Lipscomb, TW, Liao, H, Maness, P, and Lynch, MD. "Production of fungible diesel via fatty acid synthesis from hydrogen and carbon dioxide feedstocks." March 25, 2012. Link to Item
  - Watson, FD, Mercogliano, CP, Ribble, WK, Anderson, RD, Liao, HH, Lipscomb, TW, and Lynch, MD. "Enzyme engineering of malonyl coA reductase (MCR) to improve 3-hydroxypropionate (3HP) production." March 25, 2012. Link to Item
  - 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.
  - Mercogliano, CP, Liao, HH, and Lynch, MD. "Enzyme evolution of an alpha-keto decarboxylase." March 27, 2011. Link to Item
  - 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.
  - Lynch, MD, Warnecke, T, and Gill, RT. "Mixed-library parallel gene trait mapping: A quantitative micro-array technique for the genome-wide identification of trait conferring genes." March 13, 2005. Link to Item
  - Warnecke, TE, Lynch, MD, and Gill, RT. "Post-genomics approach to understanding E. Coli network architecture." March 13, 2005. Link to Item
Teaching & Mentoring
Recent Courses
Scholarly, Clinical, & Service Activities
Outreach & 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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Education, Training, & Certifications

Duke Appointment History

In the News

Selected Grants

Selected Publications

Academic Articles

Book Sections

Conference Papers

Recent Courses

Outreach & Engaged Scholarship