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Publications


  2022


43. Yang, T., Ye, Z., and Lynch MD. “Multiagent” Screening Improves Directed Enzyme Evolution by Identifying Epistatic Mutations ACS Synthetic Biology, Available Online: 5 May 2022.

42. Casadevall, A. Burnham, C., Cassell, G.H., Enquist, L. Estes, M. Golden, S., Lennon, J.T. Monack, D., Murray, B.E., Weiss, S., Weissfeld, A.S., Williams, H.N., Tiedje, J.M., Bruns, M.A., Casadevall, A., Davidson, E., Silver, P., Colwell, R.R., Criddle, C., Donohue, T., Eloe-Fadrosh, E., Falkowski, P., Frost, S., Hellweger, F., Hoehler, T.M., Jansson, J.K., Jones, A., Jiang, S., Karl, D., King, G.M., Lipp, E.K., Lynch, M.D. Martiny, J.B.H, Machlis, G.E., McFall-Ngai, M., McGovern, V. Rich V., Schuur, T., Sihi, D., Spear, J.R., Verstraete, W., Jutla, A., and Zhou J. Microbes and Climate Change – Science, People & Impacts. Report on an American Academy of Microbiology Virtual Colloquium. April 22, 2022.

41. Decker, JS., Menacho-Melgar R., and Lynch MD. 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. Available Online March 13, 2022.

40. Li, S., Ye, Z., Moreb, E.A., Menacho-Melgar, R., and Lynch MD. The Development of 2-stage Microfermentation Protocols for High Throughput Cell Factory Evaluations. BioRxiv. Feb 28 2022.

39. Moreb, E.A., and Lynch MD. 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. Feb 22 2022.

38. Menacho-Melgar R., and Lynch MD. Simple Scalable Protein Expression and Extraction Using Two-stage Autoinducible Cell Autolysis and DNA/RNA Autohydrolysis in Escherichia coli. Bio-protocol. Jan 20 2022.

37. Menacho-Melgar R., and Lynch MD. Measuring Oligonucleotide Hydrolysis in Cellular Lysates via Viscosity Measurements. Bio-protocol. Jan 20 2022.


  2021


36. Ye, Z., Li. S., Hennigan, JN., Lebeau, J., Moreb, EA., Wolf, J., and Lynch MD. Two-stage Dynamic Deregulation of Metabolism Improves Process Robustness & Scalability in Engineered E. coli. Metabolic Engineering. Available Online September 30 2021.

35. Menacho-Melgar, R. Yang, T. and Lynch MD. Instant Taq: Rapid Autoinducible Expression and Chromatography-free Purification of Taq polymerase. BioRxiv, September 25, 2021.

34. Hennigan, JN. and Lynch MD. Keynote Review: The past, present, and future of enzyme-based therapies. Drug Discovery Today, Available Online September 16, 2021.

33. Menacho-Melgar, R., Hennigan, JN., and Lynch MD. Optimization of phosphate-limited autoinduction broth for two-stage heterologous protein expression in Escherichia coli. Biotechniques, Available Online August 25, 2021.

32. Moreb, EA., and Lynch MD. Genome dependent Cas9/gRNA search time underlies sequence dependent gRNA activity. Nature Communications, Aug 19, 2021.

31. Hennigan, JN., and Lynch MD. A Compilation of Investigational, Preclinical and Clinical Enzyme Based Therapeutics Mendeley Data, May 6, 2021.

30. Rios, J., Lebeau, J., Yang, T., Li, S., and Lynch MD. A Critical Review on the Progress and Challenges to a More Sustainable, Cost Competitive Synthesis of Adipic Acid. Green Chemistry, Available Online April 13, 2021.

29. Lynch, MD., The Bioprocess TEA Calculator: An online techno-economic analysis tool to evaluate the commercial competitiveness of potential bioprocesses. Metabolic Engineering. Online 9 March 2021.

28. Efromson, JP., Li, S., and Lynch, MD., BioSamplr: An open source, low cost automated sampling system for bioreactors. Hardware X. Available online 5 February 2021.

27. Li. S., Moreb, EA., Ye, Z., Hennigan, JN., Baez Castellanos, D., Yang, T., and Lynch MD. Dynamic control over feedback regulatory mechanisms improves NADPH fluxes and xylitol biosynthesis in engineered E. coli. Metabolic Engineering. January 2021.


  2020


26. Hennigan, JN., Wagner, P., Burk, C., Efromson, JP., Ye, Z., Lipscomb, M.L., and Lynch MD. A Technoeconomic Evaluation of the Potential of Industrial Biotechnology for the Competitive Production of Commodity and Bulk Chemicals. ChemRxiv (In Review). November 2020.

25. Li. S., Ye, Z., Lebeau, J., Moreb, EA., and Lynch MD. Dynamic control over feedback regulation identifies pyruvate-ferredoxin oxidoreductase as a central metabolic enzyme in stationary phase E. coli. Biorxiv.org. (In Review) August 2020.

24. Moreb, EA., Hutmacher, M., and Lynch MD. CRISPR/Cas “non-target” sites inhibit on-target cutting rates. The CRISPR Journal, 20 December 2020.

23. Ye, Z., Moreb, EA., Li, S., Lebeau, J., Menacho-Melgar, R., Munson, M., and Lynch MD. The E. coli Cas1/2 endonuclease complex modifies self-targeting CRISPR/Cascade spacers reducing silencing guide stability. ACS Synthetic Biology, 16 December 2020.

22. Decker, JS., Menacho Melgar, R., and Lynch MD. Low-Cost, Large-Scale Production of the Anti-viral Lectin Griffithsin. Front. Bioeng. Biotechnol., 21 August 2020.

21. Moreb, EA., Ye, Z., Efromson, JP., Hennigan, JN., Menacho-Melgar, R., and Lynch, MD., Media Robustness and Scalability of Phosphate Regulated Promoters Useful for Two-Stage Autoinduction in E. coli. ACS Synthetic Biology., 30 April 2020.

20. Menacho-Melgar, R., Moreb, EA., Efromson, JP., Yang, T., Hennigan, JN., Wang, R., and Lynch, MD., 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 & Bioengineering., 28 May 2020.

19. Menacho-Melgar, R., Ye, Z., Moreb, EA., Yang, T., Efromson, JP., Decker, JS., Wang, R., and Lynch, MD., Scalable, two‐stage, autoinduction of recombinant protein expression in E. coli utilizing phosphate depletion. Biotechnology & Bioengineering., 22 May 2020.

18. Lebeau, J., Efromson, JP., and Lynch MD. A Review of the Biotechnological Production of Methacrylic Acid. Front. Bioeng. Biotechnol., 20 March 2020.


  2019


17. Menacho-Melgar, R., J., Decker, JS., Hennigan, JN., and Lynch MD. A review of lipidation in the development of advanced protein and peptide therapeutics. J. Control Release., 10 February 2019.


  2017


16. Moreb, EA., Hoover, B., Yaseen A., Valyasevi, N., Roecker, A., 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., 15 September 2017.


  2016


15. Burg, JM., Cooper, CB., Z 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., November 2016.

14. Lynch MD. Into new territory: improved microbial synthesis through engineering of the essential metabolic network. Current Opinion in Biotechnology., April 2016.


  2015 & Earlier


13. Garst, A., Lynch MD., Evans, R., and Gill, RT. Strategies for the multiplex mapping of genes to traits. Microbial Cell Factories., October 2013.

12. Boyle, NR., Reynolds, TS., Evans, R., and Lynch MD. and Gill, RT. Recombineering to homogeneity: extension of multiplex recombineering to large-scale genome editing. Biotechnology Journal., May 2013.

11. Warnecke, TE., Lipscomb, ML., Gill, RT., and Lynch MD. Metabolic Engineering of Recombinant E. coli for the Production of 3‐Hydroxypropionate. Engineering Complex Phenotypes in Industrial Strains. Chapter 7, 24 February 2012.

10. 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. Biotechnoloy & Bioengineering. January 2012.

9. Warnecke, TE., 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., May 2010.

8. Prior, JE., Lynch MD. and Gill, RT. Broad‐host‐range vectors for protein expression across gram negative hosts. Biotechnology & Bioengineering., 10 February 2010.

7. Singh, A., Lynch MD., and Gill, RT. Genes restoring redox balance in fermentation-deficient E. coli NZN111. Metabolic Engineering., November 2009.

6. Gall, S., Lynch MD., and Gill, RT. Parallel mapping of genotypes to phenotypes contributing to overall biological fitness. Metabolic Engineering., November 2008.

5. 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., May 2008.

4. Bonomo, J., Lynch MD., Warnecke, TE., Price, JV., and Gill, RT. Genome-scale analysis of anti-metabolite directed strain engineering. Metabolic Engineering., March 2008.

3. Lynch MD., Warnecke, TE., and Gill, RT. SCALEs: multiscale analysis of library enrichment. Nature Methods., November 2007.

2. Lynch MD., and Gill, RT. Broad host range vectors for stable genomic library construction. Biotechnology & Bioengineering., February 2006.

1. Lynch MD., Gill, RT., and Stephanopolous, G. Mapping phenotypic landscapes using DNA micro-arrays. Metabolic Engineering., 6 July 2004.



Copyright © Michael D. Lynch 2021