publications by Michael D Lynch.


Preprints

  1. Lynch, MD, A rational microbial design perspective in the design build test era, Metabolic Engineering X (January, 2014), pp. 505-528 .
  2. Watson, FD; Mercogliano, CP; Ribble, WK; Anderson, RD; Liao, HH; Lipscomb, TW; Lynch, MD, Enzyme engineering of malonyl coA reductase (MCR) to improve 3-hydroxypropionate (3HP) production, Abstracts of Papers of the American Chemical Society, vol. 243 (March, 2012), pp. 1 pages, AMER CHEMICAL SOC .
  3. Lipscomb, ML; Lipscomb, TW; Liao, H; Maness, P; Lynch, MD, Production of fungible diesel via fatty acid synthesis from hydrogen and carbon dioxide feedstocks, Abstracts of Papers of the American Chemical Society, vol. 243 (March, 2012), pp. 1 pages, AMER CHEMICAL SOC .
  4. Lynch, MD; Manness, PC; Lipscomb, M; Warnecke, T; Liao, H, Novel biological conversion of hydrogen and carbon dioxide directly into biodiesel, Abstracts of Papers of the American Chemical Society (December, 2011)  [abs].
  5. Lipscomb, ML; Warnecke, T; Hans, L; Maness, LP; Lynch, MD, Novel biological conversion of hydrogen and carbon dioxide directly into biodiesel, Abstracts of Papers of the American Chemical Society (August, 2011)  [abs].
  6. Mercogliano, CP; Liao, HH; Lynch, MD, Enzyme evolution of an alpha-keto decarboxylase, Abstracts of Papers of the American Chemical Society, vol. 241 (March, 2011), pp. 1 pages, AMER CHEMICAL SOC .
  7. Warnecke, T; Lynch, MD; Gill, RT, Identification of organic acid tolerance genes in E. coli for biorefinery applications, Aiche Annual Meeting, Conference Proceedings (December, 2005), pp. 8984  [abs].
  8. Lynch, MD; Warnecke, T; Singh, A; Gill, RT, Genomics tools for elucidating the function of trait conferring genes, Aiche Annual Meeting, Conference Proceedings (December, 2005), pp. 9189  [abs].
  9. Warnecke, TE; Lynch, MD; Gill, RT, Post-genomics approach to understanding E. Coli network architecture., Abstracts of Papers of the American Chemical Society, vol. 229 (March, 2005), pp. U227-U227, AMER CHEMICAL SOC .
  10. Lynch, MD; Warnecke, T; Gill, RT, Mixed-library parallel gene trait mapping: A quantitative micro-array technique for the genome-wide identification of trait conferring genes., Abstracts of Papers of the American Chemical Society, vol. 229 (March, 2005), pp. U202-U202, AMER CHEMICAL SOC .

Journal Articles

  1. Yang, T; Ye, Z; Lynch, MD, "Multiagent" Screening Improves Directed Enzyme Evolution by Identifying Epistatic Mutations., Acs Synthetic Biology, vol. 11 no. 5 (May, 2022), pp. 1971-1983 [doi]  [abs].
  2. Decker, JS; Menacho-Melgar, R; 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, vol. 181 (April, 2022), pp. 108403 [doi]  [abs].
  3. Moreb, EA; 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, vol. 5 no. 1 (February, 2022), pp. 146-154 [doi]  [abs].
  4. Decker, JS; Menacho-Melgar, R; 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., Biorxiv (January, 2022) [doi]  [abs].
  5. Hennigan, JN; Lynch, MD, The past, present, and future of enzyme-based therapies., Drug Discovery Today, vol. 27 no. 1 (January, 2022), pp. 117-133 [doi]  [abs].
  6. Menacho-Melgar, R; Lynch, MD, Simple Scalable Protein Expression and Extraction Using Two-stage Autoinducible Cell Autolysis and DNA/RNA Autohydrolysis in Escherichia coli., Bio Protocol, vol. 12 no. 2 (January, 2022), pp. e4297 [doi]  [abs].
  7. Menacho-Melgar, R; Lynch, MD, Measuring Oligonucleotide Hydrolysis in Cellular Lysates via Viscosity Measurements., Bio Protocol, vol. 12 no. 2 (January, 2022), pp. e4304 [doi]  [abs].
  8. Menacho-Melgar, R; Hennigan, JN; Lynch, MD, Optimization of phosphate-limited autoinduction broth for two-stage heterologous protein expression in Escherichia coli., Biotechniques, vol. 71 no. 5 (November, 2021), pp. 566-572 [doi]  [abs].
  9. Ye, Z; Li, S; Hennigan, JN; Lebeau, J; Moreb, EA; Wolf, J; Lynch, MD, Two-stage dynamic deregulation of metabolism improves process robustness & scalability in engineered E. coli., Metabolic Engineering, vol. 68 (September, 2021), pp. 106-118 [doi]  [abs].
  10. Moreb, EA; Lynch, MD, Genome dependent Cas9/gRNA search time underlies sequence dependent gRNA activity., Nature Communications, vol. 12 no. 1 (August, 2021), pp. 5034, Springer Science and Business Media LLC [doi]  [abs].
  11. Rios, J; Lebeau, J; Yang, T; Li, S; Lynch, MD, A critical review on the progress and challenges to a more sustainable, cost competitive synthesis of adipic acid, Green Chem., vol. 23 no. 9 (May, 2021), pp. 3172-3190 [doi]  [abs].
  12. Lynch, MD, The bioprocess TEA calculator: An online technoeconomic analysis tool to evaluate the commercial competitiveness of potential bioprocesses., Metabolic Engineering, vol. 65 (May, 2021), pp. 42-51, Elsevier BV [doi]  [abs].
  13. Efromson, JP; Li, S; Lynch, MD, BioSamplr: An open source, low cost automated sampling system for bioreactors., Hardwarex, vol. 9 (April, 2021), pp. e00177 [doi]  [abs].
  14. Li, S; Ye, Z; Moreb, EA; Hennigan, JN; Castellanos, DB; Yang, T; Lynch, MD, Dynamic control over feedback regulatory mechanisms improves NADPH flux and xylitol biosynthesis in engineered E. coli., Metabolic Engineering, vol. 64 (March, 2021), pp. 26-40 [doi]  [abs].
  15. Ye, Z; Moreb, EA; Li, S; Lebeau, J; Menacho-Melgar, R; Munson, M; Lynch, MD, Escherichia coli Cas1/2 Endonuclease Complex Modifies Self-Targeting CRISPR/Cascade Spacers Reducing Silencing Guide Stability., Acs Synthetic Biology, vol. 10 no. 1 (January, 2021), pp. 29-37 [doi]  [abs].
  16. Menacho-Melgar, R; Yang, T; Lynch, M, Instant Taq: Rapid Autoinducible Expression and Chromatography-free Purification of Taq polymerase (2021) [doi]  [abs].
  17. Menacho-Melgar, R; Hennigan, J; Lynch, M, Optimization of Phosphate Limited Autoinduction Broth for 2-Stage Heterologous Protein Expression in E. coli (2021) [doi]  [abs].
  18. Moreb, EA; Lynch, M, A meta-analysis of gRNA library screens enables an improved understanding of the impact of gRNA folding and structural stability on CRISPR-Cas9 activity (2021) [doi]  [abs].
  19. Moreb, EA; Lynch, MD, An Analysis of gRNA Sequence Dependent Cleavage Highlights the Importance of Genomic Context on CRISPR-Cas Activity (2021) [doi]  [abs].
  20. Yang, T; Ye, Z; Lynch, M, “Multi-Agent” Screening Improves the Efficiency of Directed Enzyme Evolution (2021) [doi]  [abs].
  21. Moreb, EA; Hutmacher, M; Lynch, MD, CRISPR-Cas "Non-Target" Sites Inhibit On-Target Cutting Rates., The Crispr Journal, vol. 3 no. 6 (December, 2020), pp. 550-561 [doi]  [abs].
  22. Efromson, J; Li, S; Lynch, M, BioSamplr: An open source, low cost automated sampling system for bioreactors (October, 2020) [doi]  [abs].
  23. Menacho-Melgar, R; Moreb, EA; Efromson, JP; Yang, T; Hennigan, JN; Wang, R; 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 and Bioengineering, vol. 117 no. 9 (September, 2020), pp. 2852-2860 [doi]  [abs].
  24. Menacho-Melgar, R; Ye, Z; Moreb, EA; Yang, T; Efromson, JP; Decker, JS; Wang, R; Lynch, MD, Scalable, two-stage, autoinduction of recombinant protein expression in E. coli utilizing phosphate depletion., Biotechnology and Bioengineering, vol. 117 no. 9 (September, 2020), pp. 2715-2727 [doi]  [abs].
  25. Moreb, EA; Ye, Z; Efromson, JP; Hennigan, JN; Menacho-Melgar, R; Lynch, MD, Media Robustness and Scalability of Phosphate Regulated Promoters Useful for Two-Stage Autoinduction in E. coli., Acs Synthetic Biology, vol. 9 no. 6 (June, 2020), pp. 1483-1486 [doi]  [abs].
  26. Lebeau, J; Efromson, JP; Lynch, MD, A Review of the Biotechnological Production of Methacrylic Acid., Frontiers in Bioengineering and Biotechnology, vol. 8 (January, 2020), pp. 207 [doi]  [abs].
  27. Decker, JS; Menacho-Melgar, R; Lynch, MD, Low-Cost, Large-Scale Production of the Anti-viral Lectin Griffithsin., Frontiers in Bioengineering and Biotechnology, vol. 8 (January, 2020), pp. 1020 [doi]  [abs].
  28. Moreb, E; Ye, Z; Efromson, J; Hennigan, J; Menacho-Melgar, R; Lynch, M, Robustness testing and scalability of phosphate regulated promoters useful for two-stage autoinduction in E. coli (2020) [doi]  [abs].
  29. Li, S; Moreb, E; Ye, Z; Hennigan, J; Castellanos, DB; Yang, T; Lynch, M, Dynamic control over feedback regulatory mechanisms improves NADPH fluxes and xylitol biosynthesis in engineered E. coli (2020) [doi]  [abs].
  30. Ye, Z; Lebeau, J; Moreb, E; Menacho-Melgar, R; Lynch, M, TheE. coliCas1/2 endonuclease complex reduces CRISPR/Cascade guide array stability (2020) [doi]  [abs].
  31. Li, S; Ye, Z; Lebeau, J; Moreb, E; Lynch, M, Dynamic control over feedback regulation identifies pyruvate-ferredoxin oxidoreductase as a central metabolic enzyme in stationary phase E. coli (2020) [doi]  [abs].
  32. Ye, Z; Li, S; Hennigan, J; Lebeau, J; Moreb, E; Wolf, J; Lynch, M, Two-stage Dynamic Deregulation of Metabolism Improves Process Robustness & Scalability in EngineeredE. coli (2020) [doi]  [abs].
  33. Hennigan, J; Wagner, P; Burk, C; Efromson, J; Ye, Z; Lipscomb, M; Lynch, M, A Technoeconomic Evaluation of the Potential of Industrial Biotechnology for the Competitive Production of Commodity and Bulk Chemicals (2020) [doi]  [abs].
  34. Menacho-Melgar, R; Decker, JS; Hennigan, JN; Lynch, MD, A review of lipidation in the development of advanced protein and peptide therapeutics., Journal of Controlled Release : Official Journal of the Controlled Release Society, vol. 295 (February, 2019), pp. 1-12 [doi]  [abs].
  35. Menacho-Melgar, R; Ye, Z; Moreb, E; Yang, T; Efromson, J; Decker, J; Lynch, M, Improved, scalable, two-stage, autoinduction of recombinant protein expression in E. coli utilizing phosphate depletion (2019) [doi]  [abs].
  36. Moreb, EA; Hoover, B; Yaseen, A; Valyasevi, N; Roecker, Z; Menacho-Melgar, R; 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, vol. 6 no. 12 (December, 2017), pp. 2209-2218 [doi]  [abs].
  37. Burg, JM; Cooper, CB; Ye, Z; Reed, BR; Moreb, EA; Lynch, MD, Large-scale bioprocess competitiveness: the potential of dynamic metabolic control in two-stage fermentations, Current Opinion in Chemical Engineering, vol. 14 (November, 2016), pp. 121-136, Elsevier BV [doi]  [abs].
  38. Lynch, MD, Into new territory: improved microbial synthesis through engineering of the essential metabolic network., Current Opinion in Biotechnology, vol. 38 (April, 2016), pp. 106-111 [doi]  [abs].
  39. Garst, A; Lynch, M; Evans, R; Gill, RT, Strategies for the multiplex mapping of genes to traits., Microbial Cell Factories, vol. 12 no. 1 (October, 2013), pp. 99 [doi]  [abs].
  40. Boyle, NR; Reynolds, TS; Evans, R; Lynch, M; Gill, RT, Recombineering to homogeneity: extension of multiplex recombineering to large-scale genome editing., Biotechnology Journal, vol. 8 no. 5 (May, 2013), pp. 515-522 [doi]  [abs].
  41. Warnecke, TE; Lynch, MD; Lipscomb, ML; Gill, RT, Identification of a 21 amino acid peptide conferring 3-hydroxypropionic acid stress-tolerance to Escherichia coli., Biotechnology and Bioengineering, vol. 109 no. 5 (May, 2012), pp. 1347-1352 [doi]  [abs].
  42. Prior, JE; Lynch, MD; Gill, RT, Broad-host-range vectors for protein expression across gram negative hosts., Biotechnology and Bioengineering, vol. 106 no. 2 (June, 2010), pp. 326-332 [doi]  [abs].
  43. Warnecke, TE; Lynch, MD; Karimpour-Fard, A; Lipscomb, ML; Handke, P; Mills, T; Ramey, CJ; Hoang, T; Gill, RT, Rapid dissection of a complex phenotype through genomic-scale mapping of fitness altering genes., Metabolic Engineering, vol. 12 no. 3 (May, 2010), pp. 241-250 [doi]  [abs].
  44. Singh, A; Lynch, MD; Gill, RT, Genes restoring redox balance in fermentation-deficient E. coli NZN111., Metabolic Engineering, vol. 11 no. 6 (November, 2009), pp. 347-354 [doi]  [abs].
  45. Gall, S; Lynch, MD; Sandoval, NR; Gill, RT, Parallel mapping of genotypes to phenotypes contributing to overall biological fitness., Metabolic Engineering, vol. 10 no. 6 (November, 2008), pp. 382-393 [doi]  [abs].
  46. Warnecke, TE; Lynch, MD; Karimpour-Fard, A; Sandoval, N; Gill, RT, A genomics approach to improve the analysis and design of strain selections., Metabolic Engineering, vol. 10 no. 3-4 (May, 2008), pp. 154-165 [doi]  [abs].
  47. Bonomo, J; Lynch, MD; Warnecke, T; Price, JV; Gill, RT, Genome-scale analysis of anti-metabolite directed strain engineering., Metabolic Engineering, vol. 10 no. 2 (March, 2008), pp. 109-120 [doi]  [abs].
  48. Lynch, MD; Warnecke, T; Gill, RT, SCALEs: multiscale analysis of library enrichment., Nature Methods, vol. 4 no. 1 (January, 2007), pp. 87-93 [doi]  [abs].
  49. Lynch, MD; Gill, RT, Broad host range vectors for stable genomic library construction., Biotechnology and Bioengineering, vol. 94 no. 1 (May, 2006), pp. 151-158 [doi]  [abs].
  50. Lynch, MD; Gill, RT; Stephanopoulos, G, Mapping phenotypic landscapes using DNA micro-arrays., Metabolic Engineering, vol. 6 no. 3 (July, 2004), pp. 177-185 [doi]  [abs].

Chapter in Book

  1. Lipscomb, TW; Lipscomb, ML; Gill, RT; Lynch, MD, Metabolic Engineering of Recombinant E. coli for the Production of 3-Hydroxypropionate, in Engineering Complex Phenotypes in Industrial Strains (October, 2012), pp. 185-120, JOHN WILEY & SONS INC [doi] .
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