J. Andrew Jones, Ph.D.

Portrait of Assistant Professor Andrew Jones

Assistant Professor

66 D Engineering Building

Research Interests

  • Metabolic Engineering
  • Pathway Optimization
  • Synthetic Biology


  • Ph.D., Chemical and Biological Engineering
    Rensselaer Polytechnic Institute
  • M.S., Environmental Engineering
    Mercer University
  • B.S., Engineering
    Mercer University

Education and Work Experience

  • Hamilton College: Clinton, NY (2016 – 2017)
    • Visiting Assistant Professor of Chemistry
    • Teaching Experience – Principles of Chemistry, Biophysical Chemistry, Principles of Chemistry Lab, Biological Chemistry Lab
  • Rensselaer Polytechnic Institute (RPI): Troy, NY (2012 – 2016)
    • Postdoctoral Researcher – Koffas Lab (May 2016 – Aug. 2016)
    • Ph.D. in Chemical and Biological Engineering
  • Mercer University: Macon, GA (2007 – 2012)
    • Master of Science in Environmental Engineering
      • Thesis: Equilibrium and Kinetic Analysis of Fluoride Adsorption on Bone Charcoal
    • Bachelor of Science in Engineering
      • Concentration: Biomedical Engineering →→ Minors – Chemistry, Biology
      • Senior Design: Design and Thermodynamic Modeling of a Passive Solar Desalination Unit

Awards, Honors, and Activities

  • Prior to Employment at Miami University
    • Metabolic Engineering XI (Awaji Island, Japan) – Poster Award (2016)
    • ACS BIOT – Best of BIOT Designation for Oral Presentation (2016)
    • ACS BIOT – Travel Grant (2016)
    • Phillip A. Groll Class of 1921 Undergraduate Mentorship Award (2015)
    • RPI Travel Grant (Fall 2015, Spring 2016)
    • Research Highlighted on National Public Radio (NPR) – All Things Considered (Dec. 2014) Link
    • President - Graduate Student Association (2013-2014)
    • NSF GRFP - Honorable Mention (2013)
    • Howard P. Isermann Fellowship (2012-2013)
    • Wallace Duvall Excellence in Leadership, Undergraduate Commencement Award (2012)
    • Eagle Scout, in the Boy Scouts of America (2005)


  • Jones J. A. and Koffas M. A. G. MICROBIAL POLYCULTURES AND METHODS OF USE THEREOF. Application Filed – Nov. 2nd 2016. Serial Number: 15/341,911.


Key: †Undergraduate Student *Equal Contribution
Google Scholar Profile


  • †Adams A. M., †Kaplan N. A., †Wei Z., Brinton J. D., †Monnier C. S., †Enacopol A. L., Ramelot T. A., *Jones J. A. (2019) In Vivo Production of Psilocybin in E. coli. Metabolic Engineering. 56, 111-119.


  • Jones J. A., Wang, X.(2018) Use of Bacterial Co-Cultures for the Efficient Production ofChemicals. Current Opinion in Biotechnology. 53, 33-38.

Work Completed Prior to Miami University


  • Jones J. A., †Vernacchio V. R., †Collins S. M., Shirke A. N., Xiu Y.,  Englaender J. A., Cress B. F., †McCutcheon C., Linhardt R. J., Gross R.,  Koffas M. A. G. (2017) Complete biosynthesis of anthocyanins using E. coli  polycultures. mBio. 8 (3), e00621-17.
  • *Xiu Y., *Jang S., Jones J. A., Zill N. A., Linhardt R. J., Jung G. Y.,  Yuan Q., Koffas M. A. G. (2017) Naringenin-responsive riboswitch-based  fluorescent biosensor module for Escherichia coli co-cultures.  Biotechnology and Bioengineering. 114(10), 2235-2244.
  • Englaender J. A., Jones J. A., Cress B. F., Kuhlman, T. E., Linhardt R. J., Koffas M. A. G. (2017) Effect of genomic integration location on heterogous protein expression and metabolic engineering. ACS Synthetic Biology. 6 (4), 710-720.
  • Fang Z., Jones J. A.,Zhou, J., Koffas M. A. G. (2017) Engineering Escherichia coli co-cultures for production of curcuminoids from glucose. Biotechnology Journal. 13 (5), 1700576."


  • *He L., *Yu X., *Jones J. A., Baidoo E. E. K., Keasling J. D., Tang Y. J.,  Koffas M. A. G. (2016) Deciphering flux adjustments of engineered E. coli  cells during fermentation with changing growth conditions. Metabolic  Engineering. 39, 247-256.
  • *Whitaker W. B., *Jones J. A., *Bennett R. K., Gonzalez J., †Vernacchio V. R., †Collins S. M., Palmer M. A., Schmidt S., Antoniewicz M. R., Koffas M. A. G., Papoutsakis E. T. (2016) Engineering the biological conversion of methanol to specialty chemicals in Escherichia coli. Metabolic Engineering. 39, 49-59.
  • *Shirke A. N., *Su A., Jones J. A., Butterfoss G. L., Koffas M. A. G., Kim J. R., Gross R. (2016) Comparative thermal inactivation analysis of Aspergillus oryzae and Thiellavia terrestris cutinase: role of glycosylation. Biotechnology and Bioengineering. 114 (1), 63-73.
  • Cress B. F., Jones J. A., †Kim D., †Leitz Q., Englaender J. A., †Collins S. M., Linhardt R. J., Koffas M. A. G. (2016) Rapid generation of CRISPR/dCas9-regulated, orthogonally repressible hybrid T7-lac promoters for modular, tuneable control of metabolic pathway fluxes in E. coli. Nucleic Acids Research, 44 (9), 4472-4485.
  • Jones J. A. and Koffas M. A. G. (2016) Optimizing Metabolic Pathways for the Improved Production of Natural Products. Methods in Enzymology, 575, 179-193.
  • Wu G., Yan Q., Jones J. A., Tang Y. J., Fong S. S., Koffas M. A. G. (2016) Metabolic burden and its effect in synthetic biology and metabolic engineering applications. Trends in Biotechnology, 34 (8), 652-664.
  • Jones J. A., †Vernacchio V. R., Sinkoe A. L., †Collins S. M., Ibrahim M. H. A., †Lachance D. M., Hahn J., Koffas M. A. G. (2016) Experimental and computational optimization of an E. coli co-culture for the efficient production of flavonoids. Metabolic Engineering, 35, 55-63.
  • Hess V., Gallegos R., Jones J. A., Barquera B., Malamy M. H., Müller V. (2016) Occurrence of ferredoxin:NAD+ oxidoreductase activity and its ion specificity in several Gram-positive and Gram-negative bacteria. PeerJ, 4, (e1515).


  • Jones J. A., †Collins S. M., †Lachance D. M., †Vernacchio, V. R., Koffas M. A. G. (2015) Optimization of naringenin and p-coumaric acid hydroxylation using the native E. coli hydroxylase complex, HpaBC. Biotechnology Progress. 32 (1), 21-25.
  • Jones J. A., †Vernacchio V. R., †Lachance D. M., †Lebovich M., Fu L., Shirke A. N., Schultz V., Cress B., Linhardt R. J., & Koffas M. A. G. (2015) ePathOptimize: A combinatorial approach for transcriptional balancing of metabolic pathways. Scientific Reports, 5 (11301), 1- 10.
  • Cress B. F., Toparlak Ö. D., Guleria S., †Lebovich M., †Stieglitz J. T., Englaender J. A., Jones J. A., Linhardt R. J., and Koffas M. A. G. (2015) CRISPathBrick: Modular Combinatorial Assembly of Type II-A CRISPR Arrays for dCas9-Mediated Multiplex Transcriptional Repression in E. coli. ACS Synthetic Biology, 4 (9), 987-1000.
  • *Zhao S., *Jones J. A., †Lachance D. M., Bhan N., †Khalidi O., Venkataraman S., Wang Z., & Koffas M. A. G. (2015). Improvement of catechin production in Escherichia coli through combinatorial metabolic engineering. Metabolic Engineering, 28, 43-53.
  • Jones J. A., Toparlak Ö. D., & Koffas M. A. G. (2015). Metabolic pathway balancing and its role in the production of biofuels and chemicals. Current Opinion in Biotechnology, 33, 52-59.
  • He W., Fu L., Li G., Jones J. A., Linhardt R. J., & Koffas M. A. G. (2015). Production of chondroitin in metabolically engineered E. coli. Metabolic Engineering, 27, 92-100.


  • Jones J. A., Lackey L. W., & Lindsay K. E. (2014). Effects of wind and choice of cover material on the yield of a passive solar still. Desalination and Water Treatment, 52 (1-3), 48-56.


  • Sept. 2019 – SEEC Living Learning COmmunity. Oral Presentation. Oxford, Ohio
  • Apr. 2019 – Green Ball – Miami Chemical Society. Oral Presentation. Oxford, OH
  • Apr. 2019 – ACS National Meeting. Oral Presentation. Orlando, FL. (BIOT Division)
  • Dec. 2018 – Residence Hall Program: UG Research. Oral Presentation. Oxford, OH
  • May 2018 – Miami University – Department of Microbiology. Invited Lecture. Oxford, OH
  • Nov. 2017 – University of Toledo. Invited Lecture. Toledo, OH
  • Apr. 2017 – ACS National Meeting. Oral Presentation. San Francisco, CA (BIOT Division)
  • Apr. 2017 – ACS National Meeting. Oral Presentation. San Francisco, CA  (CHED Division)
  • Mar. 2017 – San Jose State University. Invited Lecture. San Jose, CA
  • Mar. 2017 – Miami University. Invited Lecture. Oxford, OH
  • Nov. 2016 – AIChE Annual Meeting. Oral Presentation. San Francisco, CA
  • July 2016 – Hamilton College. Invited Lecture. Clinton, NY
  • July 2016 – Rowan University. Invited Lecture. Glassboro, NJ
  • June 2016 – Metabolic Engineering 11. Poster Presentation. Awaji Island, Japan (Poster Award)
  • Apr. 2016 – Guest Lecture: Microbiology - “Engineering Transcription in E. coli”, RPI. Troy, NY
  • Mar. 2016 – ACS National Meeting. Oral Presentation. San Diego, CA (Best of BIOT Designation)
  • Mar. 2016 – ACS National Meeting. Oral Presentation. San Diego, CA (CHED Division)
  • Mar. 2016 – ACS National Meeting. Poster Presentation. San Diego, CA (BIOT Division, Sci-Mix)
  • Jan. 2016 – DOE: ARPA-E Grantee Meeting. Poster Presentation. San Diego, CA
  • Nov. 2015 – AIChE Annual Meeting. Oral Presentation. Salt Lake City, UT
  • Nov. 2015 – AIChE Annual Meeting. Poster Presentation. Salt Lake City, UT
  • Nov. 2015 – Union College. Invited Lecture. Schenectady, NY
  • June 2015 – Syn. Bio. Engineering, Evolution, & Design (SEED). Poster Presentation. Boston, MA
  • April 2015 – Northeast Bioengineering Conference (NEBEC). Poster Presentation. Troy, NY
  • Nov. 2014 – Mercer University. Invited Lecture. Macon, GA
  • Nov. 2014 – AIChE Annual Meeting. Oral Presentation. Atlanta, GA
  • Nov. 2014 – AIChE Annual Meeting. Poster Presentation. Atlanta, GA
  • May 2012 – Mercer Engineering Expo. Award for Best Podium Presentation. Macon, GA