J. Andrew Jones, Ph.D.

Dr. Andrew Jones

Assistant Professor

66 D Engineering Building

Research Interests

  • Metabolic Engineering
  • Pathway Optimization
  • Synthetic Biology
  • Psychedelic Medicine


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

Research Bio

Dr. J. Andrew Jones received his B.S. in general engineering with specialization in Biomedical Engineering and his M.S. in Environmental Engineering from Mercer University (Macon, GA) in 2012. While at Mercer, Dr. Jones was a NCAA Division I cross country student-athlete and served as chief justice of the university academic honor council. Dr. Jones received his Ph.D. in Chemical and Biological Engineering from Rensselaer Polytechnic Institute (RPI) in the Spring of 2016. Prior to joining Miami, Dr. Jones spent 1 year as a Visiting Assistant Professor of Chemistry at Hamilton College in Clinton, NY.

Dr. Jones joined Miami in the Fall of 2017. His research focuses on genetic engineering of microorganism for sustainable chemical production. Using traditional and high-throughput molecular biology and biochemistry techniques, Dr. Jones takes a fine-tuned approach towards rewiring the metabolism of bacteria and yeast for more efficient chemical production. He is especially interested in the production of high-value, bioactive, natural products with medicinal applications.

Dr. Jones’ research has been highlighted on National Public Radio and in the print publication Chemical & Engineering News. Additionally, his work has been selected for multiple awards including: RPI Travel Grant (2015, 2016), ACS BIOT Travel Grant (2016), ACS ‘Best of BIOT’ designation (2016), Metabolic Engineering XI Poster Award (2016). Dr. Jones has published 20 peer-reviewed publications in top journals and has been cited over 400 times since 2014.

Dr. Jones is a member of the American Chemical Society (ACS) and the American Institute of Chemical Engineers (AIChE).

Education and Work Experience

  • PsyBio Therapeutics (2020–Present)
    • Inventor and Chairman of the Scientific Advisory Board
  • Miami University: Oxford, OH (2017–Present)
    • Assistant Professor—Chemical, Paper, and Biomedical Engineering
      Teaching Experience:
      • CPB 102–Introduction to Chemical and Bioengineering
      • CPB 244—Introduction to Environmental Engineering
      • CPB 418—Biological Transport Phenomena
      • CPB 405—Industrial Environmental Control
      • CPB 436—Principles in Fermentation
      • CPB 442—Air Pollution Control
      • CPB 451—Unit Operations Laboratory II
      • CPB 471/472—Senior Design Projects
      • CPB 600—Graduate Seminar
  • 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
      • Thesis: Pathway Optimization and Balancing for the Improved Microbial Production of High-Value Chemicals.
      • Advisor: Dr. Mattheos Koffas
  • 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

  • At Miami University:
    • American Institute of Chemical Engineers—35 under 35 Award—Bioengineering (2020)
  • 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)
    • Research Highlighted on National Public Radio (NPR) – All Things Considered (Dec. 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
Andrew Jones Google Scholar Profile


  • Hreha T. N., Foreman S., Duran-Pinedo A., Morris A. R., Diaz-Rodrigues P., Jones J. A., Ferrara K., Bourges A., Rodriguez L., Koffas M. A. G., Hann M., Houser A., Barquera B. (2020) The three NADH dehydrogenases of Pseudomonas aeruginosa: their roles in energy metabolism and links to virulence. PLOS ONE. Accepted.


  • †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.
    Research Highlighted on:

    Research Highlighted on


    • 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.


  • Feb. 2021—Vnat 2021. Invited Presentation. Online/Virtual.
  • Jan. 2021—Global Connectome - Society for Neuroscience. Online/Virtual.
  • Nov. 2020—AIChE Annual Meeting. Online/Virtual.
  • Nov. 2020—Miami University Department of Chemistry. Invited Lecture. Online/Virtual.
  • Apr. 2020—Miami University MBI 450/550. Guest Lecture. Online/Virtual.
  • Mar. 2020—Mercer University. Invited Lecture. Macon, GA.
  • Mar 2020—Shorter University. Invited Lecture. Rome, GA.
  • Dec. 2019—Miami University Board of Trustees. Invited Lecture. Oxford, OH.
  • Nov. 2019—AIChE Annual Meeting. Oral Presentation. Orlando, FL.
  • 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. col" 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