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Andrew Jones
Associate Professor (Affiliate)
Microbiology, Chemical, Paper, and Biomedical Engineering, Cell, Molecular and Structural Biology Graduate Program

J. Andrew Jones, Ph.D.

Contact Info

513-529-0756
Engineering Building 64 P

Education

  • Ph.D. Chemical and Biological Engineering, Rensselaer Polytechnic Institute (2016)
  • M.S. Environmental Engineering, Mercer University (2012)
  • B.S. Engineering, Concentration: Biomedical, Mercer University (2012)

Research Interests

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

Research Bio

Andrew Jones is an Associate Professor in the Department of Chemical, Paper, and Biomedical Engineering at 黑料社区. Prior to joining Miami, Dr. Jones spent 1 year as a Visiting Assistant Professor of Chemistry at Hamilton College (Clinton, NY). Dr. Jones completed his Ph.D. in Chemical and Biological Engineering at Rensselaer Polytechnic Institute (Troy, NY) and his M.S. in Environmental Engineering and B.S. in general engineering, with specialization in Biomedical Engineering, at Mercer University (Macon, GA).

Dr. Jones joined Miami in the Fall of 2017. His research focuses on genetically engineering microorganisms for high-value chemical production. Using traditional and high-throughput molecular biology and biochemistry techniques, Dr. Jones takes a fine-tuned approach towards rewiring cellular metabolism of bacteria for more efficient chemical production.

Dr. Jones' research has been highlighted on National Public Radio [, , , ], Chemical & Engineering News [, ], Vice News [], High Times [], and Scientific American []. Additionally, he has been selected for multiple awards including: AIChE's 35Under35 – Bioengineering (), 黑料社区's Junior Faculty Scholar Award (), and Miami's Associated Student Government – Outstanding Professor Award Nominee (2021, 2022) and the Ohio Faculty Council’s Technology Commercialization Award (2022).

Jones’ research program has attracted over $2 Million dollars in external research funding and has led to the direct training of over 40 黑料社区s and professional staff. As of 2023, Dr. Jones has published 30 peer-reviewed publications in top journals, submitted 13 families of patent applications and has been cited over 2400 times. Dr. Jones is a member of the American Chemical Society, the American Institute of Chemical Engineers, and the National Academy of Inventors. More information on Jones Lab research can be found at .

Education and Work Experience

 (2020–Present)

  • Inventor and Chairman of the Scientific Advisory Board

黑料社区: Oxford, OH (2017–Present)

  • Associate Professor – Chemical, Paper, and Biomedical Engineering (2023 – Present)
  • Assistant Professor – Chemical, Paper, and Biomedical Engineering (2017 – 2023)
    Teaching Experience:
    • CPB 102 – Introduction to Chemical and Biomedical Engineering
    • CPB 244 – Introduction to Environmental Engineering
    • CPB 418 – Biological Transport Phenomena
    • CPB 405 – Industrial Environmental Control
    • CPB 436 – Principles in Fermentation
    • CPB 441 – Pollution Prevention in Environmental Management
    • 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)

  • 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

Awards, Honors, and Activities

At 黑料社区:

  • 黑料社区 – CEC Outstanding Faculty Research Award (2023)
  • Inducted to the National Academy of Inventors – Senior Member (2023)
  • Ohio Faculty Council – Technology Commercialization Award (2022)
  • 黑料社区 – Creativity & Innovation Award (2022)
  • 黑料社区 – Student Government’s Outstanding Professor Award Nominee (2021, 2022)
  • 黑料社区 – Junior Faculty Scholar (2021)
  • American Institute of Chemical Engineers—35 under 35 Award—Bioengineering (2020)
Prior to Employment at 黑料社区:
  • 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)
  • 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)

Patents

  1. Keller M. R. and Jones J. A. ALTERNATIVE ENZYME SOURCES. US Provisional Application Number: 63/424,567
  2. Carpenter T. A., Sen A. K., and Jones J. A. IN VIVO PRODUCTION OF 5-METHOXY-N,N-DIMETHYLTRYPTAMINE IN ESCHERICHIA COLI. US Provisional Application Number: 63/424,563
  3. Abrahms Z. N. and Jones J. A. OPTIMIZING THE DE NOVO PRODUCTION OF PSILOCYBIN IN E. COLI. US Provisional Application Number: 63/424,527
  4. O’Dell P. J. and Jones J. A. OPTIMIZED METHODS FOR THE PRODUCTION OF PSILOCYBIN AND INTERMEDIATES OR SIDE PRODUCTS. Application Number: PCT/US2022/071797. Claims priority to U.S. Provisional Applications: 63
  5. Gibbons W. J. and Jones J. A. SYSTEMS AND METHODS FOR PHARMACEUTICAL PRODUCTION OF PSILOCYBIN AND INTERMEDIATES AND SIDE PRODUCTS. PCT Application Number: PCT/US2022/070132. Claims priority to U.S. Provisional Application: 63/135,864.
  6. McMurray M. S. and Jones J. A. PSILOCYBIN AND NORBAEOCYSTIN COMPOSITIONS AND METHODS OF TREATMENT. PCT Application Number: PCT/US2022/070094. Claims priority to U.S. Provisional Applications: 63/219,430; 63/146.044; and 63/135,054.
  7. McKinney M. G. and Jones J. A. METHODS FOR THE IMPROVED PRODUCTION OF PSILOCYBIN AND INTERMEDIATES OR SIDE PRODUCTS THROUGH ENZYME OPTIMIZATION. US Provisional Application Number: 63/263,607
  8. Kaplan N. A. and Jones J. A. METABOLIC ENGINEERING METHODS FOR THE PRODUCTION OF PSILOCYBIN AND INTERMEDIATES OR SIDE PRODUCTS. PCT Application Number: PCT/US2022/079314. Claims priority to U.S. Provisional Application: 63/263,614
  9. Gibbons W. J., Flower J. E., Adams A. M., and Jones J. A. METHODS FOR THE PRODUCTION OF TRYPTOPHANS, TRYPTAMINES, INTERMEDIATES, SIDE PRODUCTS, AND DERIVATIVES. PCT Application Number: PCT/US2022/079321. Claims priority to U.S. Provisional Applications: 63/263,616 and 63/263,623
  10. Kanis F. C. and Jones J. A. ALTERNATIVE BIOSYNTHESIS PATHWAYS FOR THE PRODUCTION OF PSILOCYBIN AND INTERMEDIATES OR SIDE PRODUCTS. PCT Application Number: PCT/US2022/079329. Claims priority to U.S. Provisional Application: 63/263,618
  11. Friedberg L. and Jones J. A. METHODS FOR THE PRODUCTION OF METHYLATED TRYPTAMINE DERIVATIVES, INTERMEDIATES, OR SIDE PRODUCTS. PCT Application Number: PCT/US2022/074579. Claims priority to U.S. Provisional Application: 63/203,970
  12. Adams A. M., Kaplan N. A., and Jones J. A. METHODS FOR THE PRODUCTION OF PSILOCYBIN AND INTERMEDIATES OR SIDE PRODUCTS. PCT Application Number: PCT/US2020/051543. Claims priority to U.S. Provisional Applications: 62/990,633 and 62/926,875
  13. Jones J. A. and Koffas M. A. G. MICROBIAL POLYCULTURES AND METHODS OF USE THEREOF. U.S. Patent No. 10,954,543 B2, Granted: March 25th 2021

Publications

Key: †Undergraduate Student *Equal Contribution

  1. †,*Flower J. E., *Gibbons W. J., †Adams A. M., Wang X., Broude C. N., Jones J. A. (2023) Biosynthesis of psilocybin and its non-natural derivatives by a promiscuous psilocybin synthesis pathway in E. coli. Biotechnology and Bioengineering. Accepted.
  2. †Friedberg L. M., †Sen A. K, Nguyen Q., †Tonucci G., Hellwarth E. B., Gibbons W. J., Jones J. A. (2023) Biosynthesis of N,N-dimethyltryptamine, 5-MeO-N,N-dimethyltryptamine, and Bufotenine in E. coli. Metabolic Engineering. 78, 61-71.
  3. Roberts B. F., Zylko A. L., Waters C. E., Crowder J. D., Gibbons W. J., †Sen A. K., Jones J. A., McMurray M. S. (2022) Effect of Psilocybin on Decision-Making and Motivation in the Healthy Rat. Behavioural Brain Research, 440, 114262.
  4. Jones J. A., Spigarelli M. G. (2022) Industry Highlight: Harnessing Synthetic Biology to Enable Development of Novel Psychedelic Therapies. Trends in Biotechnology.
  5. †Adams A. M., †Anas N. A., †Sen A. K., †Hinegardner-Hendricks J. D., †O’Dell P. J., Gibbons W. J., †Flower J. E., McMurray M., Jones J. A. (2022) Development of an E. coli-based Norbaeocystin Production Platform and Evaluation of Behavioral Effects in Rats. Metabolic Engineering Communications, 14, e00196.
  6. †Shinde S., †Singapuri S., Jiang Z., Long B., Wilcox D., Klatt C., Jones J. A., Yuan J. S., Wang X. (2022) Thermodynamics contributes to high terpene productivity in cyanobacteria. Metabolic Engineering Communications, 14, e00193.
  7. *Xu Y., *Geng L., *Zhang Y., Jones J. A., Zhang M., Chen Y., Tan R., Koffas M. A. G., Wang Z., Zhao S. (2022) De novo biosynthesis of salvianolic acid B in Saccharomyces cerevisiae engineered with rosmarinic acid biosynthesis pathway. Journal of Agricultural and Food Chemistry. 70(7), 2290-2302
  8. *Gibbons W., *†O’Dell P., *†Bollinger B., *†McKinney M., Jones J. A. (2021) Homebrewed Psilocybin: Can New Routes for Pharmaceutical Psilocybin Production Enable Recreational Use?. Bioengineered. 12(1), 8863-8871.
  9. 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. 16(2), e0244142
  10. †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.
  11. Jones J. A., Wang X. (2018) Use of Bacterial Co-Cultures for the Efficient Production of Chemicals. Current Opinion in Biotechnology. 53, 33-38.
  12. 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
  13. 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.
  14. *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
  15. 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 heterologous protein expression and metabolic engineering. ACS Synthetic Biology. 6 (4), 710-720.
  16. *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.
  17. *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.
  18. *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.
  19. 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.
  20. 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.
  21. 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.
  22. 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 coli co-culture for the efficient production of flavonoids. Metabolic Engineering. 35, 55-63.
  23. 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).
  24. 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.
  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.
  26. Cress B. F., 黑料社区arlak Ö. D., Guleria S., †Lebovich M., †Stieglitz J. T., Englaender J. A., Jones J. A., Linhardt R. J., 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.
  27. *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.
  28. Jones J. A., 黑料社区arlak 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.
  29. He W., Fu L., Li G., Jones J. A., Linhardt R. J., Koffas M. A. G. (2015). Production of chondroitin in metabolically engineered coli. Metabolic Engineering. 27, 92-100.
  30. 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.

Research Highlighted on:

Select Invited Lectures

  1. Mushroom Revival Podcast w/ Alex Dorr. . (Oct. 2022)
  2. Jones J. A. Engineering ‘magic’ Microbes for the Production of Therapeutic Psychedelics. Synthetic Biology Young Speakers Series. . (Jun. 2022)
  3. Jones J. A. Engineering ‘magic’ Microbes for the Production of Therapeutic Psychedelics. Washington University in St. Louis. St. Louis, MO. (Jun. 2022)
  4. Jones J. A. Engineering the Biosynthesis of Psychedelics: A New Class of Therapeutics. Sher-e-Kashmir University of Agricultural Sciences and Technology, Jammu, India. Online. (Jan. 2022)
  5. Psychedelic Diaries Podcast w/ Ray Christian. . (Dec. 2021)
  6. Significant Figures Podcast w/ Viva Horowitz. . (Sept. 2021)
  7. Jones J. A. Engineering the Biosynthesis of Psychedelic Medicines. University of Cincinnati – Department of Chemical and Environmental Engineering. Cincinnati, OH (Aug. 2021)
  8. Jones J. A. University – Industry Collaboration Case Study. 黑料社区 – Miami’s Focus on the Future Seminar. (Aug. 2021)
  9. Jones J. A. From Mercer Engineering, to Engineering Psychedelic Medicines: My Story. Mercer University. Macon, GA (Mar. 2020)
  10. Jones J. A. Metabolic Engineering: The Future of Pharmaceutical Production. Lewis to Luther Colloquium Speaker - Shorter University. Rome, GA (Mar. 2020)
  11. Jones J. A. High Value Chemical Production using a Modular E. coli Polyculture Approach. University of Toledo. Toledo, OH (Nov. 2017)