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Alumni JAMES M. CLOMBURG PABLO FUENTEALBA G JING CHEN SEUNG HWAN (ALLEN) LEE BENARD NYAWANGA FAYIN ZHU

YANG HU Yang is a graduate student in the Department of Medical Engineering at University of South Florida. She obtained her bachelor’s degree at Sichuan Agricultural University, China, and received her Master’s degree at Northwest Agriculture & Forest University, China. Her previous research focused on the identify and modification of key enzymes in the synthesis of plant natural products. Education 2020 -- M.S. in Tree Genetics &Breeding from Northwest Agriculture & Forest University 2017 -- B.S. in Horticulture in Biotechnology from Sichuan Agricultural University CONTACT INFORMATION Yang Hu PhD Student Department of Chemical, Biological, and Materials Engineering University of South Florida ENB 376 | 4202 E Fowler Ave | Tampa, FL 33620 yanghu1@usf.edu

Patents and Patent Applications Full Publication and Citation Details RESEARCH PUBLICATIONS 2025 Zhang, X.; Li, A.; Huang, X.; Guo, S.; Zhang, C.; Gonzalez, R.*; Fei, Q*. Metabolic Engineering of Methanotrophic Bacteria for De Novo Production of Taxadiene from Methane . ACS Synth. Biol. 2025. https://doi.org/10.1021/acssynbio.5c00109 . Liu, H.; Chen, Y.; Li, J.; Zhu, C.; Peng, J.; Gonzalez, R.; Bai, Y.; Tan, Z. Scavenging Intracellular Reactive Oxygen Species to Boost Methanol Assimilation . Chemical Engineering Journal 2025, 516, 164002. https://doi.org/10.1016/j.cej.2025.164002 . Zhu, C.; Chen, Y.; Sun, W.; Li, J.; Liu, H.; Peng, J.; Bai, Y.; Gonzalez, R.; Tan, Z. Repair of DNA and Protein Damages Caused by Formaldehyde Improves Methanol Assimilation . Fundamental Research 2025. https://doi.org/10.1016/j.fmre.2025.05.007 Lee, S. H.; Cirino, P. C.; Gonzalez, R*. Metabolic Engineering of Escherichia Coli for the Utilization of Methylsuccinate, the Product of Methane Activation via Fumarate Addition . Bioresource Technology 2025, 416, 131700. https://doi.org/10.1016/j.biortech.2024.131700 2024 Crumbley, A. M.; Garg, S.; Pan, J. L.; Gonzalez, R. A Synthetic Co-Culture for Bioproduction of Ammonia from Methane and Air . J. Ind. Microbiol. Biotechnol. 2024, 51, kuae044. https://doi.org/10.1093/jimb/kuae044 Gao, Z., Guo, S., Chen, Y., Chen, H., Fu, R., Song, Q., Li, S., Lou, W., Fan, D., Li, Y., Yang, S., Gonzalez, R., & Fei, Q. (2024). A novel nutritional induction strategy flexibly switching the biosynthesis of food-like products from methane by a methanotrophic bacterium . Green Chemistry. Royal Society of Chemistry (RSC). https://doi.org/10.1039/d3gc04674e Kim, Y., Lee, S.H., Gade, P. et al. Revealing reaction intermediates in one-carbon elongation by thiamine diphosphate/CoA-dependent enzyme family . Commun Chem 7, 160 (2024). https://doi.org/10.1038/s42004-024-01242-y Lee, S.H., Hu, Y., Chou, A., Chen, J., Gonzalez, R., Metabolic flux optimization of iterative pathways through orthogonal gene expression control: Application to the β- oxidation reversal , Metabolic Engineering (2024), doi: https://doi.org/10.1016/j.ymben.2024.02.007. Li, J., Mu, X., Dong, W. et al. A non-carboxylative route for the efficient synthesis of central metabolite malonyl-CoA and its derived products . Nat Catal 7, 361–374 (2024). https://doi.org/10.1038/s41929-023-01103-2 2023 Lee, S.H., Chou, A., Nattermann, M., Zhu, F., Clomburg, J.M., Paczia, N., Erb, T.J., Gonzalez, R. (2023). Identification of 2-hydroxyacyl-CoA synthases with high acyloin condensation activity for orthogonal one-carbon bioconversion . ACS Catalysis. Chen, J., and Gonzalez, R. (2023). Engineering Escherichia coli for selective 1-decanol production using the reverse β-oxidation (rBOX) pathway . Metab. Eng. 79: 173-181. Nattermann, M., Wenk, S., Pfister, P., He, H., Lee, S. H., Szymanski, W., Guntermann, N., Zhu, F., Nickel, L., Wallner, C., Zarzycki, J., Paczia, N., Gaißert, N., Franciò, G., Leitner, W., Gonzalez, R., and Erb, T.J. (2023). Engineering a new-to-nature cascade for phosphate-dependent formate to formaldehyde conversion in vitro and in vivo . Nat Commun 14, 2682 (2023). . Tan, Z., Li, J. and Gonzalez, R. (2023). Designing artificial pathways for improving chemical production . Biotechnology Advances 59, 108119. 2022 Clomburg, J., Cintolesi, A. & Gonzalez, R. (2022) In silico and in vivo analyses reveal key metabolic pathways enabling the fermentative utilization of glycerol in Escherichia coli. Micro Biotech. 15(1), 289-304. Hu, L., Guo, S., Wang, B., Fu, R., Fan, D., Jiang, M., Fei, Q. & Gonzalez, R. (2022) Bio-valorization of C1 gaseous substrates into bioalcohols: Potentials and challenges in reducing carbon emissions. Biotechnology Advances. https://doi.org/10.1016/j.biotechadv.2022.107954 Tarasava, K., Lee, S.H., Chen, J., Köpke, M., Jewett, M.C., & Gonzalez, R. (2020) Reverse β-oxidation pathways for efficient chemical production, Journal of Industrial Microbiology and Biotechnology. Journal of Industrial Microbiology and Biotechnology. https://doi.org/10.1093/jimb/kuac003 Vögeli, B., Schulz, L., Garg, S., Tarasava, K., Clomburg, J., Hwan Lee, S., Gonnot, A., Moully, E.H., Kimmel, B.R., Tran, L., Zeleznik, H., Brown, S.D., Simpson, S.D., Mrksich, M., Karim A.S., Gonzalez, R., Köpke, M. & Jewett, M.C. (2022) Cell-free prototyping enables implementation of optimized reverse β-oxidation pathways in heterotrophic and autotrophic bacteria. Nat Commun. 13, 3058. Wang, Y., Nguyen, N., Lee, S., Wang, Q., May, J.A., Gonzalez, R. & Cirino, P.C. (2022) Engineering Escherichia coli for anaerobic alkane activation: Biosynthesis of (1-methylalkyl)succinates. Biotechnol Bioeng. Biotechnol Bioeng. 119(1), 315-320. 2021 Chou, A., Lee, S.H., Zhu, F., Clomburg, J. & Gonzalez, R. (2021) An orthogonal metabolic framework for one-carbon utilization . Nat Metab 3, 1385–1399. Nattermann, M., Burgener, S., Pfister, P., Chou, A., Schulz, L., Lee, S. H., Paczia, N., Zarzycki, J., Gonzalez, R., & Erb, T. (2021) Engineering a Highly Efficient Carboligase for Synthetic One-Carbon Metabolism. ACS Catalysis, 5396–5404 Shen, B., Tang, Y., Baltz, R. H., & Gonzalez, R. (2021). Introduction to the special issue: “Natural Product Discovery and Development in the Genomic Era: 2021.” J Ind Microbiol Biotechnol. 48, 3-4. Baltz, R., Vandamme E., Bennett, J., Agathos, S., Sánchez, S., Osada, H., Deng, Z. & Gonzalez, R. (2021) Introduction and Commentaries for the Special Issue: “Arnold L. Demain - a Life Lived”. Journal of Industrial Microbiology and Biotechnology. https://doi.org/10.1093/jimb/kuab082. 2020 Tan, Z., Clomburg, J. M., Cheong, S., Qian, S., & Gonzalez, R. (2020) A polyketoacyl-CoA thiolase-dependent pathway for the synthesis of polyketide backbones. Nat Catal 3:593–603 Fei, Q., Liang, B., Tao, L., Tan, E. C. D., Gonzalez, R., Henard, C., & Guarnieri, M. (2020) Biological valorization of natural gas for the production of lactic acid: techno-economic analysis and life cycle assessment. Biochem Eng J 107500 Baltz, R. H., Kao, K., Link, A. J., Marsili, E., Reguera, G., Shao, Z., Vandamme, E. J., Jeffries T. W., & Gonzalez, R. (2020) Introduction to Special Issue on “Frontiers in Industrial Microbiology and Biotechnology 2020.” J Ind Microbiol Biotechnol 47:621–622. Baltz, R. H., Greasham, R., Schwartz, R., Rau, T., Davies, T., & Gonzalez, R. (2020) Introduction to the Special Issue on “Recent Advances in Fermentation Technology 2020.” J Ind Microbiol Biotechnol 47:909–91. ___ 2019 Chou, A., Clomburg, J. M., Qian, S., & Gonzalez, R. (2019) 2-Hydroxyacyl-CoA lyase catalyzes acyloin condensation for one-carbon bioconversion. Nat Chem Biol 15:900–906 Clomburg, J. M., Qian, S., Tan, Z., Cheong, S., & Gonzalez, R. (2019) The isoprenoid alcohol pathway, a synthetic route for isoprenoid biosynthesis. Proc Natl Acad Sci 116:12810–1281 Qian, S., Clomburg, J. M., & Gonzalez, R. (2019) Engineering Escherichia coli as a platform for the in vivo synthesis of prenylated aromatics. Biotechnol Bioeng 116:1116–1127 Baltz, R. H., & Gonzalez, R. (2019) Introduction to Special Issue on “Frontiers in Industrial Microbiology and Biotechnology 2019.” J Ind Microbiol Biotechnol 46:1237. __ 2018 Cheong, S., Clomburg, J. M., & Gonzalez, R. (2018) A synthetic pathway for the production of 2-hydroxyisovaleric acid in Escherichia coli. J Ind Microbiol Biotechnol 45:579–588. Clomburg, J. M., Contreras, S. C., Chou, A., Siegel, J. B., & Gonzalez, R. (2018) Combination of type II fatty acid biosynthesis enzymes and thiolases supports a functional β-oxidation reversal. Metab Eng 45:11–19 Crumbley, A. M., & Gonzalez, R. (2018) Cracking “Economies of Scale”: Biomanufacturing on Methane-Rich Feedstock. In: Methane Biocatalysis: Paving the Way to Sustainability. Springer, pp 271–292 Garg, S., Clomburg, J. M., & Gonzalez, R. (2018) A modular approach for high-flux lactic acid production from methane in an industrial medium using engineered Methylomicrobium buryatense 5GB1. J Ind Microbiol Biotechnol 45:379–391. Katz, L., Chen, Y. Y., Gonzalez, R., Peterson, T. C., Zhao, H., & Baltz, R. H. (2018) Synthetic biology advances and applications in the biotechnology industry: a perspective. J Ind Microbiol Biotechnol 45:449–461. Kim, S., & Gonzalez, R. (2018) Selective production of decanoic acid from iterative reversal of β‐oxidation pathway. Biotechnol Bioeng 115:1311–1320 Tan, Z., Clomburg, J. M., & Gonzalez, R. (2018) Synthetic pathway for the production of olivetolic acid in Escherichia coli. ACS Synth Biol 7:1886–1896 __ 2017 Baltz, R. H., Vandamme, E., Zhang, L., & Gonzalez, R. (2017) Introduction to the Special Issue:“Arnold Demain—Industrial Microbiologist Extraordinaire.” J Ind Microbiol Biotechnol 44:503. Clomburg, J. M., Crumbley, A. M., & Gonzalez, R. (2017) Industrial biomanufacturing: the future of chemical production. Science (80- ) 355: __ 2016 Cheong, S., Clomburg, J. M., & Gonzalez, R. (2016) Energy-and carbon-efficient synthesis of functionalized small molecules in bacteria using non-decarboxylative Claisen condensation reactions. Nat Biotechnol 34:556 Gonzalez, R. (2016) From the New Editor-in-Chief. J Ind Microbiol Biotechnol 43:1–2. Kim, S., Cheong, S., Chou, A., & Gonzalez, R. (2016) Engineered fatty acid catabolism for fuel and chemical production. Curr Opin Biotechnol 42:206–215 Kim, S., Cheong, S., & Gonzalez, R. (2016) Engineering Escherichia coli for the synthesis of short-and medium-chain α, β-unsaturated carboxylic acids. Metab Eng 36:90–98 Wittmann, C., & Gonzalez, R. (2016) Editorial overview: Chemical biotechnology . Curr Opin Biotechnol 42:iv–v. __ 2015 Clomburg, J. M., Blankschien, M. D., Vick, J. E., Chou, A., Kim, S., & Gonzalez, R. (2015) Integrated engineering of β-oxidation reversal and ω-oxidation pathways for the synthesis of medium chain ω-functionalized carboxylic acids. Metab Eng 28:202–212 Kim, S., Clomburg, J. M., & Gonzalez, R. (2015) Synthesis of medium-chain length (C6–C10) fuels and chemicals via β-oxidation reversal in Escherichia coli. J Ind Microbiol Biotechnol 42:465–475. Nielsen, J., & Gonzalez, R. (2015) Editorial – Special Issue: Metabolic Engineering. J Ind Microbiol Biotechnol 42:315–316. Rodriguez-Moya, M., & Gonzalez, R. (2015) Proteomic analysis of the response of Escherichia coli to short-chain fatty acids. J Proteomics 122:86–99 Vergara, M., Berrios, J., Martínez, I., Díaz-Barrera, A., Acevedo, C., Reyes, J. G., … Altamirano, C. (2015) Endoplasmic reticulum-Associated rht-PA Processing in CHO Cells: Influence of mild hypothermia and specific growth rates in batch and chemostat cultures. PLoS One 10:e0144224 Vick, J. E., Clomburg, J. M., Blankschien, M. D., Chou, A., Kim, S., & Gonzalez, R. (2015) Escherichia coli enoyl-acyl carrier protein reductase (FabI) supports efficient operation of a functional reversal of the β-oxidation cycle. Appl Environ Microbiol 81:1406–1416 __ 2014 Cintolesi, A, Clomburg, J. M., & Gonzalez, R. (2014) In silico assessment of the metabolic capabilities of an engineered functional reversal of the β-oxidation cycle for the synthesis of longer-chain (C≥ 4) products. Metab Eng 23:100–115 Conrado, R. J., & Gonzalez, R. (2014) Envisioning the bioconversion of methane to liquid fuels. Science (80- ) 343:621–623 Haynes, C. A., & Gonzalez, R (2014) Rethinking biological activation of methane and conversion to liquid fuels. Nat Chem Biol 10:331 Vergara, M., Becerra, S., Berrios, J., Osses, N., Reyes, J., Rodriguez-Moya, M., Gonzalez, R., & Altamirano, C. (2014) Differential effect of culture temperature and specific growth rate on CHO cell behavior in chemostat culture. PLoS One 9:e93865 Zhao, Z., Arentz, J., Pretzer, L. A., Limpornpipat, P., Clomburg, J. M., Gonzalez, R., Schweitzer, N. M. , Wu, T. , Miller J. M., & Wong, M. S. (2014) Volcano-shape glycerol oxidation activity of palladium-decorated gold nanoparticles. Chem Sci 5:3715–3728 __ 2013 Blankschien, M. D., Pretzer, L. A., Huschka, R., Halas, N. J., Gonzalez, R., & Wong, M. S (2013) Light-triggered biocatalysis using thermophilic enzyme–gold nanoparticle complexes. ACS Nano 7:654–663 Cintolesi, Angela, Rodríguez‐Moyá, M., & Gonzalez, R. (2013) Fatty acid oxidation: Systems analysis and applications. Wiley Interdiscip Rev Syst Biol Med 5:575–585 Clomburg, J. M., & Gonzalez, R. (2013) Anaerobic fermentation of glycerol: a platform for renewable fuels and chemicals. Trends Biotechnol 31:20–28 González, R. (2013) Metabolic engineering: Use of system-level approaches and application to fuel production in Escherichia coli. Electron J Biotechnol 16:17 Mattam, A. J., Clomburg, J. M., Gonzalez, R., & Yazdani, S. S. (2013) Fermentation of glycerol and production of valuable chemical and biofuel molecules. Biotechnol Lett 35:831–842 Mazumdar, S., Blankschien, M. D., Clomburg, J. M., & Gonzalez, R. (2013) Efficient synthesis of L-lactic acid from glycerol by metabolically engineered Escherichia coli. Microb Cell Fact 12:7 Vergara, M., Becerra, S., Berrios, J., Reyes, J., Acevedo, C., Gonzalez, R., Osses, N., & Altamirano, C. (2013) Protein folding and glycosylation process are influenced by mild hypothermia in batch culture and by specific growth rate in continuous cultures of CHO cells producing rht-PA. In: BMC Proceedings. Springer, p P108 Rastogi, G., Gurram, R., Bhalla, A., Gonzalez, R., Bischoff, K., Hughes, S., Kumar, S., & Sani, R. K (2013) Presence of glucose, xylose, and glycerol fermenting bacteria in the deep biosphere of the former Homestake gold mine, South Dakota. Front Microbiol 4:18 __ 2012 Cintolesi, Angela, Clomburg, J. M., Rigou, V., Zygourakis, K., & Gonzalez, R. (2012) Quantitative analysis of the fermentative metabolism of glycerol in Escherichia coli. Biotechnol Bioeng 109:187–198 Clomburg, J. M., Vick, J. E., Blankschien, M. D., Rodríguez-Moyá, M., & Gonzalez, R. (2012) A synthetic biology approach to engineer a functional reversal of the β-oxidation cycle. ACS Synth Biol 1:541–554 Park, J., Rodríguez-Moyá, M., Li, M., Pichersky, E., San, K.-Y., & Gonzalez, R. (2012) Synthesis of methyl ketones by metabolically engineered Escherichia coli. J Ind Microbiol Biotechnol 39:1703–1712. Posada, J. A., Cardona, C. A., & Gonzalez, R. (2012) Analysis of the production process of optically pure D-lactic acid from raw glycerol using engineered Escherichia coli strains. Appl Biochem Biotechnol 166:680–699 __ 2011 Becerra, S., Vergara, M., González, R., Osses, N., & Altamirano, C. (2011) Condition of mild hypothermia does not promote an increase in specific productivity of recombinant protein at high specific growth rate. Curr Opin Biotechnol S35–S36 Berrios, J., Altamirano, C., Osses, N., & Gonzalez, R. (2011) Continuous CHO cell cultures with improved recombinant protein productivity by using mannose as carbon source: Metabolic analysis and scale-up simulation. Chem Eng Sci 66:2431–2439 Clomburg, J. M., & Gonzalez, R. (2011) Metabolic engineering of Escherichia coli for the production of 1, 2‐propanediol from glycerol. Biotechnol Bioeng 108:867–879 Choudhary, M. K., Yoon, J. M., Gonzalez, R., & Shanks, J. V. (2011) Re-examination of metabolic fluxes in Escherichia coli during anaerobic fermentation of glucose using 13 C labeling experiments and 2-dimensional nuclear magnetic resonance (NMR) spectroscopy. Biotechnol Bioprocess Eng 16:419–437 Dellomonaco, C., Clomburg, J. M., Miller, E. N., & Gonzalez, R. (2011) Engineered reversal of the β-oxidation cycle for the synthesis of fuels and chemicals. Nature 476:355–359 Zhu, H., Gonzalez, R., & Bobik, T. A. (2011) Coproduction of acetaldehyde and hydrogen during glucose fermentation by Escherichia coli. Appl Environ Microbiol 77:6441–6450 __ 2010 Blankschien, M. D., Clomburg, J. M., & Gonzalez, R. (2010) Metabolic engineering of Escherichia coli for the production of succinate from glycerol. Metab Eng 12:409–419 Clomburg, J. M., & Gonzalez, R. (2010) Biofuel production in Escherichia coli: the role of metabolic engineering and synthetic biology. Appl Microbiol Biotechnol 86:419–434 Dellomonaco, C., Fava, F., & Gonzalez, R. (2010) The path to next generation biofuels: successes and challenges in the era of synthetic biology. Microb Cell Fact 9:1–15 Dellomonaco, C., Rivera, C., Campbell, P., & Gonzalez, R. (2010) Engineered respiro-fermentative metabolism for the production of biofuels and biochemicals from fatty acid-rich feedstocks. Appl Environ Microbiol 76:5067–5078 Dharmadi, Y., & Gonzalez, R. (2010) Elementary network reconstruction: A framework for the analysis of regulatory networks in biological systems. J Theor Biol 263:499–509 Gonzalez, R., Campbell, P., & Wong, M. (2010) Production of ethanol from thin stillage by metabolically engineered Escherichia coli. Biotechnol Lett 32:405–411 Murarka, A., Clomburg, J. M., & Gonzalez, R. (2010) Metabolic flux analysis of wild-type Escherichia coli and mutants deficient in pyruvate-dissimilating enzymes during the fermentative metabolism of glucuronate. Microbiology 156:1860–1872 Murarka, A., Clomburg, J. M., Moran, S., Shanks, J. V, & Gonzalez, R. (2010) Metabolic analysis of wild-type Escherichia coli and a pyruvate dehydrogenase complex (PDHC)-deficient derivative reveals the role of PDHC in the fermentative metabolism of glucose. J Biol Chem 285:31548–31558 Mazumdar, S., Clomburg, J. M., & Gonzalez, R. (2010) Escherichia coli strains engineered for homofermentative production of D-lactic acid from glycerol. Appl Environ Microbiol 76:4327–4336 Rodríguez-Moyá, M., & Gonzalez, R. (2010) Systems biology approaches for the microbial production of biofuels. Biofuels 1:291–310 Yazdani, S. S., Mattam, A. J., & Gonzalez, R. (2010) Fuel and chemical production from glycerol, a biodiesel waste product. In "Biofuels from Agric wastes Byprod" Blaschek H, Ezeji T, and Scheffran J (Eds) Blackwell Publishing. 97–116 __ 2009 Dharmadi, Y., & Gonzalez, R. (2009) Metabolic Engineering for alternative fuels. The Metabolic Pathway Engineering Handbook. Smolke CD (Ed) Cameron D and Brazeau B (Eds) CRC Press. Boca Raton. FL Durnin, G., Clomburg, J., Yeates, Z., Alvarez, P. J. J., Zygourakis, K., Campbell, P., & Gonzalez, R. (2009) Understanding and harnessing the microaerobic metabolism of glycerol in Escherichia coli. Biotechnol Bioeng 103:148–161 Gupta, A., Murarka, A., Campbell, P., & Gonzalez, R. (2009) Anaerobic fermentation of glycerol in Paenibacillus macerans: metabolic pathways and environmental determinants. Appl Environ Microbiol 75:5871–5883 __ 2008 Gonzalez, Ramon, Murarka, A., Dharmadi, Y., & Yazdani, S. S. (2008) A new model for the anaerobic fermentation of glycerol in enteric bacteria: trunk and auxiliary pathways in Escherichia coli. Metab Eng 10:234–245 Murarka, A., Dharmadi, Y., Yazdani, S. S., & Gonzalez, R. (2008) Fermentative utilization of glycerol by Escherichia coli and its implications for the production of fuels and chemicals. Appl Environ Microbiol 74:1124–1135 Yazdani, S. S., & Gonzalez, R. (2008) Engineering Escherichia coli for the efficient conversion of glycerol to ethanol and co-products. Metab Eng 10:340–351 __ 2007 Gonzalez, R. (2007) Metabolic engineering of bacteria for food ingredients. In: Functional Foods and Biotechnology. pp. 501-520. Shetty K, Paliyath G, Pometto A and Levin RE (Eds) CRC Press. Boca Raton, FL Murarka, A., & Gonzalez, R. (2007) Metabolic Engineering of Bacteria. Encyclopedia of Agricultural, Food, and Biological Engineering. Heldman DR (Ed) Taylor & Francis Group LLC. New York, NY Yazdani, S. S., & Gonzalez, R. (2007) Anaerobic fermentation of glycerol: a path to economic viability for the biofuels industry. Curr Opin Biotechnol 18:213–219 __ 2006 Dharmadi, Y., Murarka, A., & Gonzalez, R. (2006) Anaerobic fermentation of glycerol by Escherichia coli: a new platform for metabolic engineering. Biotechnol Bioeng 94:821–829 Glatz, C. E., Gonzalez, R., Huba, M. E., Mallapragada, S. K., Narasimhan, B., Reilly, P. J., Saunders, K., & Shanks, J. V. (2006) Problem‐Based Learning Biotechnology Courses in Chemical Engineering. Biotechnol Prog 22:173–178 Rollins, D. K., Zhai, D., Joe, A. L., Guidarelli, J. W., Murarka, A., & Gonzalez, R. (2006) A novel data mining method to identify assay-specific signatures in functional genomic studies. BMC Bioinformatics 7:377 __ 2005 Gonzalez, R. (2005) Metabolic Engineering of Bacteria for Food Ingredients. Food Biotechnology: Second Edition. Shetty K, Pometto A and Paliyath G (Eds) CRC Press. Boca Raton, FL Dharmadi, Y., & Gonzalez, R. (2005) A better global resolution function and a novel iterative stochastic search method for optimization of high-performance liquid chromatographic separation. J Chromatogr A 1070:89–101 __ 2004 Dharmadi, Y., & Gonzalez, R. (2004) DNA microarrays: experimental issues, data analysis, and application to bacterial systems. Biotechnol Prog 20:1309–1324 Gonzalez, Ramon, Gentina, J. C., & Acevedo, F. (2004) Biooxidation of a gold concentrate in a continuous stirred tank reactor: mathematical model and optimal configuration. Biochem Eng J 19:33–42 __ 2003 Gonzalez, Ramon, Andrews, B. A., Molitor, J., & Asenjo, J. A. (2003) Metabolic analysis of the synthesis of high levels of intracellular human SOD in Saccharomyces cerevisiae rhSOD 2060 411 SGA122. Biotechnol Bioeng 82:152–169 González, Ramón, Gentina, J. C., & Acevedo, F. (2003) Optimisation of the solids suspension conditions in a continuous stirred tank reactor for the biooxidation of refractory gold concentrates. Electron J Biotechnol 6:233–243 Gonzalez, Ramon, Tao, H., Purvis, J. E., York, S. W., Shanmugam, K. T., & Ingram, L. O. (2003) Gene array‐based identification of changes that contribute to ethanol tolerance in ethanologenic Escherichia coli: comparison of KO11 (parent) to LY01 (resistant mutant). Biotechnol Prog 19:612–623 __ 2002 Gonzalez, Ramon, Andrews, B. A., & Asenjo, J. A. (2002) Kinetic model of BiP-and PDI-mediated protein folding and assembly. J Theor Biol 214:529–537 Gonzalez, Ramon, Tao, H., Shanmugam, K. T., York, S. W., & Ingram, L. O. (2002) Global gene expression differences associated with changes in glycolytic flux and growth rate in Escherichia coli during the fermentation of glucose and xylose. Biotechnol Prog 18:6–20 __ 2001 Gonzalez, Ramon, Asenjo, J. A., & Andrews, B. A. (2001) Metabolic control analysis of monoclonal antibody synthesis. Biotechnol Prog 17:217–226 Tao, H., Gonzalez, R., Martinez, A., Rodriguez, M., Ingram, L. O., Preston, J. F., & Shanmugam, K. T. (2001) Engineering a homo-ethanol pathway inEscherichia coli: Increased glycolytic flux and levels of expression of glycolytic genes during xylose fermentation. J Bacteriol 183:2979–2988 __ 1999 Gonzalez, R, Gentina, J. C., & Acevedo, F. (1999) Attachment behaviour of Thiobacillus ferrooxidans cells to refractory gold concentrate particles. Biotechnol Lett 21:715–718 González, R, Gentina, J. C., & Acevedo, F. (1999) Continuous biooxidation of a refractory gold concentrate. In: Process Metallurgy. Elsevier, pp 309–317 PATENTS AND PATENT APPLICATIONS Gonzalez, R., Chou, A. Bioconversion of 1-carbon feedstocks to fuels and chemicals . Pub. No. WO2017210381. Gonzalez, R., Clomburg, J.M., Chou, A. Conversion of 1-carbon compounds to products . Pub. No. WO2017190056. Gonzalez, R., Cheong, S., Clomburg, J.M. Microbial synthesis of isoprenoid precursors, isoprenoids and derivatives including prenylated aromatics . Pub. No. WO2017161041. Gonzalez, R., Cheong, S., Clomburg, J.M. Biosynthesis of polyketides . Pub. No. WO2017020043. Gonzalez, R., Chou, A., Clomburg, J.M. Synthetic pathway for biosynthesis from 1-carbon compounds . Pub. No. WO2016069929. Gonzalez, R., Clomburg, J.M. Bioconversion of short-chain hydrocarbons to fuels and chemicals . Pub. No. WO2016161043. Gonzalez, R., Clomburg, J.M., Cheong, S. Synthesis of omega-phenyl products and derivatives thereof . Pub. No. WO2016176339. Gonzalez, R., Clomburg, J.M., Cheong, S. Synthesis of omega-1 functionalized products and derivatives thereof . Pub. No. WO2016176347. Gonzalez, R., Clomburg, J.M., Cheong, S. Synthesis of omega functionalized methyketones, 2-alcohols, 2-amines, and derivatives thereof . Pub. No. WO2016168708. Gonzalez, R., Clomburg, J.M., Cheong, S. Iterative platform for the synthesis of alpha functionalized products . Pub. No. WO2016168681. Gonzalez, R., Clomburg, J.M. Modified fatty acid biosynthesis with ACP-dependent thiolases . Pub. No. WO2016168247. Gonzalez, R., Clomburg, J.M. Omega-carboxylated carboxylic acids and derivatives . Pub. No. WO2015191972. Gonzalez, R., Clomburg, J.M. Omega-aminated carboxylic acids . Pub. No. WO2016007258. Gonzalez, R., Clomburg, J.M. Omega-hydroxylated carboxylic acids . Pub. No. WO2015191422. Gonzalez, R., Clomburg, J.M. Functionalized carboxylic acids and alcohols by reverse fatty acid oxidation. Patent No. US 9,994,881. Gonzalez, R., Clomburg, J.M., Vick, J. Type II fatty acid synthesis enzymes in reverse β-oxidation . Pub. No. WO2015112988. Gonzalez, R., Clomburg, J.M., Dellomonaco, C., Miller, E.N. Reverse beta oxidation pathway. Patent No. US 9,416,364 . Campbell, P., and Gonzalez, R. Microbial conversion of oils and fatty acids to high-value chemicals. Pub. No. WO2009078973. Gonzalez, R., and Campbell, P. Microaerobic cultures for converting glycerol to chemicals. Patent No. US 8,691,552. Gonzalez, R. Anaerobic fermentation of glycerol . Patent No. US 8,129,157.

FAYIN ZHU Dr. Fayin Zhu is a Postdoctoral Researcher in the Department of Chemical, Biological, and Materials Engineering at the University of South Florida. His research focuses on developing novel metabolic pathways for one-carbon feedstocks utilization in biological systems as well as natural product production in E. coli. Before joining Gonzalez lab, Fayin was a postdoctoral research associate in Dr. George Benneet lab at Rice University, where he focused on metabolic engineering of E. coli for dicarboxylic acids production. Publications Education 2008 – B.S. in Biotechnology from Huazhong Agricultural University 2014 – Ph.D. in Biochemistry and Molecular biology from Wuhan University CONTACT INFORMATION Fayin Zhu Postdoctoral Researcher Researcher Department of Chemical, Biological, and Materials Engineering University of South Florida ENB 376 | 4202 E Fowler Ave | Tampa, FL 33620 fayinzhu@usf.edu

JING CHEN Dr. Jing Chen is a Postdoctoral Researcher in the Department of Chemical, Biological, and Materials Engineering at the University of South Florida. Her research focuses on investigating bio-based chemical production using the r-BOX platform as well as the biosynthesis of natural products in E. coli. Before joining the Gonzalez lab, Jing received her Ph.D. at the Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences. Her previous research experiences include metabolic engineering of S. cerevisiae for the synthesis of natural products and metabolic engineering of E. coli for bio-based chemical production. Publications Education 2014 – M.S. in Tianjin University of Science & Technology and Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences(Joint-training) 2019 – Ph.D. in Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences CONTACT INFORMATION Jing Chen Postdoctoral Researcher Department of Chemical, Biological, and Materials Engineering University of South Florida ENB 376 | 4202 E Fowler Ave | Tampa, FL 33620 cj22@usf.edu

MOHAMMADREZA NEZAMIRAD Mohammadreza is a graduate student in the Department of Chemical, Biological, and Materials Engineering at University of South Florida. He received his bachelor and master degrees at Amirkabir University of Technology (Tehran Polytechnic). His previous research experiences mainly focused on catalytic conversion of benzene present in gasoline. He has experience in industry working with NanoAlvand pharmaceutical company, an anticancer drugs’ producer in Iran. Education 2011– Amirkabir University of Technology, B.Sc. in Chemical Engineering 2013 – Amirkabir University of T echnology, M.Sc. in Chemical Engineering CONTACT INFORMATION Mohammandreza Mezamirad PhD student Department of Chemical, Biological, and Materials Engineering University of South Florida ENB 376 | 4202 E Fowler Ave | Tampa, FL 33620 mnezamirad@usf.edu

RESEARCH Engineering metabolism for fuel, chemical, and pharmaceutical production Advancements in our knowledge and understanding of biology, coupled with the emergence of fields such as synthetic biology and metabolic engineering have led to an unprecedented ability to harness cellular metabolism. However, the full potential of biological systems remains unrealized due to critical limitations in our ability to engineer and control them. The Metabolic Engineering and Biomanufacturing Laboratory seeks to overcome these limitations by designing and implementing transformational metabolic engineering and synthetic biology approaches to engineer biological systems. Combined with advancement of our fundamental knowledge of cellular metabolism, these approaches exploit the power and diversity of biology for the development of novel technologies across a range of applications. With a focus on the biomanufacturing of small molecules, this has enabled us to engineer cellular metabolism for the production of fuel, chemical, and pharmaceutical compounds from cost-effective and sustainable feedstocks .

Gonzalez Reseach Group. Metabolic Engineering & Biomanufacturing. Engineering metabolismfor energy, chemical and pharmaceutical production. Heading 3 Welcome to the laboratory for Metabolic Engineering & Biomanufacturing Engineering metabolism for energy, chemical, and pharmaceutical production Dr. Ramon Gonzalez Principal Investigator The laboratory for Metabolic Engineering and Biomanufacturing focusses on engineering microbial systems that have the potential to revolutionize energy, chemical & pharmaceutical production, environmental remediation, and agricultural systems. Current projects include the bioconversion of C1 feedstocks, synthesis of polyketides and isoprenoids, nitrogen fixation and ammonia production, and bio-upcycling of plastic waste. Projects Social Media

PABLO FUENTEALBA GONZÁLEZ Dr Pablo Fuentealba González is a Postdoctoral Research in the Department of Chemical, Biological, and Materials Engineering at the University of South Florida. His research experiences has been mainly focused on the antigen production for the vaccines formulation in the aquaculture sector, using metabolic engineering as a tool to improve the bioprocesses. He has developed his research in the Universidad Católica de Valparaíso, Universitat Autònoma de Barcelona, Universidad de Concepción and also in the company Abbott. His main contributions have been to carry out the first genome-scale metabolic reconstruction of P. salmonis and the development of a culture technology for the production of this microorganism. Education 2008 - Universidad de Concepción, B.S. in Biotechnology Engineering - Marine and Aquaculture. 2015 - Pontificia Universidad Católica de Valparaíso - Universidad Técnica Federico Santa María, PhD in Biotechnology. Publications CONTACT INFORMATION Pablo Fuentealba Gonzalez Postdoctoral Researcher Department of Chemical, Biological, and Materials Engineering University of South Florida ENB 376 | 4202 E Fowler Ave | Tampa, FL 33620 pablof@usf.edu

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BENARD NYAWANGA Benard Nyawanga is a graduate student in the Department of Chemical, Biological, and Materials Engineering at University of South Florida. His research focuses on bioprocess design, modeling and simulation for plastic upcycling technology. Nyawanga obtained his B.S in Chemical Engineering from University of Matanzas, Cuba and currently working on his Master’s degree in Chemical Engineering. Education 2020 (Expected) – University of South Florida, M.Sc. in Chemical and Biomedical Engineering 2012 – University of Matanzas, Cuba, B.Sc. in Chemical Engineering Experience 2010-2012 – Undergraduate Research Assistant, Chemical Engineering, University of Matanzas, Cuba. 2018-2019 – Teachers Assistant, Computational Engineering , Chemical and Biomedical Engineering, University of South Florida. 2020 – Graduate Research Assistant, Metabolic Engineering and Biomanufacturing, Chemical and Biomedical Engineering, University of South Florida. CONTACT INFORMATION Benard Nyawanga Master student Department of Chemical, Biological, and Materials Engineering University of South Florida ENB 376 | 4202 E Fowler Ave | Tampa, FL 33620 nyawanga@mail.usf.edu | nyawanga@usf.edu