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Metabolic Engineering and Synthetic & Systems Biology Laboratory

Published Literature


Research Publications (click here to see publication and citation details)


63. Rodriguez-Moya, M., and Gonzalez, R. (2015). Proteomic analysis of the response of Escherichia coli to short-chain fatty acids. Journal of Proteomics. doi:10.1016/j.jprot.2015.03.033.

62. Nielsen, J., Gonzalez, R. (2015). Editorial - Special Issue: Metabolic Engineering. Journal of Industrial Microbiology and Biotechnology. doi:10.1007/s10295-015-1587-8.

61. 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. Journal of Industrial Microbiology and Biotechnology. doi:10.1007/s10295-015-1589-6.

60. 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. Metabolic Engineering. doi:10.1016/j.ymben.2015.01.007.

59. 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. Applied and Environmental Microbiology. 81(1). doi:10.1128/AEM.03521-14.

58. Zhao, Z., Arentz, J., Pretzer, L. A., Limpornpipat, P., Clomburg, J. M., Gonzalez, R., Schweitzer, N. M., Wu, T., Miller, J. T., Wong, M. S. (2014). Volcano-shape glycerol oxidation activity of palladium-decorated gold nanoparticles. Chemical Science. 5(10), 3715. doi:10.1039/C4SC01001A.

57. Haynes. C.A., and Gonzalez, R. (2014). Rethinking biological activation of methane and conversion to liquid fuels. Nat. Chem. Biol. 10, 331-339.

56. 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(4): e93865. DOI: 10.1371/journal.pone.0093865.

55. Conrado, R., and Gonzalez R. (2014). Envisioning the Bioconversion of Methane to Liquid Fuels. Science. 343(6171): 621-623.

54. 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. Metabolic Engineering. DOI: 10.1016/j.ymben.2014.02.011.

53. Gonzalez R. (2013). Metabolic engineering: Use of system-level approaches and application to fuel production in Escherichia coli. Electronic Journal of Biotechnology. 16(3): 13.

52. Mattam A.J, Clomburg J.M., Gonzalez R., Yazdani S.S. (2013). Fermentation of glycerol and production of valuable chemical and biofuel molecules. Biotechnology Letters. 35(6): 831-842.

51. Rastogi G., Gurram R., Bhalla A., Gonzalez R., Bischoff K., Hughes S., Kumar S., and Sani R.K. (2013). Presence of glucose, xylose, and glycerol fermenting bacteria in the deep biosphere of the former Homestake gold mine, South DakotaFrontier in Microbiotechnology, Ecotoxicology and Bioremediation. 4: 18.

50. Cintolesi, A., Rodriguez-Moya, M., and Gonzalez, R. (2013). Fatty Acid Oxidation: Systems Analysis and Applications. WIREs System Biology and Medicine. 5(5): 575-585.

49. Blankschien, M., Pretzer, L., Huschka, R., Halas, H., Gonzalez, R., Wong, M. (2013). Light-tiggered biocatalysis using thermophilic enzyme-gold nanoparticle complexes. ACS Nano. 7(1): 654-663.

48. Clomburg, J.M., and Gonzalez, R. (2013). Anaerobic fermentation of glycerol: a platform for renewable fuels and chemicalsTrends in Biotechnology. 31(1): 20-28.

47. Mazumdar, S., Blankschien, M. D., Clomburg, J. M., and Gonzalez, R. (2013). Efficient synthesis of L-lactic acid from glycerol by metabolically engineered Escherichia coliMicrobial Cell Factories. 12(7).

46. Clomburg, J.M., Vick, J.E., Blankschien, M. D., Rodriguez-Moya, M., Gonzalez, R. (2012). A synthetic biology approach to engineer a functional reversal of the beta-oxidation cycleACS Synthetic Biology. 1(11): 541-554.

45. Park, J., Rodríguez-Moyá, M., Li, M., Pichersky, E., San, K-Y., Gonzalez, R. (2012). Synthesis of methyl ketones by metabolically engineered Escherichia coli. Journal of Industrial Microbiology and Biotechnology. 39 (11): 1703-1712.

44. Posada, J.A., Cardona, C.A., and Gonzalez, R. (2012). Analysis of the production process of optically pure D-lactic acid from raw glycerol using engineered Escherichia coli strains. Applied Biochemistry and Biotechnology. 166 (3): 680-699.

43. Cintolesi, A., Clomburg, J.M., Rigou, V., Zygourakis, K., and Gonzalez, R. (2012). Quantitative analysis of the fermentative metabolism of glycerol in Escherichia coliBiotechnology and Bioengineering, 109 (1): 187-198.

42. Becerra, S., Vergara, M., Gonzalez, 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. Current Opinion in Biotechnology, 22 (S1): S35-S36.

41. Dellomonaco, C., Clomburg, J.M., Miller, E.N., and Gonzalez, R. (2011). Engineered reversal of the β-oxidation cycle for the synthesis of fuels and chemicals. Nature, 476: 355-359. Featured in the Research Highlights Section of the Journal Nature Chemical Biology.

40. Zhu, H., Gonzalez, R., and Bobik, T.A. (2011). Co-production of acetaldehyde and hydrogen from glucose fermentation by Escherichia coliApplied and Environmental Microbiology. 77 (18): 6441-6450.

39. 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. Chemical Engineering Science, 66 (11): 2431-2439.

38. Choudhary, M. K., Moon, J. Y., Gonzalez, R., and Shanks, J.V. (2011). Re-examination of Metabolic Fluxes in Escherichia coli during Anaerobic Fermentation of Glucose Using 13C Labeling Experiments and 2-dimensional Nuclear Magnetic Resonance (NMR) Spectroscopy. Biotechnology and Bioprocess Engineering, 16 (3): 419-437. 

37. Clomburg, J., and Gonzalez, R. (2011). Metabolic engineering of Escherichia coli for the production of 1,2-propanediol from glycerol. Biotechnology and Bioengineering, 108 (4): 867-879. Selected for the Biotechnology and Bioengineering Metabolic Engineering Virtual Issue.

36. Murarka, A., Clomburg, J. M., Moran, S., Shanks, J.V., and Gonzalez, R. (2010). Metabolic analysis of wild-type Escherichia coli and a pyruvate dehydrogenase (PDH)-deficient derivative reveals the role of PDH in the fermentative metabolism of glucose. Journal of Biologial Chemistry, 285 (41): 31548-31558.

35. Blankschien, M. D., Clomburg, J. M., and Gonzalez, R. (2010). Metabolic engineering of Escherichia coli for the production of succinate from glycerol. Metabolic Engineering, 12 (5): 409-419.

34. Yazdani, S. S., Mattam, A.J., and Gonzalez, R. (2010). Fuel and chemical production from glycerol, a biodiesel waste product. In: “Biofuels from Agricultural Wastes and Byproducts. Blaschek H., Ezeji T., and Scheffran, J. (Eds.). Blackwell Publishing, Ames, IA. (Invited).

33. Dellomonaco, C., Rivera, C., Campbell, P., and R. Gonzalez. (2010). Engineered respiro-fermentative metabolism for the production of biofuels and biochemicals from fatty acid-rich feedstocks.Applied and Environmental Microbiology, 76 (15), 5067-5078.

32. Mazumdar, S., Clomburg, J. M., and Gonzalez, R. (2010). Engineered Escherichia coli strains for the homofermentative production of D-lactic acid from glycerol. Applied and Environmental Microbiology, 76(13): 4327-4336.

31. Murarka, A., Clomburg, J., and Gonzalez, R. (2010). Metabolic flux analysis of wild-type Escherichia coli and mutants deficient in pyruvate-dissimilating enzymes during fermentative metabolism of glucuronate. Microbiology-SGM, 156 (6): 1860 - 1872.

30. Clomburg, J.M., and Gonzalez, R. (2010). Biofuel production in Escherichia coli: The role of metabolic engineering and synthetic biology. Applied Microbiology and Biotechnology, 86 (2): 419-434 (Invited).

29. Rodriguez-Moya, M., and Gonzalez, R. (2010). Systems biology approaches for the microbial production of biofuels. Biofuels, 1(2): 291–310 (Invited).

28. Dharmadi, Y., and Gonzalez, R. (2010). Elementary Network Reconstruction: A framework for the analysis of regulatory networks in biological systems. Journal of Theoretical Biology,263(4): 499-509.

27. Gonzalez R., Campbell, P., and Wong, M. (2010). Production of ethanol from thin stillage by metabolically engineered Escherichia coli. Biotechnology Letters, 32 (3), 405-411.

26. Dellomonaco, C., Fava, F., and Gonzalez, R. (2010). The path to next generation biofuels: Successes and challenges in the era of synthetic biology. Microbial Cell Factories, 9(3) (Invited). Most accessed paper in Microbial Cell Factories within the last calendar year.

25. Gupta, A., Murarka, A., Campbell, P., and Gonzalez, R. (2009).Anaerobic fermentation of glycerol in Paenibacillus macerans: metabolic pathways and environmental determinants. Applied and Environmental Microbiology, 75(18), 5871-5883. Featured in the Journal Highlights Section of the Microbe Magazine.

24. Dharmadi, Y., and Gonzalez, R. (2009). Metabolic Engineering for alternative fuels. The Metabolic Pathway Engineering Handbook. Smolke, C. D. (Ed.); Cameron, D., and Brazeau, B. ( section Eds.) CRC Press, Boca Raton, FL (Invited).

23. Durnin, G., Clomburg, J., Yeates, Z., Alvarez, P.J.J., Zygourakis, K., Campbell, P., and Gonzalez, R. (2009). Understanding and Harnessing the Microaerobic Metabolism of Glycerol in Escherichia coli. Biotechnology and Bioengineering, 103(1), 148-161. Featured as spotlight article. Top 25 most downloaded articles in Biotechnology & Bioengineering from January – April 2009.

22. Yazdani, S.S., and Gonzalez, R. (2008). Engineering Escherichia coli for the efficient conversion of glycerol to ethanol and co-products. Metabolic Engineering,10 (6), 340-351.

21. Gonzalez, R., Murarka, A., Dharmadi, Y. and Yazdani, S.S.(2008). A New Model for the Anaerobic Fermentation of Glycerol in Enteric Bacteria: Trunk and Auxiliary Pathways in Escherichia coli. Metabolic Engineering, 10(5), 234-245.

20. Murarka, A., Dharmadi, Y. Yazdani, S.S. and Gonzalez, R.(2008). Fermentative utilization of Glycerol in Escherichia coli and its Implications for the Production of Reduced Chemicals and Fuels. Applied and Environmental Microbiology, 74(4), 1124-1135.

19. Gonzalez, R. (2007). Metabolic engineering of bacteria for food ingredients. In: Functional Foods and Biotechnology. pp. 501-520. K. Shetty, G. Paliyath, A. Pometto, and R. E. Levin. (Eds.). CRC Press, Boca Raton, FL (Invited).

18. Murarka, A., and Gonzalez, R. (2007). Metabolic Engineering of Bacteria. Encyclopedia of Agricultural, Food, and Biological Engineering. . Heldman, D. R. (Ed.) Taylor & Francis Group, LLC. New York, NY (Invited).

17. Yazdani, S.S. and Gonzalez, R.(2007). Anaerobic fermentation of glycerol: a path to economic viability for the biofuels industry. Current Opinion in Biotechnology, 18(3): 213-219 (Invited). Most Cited Current Opinion in Biotechnology Article.

16. Dharmadi, Y., Murarka, A., and Gonzalez, R., (2006). Anaerobic Fermentation of Glycerol by Escherichia coli: A New Platform for Metabolic Engineering. Biotechnology & Bioengineering, 94(5), 821-829. Top 25 most downloaded articles in Biotechnology & Bioengineering in 2006 and 2007.

15. Rollins, D., Zhai, D., Joe, A. L., Guidarelli, J. W., Murarka, A., and Gonzalez, R (2006).A Novel Data Mining Method to Identify Assay-Specific Signatures in Functional Genomic Studies. BMC Bioinformatics, 7, 377.

14. Glatz, C. E., Gonzalez, R., Huba, M. E., Mallapragada, S. K. , Narasimhan, B., Reilly, P. J., Saunders, K. P., and Shanks, J.V. (2006). Problem-Based Learning Biotechnology Courses in Chemical Engineering . Biotechnology Progress 22(1), 173-178.

13. Gonzalez, R. (2005). Metabolic Engineering of Bacteria for Food Ingredients. Food Biotechnology: Second Edition . K. Shetty, A. Pometto, and G. Paliyath. (Eds.) CRC Press, Boca Raton, FL (Invited).

12. Dharmadi, Y., and R. Gonzalez . (2005). A Better Global Resolution Function and a Novel Iterative Stochastic Search Method for Optimization of HPLC Separation, Journal of Chromatography A, 1070, 89-101.

11. Dharmadi, Y., and R. Gonzalez . (2004). DNA Microarrays: Experimental Issues, Data Analysis, and Application to Bacterial Systems, Biotechnology Progress, 20 (5), 1309-1324 (Invited).

10. Gonzalez, R ., J.C. Gentina, and F. Acevedo. (2004). Biooxidation of a Gold Concentrate in a Continuous Stirred Tank Reactor: Mathematical Model and Optimal Configuration. Biochemical Engineering Journal, 19, 33-42.

9. Gonzalez, R ., H. Tao, J. E. Purvis, K.T. Shanmugam, S.W. York, and L.O. Ingram. (2003). Gene Array-Based Identification of Changes that Contribute to Ethanol Tolerance in Ethanologenic Escherichia coli : Comparison of KO11 (Parent) to LYO1 (Resistant Mutant). Biotechnology Progress, 19 (2), 612-623.

8. Gonzalez, R ., B.A. Andrews, J. Molitor, and J. A. Asenjo. (2003). Metabolic Analysis of the Synthesis of High Levels of Intracellular Human SOD in S. cerevisiae rhSOD 2060 411 SGA122. Biotechnology and Bioengineering, 82,: 152-169.

7. Gonzalez, R ., J.C. Gentina, and F. Acevedo. (2003). Optimization of the Solids Suspension Conditions in the Biooxidation of Gold Concentrates in Continuous Stirred Tank Reactors . Electronic Journal of Biotechnology, 6 (3), 233-243.

6. Gonzalez, R ., H. Tao, K.T. Shanmugam, S.W. York, and L.O. Ingram. (2002). Global Gene Expression Differences Associated with Changes in Glycolytic Flux and Growth Rate in Escherichia coli during the Fermentation of Glucose and Xylose. Biotechnology Progress, 18 (1), 6-20.

5. Gonzalez, R ., B.A. Andrews, and J. A. Asenjo. (2002). Kinetic Model of BiP- and PDI-mediated Protein Folding and Assembly. Journal of Theoretical Biology, 214, 529-537.

4. Tao, H., R. Gonzalez , A. Martinez, M. Rodriguez, L. O. Ingram, J. F. Preston, and K. T. Shanmugam. (2001). Engineering a Homo-ethanol Pathway in Escherichia coli: Increased Glycolytic Flux and Expression Levels of Glycolytic Genes During Xylose Fermentation. Journal of Bacteriology, 183 (10), 2979-2988.

3. Gonzalez, R ., B.A. Andrews, and J. A. Asenjo. (2001). Metabolic Control Analysis of Monoclonal Antibody Synthesis. Biotechnology Progress, 17 (2), 217-226.

2. Gonzalez, R ., J.C. Gentina, and F. Acevedo. (1999). Attachment Behavior of Thiobacillus ferrooxidans Cells to Refractory Gold Concentrate Particles. Biotechnology Letters, 21 (8), 715-718.

1. Gonzalez, R., J.C. Gentina and F. Acevedo. (1999). Continuous Biooxidation of a Refractory Gold Concentrate. In: Process Metallurgy Volume 9, Part 1, 309-317 (Biohydrometallurgy and the Environment Toward the Mining of the 21st Century, Proceedings of the International Biohydrometallurgy Symposium).

Patents and Patent Applications


1. Gonzalez, R., Clomburg, J.M. Functionalized carboxylic acids and alcohols by reverse fatty acid oxidation. Pub. No: WO2013036812A1. Appln No.: PCT/US12/54230.

2. Gonzalez, R., Clomburg, J.M., Vick, J. Type II fatty acid synthesis enzymes in reverse β-oxidation. Appl. No.: 61/932,057.

3. Gonzalez, R., Clomburg, J.M., Dellomonaco, C., Miller, E.N. Reverse beta oxidation pathway. Pub No.: WO2012109176A2/CN103492560A/EP2673369A2/US20130316413/ WO2012109176A3.

4. Campbell, P., and Gonzalez, R. Microbial conversion of oils and fatty acids to high-value chemicals. Pub. No.: WO2009078973A2/EP2225373A2/US20110229942/ WO2009078973A3.

5. Gonzalez, R., and Campbell, P. Microaerobic cultures for converting glycerol to chemicals. Patent No. US 8,691,552 B2.

6. Gonzalez, R. Anaerobic fermentation of glycerol. Patent No. US 8,129,157 B2.