Research

 

Publications

 

27. Dellomonaco, C., Rivera, C., Campbell, P., and R. Gonzalez. (2009). Synthetic respiro-fermentative metabolism for the conversion of bio-oils to fuels and chemicals: a new biorefinery paradigm. (MS in Review).

26. Dharmadi, Y., and Gonzalez, R. (2009). Elementary Network Reconstruction: A framework for the analysis of regulatory networks in biological systems. (MS in Review).

25. Gonzalez R., Campbell, P., and Wong, M. (2009). Production of ethanol from thin stillage by metabolically engineered Escherichia coli. Biotechnology Letters, (In Press).

24. 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.

23. 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.

22. 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.

21. 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.

20. 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.

19. 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.

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.

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.

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.

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.

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.

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: Biohydrometallurgy and the Environment toward the Mining of the 21st Century , Part A. pp. 309-317. R. Amils and A. Ballester (Eds.), Elsevier, Amsterdam.

Presentations at National / International Conferences

 

50. Gonzalez, R. Understanding and Harnessing the Microbial Fermentation of Glycerol. A New Path for the Production of Biochemicals. 2008 Annual AIChE meeting, Philadelphia, PA, November 16-21, 2008.

49. Gupta, A., and Gonzalez, R. Microbial Fermentation of Glycerol for the Production of Ethanol. 2008 Annual AIChE meeting, Philadelphia, PA, November 16-21, 2008.

48. Gonzalez, R., Clomburg, J., Yazdani, S.S., Murarka, A., and Dharmadi, Y. Understanding and harnessing the microbial fermentation of glycerol: a new path for the production of biochemicals. Metabolic Engineering VII: Health and Sustainability, Puerto Vallarta, Mexico, September 14-19, 2008.

47. Berríos, J., Gonzalez, R. and Altamirano, C. Relationship between energetic metabolism and sialic acid levels of r-tPA: flux banalysis under different hexose concentration in continuous culture of CHO cells. Metabolic Engineering VII: Health and Sustainability, Puerto Vallarta, Mexico, September 14-19, 2008.

46. Gonzalez, R. Understanding and harnessing microbial fermentation of glycerol: A new path to biofuels and biochemicals. 236th ACS National Meeting & Exposition, Philadelphia, PA, August 17-21, 2008.

45. Yazdani, S. S., and Gonzalez, R. Engineering Escherichia coli for the efficient conversion of glycerol to ethanol and co-products. 30th Symposium on Biotechnology for Fuels and Chemicals, New Orleans, LA, May 4-7, 2008.

44. Gonzalez, R., Murarka, A., Dharmadi, Y., and Yazdani, S.S. Anaerobic fermentation of Glycerol in Escherichia coli: A New Path to Biofuels and BioChemicals. 2007 Annual AICHE Meeting, November 4-9 2007, Salt Lake City, UT.

43. Gonzalez, R., Murar ka, A., Gupta, A.,Clomburg, J. and Yazdani, S.S. Anaerobic fermentation of Glycerol by Escherichia coli: A Functional Genomics Study. 2007 Annual AICHE Meeting, November 4-9 2007, Salt Lake City, UT.

42. Darmadhi,Y., Shanks, J.V., San, K-Y., and Gonzalez, R. Unraveling the Sugar Utilization Regulatory Systems in Escherichia coli. 2007 Annual AICHE Meeting, November 4-9 2007, Salt Lake City, UT.

41. Zhu, J., Shanks, J.V., Gonzalez, R. and San, K-Y. Development of a Mechanistic Model for Sugar-Utilization Regulatory Systems. 2007 Annual AICHE Meeting, November 4-9 2007, Salt Lake City, UT.

40. Gonzalez, R., Murarka, A., Dharmadi, Y., and Yazdani, S.S. Anaerobic Fermentation of Glycerol in Escherichia coli: A New Path to BioFuels and BioChemicals. 2007 Annual Meeting, Society for Industrial Microbiology, July29-August2, 2007, Denver, CO.

39. Gonzalez, R., Mura rka, A., Dharmadi, Y., and Yazdani, S.S. A new paradigm for glycerol fermentation in Escherichia coli and other enteric bacteria: Implications for the production of biofuels and biochemicals. Biochemical Engineering XV: Engineering Biology from Biomolecules to Complex Systems. Quebec City, Canada, July 15-19, 2007.

38. Rollins, D., Zhai, D., Joe, A.L., Guidarelli, J.W., Murarka, A., and Gonzalez, R. A novel data mining method to identify assay-specific signatures in functional genomics studies. Biochemical Engineering XV: Engineering B iology from Biomolecules to Complex Systems. Quebec City, Canada, July 15-19, 20 07.

37. Gonzalez, R., Mura rka, A., Dharmadi, Y., and Yazdani, S.S. Escherichia coli Ferments Glycerol in the Absence of External Electron Acceptors: A New Platform for Metabolic Engineering. 29th Symposium on Biotechnology for Fuels and Chemicals. April 29-May 2, 2007, Denver, CO.

36. Murarka, A., and Gonzalez, R. The role of pyruvate dehydrogenase in the fermentative metabolism of sugars by Escherichia coli. 232nd ACS National Meeting, San Francisco, CA, September 10-14, 2006.

35. Dharmadi, Y., and Gonzalez, R. Elementary network decomposition: A Framework for integration of knowledge on biological networks. 232nd ACS National meeting, San Francisco, CA, September 10-14, 2006.

34. Gupta, A., and Gonzalez, R. Anaerobic fermentation of glycerol by E. coli: A proteomics study. 232nd ACS National Meeting, San Francisco, CA, September 10-14, 2006.

33. Zhu, J., Peacock, R., Zhu, J., Shanks, J.V., Gonzalez, R. and San, K-Y. Development of a Mechanistic Model for Sugar-Utilization Regulatory Systems. AICHE 2006 Annual Meeting, November 12-17, San Francisco, CA.

32. Choudhary, M., Dharmadi, Y., San, K-Y., Gonzalez, R., and Shanks, J.V. Design of Isotope labeling Experiments for Metabolic Flux Analysis in Escherichia coli under Anaerobic Condition. AICHE 2006 Annual Meeting, November 12-17, San Francisco, CA.

31. Smith, K., Murarka, A., Yu, M. L., Dharmadi, Y., and Gonzalez, R. Engineering nitrate and nitrite metabolic systems in E. coli: A novel platform for the anaerobic synthesis of oxidized products. 2006 Annual Meeting, Society for Industrial Microbiology, July 30-August 3, Baltimore, MD.

30. Smith, K., Murarka, A., and Gonzalez, R. A Novel Microbial Platform for the Anaerobic Synthesis of Oxidized Chemicals: Co-Production of Acetic and Formic Acids in Escherichia coli. 28th Symposium on Biotechnology for Fuels and Chemicals. April 30- May 3, 2006, Nashville, TN.

29. Smith, K., Moon, Y., and Gonzalez, R. A novel microbial platform for the anaerobic synthesis of oxidized chemicals: Anaerobic production of acetic acid in E. coli. AIChE 2005 Annual Meeting, October 30-November 4, Cincinnati, OH.

28. Rollins, D., Zhai, D., and Gonzalez, R. An Improved PCA Approach For Microarray Data Analysis. AIChE 2005 Annual Meeting, October 30-November 4, Cincinnati, OH.

27. Murarka, A., and Gonzalez R. Role of pyruvate dehydrogenase in the anaerobic fermentation of sugars by Escherichia coli. AIChE 2005 Annual Meeting, October 30-November 4, Cincinnati, OH.

26. Dharmadi,Y., and Gonzalez, R. A network decomposition framework for integration of knowledge on regulatory networks in biological systems. AIChE 2005 Annual Meeting, October 30-November 4, Cincinnati, OH.

25. Dharmadi,Y., and Gonzalez, R. Computer-assisted optimization of HPLC separation for simultaneous quantification of substrates and products in microbial fermentation. AIChE 2005 Annual Meeting, October 30-November 4, Cincinnati, OH.

24. Peacock, R., Zhu, J., Shanks, J.V., Gonzalez, R. and San, K-Y. Development of a mechanistic model for sugar-utilization regulatory systems. AIChE 2005 Annual Meeting, October 30-November 4, Cincinnati, OH.

23. Tobelmann, M., Moon, Y., and Gonzalez, R. Metabolic Engineering of Homologous Ethanologenic Pathways in Escherichia coli. 2004 AIChE Annual Meeting, November 7 - 12, Austin, TX. (Won first place in the National Undergraduate Student Paper Competition).

22. Dharmadi, Y., Moon, Y., Shanks, J. V., San, K-Y., and Gonzalez, R. A Systems Biology Approach for Metabolic Engineering of Escherichia coli Sugar-Utilization Regulatory Systems. 2004 AIChE Annual Meeting, November 7 - 12, Austin, TX.

21. Murarka, A., Moon, Y., Shanks, J. V., and Gonzalez, R. Metabolic Flux Analysis of Escherichia coli Strains Devoid of Genes Involved in the Metabolism of Pyruvate under Anaerobic Conditions. 2004 AIChE Annual Meeting, November 7 -12, Austin, TX.

20. Dharmadi, Y., Lamm, M., and Gonzalez, R. Mesoscopic Simulation of the Hybridization Process in Oligonucleotide Microarray by Molecular Dynamics. 2004 AIChE Annual Meeting, November 7 - 12, Austin, TX.

19. Dharmadi, Y., and Gonzalez, R. A Better Global Resolution Function and a Novel Iterative Stochastic Search Method for Optimization of HPLC Separation. 2004 AIChE Annual Meeting, November 7 - 12, Austin, TX.

18. Smith, K., Moon, Y., and Gonzalez, R. Engineering an Anaerobic Homoacetogenic Pathway in E. coli. 2004 AIChE Annual Meeting, November 7 - 12, Austin, TX.

17. San, K-Y., Gonzalez, R., Shanks, J. V., and Peacock, R. Development of a genetic network driven model for sugar-utilization regulatory systems. 2004 AIChE Annual Meeting, November 7 - 12, Austin, TX.

16. Dharmadi, Y., Moon, Y., Shanks, J. V., San, K-Y., and Gonzalez, R. Metabolic Engineering of E. coli Sugar-Utilization Regulatory Systems for the Consumption of Sugar Mixtures. Metabolic Engineering V: Genome to Product. September 19-23, 2004, Lake Tahoe, CA.

15. San, K-Y., Bennett, G. N., Levanon, S. S., Cox, S, Peercy, B., Shanks, J.V., amd Gonzalez, R. A Genetic Network Driven Metabolic Flux Analysis Scheme. Metabolic Engineering V: Genome to Product. September 19-23, 2004, Lake Tahoe, CA.

14. Asenjo, J.A., Andrews, B. A., Gonzalez, R. Diaz, H. Metabolomics of Recombinant Yeast: Fluxes, Gene Expression and Discreet Mathematical Model for Gene Regulation of Metabolism. Metabolic Engineering V: Genome to Product. September 19-23, 2004, Lake Tahoe, CA.

13. Gonzalez, R., H. Tao, K. T. Shanmugam, S.W. York, and L. O. Ingram. Use of cDNA Microarrays to Study the Anaerobic Metabolism of Ethanologenic Escherichia coli Strains. Biochemical Engineering XIII: Biochemical Engineering in the Era of Genomics, Systems Biology, Genetic Medicine & Nanotechnologies. Boulder, CO, July, 2003.

12. Asenjo, J.A., Gonzalez, R., Basulto, C., and Andrews, B.A. Metabolic Fluxes, Gene Expression Profiling and Phenotype Phase Plane Analysis in the Optimization of the Synthesis of Recombinant Protein in Yeast. Biochemical Engineering XIII: Biochemical Engineering in the Era of Genomics, Systems Biology, Genetic Medicine & Nanotechnologies. Boulder, CO, July, 2003.

11. Gonzalez, R., H. Tao, K. T. Shanmugam, S.W. York, and L. O. Ingram. Transcriptome Analysis of Ethanologenic Escherichia coli Strains: Tolerance to Ethanol. 225th ACS National Meeting. New Orleans, LA, March, 2003.

10. Gonzalez, R., B. A. Andrews, and J. A. Asenjo. Kinetic Model of Monoclonal Antibody Folding and Assembly. European Symposium on Biochemical Engineering Science IV. Netherlands, August 2002.

9. Asenjo, J.A., R. Gonzalez, and B.A. Andrews. Use of Metabolic Engineering Tools and Microarrays Technology for the Optimization of the Synthesis of Recombinant Proteins in Yeast. European Symposium on Biochemical Engineering Science IV. Netherlands, August 2002.

8. Andrews, B.A., R. Gonzalez, and J. A. Asenjo. Kinetic Model of BiP- and PDI-mediated Protein Folding and Assembly. Cell Culture Engineering VIII. Sonoma, NM. April 2002.

7. Gonzalez, R., H. Tao, K. T. Shanmugam, S.W. York, and L. O. Ingram. Identification of Promoters for Programmed Expression of Recombinant Products in Escherichia coli by Transcriptome Analysis. ASM General Meeting. Orlando, FL. May 2001.

6. Gonzalez, R., H. Tao, A. Martinez, M. Rodriguez, L. O. Ingram, J. F. Preston, and K. T. Shanmugam. Gene Array Analysis of Metabolic Engineering in Escherichia coli. 23rd Symposium on Biotechnology for Fuels and Chemicals. Breckenridge, CO. May 2001.

5. Gonzalez, R., J.C. Gentina, and F. Acevedo. Selection of Agitator Type and Operating Conditions for the Biooxidation of Gold Concentrates. International Biohydrometallurgy Symposium, Ouro Preto, MG, Brazil, September 2001.

4. Gonzalez, R., H. Tao, A. Martinez, M. Rodriguez, L. O. Ingram, J. F. Preston, and K. T. Shanmugam. Gene Array Analysis of Metabolic Engineering in Escherichia coli. Third International Conference on Metabolic Engineering, Colorado Springs, CO, October 2000.

3. Andrews, B. A., R. Gonzalez, and J. A. Asenjo. Metabolic Control Analysis of Monoclonal Antibody Synthesis. Third International Conference on Metabolic Engineering, Colorado Springs, CO, October 2000.

2. Asenjo, J.A., R. Gonzalez, J. Gabelgaard, and B.A. Andrews. Use of Metabolic Flux Analysis for the Optimization of the Synthesis of Recombinant Proteins in Yeast. Third International Conference on Metabolic Engineering, Colorado Springs, CO, October 2000.

1. Gonzalez, R., B. A. Andrews and J. A. Asenjo. Metabolic Control Analysis of Monoclonal Antibody Synthesis. Cell Culture Engineering VII. Santa Fe, NM. February 2000.