RESEARCH PUBLICATIONS

2020 

• Baltz RH, Kao K, Link AJ, et al (2020) Introduction to Special Issue on “Frontiers in Industrial Microbiology and Biotechnology 2020.” J Ind Microbiol Biotechnol 47:621–622

• Baltz RH, Greasham R, Schwartz R, et al (2020) Introduction to the Special Issue on “Recent Advances in Fermentation Technology 2020.” J Ind Microbiol Biotechnol Off J Soc Ind Microbiol Biotechnol 47:909–911

• Fei Q, Liang B, Tao L, et al (2020) Biological valorization of natural gas for the production of lactic acid: techno-economic analysis and life cycle assessment. Biochem Eng J 107500

• Tan Z, Clomburg JM, Cheong S, et al (2020) A polyketoacyl-CoA thiolase-dependent pathway for the synthesis of polyketide backbones. Nat Catal 3:593–603

2019 

• Baltz RH, Gonzalez R (2019) Introduction to Special Issue on “Frontiers in Industrial Microbiology and Biotechnology 2019.” J Ind Microbiol Biotechnol 46:1237.

• Chou A, Clomburg JM, Qian S, Gonzalez R (2019) 2-Hydroxyacyl-CoA lyase catalyzes acyloin condensation for one-carbon bioconversion. Nat Chem Biol 15:900–906

• Clomburg JM, Qian S, Tan Z, et al (2019) The isoprenoid alcohol pathway, a synthetic route for isoprenoid biosynthesis. Proc Natl Acad Sci 116:12810–1281

• Qian S, Clomburg JM, Gonzalez R (2019) Engineering Escherichia coli as a platform for the in vivo synthesis of prenylated aromatics. Biotechnol Bioeng 116:1116–1127

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2018 

• Cheong S, Clomburg JM, Gonzalez R (2018) A synthetic pathway for the production of 2-hydroxyisovaleric acid in Escherichia coli. J Ind Microbiol Biotechnol 45:579–588

• Clomburg JM, Contreras SC, Chou A, et al (2018) Combination of type II fatty acid biosynthesis enzymes and thiolases supports a functional β-oxidation reversal. Metab Eng 45:11–19

• Crumbley AM, 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 JM, 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 YY, Gonzalez R, et al (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 JM, Gonzalez R (2018) Synthetic pathway for the production of olivetolic acid in Escherichia coli. ACS Synth Biol 7:1886–1896

2017

• Baltz RH, Vandamme E, Zhang L, Gonzalez R (2017) Introduction to the Special Issue:“Arnold Demain—Industrial Microbiologist Extraordinaire.” J Ind Microbiol Biotechnol 44:503

• Clomburg JM, Crumbley AM, Gonzalez R (2017) Industrial biomanufacturing: the future of chemical production. Science (80- ) 355:

2016

• Cheong S, Clomburg JM, 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 JM, Blankschien MD, Vick JE, et al (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 JM, 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, et al (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 JE, Clomburg JM, Blankschien MD, et al (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 JM, 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 RJ, Gonzalez R (2014) Envisioning the bioconversion of methane to liquid fuels. Science (80- ) 343:621–623

• Haynes CA, Gonzalez R (2014) Rethinking biological activation of methane and conversion to liquid fuels. Nat Chem Biol 10:331

• Vergara M, Becerra S, Berrios J, et al (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 LA, et al (2014) Volcano-shape glycerol oxidation activity of palladium-decorated gold nanoparticles. Chem Sci 5:3715–3728

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2013 

• Blankschien MD, Pretzer LA, Huschka R, et al (2013) Light-triggered biocatalysis using thermophilic enzyme–gold nanoparticle complexes. ACS Nano 7:654–663

• Cintolesi A, Rodríguez‐Moyá M, Gonzalez R (2013) Fatty acid oxidation: Systems analysis and applications. Wiley Interdiscip Rev Syst Biol Med 5:575–585

• Clomburg JM, 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 AJ, Clomburg JM, Gonzalez R, Yazdani SS (2013) Fermentation of glycerol and production of valuable chemical and biofuel molecules. Biotechnol Lett 35:831–842

• Mazumdar S, Blankschien MD, Clomburg JM, 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, et al (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, et al (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 A, Clomburg JM, Rigou V, et al (2012) Quantitative analysis of the fermentative metabolism of glycerol in Escherichia coli. Biotechnol Bioeng 109:187–198

• Clomburg JM, Vick JE, Blankschien MD, et al (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, et al (2012) Synthesis of methyl ketones by metabolically engineered Escherichia coli. J Ind Microbiol Biotechnol 39:1703–1712

• Posada JA, Cardona CA, 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, et al (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 JM, Gonzalez R (2011) Metabolic engineering of Escherichia coli for the production of 1, 2‐propanediol from glycerol. Biotechnol Bioeng 108:867–879

• Choudhary MK, Yoon JM, 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 JM, Miller EN, 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 TA (2011) Coproduction of acetaldehyde and hydrogen during glucose fermentation by Escherichia coli. Appl Environ Microbiol 77:6441–6450

2010

• Blankschien MD, Clomburg JM, Gonzalez R (2010) Metabolic engineering of Escherichia coli for the production of succinate from glycerol. Metab Eng 12:409–419

• Clomburg JM, 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 JM, 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, Gonzalez R (2010) Bacteria: Metabolic Engineering. In: Encyclopedia of Agricultural, Food, and Biological Engineering. CRC Press, pp 96–100

• Murarka A, Clomburg JM, Moran S, et al (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 JM, 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 SS, Mattam AJ, 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, and 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, et al (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 R (2008) Harnessing the Microbial Fermentation of Glycerol-A New Path to Biofuels and Biochemicals. 한국생물공학회 학술대회 56

• Gonzalez R, Murarka A, Dharmadi Y, Yazdani SS (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 SS, 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 SS, 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 and 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 SS, 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 CE, Gonzalez R, Huba ME, et al (2006) Problem‐Based Learning Biotechnology Courses in Chemical Engineering. Biotechnol Prog 22:173–178

• Rollins DK, Zhai D, Joe AL, et al (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 R, Gentina JC, 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 R, Andrews BA, Molitor J, Asenjo JA (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 R, Gentina JC, 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 R, Tao H, Purvis JE, et al (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

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 2002

• Gonzalez R, Andrews BA, Asenjo JA (2002) Kinetic model of BiP-and PDI-mediated protein folding and assembly. J Theor Biol 214:529–537

• Gonzalez R, Tao H, Shanmugam KT, et al (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 R, Asenjo JA, Andrews BA (2001) Metabolic control analysis of monoclonal antibody synthesis. Biotechnol Prog 17:217–226

• Tao H, Gonzalez R, Martinez A, et al (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 JC, Acevedo F (1999) Attachment behaviour of Thiobacillus ferrooxidans cells to refractory gold concentrate particles. Biotechnol Lett 21:715–718

• González R, Gentina JC, 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.