RESEARCH PUBLICATIONS

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.

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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.

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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. 

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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. 

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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

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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:

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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.

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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