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Steve Brown

Staff Scientist



The rapid speed of next-generation sequencing technologies has led to a scientific revolution and a new age of biology. The fantastic possibilities now available because of rapid, large-scale sequencing projects that generate entire, sequenced genomes presents new challenges and opportunities such as defining and understanding gene functions and coordinate regulatory networks. Current research projects in Dr. Brown’s laboratory include characterizing the dynamics of stress responses and genetic regulation for several ethanologenic bacteria using a range of systems biology tools. Dr. Brown’s laboratories house facilities for controlled cultivation, microarray studies and next-generation sequencing using the GS FLX (Roche) system. Dr. Brown has constructed whole genome microarrays for the following organisms: Clostridium thermocellum ATCC27405, Zymomonas mobilis strain ZM4 and Desulfovibrio desulfuricans strain G20. The application of microarray technologies has led to incredible progress in our understanding of microorganisms by studying total RNAs profiles. However, the application of these approaches for understanding of microbial communities and uncultured microorganisms is limited by the requirement for genome sequence for probe design. We are working on methodologies to overcome this limitation by developing methods to enrich mRNA for direct massively parallel sequencing of cDNA so we can study microbial consortia and uncultured microorganisms.


  • Ph.D.: Microbiology- University of Otago, New Zealand(2002)
  • B.S.: Microbiology- University of Otago, New Zealand(1996)


Brown SD, Nagaraju S, Utturkar SM, De Tissera S, Segovia S, Mitchell W, Land ML, Dassanayake A, Köpke M. 2014. Comparison of single-molecule sequencing and hybrid approaches for finishing the genome of Clostridium autoethanogenum and analysis of CRISPR systems in industrial relevant Clostridia. Biotechnol. Biofuels 7:40.

Wilson C, Rodriguez M, Johnson C, Martin S, Chu T, Wolfinger R, Hauser L, Land M, Klingeman D, Syed M, Ragauskas A, Tschaplinski T, Mielenz J, Brown S. 2013. Global transcriptome analysis of Clostridium thermocellum ATCC 27405 during growth on dilute acid pretreated Populus and switchgrass. Biotechnol. Biofuels 6:179.

Parks JM, Johs A, Podar M, Bridou R, Hurt RA, Smith JD, Tomanicek SJ, Qian Y, Brown SD, Brandt CC, Palumbo AV, Smith JC, Wall JD, Elias DA, Liang L. 2013. The genetic basis for bacterial mercury methylation. Science 339:1332-1335.

Brown SD, Guss A, Karpinets T, Parks J, Smolin N, Yang S, Land ML, Klingeman DM, Bhandiwad A, Rodriguez JM, Raman B, Shao X, Mielenz JR, Smith JC, M. K, Lynd LR. 2011. Mutant alcohol dehydrogenase leads to improved ethanol tolerance in Clostridium thermocellum. Proc. Natl. Acad. Sci. USA 108:13752–13757.

Yang S, Pappas KM, Hauser LJ, Land ML, Chen GL, Hurst GB, Pan C, Kouvelis VN, Typas MA, Pelletier DA, Klingeman DM, Chang YJ, Samatova NF, Brown SD. 2009. Improved genome annotation for Zymomonas mobilis. Nat Biotechnol. 27(10):893-4.

Yang, S., T. Tschaplinski, N. Engle, S. Carroll, S. Martin, B. Davison, A. Palumbo, M. Rodriguez, and S. D. Brown. 2009. Transcriptomic and metabolomic profiling of Zymomonas mobilis during aerobic and anaerobic fermentations. BMC Genomics 10:34.

Learman, D. R., H. Yi, S. D. Brown, S. L. Martin, G. G. Geesey, A. M. Stevens, and M. F. Hochella, Jr. 2009. Shewanella oneidensis MR-1 LuxS involvement in biofilm development and sulfur metabolism. Appl. Environ. Microbiol. 75:1301-7.
Brown, S. D., B. Raman, C. K. McKeown, S. P. Kale, Z. L. He, and J. R. Mielenz. 2007. Construction and evaluation of a Clostridium thermocellum ATCC 27405 whole-genome oligonucleotide microarray. Appl. Biochem. Biotechnol. 137:663-674.

Learman, D. R., S. Bose, N. S. Wigginton, S. D. Brown, and M. F. Hochella. 2007. Reduction of hematite nanoparticles by Shewanella oneidensis MR-1. Geochimica Et Cosmochimica Acta 71:A551-A551.
S. D. Brown, M. R. Thompson, N. C. VerBerkmoes, K. Chourey, M. Shah, J. Zhou, R. L. Hettich and D. K. Thompson. Molecular dynamics of the Shewanella oneidensis response to chromate stress. 2006. Mol. Cell. Proteomics 5:1054-1071.

K. Chourey, M. Thompson, J. Morrell-Falvey, N. C. VerBerkmoes, S. D. Brown, M. Shah, R. L. Hettich, M. Doktycz and D. K. Thompson. Global molecular and morphological effects of chronic chromium exposure on Shewanella oneidensis MR-1. 2006. Appl. Environ. Microbiol. 72: 6331-6344.
A. B. Leaphart, D.K. Thompson, K. Huang, E. Alm, X. Wan, A. Arkin, S. D. Brown, L. Wu, T. Yan, X. Liu1, and J. Zhou. Transcriptome analysis of Shewanella oneidensis gene expression in response to acidic and alkaline pH stress. 2006. J. Bacteriol. 188(4): 1633–1642.

S. D. Brown, M. Martin, S. Deshpande, S. Seal,  K. Huang, E. Alm, Y. Yang, L. Wu, T. Yan, X. Liu, A. Arkin J. Zhou, D. K. Thompson. Cellular response of Shewanella oneidensis to strontium stress. 2006. Appl. Environ. Microbiol. 72(1): p. 890–900.
Sullivan, J.T., Trzebiatowski, J.R., Cruickshank, R.W., Gouzy, J., Brown, S.D., Elliot, R.M., Fleetwood, D.J., McCallum, N.G., Rossbach, U., Stuart, G.S., Weaver, J.E., Webby, R.J., de Bruijn F.J., Ronson C.W. Comparative sequence analysis of the symbiosis island of Mesorhizobium loti strain R7A. 2002. J. Bacteriol. 184(11): 3086-95.

Sullivan, J.T., Brown, S.D., Yocum, R.R., Ronson, C.W. The bio operon on the acquired symbiosis island of Mesorhizobium sp. strain R7A includes a novel gene involved in pimeloyl-CoA synthesis. 2001. Microbiol. 147: 1315-22.

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