Recent Publications

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	Global Transcriptional Analysis Delineates the Differential Inflammatory Response Interleukin-15 Elicits from Cultured Human T Cells
	Christopher G Ramsborg, Eleftherios T. Papoutsakis
	submitted
	This work was supported by a grant from the National Institutes of Health (NIH R01-GM065476). CGR was supported in part by a NIH predoctoral biotechnology training grant (T32 GM-008449).
	[Paper] [Supplementary materials]

	Diffusion, Mixing, and Associated Dye Effects in DNA-Microarray Hybridizations
	Jacob R. Borden , Carlos J. Paredes, Eleftherios T. Papoutsakis
	Biophys. J. vol. 89 (5): 3277–3284 (2005).
	This work was supported by a National Science Foundation grant (BES-0331402) and a National Institutes of Health/National Institute of General Medical Sciences Biotechnology Training grant (T32-GM08449-11) fellowship to J.R. Borden.
	[Paper] [Supplementary materials]

	*Design, Optimization, and Validation of Genomic DNA Microarrays for Examining the Clostridium acetobutylicum* Transcriptome**
	Keith V. Alsaker, Carlos J. Paredes, Eleftherios T. Papoutsakis
	BBE. Vol. 10 (5):pp. 432-443 (2005).
	This work was supported by a National Science Foundation grant (BES-0418157) and an NIH/NIGMS Biotechnology Training Grant (T32-GM08449) fellowship to K.V.Alsaker.
	[Paper] [Supplementary materials]

	*The Transcriptional Program of Early Sporulation and Stationary Phase Events in Clostridium acetobutylicum.*
	Keith V. Alsaker, Eleftherios T. Papoutsakis
	J. Bacteriol., vol. 187, No. 20, 7103-7118 (2005).
	This work was supported by a National Science Foundation grant BES-0331402, a Department of Energy grant DE-FG36-03GO13160, and a NIH/NIGMS Biotechnology Training Grant (T32-GM08449) fellowship to K.V. Alsaker.
	[Paper] [Supplementary Materials ]
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	*Intracellular butyryl-phosphate and acetyl-phosphate concentrations in Clostridium acetobutylicum* and implications for solvent formation.**
	Yinsuo Zhao, Christopher A. Tomas, Fredrick B. Rudolph, Eleftherios T. Papoutsakis and George N. Bennett
	Appl. Environ. Microbiol., vol. 71: pp. 530-537 (2005)
	This work was supported by a National Science Foundation grant (BES-9905669 and BES-0001288) and by Robert A. Welch Foundation grants C-1268 and C-1372 to GNB and FBR, respectively.
	[Paper] [Supplementary Materials ]

	A model-based optimization framework for the inference on gene regulatory networks fron DNA array data.
	R. Thomas, S. Mehrotra, E. T. Papoutsakis, V. Hatzimanikatis
	Bioinformatics, vol. 20, No. 17: pp. 3221-35 (2004)
	This work was supported by a National Science Foundation grant (BES-9905669 and BES-0001288) and by Robert A. Welch Foundation grants C-1268 and C-1372 to GNB and FBR, respectively.
	[Paper]

	*Transcriptional analysis of spo0A overexpression in Clostridium acetobutylicum* sporulation and its effects on the cell's response to butanol stress.**
	Keith V. Alsaker, Thomas R. Spitzer, and Eleftherios T. Papoutsakis
	J. Bacteriol., vol. 186, No. 7, pp. 1959-1971 (2004)
	This work was supported by grants BES-9911231 and BES-0331402 from the National Science Foundation and by grant R828562 from the Environmental Protection Agency.
	[Paper] [Supplementary Materials]

	*Transcriptional organization of the Clostridium acetobutylicum* genome.**
	Carlos J. Paredes, Isidore Rigoutsos, and Eleftherios T. Papoutsakis
	Nucleic Acids Research, vol. 32, No. 6, pp. 1973-1981 (2004)
	This work was supported by grants BES-9905669 and BES-0331402 from the National Science Foundation.
	[Paper] [Supplementary Materials ]
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	*Transcriptional analysis of butanol stress and tolerance in Clostridium acetobutylicum.*
	Christopher A. Tomas, Jeffrey A. Beamish, and Eleftherios T. Papoutsakis
	J. Bacteriol., vol. 186, No. 7, pp. 2006-2018, (2004)
	This work was supported by grants BES-9911231 and BES-0331402 from the National Science Foundation and grant R828562 from the Environmental Protection Agency.
	[Paper] [Supplementary Materials ]

	Molecular understanding of oxygen-tension and patient-variability effects on ex vivo expanded T cells.
	Hadar Haddad, Dirk Windgassen, Christopher G. Ramsborg, Carlos J. Paredes and Eleftherios T. Papoutsakis
	Biotechnol. Bioeng . 87: 437-450 (2004).
	This work was supported by a grant from the National Institutes of Health (NIH R01-GM065476), a Whitaker Foundation Graduate Fellowship (HH), and an NIH predoctoral biotechnology training grant (T32 GM-008449) (CGR).
	[Paper] [Supplementary Materials]

	Molecular insights into the pleiotropic effects of plasma on ex vivo expanded T cells using DNA-microarray analysis.
	Christopher G. Ramsborg, Dirk Windgassen, Jonathan K. Fallon, Carlos J. Paredes and Eleftherios T. Papoutsakis
	Experimental Hematology, vol. 32: pp. 970-990 (2004).
	This work was supported by a grant from the National Institutes of Health (NIH R01-GM065476) and an NIH predoctoral biotechnology training grant (T32 GM-008449) (CGR).
	[Paper] [Supplementary Materials]

	A segmental nearest neighbor normalization and gene identification method gives superior results for DNA-array analysis
	He Yang, Hadar Haddad, Christopher Tomas, Keith Alsaker, and E. Terry Papoutsakis
	PNAS, vol. 100, No. 3, pp. 1122-1127 (2003)
	This work was supported by National Science Foundation Grant BES-9905669, National Institutes of Health Grant R01-GM65476, and a Whitaker Foundation Graduate Fellowship (to H.H.).
	[Paper] [Supplementary Materials]
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	*Transcriptional analysis of product-concentration driven changes in cellular programs of recombinant Clostridium acetobutylicum* strains.**
	S. B. Tummala, S. G. Junne, C. J. Paredes , E. T. Papoutsakis
	Biotechnol. Bioeng ., vol. 84, No. 7: pp. 842-54 (2003)
	[Paper]

	*Overexpression of groESL in Clostridium acetobutylicum* results in increased solvent production and tolerance, prolonged metabolism, and changes in the cell's transcriptional program.**
	C. A. Tomas, N. E. Welker, E. T. Papoutsakis
	Appl. Environ. Microbiol., vol. 69, No. 8: pp. 4951-65 (2003)
	This work was supported by grant BES-9911231 from the National Science Foundation and grant R828562 from the Environmental Protection Agency.
	[Paper]

	*DNA-array based transcriptional analysis of asporogenous, non-solventogenic Clostridium acetobutylicum* strains SKO1 and M5**
	Christopher A. Tomas, Keith V. Alsaker, Hendrik P. J. Bonarius, Wouter T. Hendriksen, He Yang, Jeffrey A. Beamish, Carlos J. Paredes, and Eleftherios T. Papoutsakis
	J. Bacteriol., vol. 185, No. 15, pp. 4539-4547 (2003)
	This work was supported by National Science Foundation grant BES-9905669.
	[Paper] [Supplementary Materials]

	*Antisense RNA downregulation of coenzyme A transferase combined with alcohol-aldehyde dehydrogenase overexpression leads to predominantly alcohologenic Clostridium acetobutylicum* fermentations.**
	S. B. Tummala, S. G. Junne, E. T. Papoutsakis
	J. Bacteriol., vol. 185, No. 12, pp. 3644-53 (2003)
	This work was supported by National Science Foundation grant BES-9905669.
	[Paper]

	Design of antisense RNA constructs for downregulation of the acetone formation pathway of Clostridium acetobutylicum.
	S. B. Tummala, N. E. Welker, E. T. Papoutsakis
	J. Bacteriol., vol. 185, No. 6, pp. 1923-34 (2003)
	This work was supported by National Science Foundation grant BES-9905669.
	[Paper] [Erratum]

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