147. Harris, L. M., Desai, R. P., Welker, N. E., Papoutsakis, E. T. "Characterization of recombinant strains of the Clostridium acetobutylicum butyrate kinase inactivation mutant: need for new phenomenological models for solventogenesis and butanol inhibition?", Biotechnol. Bioeng. 67: 1-11 (2000).(Download PDF)

148. Hevehan, D. L., Papoutsakis, E. T. & Miller W. M., "Physiologically significant effects of pH and oxygen tension on granulopoiesis", Exp. Hematol. 28: 267-275 (2000).(Download PDF)

149. McDowell, C. L., Borys,. M.C. and Papoutsakis, E T. "Animal cell culture: Physicochemical effects of pH", The Encyclopedia of Cell Technology (R. E. Spier, Ed.). Wiley, New York. pp. 63-70 (2000).

150. Carswell, K. S., and Papoutsakis, E. T., "Culture of human T-cells in stirred bioreactors for cellular immunotherapy applications: shear, proliferation, and the IL-2 receptor", Biotechnol. Bioeng. 68: 328-338 (2000).(Download PDF)

151. Carswell, K. S., Weiss, J. W. and Papoutsakis, E. T., "Low oxygen tension enhances the stimulation and proliferation of human T lymphocytes", Cytotherapy. 2: 25-37 (2000).(Download PDF)

152. Patel, S.D, Guo, R., Miller, W.M., Papoutsakis, E.T., Minster, N.I., Baum, C.M., and Winter, J.N., "Clinical-scale expansion of progenitor and post-progenitor cells using daniplestim, leridistim, progenipoietin, promegapoietin and autologous plasma", Cytotherapy. 2: 85-94 (2000).

153. Patel, S.D., Miller, W.M., Winter, J.N., and Papoutsakis E.T., "Cell density-dependent proliferation in frequently fed peripheral blood mononuclear cell cultures", Cytotherapy. 2: 267-280 (2000).

154. Hevehan, D., Miller, W.M., and Papoutsakis, E.T., "A dynamic model of Ex vivo granulocytic kinetics to examine the effects of pO2, pH and IL-3", Exp. Hematol. 28:1016-1028 (2000).(Download PDF)

155. Patel, S.D., Papoutsakis, E.T., Winter, J.N., and Miller, W.M., "The lactic acid issue revisited: novel feeding protocols to examine inhibition of cell proliferation and glucose metabolism in hematopoietic cell cultures," Biotechnol. Progr. 16: 885-892 (2000).(Download PDF)

156. Mostafa, S.S., Miller, W.M., and Papoutsakis, E.T., "Oxygen tension influences the differentiation, maturation and apoptosis of human megakaryocytes", Br. J. Haematol. 111: 879-889 (2000).(Download PDF)

157. Carswell, K. S., and Papoutsakis, E. T., "Extracellular pH affects the proliferation of cultured human T-cells and their expression of the interleukin 2 receptor", J. Immunotherapy. 23: 669-674 (2000).

158. Yang, H., Papoutsakis, E.T., and Miller, W.M., "Model-based estimation of myeloid hematopoietic progenitor cells using metabolic activities", Biotechnol. Bioeng. 72: 144-155 (2001).(Download PDF)

159. Harris, L.M., Blank, L., Desai, R.P., Welker, N.E, and E. T. Papoutsakis "Fermentation characterization and flux analysis of recombinant strains of Clostridium acetobutylicum with an inactivated solR gene", J. Ind. Microbiol. Biotechnol. 27: 322-328 (2001). (Download PDF)

160. Mostafa, S.S., Papoutsakis, E.T., and Miller, W.M., "Oxygen tension modulates the expression of cytokine receptors, transcription factors and lineage-specific markers in cultured human megakaryocytes", Exper. Hematol. 29: 873-883 (2001).(Download PDF)

161. Haddad, H, Carswell, K. S., and Papoutsakis, E. T., "Ex vivo expansion of Human T lymphocytes", in Methods in Tissue Engineering (A. Atala & R. Lanza, Eds.), Academic Press, San Diego. Chapter 41: pp. 487-502 (2002).

162. Haddad, H, and Papoutsakis, E. T., "Low oxygen tension and autologous plasma increase T-cell proliferation in serum-free media", Cytotherapy. 3: 435-447 (2001).

163. Chow, D., Miller, W.M., and Papoutsakis, E.T., "Estimation of Oxygen Tension Distributions of the Bone Marrow Hematopoietic Compartment. I. Krogh's model", Biophysical J. 81: 675-684 (2001).

164. Chow, D., Miller, W.M., and Papoutsakis, E.T., "Estimation of oxygen tension distributions of the bone marrow hematopoietic compartment. II. Modified Kroghian models", Biophysical J. 81: 685-696 (2001).(Download PDF)

165. Hevehan, D. L., Miller, W.M., and Papoutsakis, E.T., "Differential expression and phosphorylation of distinct STAT3 proteins during granulocytic differentiation", Blood. 99: 1627-1637 (2002).(Download PDF)

166. Tummala, S.B., Tomas, C., Harris, L.M., Welker, N.E., Rudolph, F.B., Bennett, G.N., Papoutsakis, E.T. "Genetic tools for solventogenic clostridia," in Clostridia: Biotechnology and Medical Applications (Bahl, H., Durre, P., Eds). New York, NY. John Wiley & Sons, Inc., 2001, pp 105-123.

167. Yang, H., Miller, W.M., and Papoutsakis, E. T., "Higher pH promotes megakaryocytic maturation and apoptosis", Stem Cells. 20: 320-328 (2002).(Download PDF)

168. L. M. Harris, N. E. Welker, and E. T. Papoutsakis "Northern, morphological and fermentation analysis of spo0A inactivation and overexpression in Clostridium acetobutylicum ATCC 824", J. Bacteriol. 184: 3586-3597 (2002).(Download PDF)

169. Yang, H., H. Haddad, C. Tomas, K. Alsaker, and E. T. Papoutsakis. "A segmental nearest neighbor normalization and gene identification method gives superior results for DNA-array analysis", Proc. Nat. Acad. Sci. (USA). 100: 1122-1127 (2003).(Download PDF)

170. Tummala, S. B., Welker, N. E., and Papoutsakis, E. T., "Design of antisense RNA constructs for the downregulation of the acetone formation pathway of Clostridium acetobutylicum," J. Bacteriol., 185: 1923-1934 (2003).(Download PDF)

171. Tomas, C., H. Bonarius, K. Alsaker, H.Yang, W. Hendriksen, J. Beamish, C. Paredes and E. T. Papoutsakis "DNA-array based transcriptional analysis of Clostridium acetobutylicum sporulation (SK01) and degenerate (M5) mutants", J. Bacteriol. 185: 4539-4547 (2003).(Download PDF)

172. Tummala, S. B., S. G. Junne, and E. T. Papoutsakis. "Antisense RNA downregulation of CoA Transferase combined with alcohol/aldehyde dehydrogenase (AAD) overexpression leads to predominantly alcohologenic Clostridium acetobutylicum fermentations", J. Bacteriol. 185: 3644-3653 (2003).(Download PDF)

173. Tummala, S.B., Junne, S.G., Paredes, C.J., Papoutsakis, E.T. "Transcriptional analysis of product concentration-driven changes in cellular programs of recombinant Clostridium acetobutylicum strains", Biotechnol Bioeng. 84: 842-854, 2003.(Download PDF)

174. Tomas, C., Welker, N. E., and Papoutsakis, E. T. "Overexpression of groESL in Clostridium acetobutylicum results in increased solvent production and tolerance, prolonged metabolism, and changes in the cell's transcriptional program", Appl. Environ. Microbiol. 69: 4951-4965 (2003).(Download PDF)

175. Tomas, C., Beamish, J, and Papoutsakis, E. T. "Transcriptional analysis of butanol stress and tolerance in Clostridium acetobutylicum", J. Bacteriol. 186: 2006-2018 (2004).(Download PDF)

176. Alsaker, K.V., Spitzer T. R. and E. T. Papoutsakis "Transcriptional analysis of spo0A overexpression in Clostridium acetobutylicum sporulation and its effects on the cell's response to butanol stress", J. Bacteriol. 186: 1959-1971 (2004).(Download PDF)

178. Tomas, C.A., S.B. Tummala, E.T. Papoutsakis. "Metabolic engineering of solventogenic Clostridia", in Handbook on Clostridia (H. Bahl and P. Durre, Eds). CRC Press, New York. 2005.(Download PDF)

179. Tummala, S.B., C.A. Tomas, E.T. Papoutsakis. "Gene analysis of clostridia", in Handbook on Clostridia (H. Bahl and P. Durre, Eds). CRC Press, New York. 2005.

180. Ramsborg CG, D. Windgassen, C. J. Paredes and E. T. Papoutsakis, "Molecular insights into the pleiotropic effects of plasma on Ex vivo expanded T-cells using DNA-microarray analysis", Exp. Hematol. 32: 970-990 (2004).(Download PDF)

181. Thomas, R., Mehrotra, S., Papoutsakis, E.T., Hatzimanikatis., V., "A model-based optimization framework for the inference of gene regulatory networks from DNA array data", Bioinformatics. 20: 3221-3235 (2004).(Download PDF)

182. Paredes, C., I. Rigoutsos, and E. T. Papoutsakis. "Transcriptional organization of the Clostridium acetobutylicum genome", Nucleic Acid Res. 32: 1973-1981 (2004).(Download PDF)

183. Zhao, Y., C. A. Tomas, Rudolph, F.B., E. T. Papoutsakis and G. N. Bennett. "Intracellular acetyl phosphate and butyryl phosphate concentrations in Clostridium acetobutylicum and implications for solvent formation", Appl. Environ. Microbiol. 71: 530-537 (2005).(Download PDF)

184. Tsaftaris S.A., Katsaggelos A.K., Pappas T.N., and Papoutsakis E.T., "DNA Based Matching of Digital Signals", Proceedings of IEEE International Conference on Acoustics, Speech, and Signal Processing, 5: 581-584 (2004).(Download PDF)

185. Tsaftaris S.A., Katsaggelos A.K., Pappas T.N., and Papoutsakis E.T., "DNA computing from a signal processing viewpoint", IEEE Signal Processing Magazine. 21 (5): 100-106 (Sep. 2004).(Download PDF)

186. Tsaftaris S.A., Katsaggelos A.K., Pappas T.N., and Papoutsakis E.T., "How can DNA computing be applied to digital signal processing?", IEEE Signal Processing Magazine. 21 (6): 57-61 (Nov. 2004).(Download PDF)

187. Borden, J.R., Paredes, C.J., Papoutsakis, E.T., "Diffusion, Mixing, and Associated Dye Effects in DNA-Microarray Hybridizations", Biophys. J. 89: 3277-3284 (2005).(Download PDF)

188. Alsaker, K., Paredes, C. and Papoutsakis, E.T., "Design, optimization and validation of genomic DNA microarrays for examining the Clostridium acetobutylicum transcriptome", Biotech. Bioproc. Eng. 10: 432-443 (2005).(Download PDF)

189. Alsaker, K., and Papoutsakis, E.T., "The transcriptional program of early sporulation and stationary phase events in Clostridium acetobutylicum", J. Bacteriol. 187:7103-7118 (2005).(Download PDF)

190. Hatzimanikatis, V. and Papoutsakis, E.T.,"Extracting networks from expression data", Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, Part 4, Sect. 5, (2005).

191. Paredes, C. J., Alsaker, K.V., and Papoutsakis, E.T., "A comparative genomic view of clostridial differentiation and physiology", Nature Reviews Microbiology. 3: 969-978 (2005).(Download PDF)

192. Lisa M. Giammona, L. M., P. G. Fuhrken, E. T. Papoutsakis, and W. M. Miller, "Nicotinamide (vitamin B3) increases the polyploidisation and proplatelet formation of cultured primary human megakaryocytes" Brit. J. of Haematol. 135, 554-566 (2006).

193. Fuhrken, P.G., C. Chen; W. M. Miller, & E. T. Papoutsakis. Comparative, genome-scale transcriptional analysis of CHRF-288-11 and primary human megakaryocytic cell cultures provides novel insights into lineage-specific differentiation. Exp. Hematology, 35: 476-489 (2007).

194. Dipankar R, Y. Terao, P. G. Fuhrken, Z-Q. Ma, F. J. DeMayo, K. Christov, N. A. Heerema, R. Franks, S. Y. Tsai, E. T. Papoutsakis and H. Kiyokawa. "Deregulated CDC25A expression promotes mammary tumorigenesis with genomic instability", Cancer Res., 67: 984-991 (2007).(Download PDF)

195 . Ramsborg CG and E. T. Papoutsakis, "Global transcriptional analysis delineates the differential inflammatory response interleukin-15 elicits from cultured human T cells", Exp. Hematol. 35: 454-464 (2007).

197. Borden J.R. and Papoutsakis, E. T. "Dynamics of genomic-library enrichment and identification of solvent-tolerance genes in Clostridium acetobutylicum", Appl. Environ. Microbiol. 73: 3061-3068 (2007). (Download PDF)

198. Thomas, R., Paredes, CJ, Mehrotra, S., Papoutsakis, E.T., Hatzimanikatis., V., "A model-based optimization framework for the inference of regulatory interactions using time-course DNA microarray expression data", BMC Bioinformatics 8: 228 (2007).(Download PDF)

199. Paredes, C. J., Senger, R.S., Borden, J.R., Sillers, R. and Papoutsakis, E.T., "A general framework for designing and validating oligomer-based DNA-microarrays and its application to Clostridium acetobutylicum", Appl. Environ. Microbiol. 73: 4631-4638 (2007).(Download PDF)

200. Chen, C, Fuhrken, P.G., Huang L.T, Paredes, C. J., Miller, W. M. & E. T. Papoutsakis. A systems-biology analysis of isogenic megakaryocytic and granulocytic cultures identifies new molecular components of megakaryocytic apoptosis. BMC Genomics 8: 384 (doi:10.1186/1471-2164-8-384) (2007).(Download PDF)

201. Huang, L.T., Paredes, C.J., Papoutsakis, E.T., Miller W.M., Gene-expression analysis illuminates the transcriptional programs underlying the functional activity of ex-vivo expanded granulocytes. Physiol Genomics. 31: 114-125 (2007).(Download PDF)

202. Wang, H., Lu, Y., Huang, W., Papoutsakis, E.T., Fuhrken, P., Eklund, E.A., HoxA10 activates transcription of the gene encoding mitogen-activated protein kinase phosphatase 2 (Mkp2) in myeloid cells. J Biol. Chem. 282: 16164-76. (2007).(Download PDF)

203. Pascoe, D.E., Arnott, D., Papoutsakis, E.T., Miller, W.M., Andersen, D.C., "Proteome analysis of antibody-producing CHO cell lines with different metabolic profiles", Biotechnol Bioeng. 92(2):391-410 (2007).

204. Paredes, C.J., Jones, S.W., Senger, R.S., Borden, J.R., Sillers, R., E.T. Papoutsakis. "Molecular aspects of butanol fermentation", in Microbial Energy Conversion (Wall, J., Harwoo, C., Demain, A. (Eds). American Society of Microbiology Press, In press.

205. Fuhrken, P. G., C. Chen, P. A. Apostolidis, M. Wang, W. M. Miller, E. T. Papoutsakis. Gene-Ontology driven transcriptional analysis of CD34+-cell initiated megakaryocytic cultures identifies new transcriptional regulators of megakaryopoiesis. Physiol. Genomics. (2008) 33: 159-69

206. Sepúlveda D.E., B. A. Andrews, J. A. Asenjo, & E. T. Papoutsakis. Comparative transcriptional analysis of embryoid body versus two-dimensional differentiation of murine embryonic stem cells. Tissue Eng. Accepted (2008).

207. Senger, R. S. and E. T. Papoutsakis. Genome-scale model for Clostridium acetobutylicum. Part 1. Metabolic network resolution and analysis. Biotechnol Bioeing. 101: 1036-52 (2008).

208. Senger, R. S. and E. T. Papoutsakis. Genome-Scale Model for Clostridium acetobutylicum. Part 2: Development of Specific Proton Flux States and Numerically-Determined Sub-Spaces. Biotechnol. Bioeng. 101: 1053-71 (2008).

209. Wang M, Windgassen D, Papoutsakis ET. "Comparative analysis of transcriptional profiling of CD3+, CD4+ and CD8+ T cells indentifies novel immune response players in T-cell activaiton" BMC Genomics. 2008 May 16:9(1):225

210. Jones, S.W., Paredes, C.J., Tracy, B., Cheng, N., Sillers, R., Senger, R. and E.T. Papoutsakis. "The transcriptional program underlying the physiology of clostridial sporulation." Genome Biol. 9(7): R114 (2008).