39. Cary, J.W., Petersen, D.J., Papoutsakis, E.T., and G.N. Bennett," Cloning and expression of Clostridium acetobutylicum phosphotransbutyrylase and butyrate kinase genes in Escherichia coli", J. Bacteriol. 170: 4613-4618 (1988). (Download PDF)

51. Cary, J.W., Petersen, D.J., Bennett, G.N. and Papoutsakis, E.T. "Methods for cloning key primary metabolic enzymes and ancillary proteins associated with the acetone-butanol fermentation of Clostridium acetobutylicum" Ann. N.Y. Acad. Sci., 589 (Biochem. Engineering VI) (St. Barbara, CA, Oct. 3-7, 1988): 67-81 (1990).

60. Cary, J.W., Petersen, D.J., Papoutsakis, E.T., and G.N. Bennett, "Cloning and expression of Clostridium acetobutylicum ATCC 824 coenzyme A: acetate/butyrate: coenzyme A-transferase in Escherichia coli", Appl. Environ. Microbiol. 56, 1576-1583 (1990). (Download PDF)

68. Petersen, D.J., Welch, R.W., Walter, K.A., Mermelstein, L.D., Papoutsakis, E.T., Rudolph, F.B., and Bennett, G.N., "Cloning of an NADH-dependent Butanol Dehydrogenase Gene from Clostridium acetobutylicum", Ann. N.Y. Acad. Sci. 646, 94-98 (1991).

70. Mermelstein, L.D., Welker, N.E., Bennett, G.N. and Papoutsakis, E.T., "Expression of Cloned Homologous Fermentative Genes in Clostridium acetobutylicum ATCC 824", Bio/Technol. 10: 190-195 (1992).

75. Lee, S.Y., Bennett. G.N. and Papoutsakis, E.T., "Construction of E. coli-Clostridium acetobutylicum shuttle vectors and transformation of C. acetobutylicum strains", Biotechnol. Lett. 14: 427-432 (1992).(Download PDF)

76. Lee, S.Y., Mermelstein, L.D., Bennett, G.N. and Papoutsakis, E.T., "Vector construction, transformation and gene amplification in Clostridium acetobutylicum ATCC 824", Ann. N.Y. Acad. Sci. 665: 39-51 (1992).

79. Walter, K.A., Bennett, G.N. and Papoutsakis, E.T., "Molecular characterization of two Clostridium acetobutylicum ATCC 824 butanol dehydrogenase isozyme genes" J. Bacteriol. 174: 7149-7158 (1992).(Download PDF)

81. Mermelstein, L.D. and Papoutsakis, E.T., "In vivo methylation in Escherichia coli by the Bacillus subtilis phage φ3T I Methyltransferase to protect plasmids from restriction upon transformation of Clostridium acetobuttylicum ATCC 824", Appl. Environ. Microbiol. 59: 1077-1081 (1993). (Download PDF)

84. Lee, S.Y., Mermelstein, L.D., Bennett, G.N., and Papoutsakis, E.T. "Determination of plasmid copy number and stability in Clostridium acetobutylicum ATCC 824", FEMS Microbiol. Lett. 108: 319-324 (1993).

86. Papoutsakis, E.T. and Bennett, G.N., "Cloning, structure, and expression of acid and solvent pathway genes of Clostridium acetobutylicum", Chapter 8 in: Clostridia and Biotechnology (Woods, D. R., ed.), pp. 157-199, Butterworth-Heinemann, Stoneham, MA (1993).

90. Mermelstein, L.D., Bennett, G.N. and Papoutsakis, E.T., "Amplification of homologous fermentative genes in Clostridium acetobutylicum ATCC 824", In: Bioproducts and Bioprocesses: Third Conference to Promote Japan/US Joint Projects and Cooperation in Biotechnology" (Tanner, R.D., ed.), pp. 317-343, Springer Verlag, New York (1993).

91. Mermelstein, L.D., Papoutsakis, E.T., Petersen, D.J. and Bennett, G.N., "Metabolic engineering of Clostridium acetobutylicum ATCC 824 for Increased Solvent Production by Enhancement of Acetone Formation Enzyme Activities using a Synthetic Acetone Operon" Biotechnol. Bioeng. 42: 1053-1060 (1993).(Download PDF)

92. Walter, K.A., Nair, R.V., Cary, J.W., Bennett, G.N., and Papoutsakis, E.T., "Sequence and arrangement of two genes encoding enzymes of the butyrate formation pathway of Clostridium acetobutylicum ATCC 824", Gene 134: 107-111 (1993). (Download PDF)

93. Mermelstein, L.D., and Papoutsakis, E.T., "Evaluation of macrolide and lincosamide antibiotics for plasmid maintenance in low pH Clostridium acetobutylicum ATCC 824 fermentations", FEMS Microbiol. Lett. 113: 71-75 (1993).

94. Walter, K.A., Mermelstein, L.D., and Papoutsakis, E.T., "Studies of recombinant Clostridium acetobutylicum with increased dosages of butyrate formation genes" Ann. N.Y. Acad. Sci. 721: 69-72 (1994).

95. Mermelstein, L.D., Welker, N.E., Petersen, D.J., Bennett, G.N., and Papoutsakis, E.T, "Genetic and metabolic engineering of Clostridium acetobutylicum ATCC 824", Ann. N.Y. Acad. Sci. 721: 54-68 (1994).

96. Nair, R.V., Bennett, G.N., and Papoutsakis, E.T., "Molecular characterization of an aldehyde/alcohol dehydrogenase gene from Clostridium acetobutylicum ATCC 824", J. Bacteriol. 176: 871-885 (1994). (Download PDF)

103. Nair, R.V. and Papoutsakis, E.T., "Expression of plasmid encoded aad in Clostridium acetobutylicum M5 restores vigorous butanol production", J. Bacteriol. 176: 5843-5846 (1994). (Download PDF)

104. Walter, K.A., Mermelstein, L.D. and Papoutsakis, E.T., "Host-plasmid interactions in recombinant strains of Clostridium acetobutylicum ATCC 824", FEMS Microbiol. Lett., 123: 335-342 (1994).

111. Stim-Herndon, K.P., Nair, R., Papoutsakis, E.T., and Bennett, G. N., "Analysis of degenerate variants of Clostridium acetobutylicum ATCC 824", Anaerobe, 2: 11-18 (1996). (Download PDF)

115. Green, E.M., Boynton, Z.L., Harris, L.M., Rudolph, F.B., Papoutsakis, E. T. and Bennett, G.N., "Genetic manipulation of acid formation pathways by gene inactivation in Clostridium acetobutylicum ATCC 824", Microbiology, 142: 2079-2986 (1996). (Download PDF)

122. Cornillot, E., Nair, R., Papoutsakis, E.T., & Soucaille, P. "The genes for butanol and acetone formation in Clostridium acetobutylicum ATCC 824 reside on a large plasmid whose loss leads to strain degeneration", J. Bacteriol. 179: 5442-5447 (1997). (Download PDF)

123. Bermejo, L.L., Welker, N.E and Papoutsakis, E.T. "Heterologous expression of Clostridium acetobutylicum ATCC824 genes in Escherichia coli for acetone production and acetate detoxification", Appl. Environ. Microbiol., 64: 1079-1085 (1998). (Download PDF)

135. Nair, R., Green E., Bennett, G. N. and Papoutsakis, E T. "Regulation of the sol locus genes for butanol and acetone production in Clostridium acetobutylicum ATCC 824 by a putative transcriptional repressor", J. Bacteriol. 181: 319-330 (1999). (Download PDF)

136. Desai, R. P. and Papoutsakis, E. T., "Antisense RNA strategies for the metabolic engineering of Clostridium acetobutylicum", Appl. Environ. Microbiol. 65: 936-945 (1999). (Download PDF)

138. Desai, R., Nielsen, L. K., and Papoutsakis, E. T. "Stoichiometric modeling of Clostridium acetobutylicum fermentations with nonlinear constraints", J. Biotechnol. 71: 191-205 (1999). (Download PDF)

142. Papoutsakis, E. T., and Bennett, G. N. "Metabolic Engineering of Clostridium acetobutylicum", pp. 253-279, Chapter 11 in "Metabolic Engineering" (S.Y. Lee and E. T. Papoutsakis, Eds), Marcel Dekker, 1999.

143. Lee, S. Y. and Papoutsakis, E. T. "The challenges and promise of metabolic engineering", pp.1-12, Chapter 1 in "Metabolic Engineering" (S.Y. Lee and E. T. Papoutsakis, Eds), Marcel Dekker, 1999.

145. Tummala, S. B., Welker, N. E., and Papoutsakis, E. T., "Development and characterization of a gene-expression reporter system for Clostridium acetobutylicum ATCC 824", Appl. Environ. Microbiol. 65: 3793-3799 (1999).(Download PDF)

146. Desai, R. P., Harris, L. M., Welker, N. E., Papoutsakis, E. T. "Metabolic flux analysis elucidates the importance of the acid-formation pathway in regulating solvent production by Clostridium acetobutylicum", Metabolic Eng. 1: 206-213 (1999). (Download PDF)

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)

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

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.

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 Butyryl Phosphate and Acetyl Phosphate Concentrations in Clostridium acetobutylicum and Their Implications for Solvent Formation", Appl. Environ. Microbiol. 71: 530-537 (2005). (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., "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)

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)

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)

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.

206. Sullivan, L., Paredes, C. J., Papoutsakis, E. T. & Bennett. G. N. Analysis of the clostridial hydrophobic with a conserved tryptophan family (ChW) of proteins in Clostridium acetobutylicum with emphasis on ChW14 and ChW16/17. Enz. Microb. Technol. 42: 29-43 (2007).(Download PDF)

207. Senger, R. S. and E. T. Papoutsakis. Genome-Scale Model for Clostridium acetobutylicum. Part 1. Reverse engineering to resolve network gaps, pathway discovery, and extrapolation to other clostridia. Biotechnol. Bioeng. in revision (2008).(Download PDF)

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. in revision (2008). (Download PDF)

213. 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: R114 (2008). (Download PDF)

214. Sillers, R., Ali Al-Hinai, M., and E. T. Papoutsakis. 2008. Aldehyde-alcohol dehydrogenase and/or thiolase overexpression coupled with CoA transferase downregulation lead to higher alcohol titers and selectivity in Clostridium acetobutylicum fermentations. Biotechnol. Bioeng.102: 38-49 (2009) (DOI: 10.1002/bit.22058). (Download PDF)

215. Sillers, R., Chow, A., Tracy, B.P., and Papoutsakis, E.T. 2008. Metabolic engineering of the non-sporulating, non-solventogenic Clostridium acetobutylicum strain M5 to produce butanol without acetone demonstrate the robustness of the acid-formation pathways and the importance of the electron balance. Metab. Eng. 10: 321-332 (2008) (doi:10.1016/j.ymben.2008.07.005). (Download PDF)

216. Papoutsakis, E. T. 2008. Engineering solventogenic clostridia. Curr. Opin. Biotechnol. 19:420–429 (doi:10.1016/j.copbio.2008.08.003). (Download PDF)

217. Tracy, B.P., Gaida, S.M. and Papoutsakis, E.T. 2008. Development and application of flow-cytometric techniques for analyzing and sorting cultures of endospore-forming clostridia. Appl. Environ. Microbiol. 74(24): 7497-7506 (2008) (doi:10.1128/AEM.01626-08). (Download PDF)

219. Borden, J. R., Jones, S. W., Indurthi, D., Chen, Y. & Papoutsakis, E. T. A genomic-library based discovery of a novel, possibly synthetic, acid tolerance mechanism in Clostridium acetobutylicum involving non-coding RNAs and ribosomal RNA processing. Metab. Engin. 12: 268–281 (2010) (doi:10.1016/j.ymben.2009.12.004). (Download PDF)

220. Alsaker, K.V., Paredes, C. J., & Papoutsakis, E.T. 2010. “Metabolite Stress and Tolerance in the Production of Biofuels and Chemicals: Gene-Expression-Based Systems Analysis of Butanol, Butyrate, and Acetate Stresses in the Anaerobe Clostridium acetobutylicum”, Biotechnol. Bioeng. 105: 1131–1147 DOI 10.1002/bit.22628. (Download PDF)

221. Tracy, BP, Gaida, S.M. and Papoutsakis, ET. Flow cytometry for bacteria: Enabling metabolic engineering, synthetic biology and the elucidation of complex phenotypes. (INVITED). Curr. Opin. Biotechnol. 21:85–99 (2010) DOI: 10.1016/j.copbio.2010.02.006. (Download PDF)

222. Nicolaou, S., Gaida, S. and Papoutsakis, E.T. “A comparative view of metabolite and substrate stress and tolerance in microbial bioprocessing: from biofuels and chemicals, to biocatalysis and bioremediation” Metab. Engin. 12: 307–331 (2010) doi:10.1016/j.ymben.2010.03.004. (Download PDF)

227. Chen, Y., Indurthi, I., Jones, S. W. and Papoutsakis, E. T. 2011. Small RNAs of the genus Clostridium. mBio 2(1):e00340-10. doi:10.1128/mBio.00340-10. (Download PDF)

229. Tracy, BP, Jones, S.W. and Papoutsakis, ET. 2011. Inactivation of σE and σG in Clostridium acetobutylicum illuminates their roles in clostridial-cell form biogenesis, granulose synthesis, solventogenesis, and spore morphogenesis. J. Bacteriol. 193 (6): 1414–1426. (Download PDF)

230. Jones, SW, Tracy, BP, Gaida, SM, and Papoutsakis, ET. 2011. Inactivation of σF in Clostridium acetobutylicum ATCC 824 blocks sporulation prior to asymmetric division, abolishes σE- and σG-protein expression, but does not block solvent formation. J. Bacteriol. 193 (10): 2429-2440 (doi:10.1128/JB.00088-11). (Download PDF)

231. Papoutsakis ET & Alsaker KV. Towards a Synthetic Biology of the Stress-Response and the Tolerance Phenotype. Book Chapter in: "Systems Metabolic engineering" (SY Lee and C. Whittmann, Eds), Springer (in press).

232. Bi, C, Jones, SW, Hess, DR,Tracy, BP, and Papoutsakis, ET. 2011. SpoIIE is necessary for asymmetric division, sporulation, and the expression of σF, σE, and σG, but does not control solvent production in Clostridium acetobutylicum. submitted.