Tracy BP, Jones SW, Fast AG, Indurthi DC, Papoutsakis ET: Clostridia: the importance of their exceptional substrate and metabolite diversity for biofuel and biorefinery applications. Curr Opin Biotechnol. 2012, 23: 364-381. 10.1016/j.copbio.2011.10.008.

Article
Google Scholar

Papoutsakis ET: Engineering solventogenic clostridia. Curr Opin Biotechnol. 2008, 19: 420-429. 10.1016/j.copbio.2008.08.003.

Article
Google Scholar

Wang Q, Venkataramanan KP, Huang H, Papoutsakis ET, Wu CH: Transcription factors and genetic circuits orchestrating the complex, multilayered response of *Clostridium acetobutylicum* to butanol and butyrate stress. BMC Syst Biol. 2013, 7: 120-10.1186/1752-0509-7-120.

Article
Google Scholar

Venkataramanan KP, Jones SW, McCormick KP, Kunjeti SG, Ralston MT, Meyers BC, Papoutsakis ET: The Clostridium small RNome that responds to stress: the paradigm and importance of toxic metabolite stress in *C. acetobutylicum*. BMC Genomics. 2013, 14: 849-10.1186/1471-2164-14-849.

Article
Google Scholar

Alsaker KV, Paredes C, Papoutsakis ET: 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. 2010, 105: 1131-1147.

Google Scholar

Schwarz KM, Kuit W, Grimmler C, Ehrenreich A, Kengen SWM: A transcriptional study of acidogenic chemostat cells of *Clostridium acetobutylicum*- cellular behavior in adaptation to n-butanol. J Biotechnol. 2012, 161: 366-377. 10.1016/j.jbiotec.2012.03.018.

Article
Google Scholar

Janssen H, Grimmler C, Ehrenreich A, Bahl H, Fischer RJ: A transcriptional study of acidogenic chemostat cells of *Clostridium acetobutylicum*-solvent stress caused by a transient n-butanol pulse. J Biotechnol. 2012, 161: 354-365. 10.1016/j.jbiotec.2012.03.027.

Article
Google Scholar

Hou S, Jones SW, Choe LH, Papoutsakis ET, Lee KH: Workflow for quantitative proteomic analysis of *Clostridium acetobutylicum* ATCC 824 using iTRAQ tags. Methods. 2013, 61: 269-276. 10.1016/j.ymeth.2013.03.013.

Article
Google Scholar

Feist AM, Herrgard MJ, Thiele I, Reed JL, Palsson BO: Reconstruction of biochemical networks in microorganisms. Nat Rev Microbiol. 2009, 7: 129-143. 10.1038/nrmicro1949.

Article
Google Scholar

Burgard AP, Pharkya P, Maranas CD: OptKnock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization. Biotechnol Bioeng. 2003, 84: 647-657. 10.1002/bit.10803.

Article
Google Scholar

Oliveira AP, Nielsen J, Forster J: Modeling *Lactococcus lactis* using a genome-scale flux model. BMC Microbiol. 2005, 5: 39-10.1186/1471-2180-5-39.

Article
Google Scholar

Alper H, Jin YS, Moxley JF, Stephanopoulos G: Identifying gene targets for the metabolic engineering of lycopene biosynthesis in *Escherichia coli*. Metab Eng. 2005, 7: 155-164. 10.1016/j.ymben.2004.12.003.

Article
Google Scholar

Pharkya P, Maranas CD: An optimization framework for identifying reaction activation/inhibition or elimination candidates for overproduction in microbial systems. Metab Eng. 2006, 8: 1-13. 10.1016/j.ymben.2005.08.003.

Article
Google Scholar

Almaas E, Kovacs B, Vicsek T, Oltvai ZN, Barabasi AL: Global organization of metabolic fluxes in the bacterium *Escherichia coli*. Nature. 2004, 427: 839-843. 10.1038/nature02289.

Article
Google Scholar

Burgard AP, Nikolaev EV, Schilling CH, Maranas CD: Flux coupling analysis of genome-scale metabolic network reconstructions. Genome Res. 2004, 14: 301-312. 10.1101/gr.1926504.

Article
Google Scholar

Motter AE, Gulbahce N, Almaas E, Barabasi AL: Predicting synthetic rescues in metabolic networks. Mol Syst Biol. 2008, 4: 168-10.1038/msb.2008.1.

Article
Google Scholar

Jin YS, Jeffries TW: Stoichiometric network constraints on xylose metabolism by recombinant *Saccharomyces cerevisiae*. Metab Eng. 2004, 6: 229-238. 10.1016/j.ymben.2003.11.006.

Article
Google Scholar

Papoutsakis ET: Equations and calculations for fermentations of butyric acid bacteria. Biotechnol Bioeng. 1984, 26: 174-187. 10.1002/bit.260260210.

Article
Google Scholar

Desai RP, Harris LM, Welker NE, Papoutsakis ET: Metabolic flux analysis elucidates the importance of the acid-formation pathways in regulating solvent production by *Clostridium acetobutylicum*. Metab Eng. 1999, 1: 206-213. 10.1006/mben.1999.0118.

Article
Google Scholar

Lee J, Yun H, Feist AM, Palsson BO, Lee SY: Genome-scale reconstruction and in silico analysis of the *Clostridium acetobutylicum* ATCC 824 metabolic network. Appl Microbiol Biotechnol. 2008, 80: 849-862. 10.1007/s00253-008-1654-4.

Article
Google Scholar

Senger RS, Papoutsakis ET: Genome-scale model for *Clostridium acetobutylicum*: Part I. Metabolic network resolution and analysis. Biotechnol Bioeng. 2008, 101: 1036-1052. 10.1002/bit.22010.

Article
Google Scholar

McAnulty MJ, Yen JY, Freedman BG, Senger RS: Genome-scale modeling using flux ratio constraints to enable metabolic engineering of clostridial metabolism in silico. BMC Syst Biol. 2012, 6: 42-10.1186/1752-0509-6-42.

Article
Google Scholar

Henry CS, DeJongh M, Best AA, Frybarger PM, Linsay B, Stevens RL: High-throughput generation, optimization and analysis of genome-scale metabolic models. Nat Biotechnol. 2010, 28: 977-982. 10.1038/nbt.1672.

Article
Google Scholar

Crown SB, Indurthi DC, Ahn WS, Choi J, Papoutsakis ET, Antoniewicz MR: Resolving the TCA cycle and pentose-phosphate pathway of *Clostridium acetobutylicum* ATCC 824: Isotopomer analysis, in vitro activities and expression analysis. Biotechnol J. 2011, 6: 300-305. 10.1002/biot.201000282.

Article
Google Scholar

Au J, Choi J, Jones SW, Venkataramanan KP, Antoniewicz MR: Parallel labeling experiments validate *Clostridium acetobutylicum* metabolic network model for 13C metabolic flux analysis. Metabolic engineering, 26: 23-33. 10.1016/j.ymben.2014.08.002.

Covert MW, Palsson BO: Transcriptional regulation in constraints-based metabolic models of *Escherichia coli*. J Biol Chem. 2002, 277: 28058-28064. 10.1074/jbc.M201691200.

Article
Google Scholar

Covert MW, Schilling CH, Palsson B: Regulation of gene expression in flux balance models of metabolism. J Theor Biol. 2001, 213: 73-88. 10.1006/jtbi.2001.2405.

Article
Google Scholar

Shlomi T, Eisenberg Y, Sharan R, Ruppin E: A genome-scale computational study of the interplay between transcriptional regulation and metabolism. Mol Syst Biol. 2007, 3: 101-10.1038/msb4100141.

Article
Google Scholar

Barua D, Kim J, Reed JL: An automated phenotype-driven approach (GeneForce) for refining metabolic and regulatory models. PLoS Comput Biol. 2010, 6: e1000970-10.1371/journal.pcbi.1000970.

Article
Google Scholar

Chandrasekaran S, Price ND: Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in *Escherichia coli* and *Mycobacterium tuberculosis*. Proc Natl Acad Sci U S A. 2010, 107: 17845-17850. 10.1073/pnas.1005139107.

Article
Google Scholar

Schmidt BJ, Ebrahim A, Metz TO, Adkins JN, Palsson BO, Hyduke DR: GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data. Bioinformatics. 2013, 29: 2900-2908. 10.1093/bioinformatics/btt493.

Article
Google Scholar

Yizhak K, Gabay O, Cohen H, Ruppin E: Model-based identification of drug targets that revert disrupted metabolism and its application to ageing. Nat Commun. 2013, 4: 2632-10.1038/ncomms3632.

Article
Google Scholar

Ranganathan S, Suthers PF, Maranas CD: OptForce: an optimization procedure for identifying all genetic manipulations leading to targeted overproductions. PLoS Comput Biol. 2010, 6: e1000744-10.1371/journal.pcbi.1000744.

Article
Google Scholar

Colijn C, Brandes A, Zucker J, Lun DS, Weiner B, Farhat MR, Cheng TY, Moody DB, Murray M, Galagan JE: Interpreting expression data with metabolic flux models: predicting *Mycobacterium tuberculosis* mycolic acid production. PLoS Comput Biol. 2009, 5: e1000489-10.1371/journal.pcbi.1000489.

Article
Google Scholar

Meyer CL, Roos JW, Papoutsakis ET: Carbon-monoxide gasing leads to alcohol production and butyrate uptake without acetone formation in continuous cultures of *Clostridium acetobutylicum*. Appl Microbiol Biotechnol. 1986, 24: 159-167. 10.1007/BF01982561.

Google Scholar

Jiang Y, Xu C, Dong F, Yang Y, Jiang W, Yang S: Disruption of the acetoacetate decarboxylase gene in solvent-producing *Clostridium acetobutylicum* increases the butanol ratio. Metab Eng. 2009, 11: 284-291. 10.1016/j.ymben.2009.06.002.

Article
Google Scholar

Lehmann D, Radomski N, Lutke-Eversloh T: New insights into the butyric acid metabolism of *Clostridium acetobutylicum*. Appl Microbiol Biotechnol. 2012, 96: 1325-1339. 10.1007/s00253-012-4109-x.

Article
Google Scholar

Meyer CL, Papoutsakis ET: Increased levels of ATP and NADH are associated with increased solvent production in continuous cultures of *Clostridium acetobutylicum*. Appl Microbiol Biotechnol. 1989, 30: 450-459.

Article
Google Scholar

Vasconcelos I, Girbal L, Soucaille P: Regulation of carbon and electron flow in *Clostridium acetobutylicum* grown in chemostat culture at neutral pH on mixtures of glucose and glycerol. J Bacteriol. 1994, 176: 1443-1450.

Google Scholar

Meyer CL, Papoutsakis ET: Continuous and biomass recycle fermentations of *Clostridium acetobutylicum*.2. Novel patterns in energetics and product-formation kinetics. Bioprocess Eng. 1989, 4: 49-55. 10.1007/BF00612664.

Article
Google Scholar

Meyer CL, Papoutsakis ET: Continuous and biomass recycle fermentations of *Clostridium acetobutylicum*.1. ATP supply and demand determines product selectivity. Bioprocess Eng. 1989, 4: 1-10. 10.1007/BF00612664.

Article
Google Scholar

Cooksley CM, Zhang Y, Wang H, Redl S, Winzer K, Minton NP: Targeted mutagenesis of the *Clostridium acetobutylicum* acetone-butanol-ethanol fermentation pathway. Metab Eng. 2012, 14: 630-641. 10.1016/j.ymben.2012.09.001.

Article
Google Scholar

Kuit W, Minton NP, Lopez-Contreras AM, Eggink G: Disruption of the acetate kinase (*ack*) gene of *Clostridium acetobutylicum* results in delayed acetate production. Appl Microbiol Biotechnol. 2012, 94: 729-741. 10.1007/s00253-011-3848-4.

Article
Google Scholar

Jang YS, Lee JY, Lee J, Park JH, Im JA, Eom MH, Lee J, Lee SH, Song H, Cho JH, Seung do Y, Lee SY: Enhanced butanol production obtained by reinforcing the direct butanol-forming route in *Clostridium acetobutylicum*. MBio. 2012, 3: e00314-12. 10.1128/mBio.00314-12.

Article
Google Scholar

Lehmann D, Lutke-Eversloh T: Switching *Clostridium acetobutylicum* to an ethanol producer by disruption of the butyrate/butanol fermentative pathway. Metab Eng. 2011, 13: 464-473. 10.1016/j.ymben.2011.04.006.

Article
Google Scholar

Jones SW, Paredes CJ, Tracy B, Cheng N, Sillers R, Senger RS, Papoutsakis ET: The transcriptional program underlying the physiology of clostridial sporulation. Genome Biology. 2008, 9: R114-10.1186/gb-2008-9-7-r114.

Article
Google Scholar

Huesemann M, Papoutsakis ET: Effect of acetoacetate, butyrate, and uncoupling ionophores on growth and product formation of *Clostridium acetobutylicum*. Biotechnol Lett. 1986, 8: 37-42. 10.1007/BF01044399.

Article
Google Scholar

Husemann MHW, Papoutsakis ET: Solventogenesis in *Clostridium acetobutylicum* fermentations related to carboxylic-acid and proton concentrations. Biotechnol Bioeng. 1988, 32: 843-852. 10.1002/bit.260320702.

Article
Google Scholar

Feist AM, Scholten JC, Palsson BO, Brockman FJ, Ideker T: Modeling methanogenesis with a genome-scale metabolic reconstruction of *Methanosarcina barkeri*. Mol Syst Biol. 2006, 2: 2006 0004-10.1038/msb4100046.

Article
Google Scholar

Reed JL, Famili I, Thiele I, Palsson BO: Towards multidimensional genome annotation. Nat Rev Genet. 2006, 7: 130-141. 10.1038/nrg1769.

Article
Google Scholar

Thiele I, Palsson BO: A protocol for generating a high-quality genome-scale metabolic reconstruction. Nat Protoc. 2010, 5: 93-121. 10.1038/nprot.2009.203.

Article
Google Scholar

Kumar A, Suthers PF, Maranas CD: MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases. BMC Bioinformatics. 2012, 13: 6-10.1186/1471-2105-13-6.

Article
Google Scholar

Childs KL, Hamilton JP, Zhu W, Ly E, Cheung F, Wu H, Rabinowicz PD, Town CD, Buell CR, Chan AP: The TIGR Plant Transcript Assemblies database. Nucleic Acids Res. 2007, 35: D846-D851. 10.1093/nar/gkl785.

Article
Google Scholar

Mueller TJ, Berla BM, Pakrasi HB, Maranas CD: Rapid construction of metabolic models for a family of Cyanobacteria using a multiple source annotation workflow. BMC Syst Biol. 2013, 7: 142-10.1186/1752-0509-7-142.

Article
Google Scholar

Schellenberger J, Lewis NE, Palsson BO: Elimination of thermodynamically infeasible loops in steady-state metabolic models. Biophys J. 2011, 100: 544-553. 10.1016/j.bpj.2010.12.3707.

Article
Google Scholar

Orth JD, Thiele I, Palsson BO: What is flux balance analysis?. Nat Biotechnol. 2010, 28: 245-248. 10.1038/nbt.1614.

Article
Google Scholar

Hou XH, Peng WF, Xiong L, Huang C, Chen XF, Chen XD, Zhang WG: Engineering *Clostridium acetobutylicum* for alcohol production. J Biotechnol. 2013, 166: 25-33. 10.1016/j.jbiotec.2013.04.013.

Article
Google Scholar

Amador-Noguez D, Brasg IA, Feng XJ, Roquet N, Rabinowitz JD: Metabolome remodeling during the acidogenic-solventogenic transition in *Clostridium acetobutylicum*. Appl Environ Microbiol. 2011, 77: 7984-7997. 10.1128/AEM.05374-11.

Article
Google Scholar

Tusher VG, Tibshirani R, Chu G: Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci U S A. 2001, 98: 5116-5121. 10.1073/pnas.091062498.

Article
Google Scholar