CASOP GS: Computing intervention strategies targeted at production improvement in genome-scale metabolic networks

GCB 2010 - German Conference on Bioinformatics 2010

Volumn , Issue , 2010, Pages 71-80

  Bohl, Katrin ^a,b   De Figueiredo, Luís F ^a   Hädicke, Oliver ^c   Klamt, Steffen ^c   Kost, Christian ^b   Schuster, Stefan ^a   Kaleta, Christoph ^a  

^a FRIEDRICH SCHILLER UNIVERSITY JENA   (Germany)

^b MAX PLANCK INSTITUTE FOR CHEMICAL ECOLOGY   (Germany)

^c MAX PLANCK INSTITUTE FOR DYNAMICS OF COMPLEX TECHNICAL SYSTEMS   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

E. COLI; FLUX DISTRIBUTIONS; GENOME-SCALE METABOLIC NETWORK; INTERVENTION STRATEGY; METABOLIC CAPABILITIES; METABOLIC NETWORK; OVER-EXPRESSION; PRODUCTION IMPROVEMENT; REACTION NETWORK; REGULATORY NETWORK; SOURCE CODES; TARGET COMPOUND;

AMINO ACIDS; BIOINFORMATICS; DESIGN; ESCHERICHIA COLI; METABOLISM;

GENES;

EID: 84856571424     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (19)

1. H. Alper and G. Stephanopoulos. Engineering for biofuels: Exploiting innate microbial capacity or importing biosynthetic potential? Nat Rev Microbiol, 7(10):715-723, Oct 2009.
2. T. Baba, T. Ara, M. Hasegawa, Y. Takai, Y. Okumura, M. Baba, K. A. Datsenko, M. Tomita, B. L. Wanner, and H. Mori. Construction of Escherichia coli K-12 inframe, single-gene knockout mutants: the Keio collection. Mol Syst Biol, 2:2006.0008, 2006.
3. A. P. Burgard, P. Pharkya, and C. D. Maranas. Optknock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization. Biotechnol Bioeng, 84(6):647-657, Dec 2003.
4. H. J. Brons and A. J. Zehnder. Aerobic nitrate and nitrite reduction in continuous cultures of Escherichia coli E4. Arch Microbiol, 153(6):531-536, 1990.
5. L. F. de Figueiredo, A. Podhorski, A. Rubio, C. Kaleta, J. E. Beasley, S. Schuster, and F. J. Planes. Computing the shortest elementary flux modes in genome-scale metabolic networks. Bioinformatics, 25(23):3158-3165, Dec 2009.
6. A. M. Feist, C. S. Henry, J. L. Reed, M. Krummenacker, A. R. Joyce, P. D. Karp, L. J. Broadbelt, V. Hatzimanikatis, and B. Ø. Palsson. A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Mol Syst Biol, 3:121, 2007.
7. O. Hadicke and S. Klamt. CASOP: A computational approach for strain optimization aiming at high productivity. J Biotechnol, 147(2):88-101, May 2010.
8. C. Kaleta, L. F. de Figueiredo, J. Behre, and S. Schuster. EFMEvolver: Computing elementary flux modes in genome-scale metabolic networks. In I. Grosse, S. Neumann, S. Posch, F. Schreiber, and P. Stadler, editors, Lecture Notes in Informatics-Proceedings, volume P-157, pages 179-189, Bonn, 2009. Gesellschaft fur Informatik.
9. C. Kaleta, L. F. de Figueiredo, and S. Schuster. Can the whole be less than the sum of its parts? Pathway analysis in genome-scale metabolic networks using elementary flux patterns. Genome Res, 19(10):1872-1883, Oct 2009.
10. S. Kind, W. K. Jeong, H. Schroder, and C. Wittmann. Systems-wide metabolic pathway engineering in Corynebacterium glutamicum for bio-based production of diaminopentane. Metab Eng, Apr 2010. In print.
11. J. Kim and J. L. Reed. OptORF: Optimal metabolic and regulatory perturbations for metabolic engineering of microbial strains. BMC Syst Biol, 4(1):53, Apr 2010.
12. S. Klamt and J. Stelling. Combinatorial complexity of pathway analysis in metabolic networks. Mol Biol Rep, 29(1-2):233-236, 2002.
13. H. Lin, G. N. Bennett, and K.-Y. San. Metabolic engineering of aerobic succinate production systems in Escherichia coli to improve process productivity and achieve the maximum theoretical succinate yield. Metab Eng, 7(2):116-127, Mar 2005.
14. S. Y. Lee. Systems biotechnology. Genome Inform, 23(1):214-216, Oct 2009.
15. E. C. C. Lin and D. R. Kuritzkes. Escherichia coli and Salmonella typhimurium-Cellular and Molecular Biology, volume I, chapter 16-Pathways for anaerobic electron transport, pages 201-221. ASM, Washington, 1987.
16. D. Na, T. Y. Kim, and S. Y. Lee. Construction and optimization of synthetic pathways in metabolic engineering. Curr Opin Microbiol, Mar 2010. In print.
17. K. R. Patil, I. Rocha, J. Forster, and J. Nielsen. Evolutionary programming as a platform for in silico metabolic engineering. BMC Bioinformatics, 6:308, 2005.
18. S. Schuster, T. Dandekar, and D. A. Fell. Detection of elementary flux modes in biochemical networks: A promising tool for pathway analysis and metabolic engineering. Trends Biotechnol, 17(2):53-60, Feb 1999.
19. N. Tepper and T. Shlomi. Predicting metabolic engineering knockout strategies for chemical production: Accounting for competing pathways. Bioinformatics, 26(4):536-543, Feb 2010.