Genome-scale modeling

Price, N. D. Reed,). L. Palsson, B. O. Genome-scale models of microbial cells evaluating the consequences of constraints. Not Rev Microbiol 2004, 2 886-897. 

This overview accounts for a total of three species represented by nine reconstructed metabolic network models Notes Genome-scale models report several different parameters characterizing them... 

Genome-scale models Improved ethanol yield Bioethanol production [232]... 

Part A From Pioneers to Visionary covers the period from the early days of industrial biotechnology (Chapter 1) till the time of development of novel concepts of strain design and production, including synthetic biology, genome-scale modeling, and cell-free production (Chapters 2-4) and bridges 100 years of discovery and innovation. 

Genome-scale model for Clostridium acetobutylicum. part 1. Metabolic network resolution and analysis. Biotechnol. Bioeng., 101, 1036-1052. 

Genome-scale metabolic models Lactococcus lactis IL1403 First LAB genome-scale model metabolic engineering of central metabolism for diacetyl production Oliveira et al. (2005)... 

Table 8.3 Flux variability analysis (FVA) of maximum growth rate (1/h), a-acetolactate production rate (mmol/gow/h), and resulting yield predicted from the genome-scale model of Lactococcus lactis MG1363...

Durot, M., Bourguignon, P. Y., Schachter, V. (2009). Genome-scale models of bacterial metabolism reconstruction and applications. FEMS Microbiology Reviews, 33, 164-190. 

Pastink, M. L, Teusink, B., Hols, R, Visser, S., De Vos, W. M., Hugenholtz, J. (2009). Genome-scale model of Streptococcus thermophilus LMG18311 for metabolic comparison of lactic acid bacteria. Applied and Environmental Microbiology, 75, 3627-3633. 

McAnulty M, Yen J, Freedman B, Senger R. (2012). Genome-scale modeling using flux ratio constraints to enable metabolic engineering of clostridial metabohsm in silico. BMC Syst... 

MUne C, Eddy J, Raju R, Ardekani S, Kim P-J, Senger R, Jin Y-S, Blaschek H, Price N. (2011). Metabohc network reconstruction and genome-scale model of butanol-producing strain Clostridium beijerinckii NCIMB 8052. BMC Syst Biol, 5,130. 

Senger RS, Papoutsakis ET. (2008b). Genome-scale model for Clostridium acetobutylicum Part II. Development of specific proton flux states and numerically determined sub-systems. Biotechnol Bioeng, 101, 1053-1071. 

Blazeck J, Alper H. Systems metabolic engineering genome-scale models and beyond. Biotechnol J 2010 5 647-59. 

Mahadevan R, Palsson BO, Lovley DR. In situ to in sUico and back elucidating the physiology and ecology of Geobacter spp. using genome-scale modelling. Nat Rev Microbiol 2011 9 39-50. 

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