Genome-scale metabolic model

Schilling CH, Covert MW, Famili I, Church GM, Edwards JS, Palsson BO. Genome-scale metabolic model of Helicobacter pylori 26695. J Bacteriol 2002 184 4582-93. 

Akesson M, Lorster J, Nielsen J (2004) Integration of gene expression data into genome-scale metabolic models. Metab Eng 6 285-293... 

Table 5 Reconstructed genome-scale metabolic models of S. cerevisiae, Aspergillus niger, and A. oryzae completed by December 2008... 

Fig. 2 Simplified workflow for the reconstruction of genome-scale metabolic models and their use in simulating cellular function through flux balance analysis...

Additionally, genome-scale metabolic models (GSMMs) provide a framework for organizing, integrating, and analyzing omics data. A figure showing the basic steps and a simplified workflow [14,110] for reconstruction of metabolic models is shown in Fig. 2. 

Mahadevan, R. and Schilling, C.H. (2003) The effects of alternate optimal solutions in constraint-based genome-scale metabolic models. Metab. Eng. 5, 264-276. 

Large-scale regulatory network reconstructions can be converted to in silico models that allow systematic analysis of network behavior in response to changes in environmental conditions. These models can be combined further with genome-scale metabolic models to build integrated models of cellular function including both metabolism and its regulation [41]. 

Gasser, B., Maurer, M. et al. (2010) Genome-scale metabolic model of methylotrophic yeast Pichia pastoris and its use for in silico analysis of heterologous protein production. Biotechnol. J., 5, 705-715. 

In the following, we will detail the DD method and then outline a new algorithm for the calculation of short EFMs that will make the DD method fit for the analysis of genome-scale metabolic models. 

Kinetic models and genome-scale metabolic models... 

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

Flahaut, N. A. L., Wiersma, A., Bunt, B., Martens, D. E., Schaap, P. J., Sijtsma, L., et al. (2013). Genome-scale metabolic model for Lactococcus lactis MG1363 and its application to the analysis of flavor formation. Applied Microbiology and Biotechnology, 1-11. 

Teusink, B., Wiersma, A., Molenaar, D., Francke, C., De Vos, W. M., Siezen, R. J., et al. (2006). Analysis of growth of Lactobacillus plantarum WCFSl on a complex medium using a genome-scale metabolic model. Journal of Biological Chemistry, 40041 0048. 

Santos F, Boele J, Teusink B (2011) A practical guide to genome-scale metabolic models and their analysis. Methods Sys Biol 500 509-532. Elsevier Inc... 

Henry CS, DeJongh M, Best AA, Frybarger PM, Linsay B, Stevens RL (2010) High-throughput generation, optimization and analysis of genome-scale metabolic models. Nat Biotech... 

Jensen P, Lutz K, Papin J (2011) Tiger toolbox for integrating genome-scale metabolic models, expression data, and transcriptional regulatory networks. BMC Syst Biol 5 147 Jevremovic D, Trinh CT, Srienc F, Boley D (2010) On algebraic properties of extreme pathways in metabolic networks. J Comput Biol 17 107-119... 

Duarte NC, Herrgard MJ, Palsson BO (2004) Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model. Genome Res 14 1298-1309... 

In Silico Prediction of Metabolic Flux Profiles Using a Genome-Scale Metabolic Model of C. glutamicum... 

Construction of genome-scale metabolic model based on steady stale assumplion -s... 

Fig. 13.7 Concept of prediction of metabolic flux profiles using genome-scale metabolic model...

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