Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0
Jan Schellenberger,Richard Que,Ronan M. T. Fleming,Ines Thiele,Jeffrey D. Orth,Adam M. Feist,Daniel C. Zielinski,Aarash Bordbar,Nathan E. Lewis,Sorena Rahmanian,Joseph Kang,Daniel R. Hyduke,Bernhard O. Palsson +12 more
TLDR
The constraint-based reconstruction and analysis toolbox as discussed by the authors is a software package running in the Matlab environment, which allows for quantitative prediction of cellular behavior using a constraintbased approach and allows predictive computations of both steady-state and dynamic optimal growth behavior, the effects of gene deletions, comprehensive robustness analyses, sampling the range of possible cellular metabolic states and the determination of network modules.Abstract:
The manner in which microorganisms utilize their metabolic processes can be predicted using constraint-based analysis of genome-scale metabolic networks. Herein, we present the constraint-based reconstruction and analysis toolbox, a software package running in the Matlab environment, which allows for quantitative prediction of cellular behavior using a constraint-based approach. Specifically, this software allows predictive computations of both steady-state and dynamic optimal growth behavior, the effects of gene deletions, comprehensive robustness analyses, sampling the range of possible cellular metabolic states and the determination of network modules. Functions enabling these calculations are included in the toolbox, allowing a user to input a genome-scale metabolic model distributed in Systems Biology Markup Language format and perform these calculations with just a few lines of code. The results are predictions of cellular behavior that have been verified as accurate in a growing body of research. After software installation, calculation time is minimal, allowing the user to focus on the interpretation of the computational results.read more
Citations
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Integration of a constraint-based metabolic model of Brassica napus developing seeds with 13C-metabolic flux analysis
TL;DR: An updated version of bna572, a bottom-up reconstruction of oilseed rape developing seeds with emphasis on representation of biomass-component biosynthesis, is reported, and improvements in predictive power of Flux Variability Analysis are demonstrated.
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Pathogenic mutations of the human mitochondrial citrate carrier SLC25A1 lead to impaired citrate export required for lipid, dolichol, ubiquinone and sterol synthesis
TL;DR: The results show that nine mutations abolish transport of citrate completely, whereas the other three reduce the transport rate by >70%, indicating that impaired citrate transport is the most likely primary cause of the disease.
Journal ArticleDOI
Comparative genome-scale metabolic modeling of actinomycetes: The topology of essential core metabolism
Mohammad Tauqeer Alam,Mohammad Tauqeer Alam,Marnix H. Medema,Eriko Takano,Rainer Breitling,Rainer Breitling +5 more
TL;DR: A comparative analysis of genome‐scale metabolic models of 37 species of actinomycetes and constructed a global enzyme association network to identify both a conserved “core network” and an “essential core network’ of the entire group.
Journal ArticleDOI
In silico identification of metabolic engineering strategies for improved lipid production in Yarrowia lipolytica by genome-scale metabolic modeling
TL;DR: This study demonstrated that eMOMA is a powerful computational method for understanding and engineering the metabolism of Y. lipolytica and potentially other oleaginous microorganisms.
Journal ArticleDOI
Reconstruction of genome-scale metabolic model of Yarrowia lipolytica and its application in overproduction of triacylglycerol
TL;DR: In this paper, a novel genome-scale metabolic model of Y. lipolytica was reconstructed based on a previous model iYL619_PCP published by our lab and another model iYali4 published by Kerkhoven et al.
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