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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Metabolic engineering of enhanced glycerol-3-phosphate synthesis to increase lipid production in Synechocystis sp. PCC 6803
TL;DR: It is demonstrated that enhanced G3P synthesis was an important factor in photosynthetic lipid production and that introducing heterologous GPD and DGAT genes was an effective strategy to increase lipid production in Synechocystis sp.
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BiologicalNetworks 2.0 - an integrative view of genome biology data
Sergey Kozhenkov,Yulia Dubinina,Mayya Sedova,Amarnath Gupta,Julia Ponomarenko,Julia Ponomarenko,Michael Baitaluk +6 more
TL;DR: The new release of BiologicalNetworks together with its back-end database introduces extensive functionality for a more efficient integrated multi-level analysis of microarray, sequence, regulatory, and other data.
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Expanding the computable reactome inPseudomonas putidareveals metabolic cycles providing robustness
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Improvement of Acetaldehyde Production in Zymomonas mobilis by Engineering of Its Aerobic Metabolism.
Uldis Kalnenieks,Elina Balodite,Steffi Strähler,Inese Strazdina,Julia Rex,Agris Pentjuss,Katsuya Fuchino,Per Bruheim,Reinis Rutkis,Katherine M. Pappas,Robert K. Poole,Oliver Sawodny,Katja Bettenbrock +12 more
TL;DR: Two mutant strains were selected, with acetaldehyde yield close to 70% of the theoretical maximum value, almost twice the previously published yield for Z. mobilis, which can serve as a basis for further development of industrial acetaldehyde producers.
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Genome-scale modelling of microbial metabolism with temporal and spatial resolution
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