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
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Cellular Plasticity in Response to Suppression of Storage Proteins in the Brassica napus Embryo.
Hardy Rolletschek,Jörg Schwender,Christina König,Kent D. Chapman,Trevor B. Romsdahl,Christin Lorenz,Hans-Peter Braun,Peter Denolf,Katrien Van Audenhove,Eberhard Munz,Nicolas Heinzel,Stefan Ortleb,Twan Rutten,Sean R. McCorkle,Taras Borysyuk,André Guendel,Hai Shi,Michiel Vander Auwermeulen,Stéphane Bourot,Ljudmilla Borisjuk +19 more
TL;DR: Cellular plasticity in seeds protects against perturbations to its storage capabilities and, hence, contributes materially to homeostasis.
Journal ArticleDOI
Proteomic and Transcriptomic Changes in Hibernating Grizzly Bears Reveal Metabolic and Signaling Pathways that Protect against Muscle Atrophy.
D. A. Mugahid,T. G. Sengul,X. You,Yongbo Wang,Leif Steil,Nora Bergmann,Michael H. Radke,Andreas Ofenbauer,M. Gesell-Salazar,András Balogh,Stefan Kempa,Baris Tursun,Charles T. Robbins,Uwe Völker,Wei Chen,L. Nelson,Michael Gotthardt,Michael Gotthardt +17 more
TL;DR: This work shows how metabolism and atrophy signaling are regulated in skeletal muscle of hibernating grizzly bear and identifies several genes differentially regulated during hibernation, including Pdk4 and Serpinf1.
Journal ArticleDOI
Gene knockout identification for metabolite production improvement using a hybrid of genetic ant colony optimization and flux balance analysis
Abdul Hakim Mohamed Salleh,Mohd Saberi Mohamad,Safaai Deris,Sigeru Omatu,Florentino Fdez-Riverola,Juan M. Corchado,Juan M. Corchado +6 more
TL;DR: This paper proposes a hybrid of Genetic Ant Colony Optimization and Flux Balance Analysis namely GACOFBA to find the optimal gene knockout that increase the production of the target metabolite and shows that the proposed hybrid algorithm able to identify the best set of genes and increase theProduction while maintaining the optimal growth rate.
Journal ArticleDOI
Using bioconductor package BiGGR for metabolic flux estimation based on gene expression changes in brain.
Anand Gavai,Farahaniza Supandi,Hannes Hettling,Paul Murrell,Jack A. M. Leunissen,Johannes H. G. M. van Beek +5 more
TL;DR: A new algorithm termed Least-squares with equalities and inequalities Flux Balance Analysis (Lsei-FBA) is introduced to predict flux changes from gene expression changes, for instance during disease.
Journal ArticleDOI
Metabolomics assisted metabolic network modeling and network wide analysis of metabolites in microbiology
TL;DR: This review will examine recent progress in the application of metabolomics approaches in metabolic network modeling and network wide analysis of microbial cell metabolism.
References
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