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Software and Methods for Computational Flux Balance Analysis
2020As genetic engineering of organisms has grown easier and more precise, computational modeling of metabolic systems has played an increasingly important role in both guiding experimental interventions and in understanding the results of metabolic perturbations.
Peter C, St John, Yannick J, Bomble
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Comparison and analysis of objective functions in flux balance analysis
Biotechnology Progress, 2014Flux balance analysis (FBA) is currently one of the most important and used techniques for estimation of metabolic reaction rates (fluxes). This mathematical approach utilizes an optimization criterion in order to select a distribution of fluxes from the feasible space delimited by the metabolic reactions and some restrictions imposed over them ...
Carlos Eduardo, García Sánchez +1 more
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Flux Balance Analysis Within Physiologically Feasible Region
2009 3rd International Conference on Bioinformatics and Biomedical Engineering, 2009Flux balance analysis (FBA) has emerged as an ef- fective means to quantitatively analyze cell steady-state metabolic behaviors. However, regardless of environmental factors, basal FBA predictions usually represent the theoretical capabilities of the cell which may not be biologically meaningful.
Haoran Zheng +3 more
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Flux Balance Analysis: Interrogating Genome-Scale Metabolic Networks
2009Flux balance analysis (FBA) is a computational method to analyze reconstructions of biochemical networks. FBA requires the formulation of a biochemical network in a precise mathematical framework called a stoichiometric matrix. An objective function is defined (e.g., growth rate) toward which the system is assumed to be optimized.
Matthew A, Oberhardt +2 more
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Robust flux balance analysis of metabolic networks
Proceedings of the 2011 American Control Conference, 2011Metabolic networks describe the set of biochemical reactions and regulatory interactions of metabolism that govern the phenotypical properties of a cell. Analysis of such networks is critical not only to promote biological knowledge, but also in drug discovery, where it can be used to identify and knockout the targeted pathways.
Michael M. Zavlanos, A. Agung Julius
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Flux Balance Analysis of Mammalian Cell Systems
Flux balance analysis (FBA) is a computational methodology to model and analyze the metabolic behavior of cells. In this chapter, we break down the key steps for formulating an FBA model and other FBA-derived methodologies in the context of mammalian cell biology, including strain design, developing cell line-specific models, and conducting flux ...James, Morrissey +2 more
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Elementary Flux Modes, Flux Balance Analysis, and Their Application to Plant Metabolism
2013In recent years the number of sequenced and annotated plant genomes has increased significantly, and novel approaches are required to retrieve valuable information from these data sets. The field of systems biology has accelerated the simulation and prediction of phenotypes derived from specific genotypic modifications under defined growth conditions ...
Katrin, Lotz +4 more
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Identification of active constraints in dynamic flux balance analysis
Biotechnology Progress, 2016This study deals with the calibration of dynamic metabolic flux models that are formulated as the maximization of an objective subject to constraints. Two approaches were applied for identifying the constraints from data. In the first approach a minimal active number of limiting constraints is found based on data that are assumed ...
Ali, Nikdel, Hector, Budman
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Flux Balance Analysis as an Alternative Method to Estimate Fluxes Without Labeling
2013The analysis of plant metabolic networks essentially contributes to the understanding of the efficiency of plant systems in terms of their biotechnological usage. Metabolic fluxes are determined by biochemical parameters such as metabolite concentrations as well as enzyme properties and activities, which in turn are the result of various regulatory ...
Eva, Grafahrend-Belau +3 more
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The application of flux balance analysis in systems biology
WIREs Systems Biology and Medicine, 2010AbstractAn increasing number of genome‐scale reconstructions of intracellular biochemical networks are being generated. Coupled with these stoichiometric models, several systems‐based approaches for probing these reconstructions in silico have been developed.
Erwin P, Gianchandani +2 more
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