Advances in flux balance analysis.

By Kenneth J. Kauffman, Purusharth Prakash, Jeremy S. Edwards. Current Opinion in Biotechnology, 2003

822 citations recorded by the source corpus.

Subfields: Biomedical Engineering, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/2d5d892d83e579348ddcd4f62086d110a31c8990

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Citations in the corpus

Flux balance analysis of biological systems: applications and challenges (2009, methodology): “Practically, a finite upper bound can be imposed, which may also be decided based on the knowledge of cellular thermodynamics or actual measurements [13].”
Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis (2010, methodology): “(17) and uses FBA (18) for modeling metabolic networks.”
Shifts in growth strategies reflect tradeoffs in cellular economics (2009, methodology): “…related to growth rate, may be maximized has been successfully applied in theoretical models of microbial growth to predict experimentally observed growth strategies related to gene expression (Dekel and Alon, 2005) and global metabolic phenomena (Pfeiffer et al, 2001; Kauffman et al, 2003).”
Generic Strategies for Chemical Space Exploration (2013, background): “Two of the most prominent ones are Flux Balance Analysis [14] and Elementary Mode Analysis [15].”
Flux balance analysis in the era of metabolomics (2006, background): “Consequently, this set of linear equations is under-determined [23].”
The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli (2008, neutral): “) that has been utilized in most of the studies reviewed here for the general application of flux balance analysis (FBA”
Reconstruction of cellular signalling networks and analysis of their properties (2005, background): “Stoichiometric models of metabolic networks are well developed and have been found to be quite informativ”
Recent Developments in Parameter Estimation and Structure Identification of Biochemical and Genomic Systems (2009, neutral): “[12].”
Putative regulatory sites unraveled by network-embedded thermodynamic analysis of metabolome data (2006, background): “FBA employs linear programming to optimize a suitable cellular objective, while assuming steady state for the mass balances (Kauffman et al , 2003; Price et al , 2003).”
A methodology for the structural and functional analysis of signaling and regulatory networks (2006, methodology): “Flux Balance Analysis is another related technique often used for phenotype predictions of metabolic mutants [11,27].”
Genome-scale models of microbial cells: evaluating the consequences of constraints (2004, neutral): “Frequently, the constraints and the objective function are linear functions, so linear optimization or linear programming (LP) can be used 20,37,38 .”
Modular epistasis in yeast metabolism (2005, methodology): “cerevisiae using the framework of flux balance analysis (FBA), a mathematical method for computing whole-cell metabolic fluxes and growth rates based on steady-state and optimality assumption”
Environments that Induce Synthetic Microbial Ecosystems (2010, methodology): “(hr)21) at a genome scale, e.g. using flux balance analysis (FBA) [56,24].”
Graph theory and networks in Biology. (2006, background): “The results of this paper indicate that, for all 43 networks studied, the distributions of in-degree, Pin(k), and out-degree, Pout(k), have tails of the form (3), with 2 γ 3.”
Evolutionary programming as a platform for in silico metabolic engineering (2005, methodology): “the fluxes through all metabolic reactions) is to use flux balance analysis (FBA) [13,14].”