Energy balance for analysis of complex metabolic networks.

By Daniel A. Beard, S. Liang, Hong Qian. Biophysical Journal, 2002

411 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/b14990c03f2ea0fd4a043ef72b3cf250ad29c0ba

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Citations in the corpus

A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information (2007, background): “Conversely, the thermodynamic properties represent physicochemical limitations that can be estimated and taken into account”
Flux balance analysis in the era of metabolomics (2006, methodology): “where c denotes the vector that defines the coefficients, or weights, for each of the fluxes in v [18].”
Genome-scale models of bacterial metabolism: reconstruction and applications (2008, methodology): “To prevent models from predicting such unrealistic metabolic modes, extensions of the modeling framework were proposed that directly enforce these laws (Beard et al ., 2002).”
Putative regulatory sites unraveled by network-embedded thermodynamic analysis of metabolome data (2006, methodology): “In this regard, the second law of thermodynamics was incorporated into stoichiometric models (Beard et al , 2002; Price et al , 2002; Yang et al , 2005) or Gibbs energies of reaction were used to analyze metabolic pathways or small networks (Mavrovouniotis, 1993; Pissarra and Nielsen, 1997; Beard…”
Evolutionary programming as a platform for in silico metabolic engineering (2005, result): “There are, however, some other approaches to determine flux distributions, especially for deletion mutants that might not be capable of realizing the same objective function as the wild-type strain [19-21].”
Flux balance analysis of biological systems: applications and challenges (2009, methodology): “Qian and co-workers have proposed an alternative method, involving an energy balance analysis, through the imposition of non-linear constraints, which arise from the introduction of free energy changes into the constraints [37].”
Thirteen Years of Building Constraint-Based In Silico Models of Escherichia coli (2003, methodology): “…constraints, osmotic balances, or electroneutrality, should further reduce the allowable solution space, resulting in more accurate predictions. framework for implementing energy balance constraints (3, 44) has already been developed and applied to the central metabolic network of E. coli (3).”
Thermodynamics-based metabolic flux analysis. (2007, neutral): “; r1 L jDrG9 i is knowng; (14) DrG9i Kyi , 0; fi 1⁄4 r; .”
Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods (2012, methodology): “2) by removing thermodynamically infeasible pathway uses 95–97 or constraining flux according to Gibbs free energy calculations 54,98,99 .”