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An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)
BackgroundDiverse datasets, including genomic, transcriptomic, proteomic and metabolomic data, are becoming readily available for specific organisms. There is currently a need to integrate theseExpand
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Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective.
Cellular metabolism is most often described and interpreted in terms of the biochemical reactions that make up the metabolic network. Genomics is providing near complete information regarding theExpand
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Flux coupling analysis of genome-scale metabolic network reconstructions.
In this paper, we introduce the Flux Coupling Finder (FCF) framework for elucidating the topological and flux connectivity features of genome-scale metabolic networks. The framework is demonstratedExpand
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Regulation of gene expression in flux balance models of metabolism.
Genome-scale metabolic networks can now be reconstructed based on annotated genomic data augmented with biochemical and physiological information about the organism. Mathematical analysis can beExpand
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Characterization of Metabolism in the Fe(III)-Reducing Organism Geobacter sulfurreducens by Constraint-Based Modeling
ABSTRACT Geobacter sulfurreducens is a well-studied representative of the Geobacteraceae, which play a critical role in organic matter oxidation coupled to Fe(III) reduction, bioremediation ofExpand
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Genome-scale Reconstruction of Metabolic Network in Bacillus subtilis Based on High-throughput Phenotyping and Gene Essentiality Data*
In this report, a genome-scale reconstruction of Bacillus subtilis metabolism and its iterative development based on the combination of genomic, biochemical, and physiological information andExpand
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Genome-scale microbial in silico models: the constraints-based approach.
Genome sequencing and annotation has enabled the reconstruction of genome-scale metabolic networks. The phenotypic functions that these networks allow for can be defined and studied usingExpand
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Combining pathway analysis with flux balance analysis for the comprehensive study of metabolic systems.
The elucidation of organism-scale metabolic networks necessitates the development of integrative methods to analyze and interpret the systemic properties of cellular metabolism. A shift in emphasisExpand
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Metabolic modeling of microbial strains in silico.
The large volume of genome-scale data that is being produced and made available in databases on the World Wide Web is demanding the development of integrated mathematical models of cellularExpand
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Metabolic Pathway Analysis: Basic Concepts and Scientific Applications in the Post‐genomic Era
This article reviews the relatively short history of metabolic pathway analysis. Computer‐aided algorithms for the synthesis of metabolic pathways are discussed. Important algebraic concepts used inExpand
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