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Dynamic flux balance analysis of diauxic growth in Escherichia coli.
Flux Balance Analysis (FBA) has been used in the past to analyze microbial metabolic networks. Typically, FBA is used to study the metabolic flux at a particular steady state of the system. However,… Expand
Advances in flux balance analysis.
- Kenneth J. Kauffman, P. Prakash, J. Edwards
- Biology, Medicine
- Current opinion in biotechnology
- 1 October 2003
Biology is going through a paradigm shift from reductionist to holistic, systems-based approaches. The complete genome sequence for a number of organisms is available and the analysis of genome… Expand
The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities.
The Escherichia coli MG1655 genome has been completely sequenced. The annotated sequence, biochemical information, and other information were used to reconstruct the E. coli metabolic map. The… Expand
In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data
A significant goal in the post-genome era is to relate the annotated genome sequence to the physiological functions of a cell. Working from the annotated genome sequence, as well as biochemical and… Expand
Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth
Annotated genome sequences can be used to reconstruct whole-cell metabolic networks. These metabolic networks can be modelled and analysed (computed) to study complex biological functions. In… Expand
Metabolic modelling of microbes: the flux-balance approach.
One area of active research in this area has focused on bacterial metabolism (van Gulik and Heijnen, 1995; Liao et al., 1996; Lee et al., 1997; Sauer et al., 1998; Edwards and Palsson, 1999; Sauer… Expand
Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions
BackgroundGenome sequencing and bioinformatics are producing detailed lists of the molecular components contained in many prokaryotic organisms. From this 'parts catalogue' of a microbial cell, in… Expand
Combining pathway analysis with flux balance analysis for the comprehensive study of metabolic systems.
- C. Schilling, J. Edwards, D. Letscher, B. Palsson
- Chemistry, Medicine
- Biotechnology and bioengineering
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 emphasis… Expand
Metabolic modeling of microbial strains in silico.
- M. Covert, C. Schilling, +4 authors B. Palsson
- Medicine, Biology
- Trends in biochemical sciences
- 1 March 2001
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 cellular… Expand
Robustness Analysis of the Escherichiacoli Metabolic Network
Genomic, biochemical, and strain‐specific data can be assembled to define an in silico representation of the metabolic network for a select group of single cellular organisms. Flux‐balance analysis… Expand