Metabolic modeling of microbial strains in silico.

By Markus W. Covert, C. Schilling, Iman Famili, Jeremy S. Edwards, Igor Goryanin, Evgeni Selkov Jr., Bernhard O. Palsson. TIBS -Trends in Biochemical Sciences. Regular ed, 2001

347 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/07b470e52841e3facc22e000e2e03ef6d1b38d0e

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Citations in the corpus

Graph theory and networks in Biology. (2006, methodology): “In [200], the protein interaction network of S. cerevisiae was analysed using data from four different sources.”
Regulation of gene expression in flux balance models of metabolism. (2001, background): “The abundance of genomic data currently available has led to the construction of genome-scale models of microbial metabolism (Covert et al., 2001).”
An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR) (2003, background): “This iterative process [2] would be likely to produce more useful results in less-characterized organisms and has already been successful in helping to identify malate dehydrogenase in Helicobacter pylori [24] and citrate synthase in Geobacter sulfurreducens (D.”
Flux balance analysis of biological systems: applications and challenges (2009, background): “A common way of relating the cell genotype to phenotype is by analysing the metabolic fluxes [6].”
Thirteen Years of Building Constraint-Based In Silico Models of Escherichia coli (2003, methodology): “…the enzymes are assigned based on sequence homology and await biochemical characterization In the case of E. coli , the genomic information, coupled with physiological and biochemical data (10), enabled reconstruction of a genome-scale metabolic model describing the E. coli metabolic network (16).”
Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth (2002, methodology): “Oxygen consumption was measured in three different ways: (1) passing the effluent gas through a Servomex oxygen analyser (model 1140C) (Servomex); (2) calculated from the dissolved oxygen reading and k la measurements; and (3) in a respirometer chamber in a separate 70-ml flask.”
Genome-Scale Metabolic Model of Helicobacter pylori 26695 (2002, background): “It has made possible studies in comparative genomics (1, 2, 17, 34), genome-wide transcriptional profiling (16), and a host of integrated analyses aimed at understanding the systems biology of organisms (14, 25, 68).”
Genome-scale models of microbial cells: evaluating the consequences of constraints (2004, methodology): “USA 99, 15112–15117 (2002). Presents a new method for predicting metabolic flux distributions of knockout strains, and shows that the predictions matched experimental data better than flux balance analysis.”
Flux coupling analysis of genome-scale metabolic network reconstructions. (2004, background): “…sequence of byproduct secretion under increasingly anaerobic conditions (Varma et al. 1993); (3) quantitatively predicting cellular growth rates (Edwards et al. 2001; Ibarra et al. 2002); (4) assessing the performance limits of metabolic networks in response to gene additions or deletions…”
Metabolic pathways in the post-genome era. (2003, background): “network is defined using genomic, biochemical, physiological and other datasets (Fig. 2a) [ 1 ].”
Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. (2003, background): “Recently, genomescale metabolic networks were reconstructed for prokaryotic cells (Edwards and Palsson 1999; Covert et al. 2001 ), and it was demonstrated how such reconstructed metabolic models allow direct correlation between the genomic information and metabolic activity at the flux level.”