Thirteen Years of Building Constraint-Based In Silico Models of Escherichia coli

By Jennie L. Reed, Bernhard O. Palsson. Journal of Bacteriology, 2003

333 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/9128021ac64e784583ad1c311bbd02633658ae64

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Citations in the corpus

Genome-scale models of microbial cells: evaluating the consequences of constraints (2004, methodology): “The analysis of microorganism phenotypic functions on a genome-scale using COBRA has developed rapidly in recent years 3,26 .”
Genome-scale models of bacterial metabolism: reconstruction and applications (2008, background): “Similarly, upper bounds on the reaction rates can be known from measurements or theory and included in the model as additional constraints on the reaction ﬂuxes (Reed & Palsson, 2003).”
Graph theory and networks in Biology. (2006, background): “However, in all four cases, the degree distribution appeared to be broad-tailed and to be best described by some form of modified power law.”
Putative regulatory sites unraveled by network-embedded thermodynamic analysis of metabolome data (2006, background): “For the E. coli data set, we employed the genome-scale model iJR904 developed by Palsson and co-workers (Reed et al , 2003), which is an elementally balanced stoichiometric network.”
The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli (2008, background): “(5) Using the network reconstruction, evolutionary studies have examined the cellular network in the context of adaptive evolution events81, horizontal gene transfer80,81 and minimal metabolic network evolution82.”
Flux coupling analysis of genome-scale metabolic network reconstructions. (2004, background): “…abundance of complete genome sequences has enabled the generation of genome-scale metabolic reconstructions for various microorganisms (Covert et al. 2001; Price et al. 2003; Reed and Palsson 2003) These models provide a largely complete skeleton of the metabolic reactions present in an organism .”
Using Genome-Scale Models to Predict Biological Capabilities (2015, positive): “Thus, a vision was laid out in 2003 that the path to whole-cell models was conceptually possible and that such models could be used as a context for mechanistically integrating disparate omic data types (Reed and Palsson, 2003).”
An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR) (2003, methodology): “Since computational models of E. coli will continue to grow in size and scope [ 7 ] it will become important to be able to distinguish between the different models - a naming convention will aid in this effort.”
Identifying global regulators in transcriptional regulatory networks in bacteria. (2003, background): “See also a historical summary account in Reed and Palsson (2003) [68].”
A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information (2007, background): “After reconstruction of the enzymatically catalyzed reactions in the pathway, there was no continuous pathway for the de novo generation of L-proline.”