Integrating high-throughput and computational data elucidates bacterial networks

By Markus W. Covert, E. M. Knight, Jennie L. Reed, Markus J. Herrgård, Bernhard O. Palsson. Nature, 2004

845 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/2053492a63f0e3a496a492549e85521721a369bb

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Citations in the corpus

The model organism as a system: integrating 'omics' data sets (2006, background): “Efforts have begun that are aimed at incorporating regulator”
A comprehensive genome-scale reconstruction of Escherichia coli metabolism—2011 (2011, background): “…network with reconstructions of other cellular systems such as transcription and translation (Thiele et al, 2009) or transcriptional regulation (Covert et al, 2004). iJO1366 is the most advanced and comprehensive metabolic reconstruction of any microorganism to date, and can thus continue to…”
Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods (2012, background): “6a) , or a mathematical representation of transcription regulation 109,110 or signalling 111,112 is interfaced directly with the metabolic network to aid in modelling (FIG.”
Modelling and analysis of gene regulatory networks (2008, background): “A more comprehensive model that accounts for 1,010 genes was later introduced by Covert and colleague”
Genome-scale models of microbial cells: evaluating the consequences of constraints (2004, methodology): “Constraint-based regulatory models have been built for central and genome-scale metabolic models of E. coli 51,89 .”
Systems biotechnology for strain improvement. (2005, neutral): “In a recent study by Covert et al. [ 37 ], a simulation of an”
Genome-scale models of bacterial metabolism: reconstruction and applications (2008, background): “A signiﬁcant proportion of inconsistent expression states could be corrected in these models by searching for missing interactions (Covert et al ., 2004; Herrg˚ard et al ., 2006b).”
Evolutionary programming as a platform for in silico metabolic engineering (2005, background): “Although there have been some attempts to simulate dynamic behavior of whole cell systems [8,9], currently these approaches enjoy limited applicability due to lack of kinetic and regulatory information on the whole genome scale.”
A Whole-Cell Computational Model Predicts Phenotype from Genotype (2012, positive): “Although we and others had previously developed methods to integrate ODEs with Boolean, probabilistic, and constraint-based submodels (Covert et al., 2001, 2004, 2008; Chandrasekaran and Price, 2010), the current effort involved so many different cellular functions and mathematical representations…”
Sparse graphical Gaussian modeling of the isoprenoid gene network in Arabidopsis thaliana (2004, methodology): “In simple eukaryotes or prokaryotes, gene-expression data has been combined with two-hybrid data [1] and phenotypic data [2] to successfully predict protein-protein interaction and transcriptional regulation on a large scale.”