Regulation of gene expression in flux balance models of metabolism.

By Markus W. Covert, C. Schilling, Bernhard O. Palsson. Journal of Theoretical Biology, 2001

468 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/435eee25b4a44b781f3ceb0db7de58adbd1a1e96

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Citations in the corpus

Flux balance analysis in the era of metabolomics (2006, unknown): “concentrations [25, 27, 30].”
Flux balance analysis of biological systems: applications and challenges (2009, background): “ENHANCEMENTSTO FBAMODELS Incorporation of regulatory information The first attempts to integrate regulatory information into metabolic networks were made by Palsson and co-workers, who integrated regulatory constraints into FBA models (regulatory FBA; rFBA), using Boolean logic operators [12, 31, 33”
Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis (2010, background): “Currently themost commonlyusedgenome-scale analysismethod that links the transcriptome of an organism with metabolism is regulatoryflux balance analysis (RFBA) (8, 10).”
Genome-scale models of microbial cells: evaluating the consequences of constraints (2004, background): “To account for the effects of transcriptional regulation, a Boolean representation of the transcriptional regulatory network can be constructed 89,97 .”
Optknock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization (2003, unknown): “coli models currently under development (Covert et al., 2001; Covert and Palsson, 2002).”
Interpreting Expression Data with Metabolic Flux Models: Predicting Mycobacterium tuberculosis Mycolic Acid Production (2009, methodology): “similar to the approach used to predict phenotypes from gene knockouts using FBA [1–3] and for coupling Boolean regulatory models with metabolic models [8].”
Integrating high-throughput and computational data elucidates bacterial networks (2004, methodology): “The whole model construction and simulation process has been described elsewhere in detai”
A Whole-Cell Computational Model Predicts Phenotype from Genotype (2012, unknown): “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…”
Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli (2008, methodology): “, 2006), and the incorporation of transcriptional regulatory network models (Covert et al., 2001; Shlomi et al., 2005, 2007).”
Genome-scale models of bacterial metabolism: reconstruction and applications (2008, methodology): “We will conclude the review with a discussion on future directions in the ﬁeld.”