Genome-scale models of microbial cells: evaluating the consequences of constraints

By Nathan D. Price, Jennie L. Reed, Bernhard O. Palsson. Nature Reviews Microbiology, 2004

1,090 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/88d6f5962c0adc754f08f43294d6c982a29d34c3

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Citations in the corpus

Advances in Host Plant and Rhizobium Genomics to Enhance Symbiotic Nitrogen Fixation in Grain Legumes (2015, background): “…approach Advances in Host Plant and Rhizobium Genomics 83 Advances in Agronomy, First Edition, 2015, 1–116 and the flux balance analysis (FBA) (Price et al., 2004; Varma and Palsson, 1994), Resendis-Antonio et al. (2007) presented a genome-scale metabolic reconstruction (iOR363) model for R.…”
Genome-scale models of bacterial metabolism: reconstruction and applications (2008, methodology): “…studies, and the resulting sets of coupled reactions were for instance compared with correlations observed in the transcriptional states of enzymes (Reed & Palsson, 2004; Notebaart et al ., 2008), interpreted with respect to the structure of the metabolic regulation (Notebaart et al ., 2008), and…”
A methodology for the structural and functional analysis of signaling and regulatory networks (2006, methodology): “Papin and coworkers [14,15] were the first to adapt methods from the constraint-based approach (frequently used for structural analysis of metabolic networks [11]) to analyze stoichiometric models of signaling pathways.”
Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0 (2007, neutral): “A wide variety of COBRA methods have been developed over the year”
Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli (2008, methodology): “Two extensions of FBA of interest here are the use of multiple FBA steps to simulate growth dynamics (Luo et al ., 2006; Mahadevan et al ., 2002; Varma and Palsson, 1994), and the incorporation of transcriptional regulatory network models (Covert et al ., 2001; Shlomi et al ., 2005, 2007).”
Permafrost Meta-Omics and Climate Change (2016, background): “Genome-scale models provide the necessary elements to translate sequence information from metagenomes into a set of possible metabolic reactions involving substrate utilization and their resulting products (metabolites and fluxes) (Price et al. 2004).”
The implications of human metabolic network topology for disease comorbidity (2008, background): “Significant improvements are expected from more accurate reconstructions of the human metabolic network, from the appearance of cell type-specific metabolic network reconstructions, and from improvements in flux balance-based modeling approaches (17, 41).”
Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis (2010, background): “Metabolic networks are typically reconstructed and analyzed by using detailed chemistry-based methods (1, 2), whereas transcriptional regulatory networks have typically been reconstructed based on high-throughput protein–DNA interaction data and statistical inference of functional relationships from”
The model organism as a system: integrating 'omics' data sets (2006, methodology): “The constraint-based reconstruction and analysis (COBRA) techniqu”
Network-based prediction of human tissue-specific metabolism (2008, background): “Specifically, a highly expressed reaction is considered to be active if it carries a significant positive flux that is greater than a positive threshold e (equation (3)) or a significant negative flux o –e (equation (4) for reversible reactions).”
The Biomass Objective Function (2010, neutral): “It is needed to perform a variety of Constraint-Based Reconstruction and Analysis (COBRA) methods [21].”
Quantifying absolute protein synthesis rates reveals principles underlying allocation of cellular resources. (2014, methodology): “In addition, the global analysis of maximum reaction velocity (V max ) can be used in concert with flux balance analysis (Price et al., 2004; Schuetz et al., 2012) to identify possible routes of metabolic flux at a given condition.”
Introduction to systems biology. (2007, background): “In much the same way as genome sequencing has lead to the emergence of the theoretical analysis of genomes (bioinformatics), has the availability of the entire metabolic, signaling, and gene networks of cells led to the development of theoretical analyses of networks [6, 54].”
Context-Specific Metabolic Networks Are Consistent with Experiments (2008, methodology): “The great majority of the lower and upper bounds do not correspond to an RMF and are set to the same value as in a standard FBA problem, usually to arbitrarily high and low values, but sometimes to finite values as for input constraints (glucose uptake, for example) and irreversible reactions.”