The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli

By Adam M. Feist, Bernhard O. Palsson. Nature Biotechnology, 2008

586 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/99bcc889a16586aa8340b381442c9a16f9e53597

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In Molecular Biology

Citations in the corpus

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0 (2007, unknown): “308" language="eng" publish="issue" relation="no"> Introduction COBRA methods have been successfully used in the field of microbial metabolic engineerin”
High-throughput generation, optimization and analysis of genome-scale metabolic models (2010, background): “A ll ri g h ts r es er ve d . nature biotechnology doi:10.1038/nbt.1672 Equation (3) enforces the bounds on the reaction fluxes (vi) and the values of the reaction use variables (zi).”
Genome-scale models of bacterial metabolism: reconstruction and applications (2008, background): “An increasing sub-set is being assessed and corrected against large-scale experimental data (see Table 4), and an impressive array of analytical studies has been applied to the most popular ones, for example E. coli (Feist & Palsson, 2008).”
The Biomass Objective Function (2010, unknown): “The constraint-based formalism has been shown to work at the genome-scale [2,3].”
Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods (2012, background): “This mathematical representation enables the computation of phenotypic state”
Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli (2013, methodology): “The following paragraphs will focus on the most recent advances in biological network analysis; the reader is referenced to Feist and Palsson (2008) and Oberhardt et al (2009) for less recent examples not covered in the main text.”
A comprehensive genome-scale reconstruction of Escherichia coli metabolism—2011 (2011, background): “coli metabolic reconstruction to date, and like its predecessors, it will likely aid in many new discoveries”
Effects of abiotic stress on plants: a systems biology perspective (2011, background): “In addition, network reconstructions at the genome-scale are key to quantifying and characterizing the genotype to phenotype relationships [2].”
Reconstruction of Genome-Scale Active Metabolic Networks for 69 Human Cell Types and 16 Cancer Types Using INIT (2012, methodology): “Understanding the function of metabolism therefore requires analysis of the complete metabolic network, and this is best done through the use of so-called genome-scale metabolic models (GEMs) [4,5,6].”
Applications of genome-scale metabolic reconstructions (2009, background): “As the applications of E. coli genome-scale models have been reviewed earlier in detail (Feist and Palsson, 2008), we specifically exclude E. coli from this review, and instead focus on the many other target organisms that have been studied.”
Bioremediation approaches for organic pollutants: a critical perspective. (2011, background): “The ‘network theory,’ thus forms a basis for studying the functional properties and mechanisms involved in the organization of biological systems and predicting their responses to environmental (both internal and external) variations (Feist and Palsson, 2008).”
COBRApy: COnstraints-Based Reconstruction and Analysis for Python (2013, methodology): “Constraint based modeling approaches have been widely applied in the field of microbial metabolic engineering [1,2] and have been employed in the analysis [3-5] and, to a lesser extent, modeling of transcriptional [6-8] and signaling [9] networks.”
BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions (2010, unknown): “Case studies have been reviewed in [10].”
Using Genome-Scale Models to Predict Biological Capabilities (2015, unknown): “It has been successfully applied to a multitude of species for modeling their cellular metabolisms (Feist and Palsson, 2008; McCloskey et al., 2013; Oberhardt et al., 2009) and therefore enabled a variety of applications such as metabolic engineering for the over-production of biochemicals (Yim et a”
A protocol for generating a high-quality genome-scale metabolic reconstruction (2010, methodology): “Often, the reconstruction process is iterative, as demonstrated by the metabolic network of Escherichia coli , whose reconstruction has been expanded and refined over the last 19 years 7 .”