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A protocol for generating a high-quality genome-scale metabolic reconstruction

Nature protocols, 2010-01, Vol.5 (1), p.93-121

2010

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Reconstruction of biochemical networks in microorganisms

Nature reviews. Microbiology, 2009-02, Vol.7 (2), p.129-143

2009

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What is flux balance analysis?

Nature biotechnology, 2010-03, Vol.28 (3), p.245-248

2010

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BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions

BMC bioinformatics, 2010-04, Vol.11 (1), p.213-213, Article 213

2010

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

Nature biotechnology, 2008-06, Vol.26 (6), p.659-667

2008

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Comparative genome-scale modelling of Staphylococcus aureus strains identifies strain-specific metabolic capabilities linked to pathogenicity

Proceedings of the National Academy of Sciences - PNAS, 2016-06, Vol.113 (26), p.E3801-E3809

2016

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Genome‐scale models of metabolism and gene expression extend and refine growth phenotype prediction

Molecular systems biology, 2013, Vol.9 (1), p.693-n/a

2013

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Basic and applied uses of genome‐scale metabolic network reconstructions of Escherichia coli

Molecular systems biology, 2013, Vol.9 (1), p.661-n/a

2013

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Drug off-target effects predicted using structural analysis in the context of a metabolic network model

PLoS computational biology, 2010-09, Vol.6 (9), p.e1000938-e1000938

2010

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Enhancement of carotenoid biosynthesis in the green microalga Dunaliella salina with light-emitting diodes and adaptive laboratory evolution

Applied microbiology and biotechnology, 2013-03, Vol.97 (6), p.2395-2403

2013

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Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments

Proceedings of the National Academy of Sciences - PNAS, 2013-12, Vol.110 (50), p.20338-20343

2013

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Use of Randomized Sampling for Analysis of Metabolic Networks

The Journal of biological chemistry, 2009-02, Vol.284 (9), p.5457-5461

2009

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Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0

Nature protocols, 2011-09, Vol.6 (9), p.1290-1307

2011

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Maximizing biomass productivity and cell density of Chlorella vulgaris by using light-emitting diode-based photobioreactor

Journal of biotechnology, 2012-10, Vol.161 (3), p.242-249

2012

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Global reconstruction of the human metabolic network based on genomic and bibliomic data

Proceedings of the National Academy of Sciences - PNAS, 2007-02, Vol.104 (6), p.1777-1782

2007

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In situ to in silico and back: elucidating the physiology and ecology of Geobacter spp. using genome-scale modelling

Nature reviews. Microbiology, 2011-01, Vol.9 (1), p.39-50

2011

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The model organism as a system: integrating 'omics' data sets

Nature reviews. Molecular cell biology, 2006-03, Vol.7 (3), p.198-210

2006

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Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways

PLoS computational biology, 2015-08, Vol.11 (8), p.e1004321-e1004321

2015

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Systems biology and biotechnology of Streptomyces species for the production of secondary metabolites

Biotechnology advances, 2014-03, Vol.32 (2), p.255-268

2014

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Adaptive Evolution of Escherichia coli K-12 MG1655 during Growth on a Nonnative Carbon Source, L-1,2-Propanediol

Applied and Environmental Microbiology, 2010-07, Vol.76 (13), p.4158-4168

2010

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Elimination of Thermodynamically Infeasible Loops in Steady-State Metabolic Models

Biophysical journal, 2011-02, Vol.100 (3), p.544-553

2011

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A comprehensive genome‐scale reconstruction of Escherichia coli metabolism—2011

Molecular systems biology, 2011-10, Vol.7 (1), p.535-n/a

2011

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Systematizing the generation of missing metabolic knowledge

Biotechnology and bioengineering, 2010-10, Vol.107 (3), p.403-412

2010

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Applications of genome-scale metabolic reconstructions

Molecular systems biology, 2009, Vol.5 (1), p.320-n/a

2009

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Reconstructing organisms in silico: genome-scale models and their emerging applications

Nature reviews. Microbiology, 2020-12, Vol.18 (12), p.731-743

2020

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A protocol for generating a high-quality genome-scale metabolic reconstruction

Reconstruction of biochemical networks in microorganisms

What is flux balance analysis?

BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions

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

Comparative genome-scale modelling of Staphylococcus aureus strains identifies strain-specific metabolic capabilities linked to pathogenicity

Genome‐scale models of metabolism and gene expression extend and refine growth phenotype prediction

Basic and applied uses of genome‐scale metabolic network reconstructions of Escherichia coli

Drug off-target effects predicted using structural analysis in the context of a metabolic network model

Enhancement of carotenoid biosynthesis in the green microalga Dunaliella salina with light-emitting diodes and adaptive laboratory evolution

Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments

Use of Randomized Sampling for Analysis of Metabolic Networks

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0

Maximizing biomass productivity and cell density of Chlorella vulgaris by using light-emitting diode-based photobioreactor

Global reconstruction of the human metabolic network based on genomic and bibliomic data

In situ to in silico and back: elucidating the physiology and ecology of Geobacter spp. using genome-scale modelling

The model organism as a system: integrating 'omics' data sets

Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways

Systems biology and biotechnology of Streptomyces species for the production of secondary metabolites

Adaptive Evolution of Escherichia coli K-12 MG1655 during Growth on a Nonnative Carbon Source, L-1,2-Propanediol

Elimination of Thermodynamically Infeasible Loops in Steady-State Metabolic Models

A comprehensive genome‐scale reconstruction of Escherichia coli metabolism—2011

Systematizing the generation of missing metabolic knowledge

Applications of genome-scale metabolic reconstructions

Reconstructing organisms in silico: genome-scale models and their emerging applications

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