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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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What is flux balance analysis?

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

2010

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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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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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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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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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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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Systematizing the generation of missing metabolic knowledge

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

2010

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Genome-scale models in human metabologenomics

Nature reviews. Genetics, 2024-09

2024

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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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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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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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Genetic basis of growth adaptation of Escherichia coli after deletion of pgi, a major metabolic gene

PLoS genetics, 2010-11, Vol.6 (11), p.e1001186

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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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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Mass Action Stoichiometric Simulation Models: Incorporating Kinetics and Regulation into Stoichiometric Models

Biophysical journal, 2010-01, Vol.98 (2), p.175-185

2010

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Comparative analysis of regulatory elements between Escherichia coli and Klebsiella pneumoniae by genome-wide transcription start site profiling

PLoS genetics, 2012-08, Vol.8 (8), p.e1002867-e1002867

2012

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RNA polymerase mutants found through adaptive evolution reprogram Escherichia coli for optimal growth in minimal media

Proceedings of the National Academy of Sciences - PNAS, 2010-11, Vol.107 (47), p.20500-20505

2010

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MS/MS networking guided analysis of molecule and gene cluster families

Proceedings of the National Academy of Sciences - PNAS, 2013-07, Vol.110 (28), p.E2611-E2620

2013

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Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions

Molecular systems biology, 2010-10, Vol.6 (1), p.422-n/a

2010

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Towards genome-scale signalling network reconstructions

Nature reviews. Genetics, 2010-04, Vol.11 (4), p.297-307

2010

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Microbial laboratory evolution in the era of genome‐scale science

Molecular systems biology, 2011, Vol.7 (1), p.509-n/a

2011

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Metabolic network reconstruction of Chlamydomonas offers insight into light‐driven algal metabolism

Molecular systems biology, 2011, Vol.7 (1), p.518-n/a

2011

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

What is flux balance analysis?

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

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

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

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

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

Systematizing the generation of missing metabolic knowledge

Genome-scale models in human metabologenomics

Use of Randomized Sampling for Analysis of Metabolic Networks

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

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

Genetic basis of growth adaptation of Escherichia coli after deletion of pgi, a major metabolic gene

Applications of genome-scale metabolic reconstructions

Elimination of Thermodynamically Infeasible Loops in Steady-State Metabolic Models

Mass Action Stoichiometric Simulation Models: Incorporating Kinetics and Regulation into Stoichiometric Models

Comparative analysis of regulatory elements between Escherichia coli and Klebsiella pneumoniae by genome-wide transcription start site profiling

RNA polymerase mutants found through adaptive evolution reprogram Escherichia coli for optimal growth in minimal media

MS/MS networking guided analysis of molecule and gene cluster families

Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions

Towards genome-scale signalling network reconstructions

Microbial laboratory evolution in the era of genome‐scale science

Metabolic network reconstruction of Chlamydomonas offers insight into light‐driven algal metabolism

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