(Q42101147)

16 October 2017

Optimal flux spaces of genome-scale stoichiometric models are determined by a few subnetworks (English)

1 reference

16 October 2017

0 references

4

Frank J Bruggeman

1 reference

16 October 2017

3

Leen Stougie

1 reference

16 October 2017

Steven M Kelk

1

1 reference

16 October 2017

Brett G Olivier

series ordinal

2

1 reference

16 October 2017

language of work or name

English

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publication date

15 August 2012

1 reference

16 October 2017

1 reference

16 October 2017

2

1 reference

16 October 2017

580

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Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported

16 October 2017

start time

15 August 2012

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

exact match

https://scigraph.springernature.com/pub.10.1038/srep00580

0 references

cites work

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3419370

Genome-scale metabolic modeling elucidates the role of proliferative adaptation in causing the Warburg effect

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3419370

Elimination of thermodynamically infeasible loops in steady-state metabolic models

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3419370

High-throughput generation, optimization and analysis of genome-scale metabolic models

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3419370

Sampling the solution space in genome-scale metabolic networks reveals transcriptional regulation in key enzymes

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3419370

The biomass objective function

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3419370

What is flux balance analysis?

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3419370

The ArcBA two-component system of Escherichia coli is regulated by the redox state of both the ubiquinone and the menaquinone pool

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3419370

Applications of genome-scale metabolic reconstructions

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3419370

Understanding the adaptive growth strategy of Lactobacillus plantarum by in silico optimisation

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3419370

Use of randomized sampling for analysis of metabolic networks

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3419370

Large-scale computation of elementary flux modes with bit pattern trees

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3419370

Intracellular crowding defines the mode and sequence of substrate uptake by Escherichia coli and constrains its metabolic activity.

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3419370

A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3419370

Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rv using the in silico strain iNJ661 and proposing alternative drug targets

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3419370

Systematic assignment of thermodynamic constraints in metabolic network models

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3419370

Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3419370

Modelling strategies for the industrial exploitation of lactic acid bacteria

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3419370

Reconstructing the metabolic network of a bacterium from its genome

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3419370

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

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3419370

Uniform sampling of steady-state flux spaces: means to design experiments and to interpret enzymopathies.

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3419370

Modelling cellular systems with PySCeS.

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3419370

Genome-scale in silico models of E. coli have multiple equivalent phenotypic states: assessment of correlated reaction subsets that comprise network states.

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3419370

Reconstruction and functional characterization of the human mitochondrial metabolic network based on proteomic and biochemical data

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3419370

Flux coupling analysis of genome-scale metabolic network reconstructions.

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3419370

The effects of alternate optimal solutions in constraint-based genome-scale metabolic models

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3419370

An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3419370

Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3419370

Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3419370

A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3419370

Multidimensional optimality of microbial metabolism

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3419370

A practical guide to genome-scale metabolic models and their analysis

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3419370

Genome-scale model of Streptococcus thermophilus LMG18311 for metabolic comparison of lactic acid bacteria

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3419370

Enumerating constrained elementary flux vectors of metabolic networks.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3419370

Functional stoichiometric analysis of metabolic networks.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3419370

Expa: a program for calculating extreme pathways in biochemical reaction networks

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3419370

An improved algorithm for stoichiometric network analysis: theory and applications.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3419370

Monte Carlo sampling can be used to determine the size and shape of the steady-state flux space

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3419370

Reconstructing metabolic flux vectors from extreme pathways: defining the alpha-spectrum

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3419370

A new constraint-based description of the steady-state flux cone of metabolic networks

17 August 2018

1 reference

Crossref

https://api.crossref.org/works/10.1038%2FSREP00580

21 January 2018

Identifiers

DOI

10.1038/SREP00580

1 reference

Dimensions Publication ID

16 October 2017

0 references

1 reference

16 October 2017

PubMed publication ID

22896812

1 reference