Genome-scale thermodynamic analysis of Escherichia coli metabolism (Q42155867)

17 October 2017

Genome-scale thermodynamic analysis of Escherichia coli metabolism (English)

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17 October 2017

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Vassily Hatzimanikatis

series ordinal

4

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17 October 2017

3

Linda J Broadbelt

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17 October 2017

Christopher S Henry

1

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PMCID

1367295

17 October 2017

Matthew D Jankowski

series ordinal

2

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PMCID

1367295

17 October 2017

language of work or name

English

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publication date

18 November 2005

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17 October 2017

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17 October 2017

90

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17 October 2017

4

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17 October 2017

1453-1461

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Metabolic control analysis under uncertainty: framework development and case studies

17 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367295

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=1367295

Identifying constraints that govern cell behavior: a key to converting conceptual to computational models in biology?

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367295

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=1367295

The first step of histidine biosynthesis.

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367295

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=1367295

Stoichiometric network theory for nonequilibrium biochemical systems

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367295

Energy balance for 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=1367295

Endothelial cell surface F1-F0 ATP synthase is active in ATP synthesis and is inhibited by angiostatin

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367295

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=1367295

KEGG: kyoto encyclopedia of genes and genomes

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367295

Metabolic flux ratio analysis of genetic and environmental modulations of Escherichia coli central carbon 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=1367295

KEGG: Kyoto Encyclopedia of Genes and Genomes

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367295

Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110.

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367295

Enzymes of clostridial purine fermentation. Methylenetetrahydrofolate dehydrogenase.

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367295

Cellular concentrations of enzymes and their substrates

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367295

Estimation of standard Gibbs energy changes of biotransformations

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367295

Metabolic capabilities of Escherichia coli: I. synthesis of biosynthetic precursors and cofactors.

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367295

Equations and calculations of product yields and preferred pathways for butanediol and mixed-acid fermentations.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367295

Construction of lycopene-overproducing E. coli strains by combining systematic and combinatorial gene knockout targets.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367295

Thermodynamic-based computational profiling of cellular regulatory control in hepatocyte metabolism

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367295

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=1367295

Thermodynamic constraints for biochemical 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=1367295

Probing the performance limits of the Escherichia coli metabolic network subject to gene additions or deletions

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367295

Robustness analysis of the Escherichia coli metabolic network

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367295

Enzymatic reaction rate limits with constraints on equilibrium constants and experimental parameters

17 August 2018

1 reference

12 December 2020

Group contributions for estimating standard gibbs energies of formation of biochemical compounds in aqueous solution

1 reference

12 December 2020

Calculation of standard transformed Gibbs energies and standard transformed enthalpies of biochemical reactants

1 reference

12 December 2020

Steady state kinetics of ATP synthesis and hydrolysis coupled calcium transport catalyzed by the reconstituted sarcoplasmic reticulum ATPase

1 reference

12 December 2020

10.1529/BIOPHYSJ.105.071720

Identifiers

DOI

1 reference

17 October 2017

1 reference

17 October 2017

1 reference

PMCID

1367295