Prediction of metabolic fluxes by incorporating genomic context and flux-converging pattern analyses (Q34093205)

31 July 2017

Prediction of metabolic fluxes by incorporating genomic context and flux-converging pattern analyses (English)

1 reference

31 July 2017

1 reference

3

1 reference

31 July 2017

Jong Myoung Park

1

1 reference

PubMed ID

20679215

31 July 2017

Tae Yong Kim

series ordinal

2

1 reference

PubMed ID

20679215

31 July 2017

language of work or name

English

0 references

publication date

2 August 2010

1 reference

Proceedings of the National Academy of Sciences of the United States of America

31 July 2017

1 reference

31 July 2017

107

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31 July 2017

33

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31 July 2017

14931-14936

1 reference

The primary transcriptome of the major human pathogen Helicobacter pylori

31 July 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930451

The transcription unit architecture of the Escherichia coli genome

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930451

Constraints-based genome-scale metabolic simulation for systems metabolic engineering

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930451

Using in silico models to simulate dual perturbation experiments: procedure development and interpretation of outcomes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930451

Genome-scale reconstruction and analysis of the Pseudomonas putida KT2440 metabolic network facilitates applications in biotechnology

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930451

STRING 8--a global view on proteins and their functional interactions in 630 organisms

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930451

Towards systems metabolic engineering of microorganisms for amino acid production

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930451

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930451

Dynamic analysis of integrated signaling, metabolic, and regulatory networks

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930451

Metabolic responses to pyruvate kinase deletion in lysine producing Corynebacterium glutamicum

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930451

Metabolic flux analysis and metabolic engineering of microorganisms

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930451

Systems metabolic engineering of Escherichia coli for L-threonine production

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930451

New surveyor tools for charting microbial metabolic maps.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930451

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930451

Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930451

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930451

Metabolic engineering of Escherichia coli for the production of L-valine based on transcriptome analysis and in silico gene knockout simulation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930451

Thermodynamics-based metabolic flux analysis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930451

Systematic assignment of thermodynamic constraints in metabolic network models

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930451

Metabolic networks in motion: 13C-based flux analysis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930451

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930451

The global transcriptional regulatory network for metabolism in Escherichia coli exhibits few dominant functional states.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930451

Large-scale 13C-flux analysis reveals mechanistic principles of metabolic network robustness to null mutations in yeast

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930451

Systems biotechnology for strain improvement

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930451

Hierarchical thinking in network biology: the unbiased modularization of biochemical networks.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930451

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930451

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930451

Integrating high-throughput and computational data elucidates bacterial networks

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930451

In-depth profiling of lysine-producing Corynebacterium glutamicum by combined analysis of the transcriptome, metabolome, and fluxome

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930451

Flux coupling analysis of genome-scale metabolic network reconstructions.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930451

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930451

Description and Interpretation of Adaptive Evolution of Escherichia coli K-12 MG1655 by Using a Genome-Scale In Silico Metabolic Model

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930451

Metabolic flux analysis of pykF gene knockout Escherichia coli based on 13C-labeling experiments together with measurements of enzyme activities and intracellular metabolite concentrations

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930451

In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930451

A functional genomics strategy that uses metabolome data to reveal the phenotype of silent mutations

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930451

Molecular characterization of glucokinase from Escherichia coli K-12.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930451

Towards a metabolic and isotopic steady state in CHO batch cultures for reliable isotope-based metabolic profiling.

5 July 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1003740107

Large-scale in vivo flux analysis shows rigidity and suboptimal performance of Bacillus subtilis metabolism

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1003740107

A genome-scale computational study of the interplay between transcriptional regulation and metabolism

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1003740107

Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1003740107

Effect of zwf gene knockout on the metabolism of Escherichia coli grown on glucose or acetate

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1003740107

Metabolic flux analysis for a ppc mutant Escherichia coli based on 13C-labelling experiments together with enzyme activity assays and intracellular metabolite measurements.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1003740107

Transcriptome Complexity in a Genome-Reduced Bacterium

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1003740107

Effect of lpdA gene knockout on the metabolism in Escherichia coli based on enzyme activities, intracellular metabolite concentrations and metabolic flux analysis by 13C-labeling experiments

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2930451

Ab initio prediction of thermodynamically feasible reaction directions from biochemical network stoichiometry

28 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20679215

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1073/PNAS.1003740107

1 reference

31 July 2017

0 references

1 reference

31 July 2017

1 reference

PubMed ID

20679215