(Q31150221)

15 September 2017

A genome-scale Escherichia coli kinetic metabolic model k-ecoli457 satisfying flux data for multiple mutant strains (English)

1 reference

15 September 2017

1 reference

Ali Khodayari

1

1 reference

PMCID

5187423

15 September 2017

Costas D Maranas

series ordinal

2

1 reference

PMCID

5187423

15 September 2017

language of work or name

English

0 references

publication date

20 December 2016

1 reference

15 September 2017

Nature Communications

1 reference

15 September 2017

7

1 reference

15 September 2017

13806

1 reference

Creative Commons Attribution 4.0 International

15 September 2017

start time

1 December 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Metabolite concentrations, fluxes and free energies imply efficient enzyme usage

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187423

Personalized Whole-Cell Kinetic Models of Metabolism for Discovery in Genomics and Pharmacodynamics

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187423

Pseudo-transition Analysis Identifies the Key Regulators of Dynamic Metabolic Adaptations from Steady-State Data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187423

2P2Idb v2: update of a structural database dedicated to orthosteric modulation of protein-protein interactions.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187423

Software-aided cytochrome P450 reaction phenotyping and kinetic analysis in early drug discovery.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187423

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187423

The application of multi-omics and systems biology to identify therapeutic targets in chronic kidney disease

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187423

13C metabolic flux analysis at a genome-scale

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187423

Improving prediction fidelity of cellular metabolism with kinetic descriptions

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187423

Rapid Multiplex Creation of Escherichia coli Strains Capable of Interfering with Phage Infection Through CRISPR.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187423

A general framework for thermodynamically consistent parameterization and efficient sampling of enzymatic reactions

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187423

Succinate Overproduction: A Case Study of Computational Strain Design Using a Comprehensive Escherichia coli Kinetic Model

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187423

CeCaFDB: a curated database for the documentation, visualization and comparative analysis of central carbon metabolic flux distributions explored by 13C-fluxomics

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187423

The genome editing toolbox: a spectrum of approaches for targeted modification

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187423

A kinetic model of Escherichia coli core metabolism satisfying multiple sets of mutant flux data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187423

d-OptCom: Dynamic multi-level and multi-objective metabolic modeling of microbial communities

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187423

Pathway thermodynamics highlights kinetic obstacles in central metabolism

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187423

Improving fatty acid availability for bio-hydrocarbon production in Escherichia coli by metabolic engineering

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187423

The MetaboLights repository: curation challenges in metabolomics

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187423

De novo production of the flavonoid naringenin in engineered Saccharomyces cerevisiae

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187423

BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187423

EcoCyc: fusing model organism databases with systems biology

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187423

Parallel labeling experiments with [U-13C]glucose validate E. coli metabolic network model for 13C metabolic flux analysis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187423

SABIO-RK--database for biochemical reaction kinetics

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187423

Metabolic ensemble modeling for strain engineers

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187423

Large-scale 13C-flux analysis reveals distinct transcriptional control of respiratory and fermentative metabolism in Escherichia coli

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187423

Unraveling condition-dependent networks of transcription factors that control metabolic pathway activity in yeast

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187423

Modeling and simulation of the main metabolism in Escherichia coli and its several single-gene knockout mutants with experimental verification

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187423

PRIDB: a Protein-RNA interface database

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187423

OptForce: an optimization procedure for identifying all genetic manipulations leading to targeted overproductions

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187423

Towards a genome-scale kinetic model of cellular metabolism

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187423

Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187423

Acyl-CoA synthetases: fatty acid uptake and metabolic channeling

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187423

Ensemble modeling of metabolic networks

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187423

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187423

Multiple high-throughput analyses monitor the response of E. coli to perturbations

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187423

Metabolic regulation analysis of icd-gene knockout Escherichia coli based on 2D electrophoresis with MALDI-TOF mass spectrometry and enzyme activity measurements

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187423

Flux coupling analysis of genome-scale metabolic network reconstructions.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187423

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187423

Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187423

Global gene expression profiling in Escherichia coli K12. The effects of oxygen availability and FNR.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187423

Analysis of optimality in natural and perturbed metabolic networks

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187423

Genetics of pentose-phosphate pathway enzymes of Escherichia coli K-12.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187423

Regulation of the amount and of the activity of phosphofructokinases and pyruvate kinases in Escherichia coli

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187423

Bricks and blueprints: methods and standards for DNA assembly.

21 June 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS13806

Metabolic engineering of Saccharomyces cerevisiae for the production of triacetic acid lactone

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS13806

Genome-scale metabolic network modeling results in minimal interventions that cooperatively force carbon flux towards malonyl-CoA.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS13806

Towards kinetic modeling of genome-scale metabolic networks without sacrificing stoichiometric, thermodynamic and physiological constraints.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS13806

Dynamic modeling of the central carbon metabolism of Escherichia coli.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS13806

Modeling of uncertainties in biochemical reactions.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS13806

Global metabolic response of Escherichia coli to gnd or zwf gene-knockout, based on 13C-labeling experiments and the measurement of enzyme activities

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS13806

Metabolic flux analysis of Escherichia coli K12 grown on 13C-labeled acetate and glucose using GC-MS and powerful flux calculation method

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS13806

Quantitative estimation of channeling from early glycolytic intermediates to CO in intact Escherichia coli

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS13806

Analysis of Escherichia coli anaplerotic metabolism and its regulation mechanisms from the metabolic responses to altered dilution rates and phosphoenolpyruvate carboxykinase knockout

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS13806

Somewhat in control--the role of transcription in regulating microbial metabolic fluxes

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/27996047

12 December 2020

inferred from PubMed ID database lookup

Thermodynamic constraints shape the structure of carbon fixation pathways

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/27996047

12 December 2020

inferred from PubMed ID database lookup

Re-examination of metabolic fluxes in Escherichia coli during anaerobic fermentation of glucose using 13C labeling experiments and 2-dimensional nuclear magnetic resonance (NMR) spectroscopy

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS13806

7 January 2021

inferred from DOI database lookup

Effect of fadR gene knockout on the metabolism of Escherichia coli based on analyses of protein expressions, enzyme activities and intracellular metabolite concentrations

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS13806

7 January 2021

inferred from DOI database lookup

Identifiers

DOI

10.1038/NCOMMS13806

1 reference

Dimensions Publication ID

15 September 2017

0 references

0 references

1 reference

15 September 2017

1 reference

PMCID

5187423