Use of genome-scale metabolic models for understanding microbial physiology (Q37737389)

22 August 2017

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title

Use of genome-scale metabolic models for understanding microbial physiology (English)

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22 August 2017

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22 August 2017

Sergio Bordel

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22 August 2017

Liming Liu

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Rasmus Agren

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22 August 2017

language of work or name

English

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publication date

24 April 2010

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22 August 2017

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22 August 2017

volume

584

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22 August 2017

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22 August 2017

page(s)

2556-2564

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Industrial systems biology

22 August 2017

cites work

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

Towards systems metabolic engineering of microorganisms for amino acid production

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

Fed-batch culture of a metabolically engineered Escherichia coli strain designed for high-level succinate production and yield under aerobic conditions

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

Metabolic engineering of Escherichia coli and Corynebacterium glutamicum for biotechnological production of organic acids and amino acids

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

Metabolic engineering for advanced biofuels production from Escherichia coli

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

Metabolic engineering and directed evolution for the production of pharmaceuticals

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

Significant increase of glycolytic flux in Torulopsis glabrata by inhibition of oxidative phosphorylation.

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

Multiple redundant stress resistance mechanisms are induced in Salmonella enterica serovar Typhimurium in response to alteration of the intracellular environment via TLR4 signalling.

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

The role of NFAT5/TonEBP in establishing an optimal intracellular environment

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

Cell envelope stress response in Gram-positive bacteria

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

Sensing external stress: watchdogs of the Escherichia coli cell envelope

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

Use of genome-scale microbial models for metabolic engineering

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

Cofactor biosynthesis--still yielding fascinating new biological chemistry

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

Energy converting NADH:quinone oxidoreductase (complex I).

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

Availability and applications of ATP-binding cassette (ABC) transporter blockers

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

Mechanism of coupling of transport to hydrolysis in bacterial ATP-binding cassette transporters

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

ATP-dependent chromatin remodeling factors and DNA damage repair

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

Roles of NAD(+) / NADH and NADP(+) / NADPH in cell death.

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

Metabolic engineering in the -omics era: elucidating and modulating regulatory networks

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

Improving lycopene production in Escherichia coli by engineering metabolic control

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

Transcriptional regulation of nonfermentable carbon utilization in budding yeast

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

NADP Regulates the Yeast GAL Induction System

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

Regulatory genes controlling fatty acid catabolism and peroxisomal functions in the filamentous fungus Aspergillus nidulans

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

Translational regulation of GCN4 and the general amino acid control of yeast

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

Central role of Ifh1p-Fhl1p interaction in the synthesis of yeast ribosomal proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

EBIMed--text crunching to gather facts for proteins from Medline

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

Text-mining and information-retrieval services for molecular biology

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

KiPar, a tool for systematic information retrieval regarding parameters for kinetic modelling of yeast metabolic pathways

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

PPI finder: a mining tool for human protein-protein interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

Text mining and its potential applications in systems biology

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

Textpresso: an ontology-based information retrieval and extraction system for biological literature

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

PubFinder: a tool for improving retrieval rate of relevant PubMed abstracts

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

GapCoder automates the use of indel characters in phylogenetic analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

LitMiner and WikiGene: identifying problem-related key players of gene regulation using publication abstracts

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

MineBlast: a literature presentation service supporting protein annotation by data mining of BLAST results

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

KEGG Atlas mapping for global analysis of metabolic pathways

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

Flux balance analysis in the era of metabolomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

Flux balance analysis of biological systems: applications and challenges.

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

Comparative genome-scale metabolic reconstruction and flux balance analysis of multiple Staphylococcus aureus genomes identify novel antimicrobial drug targets

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

Flux balance analysis of a genome-scale yeast model constrained by exometabolomic data allows metabolic system identification of genetically different strains

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

Analysis of optimality in natural and perturbed metabolic networks

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

Exploring the overproduction of amino acids using the bilevel optimization framework OptKnock

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

An optimization framework for identifying reaction activation/inhibition or elimination candidates for overproduction in microbial systems

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

High-throughput metabolic flux analysis based on gas chromatography-mass spectrometry derived 13C constraints.

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

OptStrain: a computational framework for redesign of microbial production systems.

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

MILANO--custom annotation of microarray results using automatic literature searches

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

Identification of genome-scale metabolic network models using experimentally measured flux profiles

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

Quantitative assignment of reaction directionality in constraint-based models of metabolism: application to Escherichia coli

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

Regulatory on/off minimization of metabolic flux changes after genetic perturbations

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

Systematic phenome analysis of Escherichia coli multiple-knockout mutants reveals hidden reactions in central carbon metabolism.

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

Genetic modification of flux for flux prediction of mutants

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

Natural computation meta-heuristics for the in silico optimization of microbial strains

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

Parameter estimation using Simulated Annealing for S-system models of biochemical networks

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

Investigating metabolite essentiality through genome-scale analysis of Escherichia coli production capabilities

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

Genome-scale models of bacterial metabolism: reconstruction and applications

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

Identification of essential genes in bacteria

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

Essential genes on metabolic maps.

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

How many genes can make a cell: the minimal-gene-set concept

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

Prediction of conditional gene essentiality through graph theoretical analysis of genome-wide functional linkages

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

Experimental and computational assessment of conditionally essential genes in Escherichia coli

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

Systematic genome-wide scanning for genes involved in ATP generation in Escherichia coli

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

Exploiting the pathway structure of metabolism to reveal high-order epistasis

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

Optimal in silico target gene deletion through nonlinear programming for genetic engineering

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

A network-based method for predicting gene-nutrient interactions and its application to yeast amino-acid metabolism

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

Genome-scale analysis of Streptomyces coelicolor A3(2) metabolism

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

Systematic analysis of conservation relations in Escherichia coli genome-scale metabolic network reveals novel growth media

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

Putative regulatory sites unraveled by network-embedded thermodynamic analysis of metabolome data

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

Local protein structure prediction using discriminative models

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

Elucidation and structural analysis of conserved pools for genome-scale metabolic reconstructions

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

Global organization of metabolic fluxes in the bacterium Escherichia coli

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

Impact of global transcriptional regulation by ArcA, ArcB, Cra, Crp, Cya, Fnr, and Mlc on glucose catabolism in Escherichia coli

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

Disruption of a global regulatory gene to enhance central carbon flux into phenylalanine biosynthesis in Escherichia coli

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

Serial 13C-based flux analysis of an L-phenylalanine-producing E. coli strain using the sensor reactor.

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

Co-regulation of metabolic genes is better explained by flux coupling than by network distance

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

Global transcriptional and physiological responses of Saccharomyces cerevisiae to ammonium, L-alanine, or L-glutamine limitation

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

Increasing galactose consumption by Saccharomyces cerevisiae through metabolic engineering of the GAL gene regulatory network

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2010.04.052

10.1016/J.FEBSLET.2010.04.052

21 January 2018

Identifiers

DOI

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22 August 2017

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