Accomplishments in genome-scale in silico modeling for industrial and medical biotechnology (Q35178614)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19946878%20AND%20SRC:MED&resulttype=core&format=json

13 February 2020

review article

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title

Accomplishments in genome-scale in silico modeling for industrial and medical biotechnology (English)

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13 February 2020

0 references

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13 February 2020

Nathan D Price

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4

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13 February 2020

author name string

Caroline B Milne

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1

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13 February 2020

James A Eddy

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3

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13 February 2020

publication date

1 December 2009

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13 February 2020

published in

Biotechnology Journal

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13 February 2020

volume

4

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13 February 2020

issue

12

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13 February 2020

page(s)

1653-1670

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Genome-scale gene/reaction essentiality and synthetic lethality analysis

13 February 2020

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

28 July 2018

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Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction

28 July 2018

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Connecting extracellular metabolomic measurements to intracellular flux states in yeast

28 July 2018

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Genome-scale reconstruction of Escherichia coli's transcriptional and translational machinery: a knowledge base, its mathematical formulation, and its functional characterization

28 July 2018

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A fragile metabolic network adapted for cooperation in the symbiotic bacterium Buchnera aphidicola

28 July 2018

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A genome-scale metabolic reconstruction of Mycoplasma genitalium, iPS189

28 July 2018

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Genome-scale constraint-based modeling of Geobacter metallireducens

28 July 2018

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targetTB: a target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis

28 July 2018

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Genome-scale models of bacterial metabolism: reconstruction and applications

28 July 2018

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Systems biology approaches to bioremediation

28 July 2018

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

28 July 2018

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A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology

28 July 2018

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Iterative reconstruction of a global metabolic model of Acinetobacter baylyi ADP1 using high-throughput growth phenotype and gene essentiality data

28 July 2018

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Genome-scale model for Clostridium acetobutylicum: Part I. Metabolic network resolution and analysis

28 July 2018

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The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation: a scaffold to query lipid metabolism

28 July 2018

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The implications of human metabolic network topology for disease comorbidity

28 July 2018

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

28 July 2018

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Improved annotation through genome-scale metabolic modeling of Aspergillus oryzae

28 July 2018

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28 July 2018

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Human metabolic network reconstruction and its impact on drug discovery and development

28 July 2018

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28 July 2018

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28 July 2018

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28 July 2018

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28 July 2018

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Genome-scale metabolic network analysis of the opportunistic pathogen Pseudomonas aeruginosa PAO1

28 July 2018

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Systems metabolic engineering of Escherichia coli for L-threonine production

28 July 2018

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Metabolic reconstruction and modeling of nitrogen fixation in Rhizobium etli

28 July 2018

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The Edinburgh human metabolic network reconstruction and its functional analysis

28 July 2018

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Impact of systems biology on metabolic engineering of Saccharomyces cerevisiae

28 July 2018

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Metabolite essentiality elucidates robustness of Escherichia coli metabolism

28 July 2018

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Modeling Neisseria meningitidis metabolism: from genome to metabolic fluxes

28 July 2018

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Genome-scale reconstruction of metabolic network in Bacillus subtilis based on high-throughput phenotyping and gene essentiality data

28 July 2018

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

28 July 2018

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28 July 2018

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

28 July 2018

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Metabolic modeling of a mutualistic microbial community.

28 July 2018

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Systems analysis of energy metabolism elucidates the affected respiratory chain complex in Leigh's syndrome

28 July 2018

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Global reconstruction of the human metabolic network based on genomic and bibliomic data

28 July 2018

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Matrix formalism to describe functional states of transcriptional regulatory systems

28 July 2018

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

28 July 2018

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

28 July 2018

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Chance and necessity in the evolution of minimal metabolic networks

28 July 2018

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Evolutionary programming as a platform for in silico metabolic engineering

28 July 2018

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Metabolic engineering of Escherichia coli for enhanced production of succinic acid, based on genome comparison and in silico gene knockout simulation

28 July 2018

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Use of constraint-based modeling for the prediction and validation of antimicrobial targets

28 July 2018

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In silico genome-scale reconstruction and validation of the Staphylococcus aureus metabolic network.

28 July 2018

1 reference

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Expanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an in silico genome-scale characterization of single- and double-deletion mutants

28 July 2018

1 reference

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Modeling Lactococcus lactis using a genome-scale flux model

28 July 2018

1 reference

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Metabolic footprinting and systems biology: the medium is the message

28 July 2018

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

28 July 2018

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Modeling hybridoma cell metabolism using a generic genome-scale metabolic model of Mus musculus

28 July 2018

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Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: an initial draft to the two-dimensional annotation

28 July 2018

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

28 July 2018

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Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model

28 July 2018

1 reference

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Integrating high-throughput and computational data elucidates bacterial networks

28 July 2018

1 reference

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Advances in flux balance analysis

28 July 2018

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Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network

28 July 2018

1 reference

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

28 July 2018

1 reference

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Initial sequencing and comparative analysis of the mouse genome

28 July 2018

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Analysis of optimality in natural and perturbed metabolic networks

28 July 2018

1 reference

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Dynamic flux balance analysis of diauxic growth in Escherichia coli

28 July 2018

1 reference

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Genome-scale metabolic model of Helicobacter pylori 26695.

28 July 2018

1 reference

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Regulation of gene expression in flux balance models of metabolism

28 July 2018

1 reference

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

28 July 2018

1 reference

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The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities

28 July 2018

1 reference

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Assessment of the metabolic capabilities of Haemophilus influenzae Rd through a genome-scale pathway analysis

28 July 2018

1 reference

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Interpreting expression data with metabolic flux models: predicting Mycobacterium tuberculosis mycolic acid production

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160784

A dynamic, genome-scale flux model of Lactococcus lactis to increase specific recombinant protein expression

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160784

Enhancing sesquiterpene production in Saccharomyces cerevisiae through in silico driven metabolic engineering.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160784

Gene deletion of cytosolic ATP: citrate lyase leads to altered organic acid production in Aspergillus niger

27 September 2018

1 reference

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In silico analysis of the effects of H2 and CO2 on the metabolism of a capnophilic bacterium Mannheimia succiniciproducens.

27 September 2018

1 reference

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Metabolite-centric approaches for the discovery of antibacterials using genome-scale metabolic networks

27 September 2018

1 reference

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Steady-state and dynamic flux balance analysis of ethanol production by Saccharomyces cerevisiae.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160784

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

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160784

Reconstruction of biochemical networks in microorganisms

27 September 2018

1 reference

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Elucidation of metabolism in hybridoma cells grown in fed-batch culture by genome-scale modeling.

27 September 2018

1 reference

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Metabolic engineering of microorganisms for biofuels production: from bugs to synthetic biology to fuels

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160784

In silico genome-scale reconstruction and validation of the Corynebacterium glutamicum metabolic network

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160784

Metabolic network model of a human oral pathogen.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160784

A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160784

Genome-scale reconstruction and in silico analysis of the Clostridium acetobutylicum ATCC 824 metabolic network

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160784

Geobacter sulfurreducens strain engineered for increased rates of respiration

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160784

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

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160784

Selection of objective function in genome scale flux balance analysis for process feed development in antibiotic production

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160784

Antibiotic overproduction in Streptomyces coelicolor A3 2 mediated by phosphofructokinase deletion

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160784

Reconstruction, modeling & analysis of Halobacterium salinarum R-1 metabolism

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160784

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

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160784

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

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160784

Genome-scale analysis of Mannheimia succiniciproducens metabolism.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160784

Analysis of growth of Lactobacillus plantarum WCFS1 on a complex medium using a genome-scale metabolic model.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160784

Genome-scale in silico aided metabolic analysis and flux comparisons of Escherichia coli to improve succinate production.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160784

Characterization of metabolism in the Fe(III)-reducing organism Geobacter sulfurreducens by constraint-based modeling

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160784

In silico aided metabolic engineering of Saccharomyces cerevisiae for improved bioethanol production

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160784

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

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160784

Lethality and synthetic lethality in the genome-wide metabolic network of Escherichia coli.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160784

In silico design and adaptive evolution of Escherichia coli for production of lactic acid.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160784

Identifying gene targets for the metabolic engineering of lycopene biosynthesis in Escherichia coli.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160784

Animal cell cultures: recent achievements and perspectives in the production of biopharmaceuticals

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160784

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

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160784

Modular epistasis in yeast metabolism.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160784

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

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160784

In Silico Metabolic Model and Protein Expression of Haemophilus influenzae Strain Rd KW20 in Rich Medium

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160784

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

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160784

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

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160784

Experimental Determination and System Level Analysis of Essential Genes in Escherichia coli MG1655

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160784

Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160784

Multiple knockout analysis of genetic robustness in the yeast metabolic network

27 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19946878

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Network-based prediction of human tissue-specific metabolism

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19946878

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1002/BIOT.200900234

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19946878%20AND%20SRC:MED&resulttype=core&format=json

13 February 2020

1 reference

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19946878%20AND%20SRC:MED&resulttype=core&format=json

13 February 2020

PubMed publication ID

19946878

1 reference