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Using Genome-scale Models to Predict Biological Capabilities
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20 November 2019
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title
Using Genome-scale Models to Predict Biological Capabilities
(English)
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20 November 2019
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Jonathan M Monk
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20 November 2019
Bernhard Palsson
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Bernhard O Palsson
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20 November 2019
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Edward J O'Brien
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20 November 2019
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1 May 2015
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20 November 2019
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Cell
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Europe PubMed Central
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4451052
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20 November 2019
volume
161
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20 November 2019
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5
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20 November 2019
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971-987
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20 November 2019
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Functional characterization of alternate optimal solutions of Escherichia coli's transcriptional and translational machinery
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Systematic phenome analysis of Escherichia coli multiple-knockout mutants reveals hidden reactions in central carbon metabolism.
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Connecting extracellular metabolomic measurements to intracellular flux states in yeast
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Use of randomized sampling for analysis of metabolic networks
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The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli
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Intracellular crowding defines the mode and sequence of substrate uptake by Escherichia coli and constrains its metabolic activity.
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Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli
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Metabolic modeling of a mutualistic microbial community.
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Systems approach to refining genome annotation
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Integrating high-throughput and computational data elucidates bacterial networks
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Thirteen years of building constraint-based in silico models of Escherichia coli
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4451052
retrieved
29 September 2017
Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4451052
retrieved
2 June 2018
Computational reconstruction of tissue‐specific metabolic models: application to human liver metabolism
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4451052
retrieved
2 June 2018
Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4451052
retrieved
2 June 2018
Update on the Keio collection of Escherichia coli single-gene deletion mutants
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4451052
retrieved
2 June 2018
Thermodynamics-based metabolic flux analysis
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4451052
retrieved
2 June 2018
Parallel adaptive evolution cultures of Escherichia coli lead to convergent growth phenotypes with different gene expression states
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4451052
retrieved
2 June 2018
Systems properties of the Haemophilus influenzae Rd metabolic genotype
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4451052
retrieved
2 June 2018
Long-term phenotypic evolution of bacteria.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4451052
retrieved
27 November 2018
Generation of an atlas for commodity chemical production in Escherichia coli and a novel pathway prediction algorithm, GEM-Path
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4451052
retrieved
27 November 2018
Genetics. Predicting microbial growth
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4451052
retrieved
27 November 2018
Optimizing genome-scale network reconstructions
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4451052
retrieved
27 November 2018
Characterization and modelling of interspecies electron transfer mechanisms and microbial community dynamics of a syntrophic association
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4451052
retrieved
27 November 2018
Multidimensional optimality of microbial metabolism
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4451052
retrieved
27 November 2018
Evolutionary trade-offs, Pareto optimality, and the geometry of phenotype space.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4451052
retrieved
27 November 2018
rBioNet: A COBRA toolbox extension for reconstructing high-quality biochemical networks
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4451052
retrieved
27 November 2018
Emergent cooperation in microbial metabolism
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4451052
retrieved
27 November 2018
A genome-scale metabolic model accurately predicts fluxes in central carbon metabolism under stress conditions.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4451052
retrieved
27 November 2018
(13)C-based metabolic flux analysis.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4451052
retrieved
27 November 2018
Metabolic gene-deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4451052
retrieved
27 November 2018
The challenges of in silico biology
1 reference
stated in
PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4451052
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27 November 2018
Network-based prediction of human tissue-specific metabolism
1 reference
stated in
PubMed
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https://pubmed.ncbi.nlm.nih.gov/26000478
retrieved
12 December 2020
based on heuristic
inferred from PubMed ID database lookup
Identifiers
DOI
10.1016/J.CELL.2015.05.019
2 references
stated in
Consolidated OpenCitations Corpus – April 2017
OpenCitations bibliographic resource ID
454678
stated in
Europe PubMed Central
PMC publication ID
4451052
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26000478%20AND%20SRC:MED&resulttype=core&format=json
retrieved
20 November 2019
OpenCitations bibliographic resource ID
454678
1 reference
stated in
Consolidated OpenCitations Corpus – April 2017
OpenCitations bibliographic resource ID
454678
PMC publication ID
4451052
2 references
stated in
Consolidated OpenCitations Corpus – April 2017
OpenCitations bibliographic resource ID
454678
stated in
Europe PubMed Central
PMC publication ID
4451052
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26000478%20AND%20SRC:MED&resulttype=core&format=json
retrieved
20 November 2019
PubMed publication ID
26000478
2 references
stated in
Consolidated OpenCitations Corpus – April 2017
OpenCitations bibliographic resource ID
454678
stated in
Europe PubMed Central
PMC publication ID
4451052
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26000478%20AND%20SRC:MED&resulttype=core&format=json
retrieved
20 November 2019
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