(Q37023365)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23870272%20AND%20SRC:MED&resulttype=core&format=json

5 March 2020

title

Quantitative assessment of thermodynamic constraints on the solution space of genome-scale metabolic models (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23870272%20AND%20SRC:MED&resulttype=core&format=json

5 March 2020

1

Joshua J Hamilton

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23870272%20AND%20SRC:MED&resulttype=core&format=json

5 March 2020

2

Vivek Dwivedi

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23870272%20AND%20SRC:MED&resulttype=core&format=json

5 March 2020

3

Jennifer L Reed

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23870272%20AND%20SRC:MED&resulttype=core&format=json

5 March 2020

language of work or name

English

0 references

publication date

1 July 2013

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23870272%20AND%20SRC:MED&resulttype=core&format=json

5 March 2020

number of pages

11

1 reference

based on heuristic

inferred from page(s)

published in

Biophysical Journal

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23870272%20AND%20SRC:MED&resulttype=core&format=json

5 March 2020

volume

105

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23870272%20AND%20SRC:MED&resulttype=core&format=json

5 March 2020

page(s)

512-522

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23870272%20AND%20SRC:MED&resulttype=core&format=json

5 March 2020

issue

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23870272%20AND%20SRC:MED&resulttype=core&format=json

Quantitative assignment of reaction directionality in a multicompartmental human metabolic reconstruction.

5 March 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3714879

Identification of functional differences in metabolic networks using comparative genomics and constraint-based models

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3714879

An integrated open framework for thermodynamics of reactions that combines accuracy and coverage.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3714879

Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3714879

Chemical basis of metabolic network organization

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3714879

Hydrophobicity and charge shape cellular metabolite concentrations

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3714879

Engineered reversal of the β-oxidation cycle for the synthesis of fuels and chemicals

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3714879

Elimination of thermodynamically infeasible loops in steady-state metabolic models

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3714879

Thermodynamic analysis of regulation in metabolic networks using constraint-based modeling

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3714879

OptORF: Optimal metabolic and regulatory perturbations for metabolic engineering of microbial strains

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3714879

What is flux balance analysis?

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3714879

Applications of genome-scale metabolic reconstructions

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3714879

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3714879

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3714879

Thermodynamic analysis of biodegradation pathways

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3714879

Group contribution method for thermodynamic analysis of complex metabolic networks

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3714879

Multicopy suppression underpins metabolic evolvability

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3714879

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3714879

Including metabolite concentrations into flux balance analysis: thermodynamic realizability as a constraint on flux distributions in metabolic networks

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3714879

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3714879

Systematic assignment of thermodynamic constraints in metabolic network models

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3714879

Experimental and computational assessment of conditionally essential genes in Escherichia coli

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3714879

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3714879

Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3714879

Thermodynamics of enzyme-catalyzed reactions--a database for quantitative biochemistry

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3714879

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3714879

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3714879

Stoichiometric network theory for nonequilibrium biochemical systems

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3714879

Energy balance for analysis of complex metabolic networks

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3714879

Culture medium for enterobacteria

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3714879

Isolation and characterization of acetylornithine δ-transaminase of wild-type Escherichia coli W. Comparison with arginine-inducible acetylornithine δ-transaminase

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3714879

Escherichia coli mutants deficient in the aspartate and aromatic amino acid aminotransferases

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3714879

Ornithine delta-transaminase activity in Escherichia coli: its identity with acetylornithine delta-transaminase

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3714879

Update on the Keio collection of Escherichia coli single-gene deletion mutants

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3714879

Genome-scale gene/reaction essentiality and synthetic lethality analysis

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3714879

Thermodynamics-based metabolic flux analysis

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3714879

Genome-scale thermodynamic analysis of Escherichia coli metabolism

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3714879

Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3714879

Acquisition of new metabolic capabilities: multicopy suppression by cloned transaminase genes in Escherichia coli K-12.

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3714879

Estimation of standard Gibbs energy changes of biotransformations

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3714879

Driving forces enable high-titer anaerobic 1-butanol synthesis in Escherichia coli

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3714879

Combining flux and energy balance analysis to model large-scale biochemical networks.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3714879

Thermodynamic-based computational profiling of cellular regulatory control in hepatocyte metabolism

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3714879

Thermodynamic constraints for biochemical networks.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3714879

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

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3714879

Identification of localized and distributed bottlenecks in metabolic pathways.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3714879

Group contributions for estimating standard gibbs energies of formation of biochemical compounds in aqueous solution

4 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23870272

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

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

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23870272

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1016/J.BPJ.2013.06.011

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23870272%20AND%20SRC:MED&resulttype=core&format=json

5 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23870272%20AND%20SRC:MED&resulttype=core&format=json

5 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23870272%20AND%20SRC:MED&resulttype=core&format=json