(Q37279487)

19 August 2017

Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction (English)

1 reference

19 August 2017

1 reference

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24084808%20AND%20SRC:MED&resulttype=core&format=json

31 May 2020

Roger Chang

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24084808%20AND%20SRC:MED&resulttype=core&format=json

31 May 2020

author name string

Edward J O'Brien

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24084808%20AND%20SRC:MED&resulttype=core&format=json

31 May 2020

Daniel R Hyduke

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24084808%20AND%20SRC:MED&resulttype=core&format=json

31 May 2020

Bernhard Ø Palsson

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24084808%20AND%20SRC:MED&resulttype=core&format=json

31 May 2020

language of work or name

1 reference

1 October 2013

1 reference

Molecular Systems Biology

19 August 2017

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24084808%20AND%20SRC:MED&resulttype=core&format=json

31 May 2020

volume

9

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24084808%20AND%20SRC:MED&resulttype=core&format=json

31 May 2020

page(s)

693

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24084808%20AND%20SRC:MED&resulttype=core&format=json

The ability of flux balance analysis to predict evolution of central metabolism scales with the initial distance to the optimum

31 May 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3817402

EcoCyc: fusing model organism databases with systems biology

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3817402

Multiscale modeling of metabolism and macromolecular synthesis in E. coli and its application to the evolution of codon usage

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3817402

A whole-cell computational model predicts phenotype from genotype

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3817402

Prediction of microbial growth rate versus biomass yield by a metabolic network with kinetic parameters

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3817402

In silico method for modelling metabolism and gene product expression at genome scale

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3817402

The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3817402

Modeling formalisms in Systems Biology

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3817402

Economics of membrane occupancy and respiro-fermentation

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3817402

The PurR regulon in Escherichia coli K-12 MG1655.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3817402

Functional characterization of alternate optimal solutions of Escherichia coli's transcriptional and translational machinery

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3817402

The biomass objective function

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3817402

An evolutionarily conserved mechanism for controlling the efficiency of protein translation

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3817402

Growth-limiting intracellular metabolites in yeast growing under diverse nutrient limitations

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3817402

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3817402

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3817402

WGCNA: an R package for weighted correlation network analysis

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3817402

Growth-rate-dependent partitioning of RNA polymerases in bacteria

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3817402

Intracellular crowding defines the mode and sequence of substrate uptake by Escherichia coli and constrains its metabolic activity.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3817402

Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3817402

Escherichia coli K-12: a cooperatively developed annotation snapshot--2005

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3817402

Determination of the core of a minimal bacterial gene set

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3817402

A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3817402

Microbial physiology and ecology of slow growth.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3817402

Dissecting specific and global transcriptional regulation of bacterial gene expression

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3817402

Analysis of gene expression in Escherichia coli in response to changes of growth-limiting nutrient in chemostat cultures

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3817402

Shared control of gene expression in bacteria by transcription factors and global physiology of the cell.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3817402

Need-based activation of ammonium uptake in Escherichia coli

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3817402

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

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3817402

Cooperation between translating ribosomes and RNA polymerase in transcription elongation

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3817402

Growth rate-dependent global effects on gene expression in bacteria

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3817402

Shifts in growth strategies reflect tradeoffs in cellular economics

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3817402

Construction of consecutive deletions of the Escherichia coli chromosome

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3817402

Overflow metabolism in Escherichia coli during steady-state growth: transcriptional regulation and effect of the redox ratio

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3817402

Nonlinear dependency of intracellular fluxes on growth rate in miniaturized continuous cultures of Escherichia coli

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3817402

Glucose phosphoenolpyruvate phosphotransferase activity and glucose uptake rate of Klebsiella aerogenes growing in chemostat culture

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3817402

Polypeptide-chain-elongation rate in Escherichia coli B/r as a function of growth rate

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3817402

Escherichia coli achieves faster growth by increasing catalytic and translation rates of proteins

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3817402

Multidimensional optimality of microbial metabolism

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3817402

Interdependence of cell growth and gene expression: origins and consequences.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3817402

Specific growth rate dependent transcriptome profiling of Escherichia coli K12 MG1655 in accelerostat cultures.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3817402

Transcriptional regulation of the fad regulon genes of Escherichia coli by ArcA.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3817402

Biochemical basis for whole-cell uptake kinetics: specific affinity, oligotrophic capacity, and the meaning of the michaelis constant

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3817402

Characterization of diverse natural variants of CYP102A1 found within a species of Bacillus megaterium.

3 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1038%2FMSB.2013.52

On the complete determination of biological systems

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1038%2FMSB.2013.52

-Galactosidase Synthesis in Klebsiella aerogenes Growing in Continuous Culture

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24084808

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

The maintenance energy of bacteria in growing cultures

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24084808

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1038/MSB.2013.52

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24084808%20AND%20SRC:MED&resulttype=core&format=json

31 May 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24084808%20AND%20SRC:MED&resulttype=core&format=json

31 May 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24084808%20AND%20SRC:MED&resulttype=core&format=json