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English
Codon bias in Escherichia coli: the influence of codon context on mutation and selection.
scientific article published on April 1997
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instance of
scholarly article
1 reference
stated in
Europe PubMed Central
PMCID
146607
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:9060435%20AND%20SRC:MED&resulttype=core&format=json
retrieved
1 November 2019
title
Codon bias in Escherichia coli: the influence of codon context on mutation and selection
(English)
1 reference
stated in
Europe PubMed Central
PMCID
146607
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:9060435%20AND%20SRC:MED&resulttype=core&format=json
retrieved
1 November 2019
main subject
bias
1 reference
based on heuristic
inferred from title
Escherichia coli
1 reference
based on heuristic
inferred from title
author
Pedro Silva
series ordinal
2
1 reference
stated in
Europe PubMed Central
PMCID
146607
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:9060435%20AND%20SRC:MED&resulttype=core&format=json
retrieved
1 November 2019
author name string
O G Berg
series ordinal
1
1 reference
stated in
Europe PubMed Central
PMCID
146607
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:9060435%20AND%20SRC:MED&resulttype=core&format=json
retrieved
1 November 2019
language of work or name
English
0 references
publication date
1 April 1997
1 reference
stated in
Europe PubMed Central
PMCID
146607
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:9060435%20AND%20SRC:MED&resulttype=core&format=json
retrieved
1 November 2019
published in
Nucleic Acids Research
1 reference
stated in
Europe PubMed Central
PMCID
146607
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:9060435%20AND%20SRC:MED&resulttype=core&format=json
retrieved
1 November 2019
volume
25
1 reference
stated in
Europe PubMed Central
PMCID
146607
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:9060435%20AND%20SRC:MED&resulttype=core&format=json
retrieved
1 November 2019
page(s)
1397-1404
1 reference
stated in
Europe PubMed Central
PMCID
146607
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:9060435%20AND%20SRC:MED&resulttype=core&format=json
retrieved
1 November 2019
issue
7
1 reference
stated in
Europe PubMed Central
PMCID
146607
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:9060435%20AND%20SRC:MED&resulttype=core&format=json
retrieved
1 November 2019
cites work
Selection intensity for codon bias and the effective population size of Escherichia coli
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=146607
retrieved
29 September 2017
Synonymous codon bias is related to gene length in Escherichia coli: selection for translational accuracy?
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=146607
retrieved
29 September 2017
Very short patch repair: reducing the cost of cytosine methylation
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=146607
retrieved
29 September 2017
The European Bioinformatics Institute (EBI) databases
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=146607
retrieved
29 September 2017
Compilation of DNA sequences of Escherichia coli K12 (ECD and ECDC; update 1995).
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=146607
retrieved
29 September 2017
The SWISS-PROT protein sequence data bank and its new supplement TREMBL
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=146607
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29 September 2017
Transcription-repair coupling and mutation frequency decline
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=146607
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29 September 2017
Reduced synonymous substitution rate at the start of enterobacterial genes
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=146607
retrieved
29 September 2017
Selection intensity for codon bias
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=146607
retrieved
29 September 2017
Very short patch repair of T:G mismatches in vivo: importance of context and accessory proteins
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=146607
retrieved
29 September 2017
Codon usage in bacteria: correlation with gene expressivity
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=146607
retrieved
29 September 2017
Codon usage and tRNA content in unicellular and multicellular organisms
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=146607
retrieved
29 September 2017
The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications
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=146607
retrieved
29 September 2017
Translation of the sequence AGG-AGG yields 50% ribosomal frameshift
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=146607
retrieved
29 September 2017
An evolutionary perspective on synonymous codon usage in unicellular organisms
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=146607
retrieved
29 September 2017
Reading frame switch caused by base-pair formation between the 3' end of 16S rRNA and the mRNA during elongation of protein synthesis in Escherichia coli
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=146607
retrieved
29 September 2017
Growth rate dependence of transfer RNA abundance in Escherichia coli
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=146607
retrieved
29 September 2017
Codon context
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=146607
retrieved
29 September 2017
The effect of context on synonymous codon usage in genes with low codon usage bias
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=146607
retrieved
29 September 2017
The selection-mutation-drift theory of synonymous codon usage
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=146607
retrieved
29 September 2017
DNA mismatch correction by Very Short Patch repair may have altered the abundance of oligonucleotides in the E. coli genome
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=146607
retrieved
29 September 2017
Statistical evaluation and biological interpretation of non-random abundance in the E. coli K-12 genome of tetra- and pentanucleotide sequences related to VSP DNA mismatch repair
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=146607
retrieved
29 September 2017
Molecular basis of base substitution hotspots in Escherichia coli
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=146607
retrieved
29 September 2017
Constraints on codon context in Escherichia coli genes. Their possible role in modulating the efficiency of translation
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=146607
retrieved
29 September 2017
The close proximity of Escherichia coli genes: consequences for stop codon and synonymous codon use.
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=146607
retrieved
27 June 2018
Synonymous substitution-rate constants in Escherichia coli and Salmonella typhimurium and their relationship to gene expression and selection pressure.
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=146607
retrieved
27 June 2018
Sense codons are found in specific contexts.
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=146607
retrieved
27 June 2018
Codon contexts in enterobacterial and coliphage genes.
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=146607
retrieved
27 June 2018
Use of tRNA suppressors to probe regulation of Escherichia coli release factor 2.
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=146607
retrieved
27 June 2018
Absolute in vivo translation rates of individual codons in Escherichia coli. The two glutamic acid codons GAA and GAG are translated with a threefold difference in rate.
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=146607
retrieved
27 June 2018
Co-variation of tRNA abundance and codon usage in Escherichia coli at different growth rates.
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=146607
retrieved
5 September 2018
A possible relationship between VSP mismatch repair and gene expression level.
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=146607
retrieved
5 September 2018
Growth and translation elongation rate are sensitive to the concentration of EF-Tu.
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=146607
retrieved
5 September 2018
Base selection, proofreading, and mismatch repair during DNA replication in Escherichia coli.
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=146607
retrieved
5 September 2018
Compositional heterogeneity of the Escherichia coli genome: a role for VSP repair?
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=146607
retrieved
5 September 2018
Substrate preferences of Vsr DNA mismatch endonuclease and their consequences for the evolution of the Escherichia coli K-12 genome.
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=146607
retrieved
5 September 2018
Growth-rate-dependent accumulation of twelve tRNA species in Escherichia coli.
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=146607
retrieved
5 September 2018
Codon usage and intragenic position
1 reference
stated in
PubMed
reference URL
https://pubmed.ncbi.nlm.nih.gov/9060435
retrieved
12 December 2020
based on heuristic
inferred from PubMed ID database lookup
Selection of laboratory wild-type phenotype from natural isolates of Escherichia coli in chemostats
1 reference
stated in
PubMed
reference URL
https://pubmed.ncbi.nlm.nih.gov/9060435
retrieved
12 December 2020
based on heuristic
inferred from PubMed ID database lookup
Does very short patch (VSP) repair efficiency vary in relation to gene expression levels?
1 reference
stated in
PubMed
reference URL
https://pubmed.ncbi.nlm.nih.gov/9060435
retrieved
12 December 2020
based on heuristic
inferred from PubMed ID database lookup
Costs of accuracy determined by a maximal growth rate constraint
1 reference
stated in
PubMed
reference URL
https://pubmed.ncbi.nlm.nih.gov/9060435
retrieved
12 December 2020
based on heuristic
inferred from PubMed ID database lookup
Identifiers
DOI
10.1093/NAR/25.7.1397
1 reference
stated in
Europe PubMed Central
PMCID
146607
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:9060435%20AND%20SRC:MED&resulttype=core&format=json
retrieved
1 November 2019
PMCID
146607
1 reference
stated in
Europe PubMed Central
PMCID
146607
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:9060435%20AND%20SRC:MED&resulttype=core&format=json
retrieved
1 November 2019
PubMed ID
9060435
1 reference
stated in
Europe PubMed Central
PMCID
146607
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:9060435%20AND%20SRC:MED&resulttype=core&format=json
retrieved
1 November 2019
ResearchGate publication ID
14152329
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