Forces that influence the evolution of codon bias (Q33856645)

29 July 2017

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title

Forces that influence the evolution of codon bias (English)

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29 July 2017

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1

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29 July 2017

Laura R Emery

2

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author name string

Kai Zeng

series ordinal

3

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PubMed ID

20308095

29 July 2017

language of work or name

English

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publication date

1 April 2010

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Philosophical Transactions of the Royal Society B

29 July 2017

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29 July 2017

365

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29 July 2017

1544

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29 July 2017

1203-1212

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Estimating selection intensity on synonymous codon usage in a nonequilibrium population

29 July 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2871821

Coding-sequence determinants of gene expression in Escherichia coli

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2871821

Estimating translational selection in eukaryotic genomes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2871821

The effects of deleterious mutations on evolution in non-recombining genomes.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2871821

Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2871821

SCUMBLE: a method for systematic and accurate detection of codon usage bias by maximum likelihood estimation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2871821

Protein abundance profiling of the Escherichia coli cytosol

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2871821

Multilocus patterns of polymorphism and selection across the X chromosome of Caenorhabditis remanei

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2871821

Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2871821

Synonymous codon usage in Escherichia coli: selection for translational accuracy.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2871821

The 160-Kilobase Genome of the Bacterial Endosymbiont Carsonella

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2871821

Analysis of core housekeeping and virulence genes reveals cryptic lineages of Clostridium perfringens that are associated with distinct disease presentations.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2871821

Variation in the strength of selected codon usage bias among bacteria

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2871821

Microevolution and history of the plague bacillus, Yersinia pestis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2871821

Codon usage bias from tRNA's point of view: redundancy, specialization, and efficient decoding for translation optimization

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2871821

Codon usage between genomes is constrained by genome-wide mutational processes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2871821

On the genetic basis of variation and heterogeneity of DNA base composition

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2871821

Synonymous codon usage is subject to selection in thermophilic bacteria

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2871821

The effects of Hill-Robertson interference between weakly selected mutations on patterns of molecular evolution and variation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2871821

Studies of codon usage and tRNA genes of 18 unicellular organisms and quantification of Bacillus subtilis tRNAs: gene expression level and species-specific diversity of codon usage based on multivariate analysis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2871821

Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2871821

Proteome composition and codon usage in spirochaetes: species-specific and DNA strand-specific mutational biases

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2871821

Base composition skews, replication orientation, and gene orientation in 12 prokaryote genomes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2871821

Free recombination within Helicobacter pylori

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2871821

Unequal fidelity of leading strand and lagging strand DNA replication on the Escherichia coli chromosome

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2871821

Relationships between genomic G+C content, RNA secondary structures, and optimal growth temperature in prokaryotes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2871821

Amelioration of bacterial genomes: rates of change and exchange

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2871821

Codon bias in Escherichia coli: the influence of codon context on mutation and selection.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2871821

Asymmetric substitution patterns in the two DNA strands of bacteria

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2871821

Reduced synonymous substitution rate at the start of enterobacterial genes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2871821

Synonymous codon usage in Drosophila melanogaster: natural selection and translational accuracy.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2871821

Synonymous substitution-rate constants in Escherichia coli and Salmonella typhimurium and their relationship to gene expression and selection pressure.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2871821

Synonymous substitution rates in enterobacteria.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2871821

Codon catalog usage and the genome hypothesis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2871821

Codon usage in bacteria: correlation with gene expressivity

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2871821

The relationship between base composition and codon usage in bacterial genes and its use for the simple and reliable identification of protein-coding sequences

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2871821

Codon usage and tRNA content in unicellular and multicellular organisms

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2871821

The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2871821

The guanine and cytosine content of genomic DNA and bacterial evolution

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2871821

When polymerases collide: replication and the transcriptional organization of the E. coli chromosome

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2871821

"Silent" sites in Drosophila genes are not neutral: evidence of selection among synonymous codons

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2871821

Models of nearly neutral mutations with particular implications for nonrandom usage of synonymous codons.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2871821

Compositional constraints and genome evolution

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2871821

Chromosomal location and evolutionary rate variation in enterobacterial genes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2871821

Codon preferences in free-living microorganisms

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2871821

Switches in species-specific codon preferences: the influence of mutation biases

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2871821

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.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2871821

Determinants of DNA sequence divergence between Escherichia coli and Salmonella typhimurium: codon usage, map position, and concerted evolution

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2871821

The selection-mutation-drift theory of synonymous codon usage

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2871821

Patterns of protein synthesis in E. coli: a catalog of the amount of 140 individual proteins at different growth rates

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2871821

A correlation between the compositions of deoxyribonucleic and ribonucleic acids.

5 July 2018

1 reference

https://api.crossref.org/works/10.1098%2FRSTB.2009.0305

Selection intensity on preferred codons correlates with overall codon usage bias in Caenorhabditis remanei.

21 January 2018

1 reference

https://api.crossref.org/works/10.1098%2FRSTB.2009.0305

Predicting gene expression level from codon usage bias.

21 January 2018

1 reference

https://api.crossref.org/works/10.1098%2FRSTB.2009.0305

Absence of translationally selected synonymous codon usage bias in Helicobacter pylori.

21 January 2018

1 reference

https://api.crossref.org/works/10.1098%2FRSTB.2009.0305

Selection on codon usage in Drosophila americana.

21 January 2018

1 reference

https://api.crossref.org/works/10.1098%2FRSTB.2009.0305

Lifestyle evolution in symbiotic bacteria: insights from genomics.

21 January 2018

1 reference

https://api.crossref.org/works/10.1098%2FRSTB.2009.0305

Translational selection is operative for synonymous codon usage in Clostridium perfringens and Clostridium acetobutylicum.

21 January 2018

1 reference

https://api.crossref.org/works/10.1098%2FRSTB.2009.0305

Mutation exposed: a neutral explanation for extreme base composition of an endosymbiont genome.

21 January 2018

1 reference

https://api.crossref.org/works/10.1098%2FRSTB.2009.0305

Site-specific codon bias in bacteria.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2871821

Asymmetries generated by transcription-coupled repair in enterobacterial genes.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2871821

DNA sequences from the str operon of Escherichia coli.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2871821

Replication-associated gene dosage effects shape the genomes of fast-growing bacteria but only for transcription and translation genes

29 October 2018

1 reference

https://api.crossref.org/works/10.1098%2FRSTB.2009.0305

The effect of linkage on limits to artificial selection

21 January 2018

1 reference

12 December 2020

Correlations between genomic GC levels and optimal growth temperatures in prokaryotes

1 reference

12 December 2020

The contributions of replication orientation, gene direction, and signal sequences to base-composition asymmetries in bacterial genomes

1 reference

12 December 2020

Costs of accuracy determined by a maximal growth rate constraint

1 reference

12 December 2020

Nonhomogeneous model of sequence evolution indicates independent origins of primary endosymbionts within the enterobacteriales (gamma-Proteobacteria)

1 reference

12 December 2020

Identifiers

DOI

10.1098/RSTB.2009.0305

1 reference

release_ml6a7pxrzzdw3o6o6mgggnbjze

29 July 2017

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/ml6a7pxrzzdw3o6o6mgggnbjze

24 November 2022

mapped directly with Wikidata item

PMCID

2871821

1 reference

29 July 2017

1 reference

PubMed ID

20308095