(Q35064398)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21646514%20AND%20SRC:MED&resulttype=core&format=json

3 February 2020

title

Explaining complex codon usage patterns with selection for translational efficiency, mutation bias, and genetic drift (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21646514%20AND%20SRC:MED&resulttype=core&format=json

3 February 2020

1 reference

1 reference

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21646514%20AND%20SRC:MED&resulttype=core&format=json

3 February 2020

author name string

Michael A Gilchrist

series ordinal

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21646514%20AND%20SRC:MED&resulttype=core&format=json

3 February 2020

language of work or name

English

0 references

publication date

6 June 2011

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21646514%20AND%20SRC:MED&resulttype=core&format=json

Proceedings of the National Academy of Sciences of the United States of America

3 February 2020

published in

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21646514%20AND%20SRC:MED&resulttype=core&format=json

3 February 2020

volume

108

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21646514%20AND%20SRC:MED&resulttype=core&format=json

3 February 2020

issue

25

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21646514%20AND%20SRC:MED&resulttype=core&format=json

3 February 2020

page(s)

10231-10236

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21646514%20AND%20SRC:MED&resulttype=core&format=json

Synonymous but not the same: the causes and consequences of codon bias

3 February 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3121864

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3121864

Translation efficiency is determined by both codon bias and folding energy

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3121864

Measuring and detecting molecular adaptation in codon usage against nonsense errors during protein translation.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3121864

The evolutionary consequences of erroneous protein synthesis.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3121864

Coding-sequence determinants of gene expression in Escherichia coli

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3121864

GtRNAdb: a database of transfer RNA genes detected in genomic sequence

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3121864

8 July 2018

Selection on Codon Bias

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3121864

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3121864

Virus attenuation by genome-scale changes in codon pair bias

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3121864

A "silent" polymorphism in the MDR1 gene changes substrate specificity

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3121864

Rate, accuracy and cost of ribosomes in bacterial cells

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3121864

Why highly expressed proteins evolve slowly

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3121864

The application of statistical physics to evolutionary biology

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3121864

Dissecting eukaryotic translation and its control by ribosome density mapping

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3121864

Intragenic spatial patterns of codon usage bias in prokaryotic and eukaryotic genomes

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3121864

Solving the riddle of codon usage preferences: a test for translational selection

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3121864

Protein tolerance to random amino acid change

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3121864

Translational selection and yeast proteome evolution

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3121864

Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3121864

Analysis of codon:anticodon interactions within the ribosome provides new insights into codon reading and the genetic code structure

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3121864

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3121864

The economics of ribosome biosynthesis in yeast

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3121864

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3121864

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3121864

8 July 2018

Codon selection in yeast

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3121864

Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: A proposal for a synonymous codon choice that is optimal for the E. coli translational system

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3121864

An evolutionary perspective on synonymous codon usage in unicellular organisms

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3121864

Codon usage and gene expression level in Dictyostelium discoideum: highly expressed genes do 'prefer' optimal codons

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3121864

Rates of aminoacyl-tRNA selection at 29 sense codons in vivo.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3121864

The selection-mutation-drift theory of synonymous codon usage

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3121864

Combining models of protein translation and population genetics to predict protein production rates from codon usage patterns.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3121864

Post-transcriptional expression regulation in the yeast Saccharomyces cerevisiae on a genomic scale.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3121864

The effect of expression levels on codon usage in Plasmodium falciparum

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3121864

Gene expression analyzed by high-resolution state array analysis and quantitative proteomics: response of yeast to mating pheromone

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3121864

Kinetic determinants of high-fidelity tRNA discrimination on the ribosome

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3121864

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

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3121864

Co-variation of tRNA abundance and codon usage in Escherichia coli at different growth rates.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3121864

Genetic studies of the lac repressor. XIV. Analysis of 4000 altered Escherichia coli lac repressors reveals essential and non-essential residues, as well as "spacers" which do not require a specific sequence.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3121864

Translational selection and molecular evolution

27 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1073%2FPNAS.1016719108

Energy constraints on the evolution of gene expression

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21646514

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

A model of protein translation including codon bias, nonsense errors, and ribosome recycling

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21646514

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1073/PNAS.1016719108

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21646514%20AND%20SRC:MED&resulttype=core&format=json

3 February 2020

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21646514%20AND%20SRC:MED&resulttype=core&format=json

3 February 2020

PubMed publication ID

21646514

1 reference