(Q36387310)

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Gene expression levels are correlated with synonymous codon usage, amino acid composition, and gene architecture in the red flour beetle, Tribolium castaneum

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scholarly article

1 reference

Europe PubMed Central

PMC publication ID

13 August 2017

Gene expression levels are correlated with synonymous codon usage, amino acid composition, and gene architecture in the red flour beetle, Tribolium castaneum (English)

1 reference

Europe PubMed Central

PMC publication ID

13 August 2017

red flour beetle

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author name string

Anna Williford

1

1 reference

Europe PubMed Central

PMC publication ID

13 August 2017

Jeffery P Demuth

2

1 reference

Europe PubMed Central

PMC publication ID

13 August 2017

publication date

23 July 2012

1 reference

Europe PubMed Central

PMC publication ID

13 August 2017

Molecular Biology and Evolution

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Europe PubMed Central

PMC publication ID

13 August 2017

29

1 reference

Europe PubMed Central

PMC publication ID

13 August 2017

12

1 reference

Europe PubMed Central

PMC publication ID

13 August 2017

3755-3766

1 reference

Europe PubMed Central

PMC publication ID

13 August 2017

The 3-base periodicity and codon usage of coding sequences are correlated with gene expression at the level of transcription elongation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3494272

30 September 2017

Global quantification of mammalian gene expression control

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3494272

30 September 2017

Misfolded proteins impose a dosage-dependent fitness cost and trigger a cytosolic unfolded protein response in yeast

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3494272

30 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3494272

30 September 2017

Effect of correlated tRNA abundances on translation errors and evolution of codon usage bias

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3494272

30 September 2017

Hyperexpression of the X chromosome in both sexes results in extensive female bias of X-linked genes in the flour beetle

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3494272

30 September 2017

A universal nonmonotonic relationship between gene compactness and expression levels in multicellular eukaryotes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3494272

30 September 2017

BeetleBase in 2010: revisions to provide comprehensive genomic information for Tribolium castaneum.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3494272

30 September 2017

Molecular evolution of synonymous codon usage in Populus

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3494272

30 September 2017

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=3494272

30 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3494272

30 September 2017

EST analysis of Ostreococcus lucimarinus, the most compact eukaryotic genome, shows an excess of introns in highly expressed genes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3494272

30 September 2017

The genome of the model beetle and pest Tribolium castaneum

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3494272

30 September 2017

Protecting exons from deleterious R-loops: a potential advantage of having introns

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3494272

30 September 2017

Transcription-associated mutagenesis in yeast is directly proportional to the level of gene expression and influenced by the direction of DNA replication

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3494272

30 September 2017

Reinvestigating the codon and amino acid usage of S. cerevisiae genome: a new insight from protein secondary structure analysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3494272

30 September 2017

Gene expression and protein length influence codon usage and rates of sequence evolution in Populus tremula

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3494272

30 September 2017

tRNA's wobble decoding of the genome: 40 years of modification

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3494272

30 September 2017

Amino acid cost and codon-usage biases in 6 prokaryotic genomes: a whole-genome analysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3494272

30 September 2017

Weak selection and recent mutational changes influence polymorphic synonymous mutations in humans

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3494272

30 September 2017

The evolution of spliceosomal introns: patterns, puzzles and progress

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3494272

30 September 2017

Hearing silence: non-neutral evolution at synonymous sites in mammals

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3494272

30 September 2017

Gene expression intensity shapes evolutionary rates of the proteins encoded by the vertebrate genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3494272

30 September 2017

Selective and mutational patterns associated with gene expression in humans: influences on synonymous composition and intron presence

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3494272

30 September 2017

Global analysis of protein expression in yeast

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3494272

30 September 2017

The signature of selection mediated by expression on human genes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3494272

30 September 2017

Translational selection and yeast proteome evolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3494272

30 September 2017

Introns in gene evolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3494272

30 September 2017

Biased gene conversion: implications for genome and sex evolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3494272

30 September 2017

Cost-minimization of amino acid usage.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3494272

30 September 2017

Evolution of synonymous codon usage in metazoans

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3494272

30 September 2017

Selection for short introns in highly expressed genes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3494272

30 September 2017

Population, evolutionary and genomic consequences of interference selection

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3494272

30 September 2017

Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3494272

30 September 2017

Gene expression and molecular evolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3494272

30 September 2017

Codon usage and tRNA genes in eukaryotes: correlation of codon usage diversity with translation efficiency and with CG-dinucleotide usage as assessed by multivariate analysis.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3494272

30 September 2017

The correlation between intron length and recombination in drosophila. Dynamic equilibrium between mutational and selective forces.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3494272

30 September 2017

tRNA gene number and codon usage in the C. elegans genome are co-adapted for optimal translation of highly expressed genes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3494272

30 September 2017

Analysis of the yeast transcriptome with structural and functional categories: characterizing highly expressed proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3494272

30 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3494272

30 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3494272

30 September 2017

Codon usage bias and tRNA abundance in Drosophila

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3494272

30 September 2017

Evolution of codon usage bias in Drosophila

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3494272

30 September 2017

tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3494272

30 September 2017

Transcription-induced mutations: increase in C to T mutations in the nontranscribed strand during transcription in Escherichia coli

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3494272

30 September 2017

Hydrophobicity, expressivity and aromaticity are the major trends of amino-acid usage in 999 Escherichia coli chromosome-encoded genes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3494272

30 September 2017

Inferring weak selection from patterns of polymorphism and divergence at "silent" sites in Drosophila DNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3494272

30 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3494272

30 September 2017

Codon frequencies in 119 individual genes confirm consistent choices of degenerate bases according to genome type.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3494272

30 September 2017

Codon--anticodon pairing: the wobble hypothesis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3494272

30 September 2017

Non-Darwinian Evolution: A Critique

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3494272

30 September 2017

Codon usage and tRNA content in unicellular and multicellular organisms

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3494272

30 September 2017

Codon preferences in free-living microorganisms

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3494272

30 September 2017

The selection-mutation-drift theory of synonymous codon usage

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3494272

30 September 2017

Selection at the wobble position of codons read by the same tRNA in Saccharomyces cerevisiae

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3494272

28 June 2018

Reduced natural selection associated with low recombination in Drosophila melanogaster.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3494272

28 June 2018

The usage of oligopeptides in proteins correlates negatively with molecular weight

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3494272

28 June 2018

Codon usage in Aspergillus nidulans

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3494272

28 June 2018

Patterns of Codon Usage Bias in Silene latifolia

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3494272

21 September 2018

Do amino acid biosynthetic costs constrain protein evolution in Saccharomyces cerevisiae?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3494272

21 September 2018

Gene expression, intron density, and splice site strength in Drosophila and Caenorhabditis.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3494272

21 September 2018

The evolution of biased codon and amino acid usage in nematode genomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3494272

21 September 2018

Evolution of proteins and gene expression levels are coupled in Drosophila and are independently associated with mRNA abundance, protein length, and number of protein-protein interactions.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3494272

21 September 2018

Relationship of codon bias to mRNA concentration and protein length in Saccharomyces cerevisiae

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3494272

21 September 2018

Transfer RNA gene redundancy and translational selection in Saccharomyces cerevisiae.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3494272

21 September 2018

Similar amino acid sequences: chance or common ancestry?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3494272

21 September 2018

Restricted wobble rules for eukaryotic genomes

1 reference

https://pubmed.ncbi.nlm.nih.gov/22826459

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Energy constraints on the evolution of gene expression

1 reference

https://pubmed.ncbi.nlm.nih.gov/22826459

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

In plants, highly expressed genes are the least compact

1 reference

https://pubmed.ncbi.nlm.nih.gov/22826459

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Selection on synthesis cost affects interprotein amino acid usage in all three domains of life

1 reference

https://pubmed.ncbi.nlm.nih.gov/22826459

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

ANALYZING TABLES OF STATISTICAL TESTS

1 reference

https://pubmed.ncbi.nlm.nih.gov/22826459

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Genetic code synonym quotas and amino acid complexity: cutting the cost of proteins?

1 reference

https://pubmed.ncbi.nlm.nih.gov/22826459

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1093/MOLBEV/MSS184

1 reference

Europe PubMed Central

PMC publication ID

13 August 2017

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

13 August 2017

PubMed publication ID

1 reference

Europe PubMed Central

PMC publication ID

13 August 2017

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