(Q34033113)

30 July 2017

title

Codon usage bias: causative factors, quantification methods and genome-wide patterns: with emphasis on insect genomes (English)

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30 July 2017

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Susanta K Behura

1

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David Severson

series ordinal

2

object named as

David W Severson

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30 July 2017

publication date

14 August 2012

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30 July 2017

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30 July 2017

volume

88

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30 July 2017

issue

1

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30 July 2017

page(s)

49-61

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Codon bias evolution in Drosophila. Population genetics of mutation-selection drift

30 July 2017

cites work

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

Gene expression and molecular evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

Mutation pressure, natural selection, and the evolution of base composition in Drosophila

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

CodonO: codon usage bias analysis within and across genomes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

Sequencing of Culex quinquefasciatus establishes a platform for mosquito comparative genomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

Coadaptation of isoacceptor tRNA genes and codon usage bias for translation efficiency in Aedes aegypti and Anopheles gambiae

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

Genome-wide comparative analysis of simple sequence coding repeats among 25 insect species

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

Intrinsic features of Aedes aegypti genes affect transcriptional responsiveness of mosquito genes to dengue virus infection.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

Comparative analysis of codon usage bias and codon context patterns between dipteran and hymenopteran sequenced genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

Comparative analysis of nuclear tRNA genes of Nasonia vitripennis and other arthropods, and relationships to codon usage bias

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

Linkage limits the power of natural selection in Drosophila

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

Codon context and protein synthesis: enhancements of the genetic code

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

A role for codon order in translation dynamics.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

Codon adaptation index as a measure of dominating codon bias.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

Biased codon usage near intron-exon junctions: selection on splicing enhancers, splice-site recognition or something else?

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

Online synonymous codon usage analyses with the ade4 and seqinR packages.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

RNA secondary structure and compensatory evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

Virus attenuation by genome-scale changes in codon pair bias

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

The origin of the genetic code

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

General nature of the genetic code for proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

The effect of local nucleotides on synonymous codon usage in the honeybee (Apis mellifera L.) genome.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

Why highly expressed proteins evolve slowly

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

Evolution of synonymous codon usage in metazoans

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

The evolution of sex-biased genes and sex-biased gene expression

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

A role for initiation codon context in chloroplast translation.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

Optimization of recombinant protein expression in the chloroplasts of green algae

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

Gene conversion drives GC content evolution in mammalian histones

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

Amino acid and codon usage profiles: adaptive changes in the frequency of amino acids and codons.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

Codon usage in bacteria: correlation with gene expressivity

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

The codon preference plot: graphic analysis of protein coding sequences and prediction of gene expression.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

Preferential codon usage in prokaryotic genes: the optimal codon-anticodon interaction energy and the selective codon usage in efficiently expressed genes

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

JCat: a novel tool to adapt codon usage of a target gene to its potential expression host

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

Codon bias and heterologous protein expression

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

Patterns of synonymous codon usage in Drosophila melanogaster genes with sex-biased expression

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

Variable strength of translational selection among 12 Drosophila species

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

Differential usage of iso-accepting tRNASer species in silk glands of Bombyx mori

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

21 January 2018

Selection on Codon Bias

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

Incorporating PCA and fuzzy-ART techniques into achieve organism classification based on codon usage consideration.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

Codon pair utilization biases influence translational elongation step times

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

Heterogeneity in regional GC content and differential usage of codons and amino acids in GC-poor and GC-rich regions of the genome of Apis mellifera

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

Effects of rare codon clusters on high-level expression of heterologous proteins in Escherichia coli

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

Origin and evolution of the genetic code: the universal enigma

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

DnaSP v5: a software for comprehensive analysis of DNA polymorphism data

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

Does recombination improve selection on codon usage? Lessons from nematode and fly complete genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

Toward engineering synthetic microbial metabolism

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

GCUA: general codon usage analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

A method for measuring the non-random bias of a codon usage table

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

Codon usage bias and tRNA abundance in Drosophila

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

Gene length and codon usage bias in Drosophila melanogaster, Saccharomyces cerevisiae and Escherichia coli

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

Codon-triplet context unveils unique features of the Candida albicans protein coding genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

Large scale comparative codon-pair context analysis unveils general rules that fine-tune evolution of mRNA primary structure.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

Comparative context analysis of codon pairs on an ORFeome scale

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

Reduction of the rate of poliovirus protein synthesis through large-scale codon deoptimization causes attenuation of viral virulence by lowering specific infectivity

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

Tracing specific synonymous codon-secondary structure correlations through evolution.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

Use and misuse of correspondence analysis in codon usage studies

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

Evolution of codon usage bias in Drosophila

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

Analysis of a shift in codon usage in Drosophila.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

Codon usage is associated with the evolutionary age of genes in metazoan genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

RCDI/eRCDI: a web-server to estimate codon usage deoptimization.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

E-CAI: a novel server to estimate an expected value of Codon Adaptation Index (eCAI).

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

Creating a buzz about insect genomes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

Translational selection of genes coding for perfectly conserved proteins among three mosquito vectors

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

Information content of binding sites on nucleotide sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

A Mathematical Theory of Communication

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

Forces that influence the evolution of codon bias

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

An evolutionary perspective on synonymous codon usage in unicellular organisms

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

Codon usage and genome evolution.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

Synonymous codon usage in Bacillus subtilis reflects both translational selection and mutational biases

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

Codon usage: mutational bias, translational selection, or both?

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

Categorizing host-dependent RNA viruses by principal component analysis of their codon usage preferences

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

INCA: synonymous codon usage analysis and clustering by means of self-organizing map.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

Preferred and avoided codon pairs in three domains of life

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

ACUA: a software tool for automated codon usage analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

Codon usage in twelve species of Drosophila

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

Quantitative relationship between synonymous codon usage bias and GC composition across unicellular genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

On the evolution of the genetic code

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

A co-evolution theory of the genetic code

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

The 'effective number of codons' used in a gene

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

Preferential codon usage and two types of repetitive motifs in the fibroin gene of the Chinese oak silkworm, Antheraea pernyi

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

Shannon information theoretic computation of synonymous codon usage biases in coding regions of human and mouse genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

The influence of codon context on genetic code translation

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

Possible Relation between Deoxyribonucleic Acid and Protein Structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

Correlation between Coding-Triplets and Amino-Acids

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1469-185X.2012.00242.X

10.1111/J.1469-185X.2012.00242.X

21 January 2018

Identifiers

DOI

1 reference

30 July 2017

1 reference