(Q39687202)

14 September 2017

Use and misuse of correspondence analysis in codon usage studies (English)

1 reference

14 September 2017

Jean Thioulouse

2

0 references

author name string

Guy Perrière

series ordinal

1

1 reference

PMC publication ID

137129

14 September 2017

language of work or name

English

0 references

publication date

1 October 2002

1 reference

14 September 2017

Nucleic Acids Research

1 reference

14 September 2017

30

1 reference

14 September 2017

20

1 reference

14 September 2017

4548-4555

1 reference

Conserved codon composition of ribosomal protein coding genes in Escherichia coli, Mycobacterium tuberculosis and Saccharomyces cerevisiae: lessons from supervised machine learning in functional genomics

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=137129

High-density microarray-mediated gene expression profiling of Escherichia coli

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=137129

Codon usage in Chlamydia trachomatis is the result of strand-specific mutational biases and a complex pattern of selective forces

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=137129

EMGLib: the enhanced microbial genomes library (update 2000).

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=137129

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

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=137129

Codon usage and lateral gene transfer in Bacillus subtilis

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=137129

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

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=137129

Replicational and transcriptional selection on codon usage in Borrelia burgdorferi

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=137129

NRSub: a non-redundant data base for the Bacillus subtilis genome

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=137129

SubtiList: a relational database for the Bacillus subtilis genome

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=137129

A frameshift error detection algorithm for DNA sequencing projects.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=137129

A simple method for displaying the hydropathic character of a protein

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=137129

14 September 2017

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=137129

Codon usage in bacteria: correlation with gene expressivity

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=137129

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

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=137129

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

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=137129

Evidence for horizontal gene transfer in Escherichia coli speciation

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=137129

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

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=137129

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

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=137129

Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=137129

Codon usage and gene expression

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=137129

Detection of genes in Escherichia coli sequences determined by genome projects and prediction of protein production levels, based on multivariate diversity in codon usage.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=137129

Statistical method for predicting protein coding regions in nucleic acid sequences.

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=137129

Gene expressivity is the main factor in dictating the codon usage variation among the genes in Pseudomonas aeruginosa.

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=137129

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

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=137129

Gene expression, amino acid conservation, and hydrophobicity are the main factors shaping codon preferences in Mycobacterium tuberculosis and Mycobacterium leprae

20 August 2018

1 reference

https://pubmed.ncbi.nlm.nih.gov/12384602

12 December 2020

Codon usage and the origin of P elements

1 reference

https://pubmed.ncbi.nlm.nih.gov/12384602

12 December 2020

Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes

1 reference

https://pubmed.ncbi.nlm.nih.gov/12384602

12 December 2020

Correlation between the abundance of yeast transfer RNAs and the occurrence of the respective codons in protein genes. Differences in synonymous codon choice patterns of yeast and Escherichia coli with reference to the abundance of isoaccepting tran

1 reference

https://pubmed.ncbi.nlm.nih.gov/12384602

12 December 2020

The Alu family developed through successive waves of fixation closely connected with primate lineage history

1 reference

https://pubmed.ncbi.nlm.nih.gov/12384602

12 December 2020

Successive waves of fixation of B1 variants in rodent lineage history

1 reference

https://pubmed.ncbi.nlm.nih.gov/12384602

12 December 2020

Identifiers

DOI

10.1093/NAR/GKF565

1 reference

14 September 2017

1 reference

PMC publication ID

137129

14 September 2017

PubMed publication ID

12384602

1 reference

PMC publication ID

137129