(Q33297007)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17786218%20AND%20SRC:MED&resulttype=core&format=json

5 January 2020

title

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

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17786218%20AND%20SRC:MED&resulttype=core&format=json

5 January 2020

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17786218%20AND%20SRC:MED&resulttype=core&format=json

5 January 2020

Joel P. Arrais

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17786218%20AND%20SRC:MED&resulttype=core&format=json

5 January 2020

Adelaide Freitas

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17786218%20AND%20SRC:MED&resulttype=core&format=json

5 January 2020

José Luís Oliveira

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17786218%20AND%20SRC:MED&resulttype=core&format=json

5 January 2020

Manuel Santos

8

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17786218%20AND%20SRC:MED&resulttype=core&format=json

5 January 2020

author name string

Miguel Pinheiro

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17786218%20AND%20SRC:MED&resulttype=core&format=json

5 January 2020

Ana Cristina Gomes

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17786218%20AND%20SRC:MED&resulttype=core&format=json

5 January 2020

Laura Carreto

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17786218%20AND%20SRC:MED&resulttype=core&format=json

5 January 2020

language of work or name

English

0 references

publication date

5 September 2007

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17786218%20AND%20SRC:MED&resulttype=core&format=json

5 January 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17786218%20AND%20SRC:MED&resulttype=core&format=json

5 January 2020

volume

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17786218%20AND%20SRC:MED&resulttype=core&format=json

5 January 2020

issue

9

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17786218%20AND%20SRC:MED&resulttype=core&format=json

5 January 2020

page(s)

e847

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17786218%20AND%20SRC:MED&resulttype=core&format=json

Creative Commons Attribution 4.0 International

5 January 2020

copyright license

start time

5 September 2007

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

The frequency of translational misreading errors in E. coli is largely determined by tRNA competition.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1952141

tRNA properties help shape codon pair preferences in open reading frames

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1952141

After the duplication: gene loss and adaptation in Saccharomyces genomes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1952141

Genomic deletions and precise removal of transposable elements mediated by short identical DNA segments in primates

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1952141

DNA methylation and human disease

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1952141

Structural insights into translational fidelity

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1952141

Gardening the genome: DNA methylation in Arabidopsis thaliana

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1952141

Comparative context analysis of codon pairs on an ORFeome scale

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1952141

A genomic basis for the evolution of vertebrate transcription factors containing amino Acid runs

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1952141

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1952141

The major 5' determinant in stop codon read-through involves two adjacent adenines

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1952141

Quantitating protein synthesis, degradation, and endogenous antigen processing

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1952141

tRNomics: analysis of tRNA genes from 50 genomes of Eukarya, Archaea, and Bacteria reveals anticodon-sparing strategies and domain-specific features

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1952141

Computational identification of putative programmed translational frameshift sites

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1952141

Tandem repeats in protein coding regions of primate genes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1952141

Over-representation of repeats in stress response genes: a strategy to increase versatility under stressful conditions?

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1952141

Regularities of context-dependent codon bias in eukaryotic genes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1952141

Detection of genes with atypical nucleotide sequence in microbial genomes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1952141

Understanding the adaptation of Halobacterium species NRC-1 to its extreme environment through computational analysis of its genome sequence

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1952141

Fidelity of aminoacyl-tRNA selection on the ribosome: kinetic and structural mechanisms

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1952141

Gradients in nucleotide and codon usage along Escherichia coli genes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1952141

The accuracy of codon recognition by polypeptide release factors

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1952141

Thermophilic bacteria strictly obey Szybalski's transcription direction rule and politely purine-load RNAs with both adenine and guanine

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1952141

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1952141

Genome signature comparisons among prokaryote, plasmid, and mitochondrial DNA

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1952141

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1952141

Hidden infidelities of the translational stop signal

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1952141

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1952141

Codon pair utilization biases influence translational elongation step times

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1952141

Selection of aminoacyl-tRNAs at sense codons: the size of the tRNA variable loop determines whether the immediate 3' nucleotide to the codon has a context effect

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1952141

Codon catalog usage and the genome hypothesis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1952141

Codon--anticodon pairing: the wobble hypothesis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1952141

Codon choice and gene expression: synonymous codons differ in translational accuracy

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1952141

Nonrandom utilization of codon pairs in Escherichia coli

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1952141

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1952141

Evolution of the genome and the genetic code: selection at the dinucleotide level by methylation and polyribonucleotide cleavage

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1952141

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1952141

Towards a genetic dissection of the basis of triplet decoding, and its natural subversion: programmed reading frame shifts and hops

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1952141

Polymorphisms associated with the DAZ genes on the human Y chromosome.

21 June 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0000847

Mammalian mutation pressure, synonymous codon choice, and mRNA degradation

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0000847

Codon pairs in the genome of Escherichia coli.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0000847

Transfer RNA gene redundancy and translational selection in Saccharomyces cerevisiae.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0000847

Differences in dinucleotide frequencies of human, yeast, and Escherichia coli genes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0000847

Evolutionary lability of context-dependent codon bias in bacteria.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0000847

Amino acid composition of genomes, lifestyles of organisms, and evolutionary trends: a global picture with correspondence analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0000847

Universal replication biases in bacteria

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0000847

Statistical, computational and visualization methodologies to unveil gene primary structure features.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1952141

Ribosome structure: revisiting the connection between translational accuracy and unconventional decoding

31 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17786218

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Genes from nine genomes are separated into their organisms in the dinucleotide composition space

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17786218

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Codon context effects in missense suppression

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17786218

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PONE.0000847

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17786218%20AND%20SRC:MED&resulttype=core&format=json

5 January 2020

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17786218%20AND%20SRC:MED&resulttype=core&format=json

5 January 2020

PubMed publication ID

17786218

1 reference