(Q34064720)

30 July 2017

title

Species-specific codon context rules unveil non-neutrality effects of synonymous mutations (English)

1 reference

30 July 2017

Ana R Bezerra

8

0 references

Ana R Soares

Ana R Soares

7

0 references

Gabriela Moura

Gabriela R Moura

1

0 references

Adelaide Freitas

Adelaide Freitas

3

0 references

José Luís Oliveira

José L Oliveira

4

0 references

author name string

Miguel Pinheiro

2

1 reference

30 July 2017

Jörg C Frommlet

5

1 reference

30 July 2017

Laura Carreto

6

1 reference

30 July 2017

Manuel A S Santos

9

1 reference

30 July 2017

language of work or name

English

0 references

publication date

26 October 2011

1 reference

30 July 2017

1 reference

30 July 2017

volume

6

1 reference

30 July 2017

issue

10

1 reference

30 July 2017

page(s)

e26817

1 reference

Creative Commons Attribution 4.0 International

30 July 2017

copyright license

start time

26 October 2011

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Evidence that mutation is universally biased towards AT in bacteria

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202573

Evidence of Selection upon Genomic GC-Content in Bacteria

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202573

Mutational patterns cannot explain genome composition: Are there any neutral sites in the genomes of bacteria?

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202573

Live attenuated influenza virus vaccines by computer-aided rational design

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202573

General rules for optimal codon choice

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202573

5 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=3202573

Preferred and avoided codon pairs in three domains of life

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202573

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202573

Virus attenuation by genome-scale changes in codon pair bias

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202573

Analysis of the distribution of functionally relevant rare codons

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202573

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202573

A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202573

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202573

DNA methylation and human disease

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202573

Gardening the genome: DNA methylation in Arabidopsis thaliana

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202573

Comparative context analysis of codon pairs on an ORFeome scale

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202573

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202573

A programmed -1 ribosomal frameshift signal can function as a cis-acting mRNA destabilizing element

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202573

Sequences that direct significant levels of frameshifting are frequent in coding regions of Escherichia coli.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202573

Programmed translational -1 frameshifting on hexanucleotide motifs and the wobble properties of tRNAs

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202573

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202573

Computational identification of putative programmed translational frameshift sites

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202573

High level, context dependent misincorporation of lysine for arginine in Saccharomyces cerevisiae a1 homeodomain expressed in Escherichia coli

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202573

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202573

Codon pair utilization biases influence translational elongation step times

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202573

Decoding with the A:I wobble pair is inefficient

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202573

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202573

Missense misreading of asparagine codons as a function of codon identity and context

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202573

Errors and alternatives in reading the universal genetic code.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202573

Nonrandom utilization of codon pairs in Escherichia coli

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202573

Influence of codon context on UGA suppression and readthrough

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202573

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202573

Adjusting for selection on synonymous sites in estimates of evolutionary distance

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202573

Mammalian mutation pressure, synonymous codon choice, and mRNA degradation

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202573

Charging levels of four tRNA species in Escherichia coli Rel(+) and Rel(-) strains during amino acid starvation: a simple model for the effect of ppGpp on translational accuracy.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202573

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

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202573

The influence of codon context on genetic code translation

28 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22046369

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/22046369

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Computational and statistical methodologies for ORFeome primary structure analysis

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22046369

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PONE.0026817

1 reference

30 July 2017

0 references

1 reference

30 July 2017

1 reference