(Q33478380)

27 July 2017

title

Clustering of codons with rare cognate tRNAs in human genes suggests an extra level of expression regulation (English)

1 reference

27 July 2017

Martijn A Huynen

2

0 references

author name string

Joanna L Parmley

series ordinal

1

1 reference

27 July 2017

publication date

3 July 2009

1 reference

27 July 2017

1 reference

27 July 2017

volume

5

1 reference

27 July 2017

issue

7

1 reference

27 July 2017

page(s)

e1000548

1 reference

Creative Commons Attribution 4.0 International

27 July 2017

copyright license

start time

3 July 2009

1 reference

April 2022 Public Data File from Crossref

0 references

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2697378

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2697378

Analysis of the distribution of functionally relevant rare codons

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2697378

A novel CpG island set identifies tissue-specific methylation at developmental gene loci

21 June 2018

1 reference

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Codon usage suggests that translational selection has a major impact on protein expression in trypanosomatids

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2697378

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2697378

Quality control of eukaryotic mRNA: safeguarding cells from abnormal mRNA function

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2697378

Cotranslational protein folding--fact or fiction?

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2697378

Posttranscriptional expression regulation: what determines translation rates?

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2697378

Experimental confirmation of a key role for non-optimal codons in protein export

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2697378

A "silent" polymorphism in the MDR1 gene changes substrate specificity

21 June 2018

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BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2697378

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2697378

Evidence for widespread degradation of gene control regions in hominid 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=2697378

Solving the riddle of codon usage preferences: a test for translational 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=2697378

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2697378

A gene atlas of the mouse and human protein-encoding transcriptomes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2697378

MUSCLE: multiple sequence alignment with high accuracy and high throughput

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2697378

Statistical significance for genomewide studies

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2697378

The UCSC Genome Browser Database

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2697378

Distribution and characterization of regulatory elements in the human genome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2697378

Evolution of synonymous codon usage in metazoans

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2697378

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.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2697378

Initial sequencing and analysis of the human genome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2697378

tRNA gene number and codon usage in the C. elegans genome are co-adapted for optimal translation of highly expressed 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=2697378

A systematic analysis of the factors that determine the strength of pre-mRNA splicing enhancers.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2697378

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

21 June 2018

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2697378

21 June 2018

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1000548

Protein secondary structural types are differentially coded on messenger RNA.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2697378

Ribosome-mediated translational pause and protein domain organization

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2697378

DNA sequence evolution: the sounds of silence

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2697378

SCOP: a structural classification of proteins database for the investigation of sequences and structures

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2697378

Preferential codon usage in prokaryotic genes: the optimal codon-anticodon interaction energy and the selective codon usage in efficiently expressed 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=2697378

Evidence for use of rare codons in the dnaG gene and other regulatory genes of 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=2697378

Codon usage and tRNA content in unicellular and multicellular organisms

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2697378

Codon usage in regulatory genes in Escherichia coli does not reflect selection for 'rare' codons

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2697378

Codon preferences in free-living microorganisms

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2697378

Nonuniform size distribution of nascent globin peptides, evidence for pause localization sites, and a cotranslational protein-folding model

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2697378

The selection-mutation-drift theory of synonymous codon usage

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2697378

Translational selection and molecular evolution

21 June 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1000548

Effects of gene expression on molecular evolution in Arabidopsis thaliana and Arabidopsis lyrata.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1000548

Rare codons in E. coli and S. typhimurium signal sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1000548

Post-transcriptional expression regulation in the yeast Saccharomyces cerevisiae on a genomic scale.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1000548

Codon bias as a factor in regulating expression via translation rate in the human genome.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1000548

A direct approach to false discovery rates

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1000548

Evidence for codon bias selection at the pre-mRNA level in eukaryotes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1000548

Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1000548

A single determinant dominates the rate of yeast protein evolution

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2697378

Exonic Splicing Regulatory Elements Skew Synonymous Codon Usage near Intron-exon Boundaries in Mammals

31 October 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1000548

Synonymous codon substitutions affect ribosome traffic and protein folding during in vitro translation

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19578405

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Frequency of using codons in mRNA and coding of the domain structure of proteins

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19578405

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Evidence for Purifying Selection Against Synonymous Mutations in Mammalian Exonic Splicing Enhancers

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19578405

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PGEN.1000548

1 reference

27 July 2017

1 reference

27 July 2017

1 reference