(Q37405617)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24363105%20AND%20SRC:MED&resulttype=core&format=json

3 March 2020

title

tRNA genes rapidly change in evolution to meet novel translational demands (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24363105%20AND%20SRC:MED&resulttype=core&format=json

3 March 2020

author name string

Avihu H Yona

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24363105%20AND%20SRC:MED&resulttype=core&format=json

3 March 2020

Idan Frumkin

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24363105%20AND%20SRC:MED&resulttype=core&format=json

3 March 2020

Victor Hanson-Smith

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24363105%20AND%20SRC:MED&resulttype=core&format=json

3 March 2020

Yoav Charpak-Amikam

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24363105%20AND%20SRC:MED&resulttype=core&format=json

3 March 2020

Qinghua Feng

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24363105%20AND%20SRC:MED&resulttype=core&format=json

3 March 2020

Jef D Boeke

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24363105%20AND%20SRC:MED&resulttype=core&format=json

3 March 2020

Orna Dahan

8

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24363105%20AND%20SRC:MED&resulttype=core&format=json

3 March 2020

language of work or name

English

0 references

publication date

20 December 2013

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24363105%20AND%20SRC:MED&resulttype=core&format=json

3 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24363105%20AND%20SRC:MED&resulttype=core&format=json

3 March 2020

volume

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24363105%20AND%20SRC:MED&resulttype=core&format=json

3 March 2020

page(s)

e01339

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24363105%20AND%20SRC:MED&resulttype=core&format=json

describes a project that uses

3 March 2020

ImageJ

1 reference

11 June 2022

https://www.ebi.ac.uk/europepmc/webservices/rest/PMC3868979/fullTextXML

inferred from PubMed Central ID database lookup

cites work

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6 September 2017

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6 September 2017

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Non-optimal codon usage affects expression, structure and function of clock protein FRQ

6 September 2017

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Vaccinia and influenza A viruses select rather than adjust tRNAs to optimize translation.

6 September 2017

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Genome-wide identification and quantitative analysis of cleaved tRNA fragments induced by cellular stress

6 September 2017

1 reference

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Dynamic changes in translational efficiency are deduced from codon usage of the transcriptome

6 September 2017

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Mutation bias is the driving force of codon usage in the Gallus gallus genome

6 September 2017

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Eukaryotic evolutionary transitions are associated with extreme codon bias in functionally-related proteins

6 September 2017

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How mutations in tRNA distant from the anticodon affect the fidelity of decoding

6 September 2017

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The evolution of tRNA genes in Drosophila

6 September 2017

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Genomic organization of eukaryotic tRNAs

6 September 2017

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DendroPy: a Python library for phylogenetic computing

6 September 2017

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An evolutionarily conserved mechanism for controlling the efficiency of protein translation

6 September 2017

1 reference

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Signatures of protein biophysics in coding sequence evolution

6 September 2017

1 reference

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Protein folding on the ribosome

6 September 2017

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Eukaryotic initiator tRNA: finely tuned and ready for action

6 September 2017

1 reference

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The ribosome as a platform for co-translational processing, folding and targeting of newly synthesized proteins

6 September 2017

1 reference

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Coding-sequence determinants of gene expression in Escherichia coli

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3868979

Translationally optimal codons associate with structurally sensitive sites in proteins

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3868979

Misfolded proteins partition between two distinct quality control compartments

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3868979

Synonymous mutations and ribosome stalling can lead to altered folding pathways and distinct minima

6 September 2017

1 reference

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

6 September 2017

1 reference

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Synonymous codon usage in Escherichia coli: selection for translational accuracy.

6 September 2017

1 reference

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RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3868979

Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative

6 September 2017

1 reference

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3868979

MUSCLE: multiple sequence alignment with high accuracy and high throughput

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3868979

Purine bases at position 37 of tRNA stabilize codon-anticodon interaction in the ribosomal A site by stacking and Mg2+-dependent interactions

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3868979

Changing identities: tRNA duplication and remolding within animal mitochondrial genomes

6 September 2017

1 reference

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Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context

6 September 2017

1 reference

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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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3868979

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

6 September 2017

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3868979

6 September 2017

https://api.crossref.org/works/10.7554%2FELIFE.01339

Ribosome-mediated translational pause and protein domain organization

21 January 2018

1 reference

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A rare tRNA-Arg(CCU) that regulates Ty1 element ribosomal frameshifting is essential for Ty1 retrotransposition in Saccharomyces cerevisiae

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3868979

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3868979

A positive selection for mutants lacking orotidine-5'-phosphate decarboxylase activity in yeast: 5-fluoro-orotic acid resistance

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3868979

Translation is a non-uniform process. Effect of tRNA availability on the rate of elongation of nascent polypeptide chains

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3868979

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3868979

An evolutionary perspective on synonymous codon usage in unicellular organisms

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3868979

Efficient translational frameshifting occurs within a conserved sequence of the overlap between the two genes of a yeast Ty1 transposon

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3868979

The selection-mutation-drift theory of synonymous codon usage

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3868979

Mutational analysis of conserved positions potentially important for initiator tRNA function in Saccharomyces cerevisiae

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3868979

Silent mutations affect in vivo protein folding in Escherichia coli

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3868979

Codon usage bias covaries with expression breadth and the rate of synonymous evolution in humans, but this is not evidence for selection

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3868979

Anticodon-dependent conservation of bacterial tRNA gene sequences

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3868979

An active role for tRNA in decoding beyond codon:anticodon pairing

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3868979

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

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3868979

Stable tRNA-based phylogenies using only 76 nucleotides

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3868979

GtRNAdb: a database of transfer RNA genes detected in genomic sequence

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3868979

Trm9-catalyzed tRNA modifications link translation to the DNA damage response

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3868979

The effect of gene conversion on the divergence between duplicated genes

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3868979

Concerted evolution of tRNA genes: intergenic conversion among three unlinked serine tRNA genes in S. pombe

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3868979

Protein folding within the cell is influenced by controlled rates of polypeptide elongation

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3868979

Translational selection frequently overcomes genetic drift in shaping synonymous codon usage patterns in vertebrates

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3868979

Evolutionary conservation of codon optimality reveals hidden signatures of cotranslational folding

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3868979

Transient ribosomal attenuation coordinates protein synthesis and co-translational folding.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3868979

Coevolution of codon usage and tRNA genes leads to alternative stable states of biased codon usage

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3868979

Archaeology and evolution of transfer RNA genes in the Escherichia coli genome

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3868979

Evolutionary instability of operon structures disclosed by sequence comparisons of complete microbial genomes.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3868979

Evolution of a transfer RNA gene through a point mutation in the anticodon

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3868979

Transfer RNA gene redundancy and translational selection in Saccharomyces cerevisiae.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3868979

Co-variation of tRNA abundance and codon usage in Escherichia coli at different growth rates.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3868979

The yeast initiator tRNAMet can act as an elongator tRNA(Met) in vivo

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3868979

tRNA structure and ribosomal function. I. tRNA nucleotide 27-43 mutations enhance first position wobble.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3868979

Recombination between dispersed serine tRNA genes in Schizosaccharomyces pombe

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3868979

Long-Term Experimental Evolution in Escherichia coli. I. Adaptation and Divergence During 2,000 Generations

2 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.7554%2FELIFE.01339

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

21 January 2018

1 reference

12 December 2020

Phylogenetic relationship of organisms obtained by ribosomal protein comparison

1 reference

12 December 2020

Folding and quality control of the VHL tumor suppressor proceed through distinct chaperone pathways

1 reference

12 December 2020

Idiosyncratic tuning of tRNAs to achieve uniform ribosome binding

1 reference

12 December 2020

Differential translation efficiency of orthologous genes is involved in phenotypic divergence of yeast species

1 reference

12 December 2020

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

1 reference

12 December 2020

tRNA genes in eukaryotic genome organization and reorganization

1 reference

12 December 2020

A functional analysis of the repeated methionine initiator tRNA genes (IMT) in yeast

1 reference

12 December 2020

Identifiers

DOI

10.7554/ELIFE.01339

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24363105%20AND%20SRC:MED&resulttype=core&format=json

3 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24363105%20AND%20SRC:MED&resulttype=core&format=json

3 March 2020

PubMed publication ID

24363105

1 reference