(Q34331153)

1 August 2017

title

Modelling the efficiency of codon-tRNA interactions based on codon usage bias (English)

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1 August 2017

1 reference

Tamir Tuller

2

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author name string

Renana Sabi

series ordinal

1

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1 August 2017

publication date

6 June 2014

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1 August 2017

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1 August 2017

volume

21

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1 August 2017

issue

5

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1 August 2017

page(s)

511-526

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Transcript features alone enable accurate prediction and understanding of gene expression in S. cerevisiae

1 August 2017

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6 July 2018

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6 July 2018

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6 July 2018

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6 July 2018

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6 July 2018

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6 July 2018

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Coadaptation of isoacceptor tRNA genes and codon usage bias for translation efficiency in Aedes aegypti and Anopheles gambiae

6 July 2018

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6 July 2018

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6 July 2018

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6 July 2018

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Comparative analysis of nuclear tRNA genes of Nasonia vitripennis and other arthropods, and relationships to codon usage bias

6 July 2018

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Agmatidine, a modified cytidine in the anticodon of archaeal tRNA(Ile), base pairs with adenosine but not with guanosine

6 July 2018

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Translation efficiency is determined by both codon bias and folding energy

6 July 2018

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6 July 2018

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Reconstructing ancestral gene content by coevolution

6 July 2018

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Coalescent simulation of intracodon recombination

6 July 2018

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Arabidopsis tRNA adenosine deaminase arginine edits the wobble nucleotide of chloroplast tRNAArg(ACG) and is essential for efficient chloroplast translation.

6 July 2018

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Coding-sequence determinants of gene expression in Escherichia coli

6 July 2018

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Predicting gene expression level from relative codon usage bias: an application to Escherichia coli genome

6 July 2018

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Protein abundance profiling of the Escherichia coli cytosol

6 July 2018

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Determinants of protein abundance and translation efficiency in S. cerevisiae

6 July 2018

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Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation.

6 July 2018

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

6 July 2018

1 reference

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A periodic pattern of mRNA secondary structure created by the genetic code

6 July 2018

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

6 July 2018

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6 July 2018

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molecular mechanism of lysidine synthesis that determines tRNA identity and codon recognition.

6 July 2018

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Variation in the strength of selected codon usage bias among bacteria

6 July 2018

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Structure of a purine-purine wobble base pair in the decoding center of the ribosome

6 July 2018

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Codon usage bias from tRNA's point of view: redundancy, specialization, and efficient decoding for translation optimization

6 July 2018

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

6 July 2018

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Unexpected correlations between gene expression and codon usage bias from microarray data for the whole Escherichia coli K-12 genome

6 July 2018

1 reference

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Global analysis of protein expression in yeast

6 July 2018

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Comparing protein abundance and mRNA expression levels on a genomic scale

6 July 2018

1 reference

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tadA, an essential tRNA-specific adenosine deaminase from Escherichia coli

6 July 2018

1 reference

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Analysis of codon:anticodon interactions within the ribosome provides new insights into codon reading and the genetic code structure

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4195497

Large-scale analysis of the yeast proteome by multidimensional protein identification technology

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4195497

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 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4195497

A sampling of the yeast proteome

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4195497

Identification and characterization of a human tRNA-specific adenosine deaminase related to the ADAR family of pre-mRNA editing enzymes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4195497

Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4195497

mRNAs have greater negative folding free energies than shuffled or codon choice randomized sequences

6 July 2018

1 reference

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The complete genome sequence of Escherichia coli K-12

6 July 2018

1 reference

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Codon usage in Caenorhabditis elegans: delineation of translational selection and mutational biases

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4195497

6 July 2018

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=4195497

Codon catalog usage and the genome hypothesis

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4195497

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4195497

Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: A proposal for a synonymous codon choice that is optimal for the E. coli translational system

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4195497

Codon--anticodon pairing: the wobble hypothesis

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4195497

Codon usage and tRNA content in unicellular and multicellular organisms

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4195497

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4195497

Role of GC-biased mutation pressure on synonymous codon choice in Micrococcus luteus, a bacterium with a high genomic GC-content

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4195497

The 'effective number of codons' used in a gene

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4195497

Codon bias and gene expression

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4195497

Wobble position modified nucleosides evolved to select transfer RNA codon recognition: A modified-wobble hypothesis

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4195497

Transfer RNA gene redundancy and translational selection in Saccharomyces cerevisiae.

6 July 2018

1 reference

https://api.crossref.org/works/10.1093%2FDNARES%2FDSU017

Wobble inosine tRNA modification is essential to cell cycle progression in G(1)/S and G(2)/M transitions in fission yeast.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FDNARES%2FDSU017

A Simplex Method for Function Minimization

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FDNARES%2FDSU017

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FDNARES%2FDSU017

Comparative proteomic and transcriptomic profiling of the fission yeast Schizosaccharomyces pombe

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4195497

Modified bases and aminoacylation

27 October 2018

1 reference

https://api.crossref.org/works/10.1093%2FDNARES%2FDSU017

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

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24906480

12 December 2020

inferred from PubMed ID database lookup

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

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24906480

12 December 2020

inferred from PubMed ID database lookup

Genetic variability maintained in a finite population due to mutational production of neutral and nearly neutral isoalleles

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24906480

12 December 2020

inferred from PubMed ID database lookup

Identifiers

DOI

10.1093/DNARES/DSU017

1 reference

release_yzz2ksm46raoxmve6edzjnml5m

1 August 2017

Fatcat ID

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/yzz2ksm46raoxmve6edzjnml5m

24 November 2022

mapped directly with Wikidata item

PMC publication ID

4195497

1 reference

1 August 2017

1 reference