(Q41652908)

6 October 2017

Causal signals between codon bias, mRNA structure, and the efficiency of translation and elongation (English)

1 reference

6 October 2017

1 reference

7

Daphne Koller

1 reference

6 October 2017

6

Jonathan S Weissman

1 reference

6 October 2017

Cristina Pop

1

1 reference

6 October 2017

Silvi Rouskin

2

1 reference

6 October 2017

Nicholas T Ingolia

3

1 reference

6 October 2017

Lu Han

4

1 reference

6 October 2017

Eric M Phizicky

5

1 reference

6 October 2017

23 December 2014

1 reference

Molecular Systems Biology

6 October 2017

1 reference

6 October 2017

10

1 reference

6 October 2017

770

1 reference

describes a project that uses

6 October 2017

ImageQuant

object named as

ImageQuant

2 references

11 June 2022

https://www.ebi.ac.uk/europepmc/webservices/rest/PMC4300493/fullTextXML

inferred from PubMed Central ID database lookup

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

cites work

Measurement of average decoding rates of the 61 sense codons in vivo.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

Distinct stages of the translation elongation cycle revealed by sequencing ribosome-protected mRNA fragments

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

Scp160p is required for translational efficiency of codon-optimized mRNAs in yeast.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

Control of ribosome traffic by position-dependent choice of synonymous codons

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

Rate-limiting steps in yeast protein translation

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

Efficient translation initiation dictates codon usage at gene start

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

Positively charged residues are the major determinants of ribosomal velocity

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

Dynamics of translation by single ribosomes through mRNA secondary structures

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

Nascent peptides that block protein synthesis in bacteria

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

An in vivo control map for the eukaryotic mRNA translation machinery

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

Weak 5'-mRNA secondary structures in short eukaryotic genes.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

The architecture of eukaryotic translation

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

Balanced codon usage optimizes eukaryotic translational efficiency

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

Functional complexity and regulation through RNA dynamics

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

Strong association between mRNA folding strength and protein abundance in S. cerevisiae

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

Reduced mRNA secondary-structure stability near the start codon indicates functional genes in prokaryotes

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

Composite effects of gene determinants on the translation speed and density of ribosomes.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

Wobble base-pairing slows in vivo translation elongation in metazoans

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

Genome-scale analysis of translation elongation with a ribosome flow model

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

The role of tRNA and ribosome competition in coupling the expression of different mRNAs in Saccharomyces cerevisiae

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

Reduced stability of mRNA secondary structure near the translation-initiation site in dsDNA viruses

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

Synonymous but not the same: the causes and consequences of codon bias

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

Control of translation efficiency in yeast by codon-anticodon interactions

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

Genome-wide measurement of RNA secondary structure in yeast

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

On relevance of codon usage to expression of synthetic and natural genes in Escherichia coli

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

An evolutionarily conserved mechanism for controlling the efficiency of protein translation

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

How the sequence of a gene can tune its translation

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

Real-time tRNA transit on single translating ribosomes at codon resolution

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

A universal trend of reduced mRNA stability near the translation-initiation site in prokaryotes and eukaryotes

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

Translation efficiency is determined by both codon bias and folding energy

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

Experimentally increased codon bias in the Drosophila Adh gene leads to an increase in larval, but not adult, alcohol dehydrogenase activity

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

Design parameters to control synthetic gene expression in Escherichia coli

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

Coding-sequence determinants of gene expression in Escherichia coli

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

Translational control of gene expression from transcripts to transcriptomes

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

6 June 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=4300493

Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

The transcriptional landscape of the yeast genome defined by RNA sequencing

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

Following translation by single ribosomes one codon at a time.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

AUG_hairpin: prediction of a downstream secondary structure influencing the recognition of a translation start site

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

A network of multiple regulatory layers shapes gene expression in fission yeast.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

Dissecting eukaryotic translation and its control by ribosome density mapping

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

Codon bias and heterologous protein expression

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

Influence of the three nucleotides upstream of the initiation codon on expression of the Escherichia coli lacZ gene in Saccharomyces cerevisiae

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

Possible role of flanking nucleotides in recognition of the AUG initiator codon by eukaryotic ribosomes

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

Compilation and comparison of the sequence context around the AUG startcodons in Saccharomyces cerevisiae mRNAs

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

Translation rates of individual codons are not correlated with tRNA abundances or with frequencies of utilization in Escherichia coli

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

Downstream secondary structure facilitates recognition of initiator codons by eukaryotic ribosomes

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

Codon preferences in free-living microorganisms

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

Absolute in vivo translation rates of individual codons in Escherichia coli. The two glutamic acid codons GAA and GAG are translated with a threefold difference in rate.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

The selection-mutation-drift theory of synonymous codon usage

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

Positive charge loading at protein termini is due to membrane protein topology, not a translational ramp

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

The mRNA landscape at yeast translation initiation sites.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

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

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

Codon optimization can improve expression of human genes in Escherichia coli: A multi-gene study.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

Rapid tRNA decay can result from lack of nonessential modifications.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

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

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

Codon optimization reveals critical factors for high level expression of two rare codon genes in Escherichia coli: RNA stability and secondary structure but not tRNA abundance.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

mRNA sequences influencing translation and the selection of AUG initiator codons in the yeast Saccharomyces cerevisiae.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300493

Exploring the regulation of tRNA distribution on the genomic scale

18 August 2018

1 reference

12 December 2020

Codon usage determines translation rate in Escherichia coli

1 reference

12 December 2020

Clustering of low usage codons and ribosome movement

1 reference

12 December 2020

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

1 reference

12 December 2020

Identifiers

DOI

10.15252/MSB.20145524

1 reference

release_b22ya3kxjbcsjb2pmwrkomoxxy

6 October 2017

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/b22ya3kxjbcsjb2pmwrkomoxxy

24 November 2022

mapped directly with Wikidata item

1 reference

6 October 2017

PubMed publication ID

25538139

1 reference