Composite effects of gene determinants on the translation speed and density of ribosomes. (Q35907619)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22050731 AND SRC:MED&resulttype=core&format=json

15 January 2020

title

Composite effects of gene determinants on the translation speed and density of ribosomes (English)

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15 January 2020

1

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15 January 2020

Isana Veksler-Lublinsky

2

1 reference

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15 January 2020

5

Eytan Ruppin

1 reference

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15 January 2020

author name string

Nir Gazit

3

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15 January 2020

Martin Kupiec

4

1 reference

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15 January 2020

Michal Ziv-Ukelson

6

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15 January 2020

publication date

3 November 2011

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15 January 2020

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15 January 2020

volume

12

1 reference

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15 January 2020

issue

11

1 reference

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15 January 2020

page(s)

R110

1 reference

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

15 January 2020

cites work

1 reference

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Nonsense-mediated decay targets have multiple sequence-related features that can inhibit translation

11 July 2018

1 reference

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Differential arginylation of actin isoforms is regulated by coding sequence-dependent degradation

11 July 2018

1 reference

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Genome-wide measurement of RNA secondary structure in yeast

11 July 2018

1 reference

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Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line

11 July 2018

1 reference

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

11 July 2018

1 reference

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A role for codon order in translation dynamics.

11 July 2018

1 reference

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An evolutionarily conserved mechanism for controlling the efficiency of protein translation

11 July 2018

1 reference

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How the sequence of a gene can tune its translation

11 July 2018

1 reference

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3334596

Translation efficiency is determined by both codon bias and folding energy

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3334596

Translation efficiency in humans: tissue specificity, global optimization and differences between developmental stages

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3334596

GroEL dependency affects codon usage--support for a critical role of misfolding in gene evolution

11 July 2018

1 reference

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Viral adaptation to host: a proteome-based analysis of codon usage and amino acid preferences

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3334596

The evolutionary consequences of erroneous protein synthesis.

11 July 2018

1 reference

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Design parameters to control synthetic gene expression in Escherichia coli

11 July 2018

1 reference

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Coding-sequence determinants of gene expression in Escherichia coli

11 July 2018

1 reference

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3334596

Single-RNA counting reveals alternative modes of gene expression in yeast

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3334596

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3334596

Electrostatics in the ribosomal tunnel modulate chain elongation rates

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3334596

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3334596

Following translation by single ribosomes one codon at a time.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3334596

Determinants of protein abundance and translation efficiency in S. cerevisiae

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3334596

Ribosome biogenesis and the translation process in Escherichia coli

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3334596

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3334596

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3334596

NCBI GEO: mining tens of millions of expression profiles--database and tools update

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3334596

A genomic code for nucleosome positioning

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3334596

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3334596

Codon modification of T cell receptors allows enhanced functional expression in transgenic human T cells

11 July 2018

1 reference

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Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome

11 July 2018

1 reference

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Recent developments towards the heterologous expression of complex bacterial natural product biosynthetic pathways.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3334596

Expression levels influence ribosomal frameshifting at the tandem rare arginine codons AGG_AGG and AGA_AGA in Escherichia coli

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3334596

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

11 July 2018

1 reference

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Codon bias and heterologous protein expression

11 July 2018

1 reference

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The molecular mechanics of eukaryotic translation

11 July 2018

1 reference

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Vienna RNA secondary structure server

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3334596

Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3334596

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3334596

Complete suboptimal folding of RNA and the stability of secondary structures.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3334596

The genetic code is one in a million

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3334596

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3334596

Amino acid difference formula to help explain protein evolution

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3334596

Point mutations define a sequence flanking the AUG initiator codon that modulates translation by eukaryotic ribosomes

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3334596

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.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3334596

Amino acid substitution matrices from protein blocks

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3334596

Rapid and easy thermodynamic optimization of the 5'-end of mRNA dramatically increases the level of wild type protein expression in Escherichia coli

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3334596

Ribosome motions modulate electrostatic properties

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3334596

Enhancement of translation initiation by A/T-rich sequences downstream of the initiation codon in Escherichia coli

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3334596

Transfer RNA gene redundancy and translational selection in Saccharomyces cerevisiae.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3334596

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

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3334596

The Geometry of the Ribosomal Polypeptide Exit Tunnel

24 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1186/GB-2011-12-11-R110

Clustering of low usage codons and ribosome movement

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22050731

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

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

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22050731

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/GB-2011-12-11-R110

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22050731 AND SRC:MED&resulttype=core&format=json

Dimensions Publication ID

15 January 2020

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22050731 AND SRC:MED&resulttype=core&format=json

15 January 2020

PubMed publication ID

22050731

1 reference