Determinants of translation elongation speed and ribosomal profiling biases in mouse embryonic stem cells (Q34468894)

2 August 2017

title

Determinants of translation elongation speed and ribosomal profiling biases in mouse embryonic stem cells (English)

1 reference

2 August 2017

1 reference

Tamir Tuller

0 references

Alexandra Dana

1 reference

2 August 2017

language of work or name

1 reference

1 November 2012

1 reference

PLOS Computational Biology

2 August 2017

published in

1 reference

2 August 2017

1 reference

2 August 2017

1 reference

2 August 2017

page(s)

e1002755

1 reference

Creative Commons Attribution 4.0 International

2 August 2017

start time

1 November 2012

1 reference

April 2022 Public Data File from Crossref

copyrighted

0 references

cites work

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3486846

Ribosome profiling shows that miR-430 reduces translation before causing mRNA decay in zebrafish

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3486846

Genes adopt non-optimal codon usage to generate cell cycle-dependent oscillations in protein levels

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3486846

Primary role for endoplasmic reticulum-bound ribosomes in cellular translation identified by ribosome profiling

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3486846

High-resolution view of the yeast meiotic program revealed by ribosome profiling

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3486846

Selective ribosome profiling reveals the cotranslational chaperone action of trigger factor in vivo

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3486846

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3486846

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3486846

Wobble base-pairing slows in vivo translation elongation in metazoans

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3486846

Explaining complex codon usage patterns with selection for translational efficiency, mutation bias, and genetic drift.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3486846

Genome-Wide Translational Profiling by Ribosome Footprinting

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3486846

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3486846

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3486846

Mammalian microRNAs predominantly act to decrease target mRNA levels

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3486846

An evolutionarily conserved mechanism for controlling the efficiency of protein translation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3486846

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3486846

Selection for minimization of translational frameshifting errors as a factor in the evolution of codon usage

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3486846

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3486846

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3486846

Electrostatics in the ribosomal tunnel modulate chain elongation rates

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3486846

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3486846

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3486846

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3486846

Weak selection and recent mutational changes influence polymorphic synonymous mutations in humans

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3486846

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3486846

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3486846

Codon bias and heterologous protein 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=3486846

Human housekeeping genes are compact

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3486846

Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary 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=3486846

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=3486846

Ribosome pausing and stacking during translation of a eukaryotic mRNA.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3486846

Ribosome motions modulate electrostatic properties

6 July 2018

1 reference

Crossref

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002755

Both temperature and medium composition regulate RNase E processing efficiency of the rpsO mRNA coding for ribosomal protein S15 of Escherichia coli.

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002755

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002755

Totally asymmetric exclusion process with extended objects: A model for protein synthesis

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002755

10.1371/JOURNAL.PCBI.1002755

21 January 2018

Identifiers

DOI

1 reference

2 August 2017

DBLP publication ID

journals/ploscb/DanaT12

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

2 August 2017

1 reference