(Q36014081)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27166679%20AND%20SRC:MED&resulttype=core&format=json

4 April 2020

title

Codon-Driven Translational Efficiency Is Stable across Diverse Mammalian Cell States (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27166679%20AND%20SRC:MED&resulttype=core&format=json

4 April 2020

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27166679%20AND%20SRC:MED&resulttype=core&format=json

4 April 2020

Duncan Odom

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27166679%20AND%20SRC:MED&resulttype=core&format=json

4 April 2020

Konrad L M Rudolph

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27166679%20AND%20SRC:MED&resulttype=core&format=json

4 April 2020

Bianca M Schmitt

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27166679%20AND%20SRC:MED&resulttype=core&format=json

4 April 2020

John Marioni

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27166679%20AND%20SRC:MED&resulttype=core&format=json

4 April 2020

Claudia Kutter

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27166679%20AND%20SRC:MED&resulttype=core&format=json

4 April 2020

author name string

Robert J White

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27166679%20AND%20SRC:MED&resulttype=core&format=json

4 April 2020

language of work or name

English

0 references

publication date

11 May 2016

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27166679%20AND%20SRC:MED&resulttype=core&format=json

4 April 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27166679%20AND%20SRC:MED&resulttype=core&format=json

4 April 2020

volume

12

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27166679%20AND%20SRC:MED&resulttype=core&format=json

4 April 2020

issue

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27166679%20AND%20SRC:MED&resulttype=core&format=json

4 April 2020

page(s)

e1006024

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27166679%20AND%20SRC:MED&resulttype=core&format=json

Creative Commons Attribution 4.0 International

4 April 2020

copyright license

start time

11 May 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

describes a project that uses

DESeq2

object named as

DESeq2

1 reference

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

cites work

The Code of Silence: Widespread Associations Between Synonymous Codon Biases and Gene Function

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4864286

Quantification of GC-biased gene conversion in the human genome

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4864286

Codon-biased translation can be regulated by wobble-base tRNA modification systems during cellular stress responses

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4864286

Emerging roles of tRNA in adaptive translation, signalling dynamics and disease

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4864286

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4864286

RNA-Seq gene profiling--a systematic empirical comparison

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4864286

A dual program for translation regulation in cellular proliferation and differentiation

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4864286

High-resolution mapping of transcriptional dynamics across tissue development reveals a stable mRNA-tRNA interface

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4864286

Aberrant methylation of tRNAs links cellular stress to neuro-developmental disorders

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4864286

Translational selection in human: more pronounced in housekeeping genes

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4864286

A comprehensive tRNA deletion library unravels the genetic architecture of the tRNA pool

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4864286

Exonic transcription factor binding directs codon choice and affects protein evolution

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4864286

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4864286

Gene duplication and neofunctionalization: POLR3G and POLR3GL

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4864286

A genome-wide systematic analysis reveals different and predictive proliferation expression signatures of cancerous vs. non-cancerous cells

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4864286

Environmental shaping of codon usage and functional adaptation across microbial communities

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4864286

Kraken: a set of tools for quality control and analysis of high-throughput sequence data

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4864286

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4864286

Enriching the gene set analysis of genome-wide data by incorporating directionality of gene expression and combining statistical hypotheses and methods

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4864286

Rapid turnover of long noncoding RNAs and the evolution of gene expression

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4864286

A role for tRNA modifications in genome structure and codon usage

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4864286

A multiplicity of factors contributes to selective RNA polymerase III occupancy of a subset of RNA polymerase III genes in mouse liver

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4864286

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4864286

Wobble base-pairing slows in vivo translation elongation in metazoans

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4864286

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4864286

The evolution of gene expression levels in mammalian organs

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4864286

Genomic binding of Pol III transcription machinery and relationship with TFIIS transcription factor distribution in mouse embryonic stem cells

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4864286

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4864286

Pol III binding in six mammals shows conservation among amino acid isotypes despite divergence among tRNA genes.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4864286

Determinants of translation efficiency and accuracy

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4864286

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4864286

Differential expression analysis for sequence count data

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4864286

RNA processing and export

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4864286

tRNA biology charges to the front

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4864286

Genomic binding profiles of functionally distinct RNA polymerase III transcription complexes in human cells

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4864286

Human RNA polymerase III transcriptomes and relationships to Pol II promoter chromatin and enhancer-binding factors

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4864286

Pol II and its associated epigenetic marks are present at Pol III-transcribed noncoding RNA genes.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4864286

An evolutionarily conserved mechanism for controlling the efficiency of protein translation

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4864286

Translation efficiency is determined by both codon bias and folding energy

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4864286

Biased gene conversion and the evolution of mammalian genomic landscapes

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4864286

Fast and accurate short read alignment with Burrows-Wheeler transform

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4864286

Estimating translational selection in eukaryotic genomes

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4864286

2 October 2017

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=4864286

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4864286

The impact of recombination on nucleotide substitutions in the human genome

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4864286

How many human genes can be defined as housekeeping with current expression data?

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4864286

Codon usage suggests that translational selection has a major impact on protein expression in trypanosomatids

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4864286

Tissue-specific differences in human transfer RNA expression

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4864286

tRNA's wobble decoding of the genome: 40 years of modification

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4864286

The action of selection on codon bias in the human genome is related to frequency, complexity, and chronology of amino acids

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4864286

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4864286

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4864286

Tissue-specific codon usage and the expression of human genes

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4864286

Codon usage between genomes is constrained by genome-wide mutational processes

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4864286

RPG: the Ribosomal Protein Gene database

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4864286

Evolution of synonymous codon usage in metazoans

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4864286

Codon usage and tRNA genes in eukaryotes: correlation of codon usage diversity with translation efficiency and with CG-dinucleotide usage as assessed by multivariate analysis.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4864286

Diversity in G + C content at the third position of codons in vertebrate genes and its cause

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4864286

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4864286

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4864286

Codon-anticodon assignment and detection of codon usage trends in seven microbial genomes

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4864286

Synonymous Mutations Frequently Act as Driver Mutations in Human Cancers

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4864286

Evolutionary conservation of codon optimality reveals hidden signatures of cotranslational folding

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4864286

RNA cytosine methylation by Dnmt2 and NSun2 promotes tRNA stability and protein synthesis.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4864286

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

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4864286

Mammalian mutation pressure, synonymous codon choice, and mRNA degradation

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4864286

The compositional properties of human genes

23 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/27166679

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

No Evidence for Tissue-Specific Adaptation of Synonymous Codon Usage in Humans

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/27166679

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/27166679

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PGEN.1006024

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27166679%20AND%20SRC:MED&resulttype=core&format=json

4 April 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27166679%20AND%20SRC:MED&resulttype=core&format=json

4 April 2020

PubMed publication ID

27166679

1 reference