(Q35181397)

7 August 2017

title

Unraveling patterns of site-to-site synonymous rates variation and associated gene properties of protein domains and families (English)

1 reference

7 August 2017

Slavica Dimitrieva

1

1 reference

7 August 2017

Maria Anisimova

series ordinal

2

1 reference

7 August 2017

language of work or name

English

0 references

publication date

4 June 2014

1 reference

7 August 2017

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7 August 2017

volume

9

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7 August 2017

issue

6

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7 August 2017

page(s)

e95034

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Creative Commons Attribution 4.0 International

7 August 2017

copyright license

start time

4 June 2014

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Positively charged residues are the major determinants of ribosomal velocity

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4045579

Balanced codon usage optimizes eukaryotic translational efficiency

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4045579

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4045579

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4045579

The Pfam protein families database

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4045579

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4045579

Understanding the contribution of synonymous mutations to human disease

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4045579

Complex interplay of evolutionary forces in the ladybird homeobox genes of Drosophila melanogaster

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4045579

Determinants of translation efficiency and accuracy

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4045579

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4045579

Non-synonymous and synonymous coding SNPs show similar likelihood and effect size of human disease association

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4045579

Expression breadth and expression abundance behave differently in correlations with evolutionary rates

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4045579

Detecting positive and purifying selection at synonymous sites in yeast and worm

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4045579

Predicting functional alternative splicing by measuring RNA selection pressure from multigenome alignments

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4045579

A pause for thought along the co-translational folding pathway

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4045579

Human Proteinpedia: a unified discovery resource for proteomics research

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4045579

Synonymous mutations and ribosome stalling can lead to altered folding pathways and distinct minima

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4045579

Patterns of positive selection in six Mammalian genomes

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4045579

Silent polymorphisms speak: how they affect pharmacogenomics and the treatment of cancer

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4045579

Widespread positive selection in synonymous sites of mammalian genes

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4045579

PAML 4: phylogenetic analysis by maximum likelihood

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4045579

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4045579

Genetics. SNPs, silent but not invisible.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4045579

Alternative splicing and RNA selection pressure--evolutionary consequences for eukaryotic genomes

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4045579

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4045579

PANDIT: an evolution-centric database of protein and associated nucleotide domains with inferred trees

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4045579

A scan for positively selected genes in the genomes of humans and chimpanzees

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4045579

Systematic identification and analysis of exonic splicing silencers.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4045579

Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4045579

HyPhy: hypothesis testing using phylogenies

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4045579

Determinants of adaptive evolution at the molecular level: the extended complexity hypothesis

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4045579

A synonymous SNP of the corneodesmosin gene leads to increased mRNA stability and demonstrates association with psoriasis across diverse ethnic groups

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4045579

Natural selection affects frequencies of AG and GT dinucleotides at the 5' and 3' ends of exons

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4045579

A gene atlas of the mouse and human protein-encoding transcriptomes

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4045579

Synonymous mutations in the human dopamine receptor D2 (DRD2) affect mRNA stability and synthesis of the receptor

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4045579

Evolution of synonymous codon usage in metazoans

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4045579

Predictive identification of exonic splicing enhancers in human genes

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4045579

Darwin v. 2.0: an interpreted computer language for the biosciences

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4045579

Gene ontology: tool for the unification of biology

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4045579

Codon-substitution models for heterogeneous selection pressure at amino acid sites

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4045579

Evidence of selection on silent site base composition in mammals: potential implications for the evolution of isochores and junk DNA.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4045579

Ribosome-mediated translational pause and protein domain organization

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4045579

28 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=4045579

Darwinian Evolution of Proteins

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4045579

Principles that govern the folding of protein chains

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4045579

The 'effective number of codons' used in a gene

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4045579

Effects of gene expression on molecular evolution in Arabidopsis thaliana and Arabidopsis lyrata.

28 July 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0095034

A test of translational selection at 'silent' sites in the human genome: base composition comparisons in alternatively spliced genes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0095034

Human catechol-O-methyltransferase haplotypes modulate protein expression by altering mRNA secondary structure.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0095034

Specific correlations between relative synonymous codon usage and protein secondary structure

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0095034

Statistical methods for detecting molecular adaptation

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0095034

New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0095034

Accuracy and power of bayes prediction of amino acid sites under positive selection

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0095034

A role for codon order in translation dynamics.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0095034

Biased codon usage near intron-exon junctions: selection on splicing enhancers, splice-site recognition or something else?

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0095034

Sequence-based prediction of protein-protein interactions by means of codon usage.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0095034

Mammalian housekeeping genes evolve more slowly than tissue-specific genes

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0095034

Evolutionary rate in the protein interaction network

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0095034

Functional and topological characterization of protein interaction networks

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0095034

Pervasive adaptive evolution among interactors of the Drosophila hybrid inviability gene, Nup96.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0095034

Silent SNPs: impact on gene function and phenotype

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0095034

Prion sequence polymorphisms and chronic wasting disease resistance in Illinois white-tailed deer (Odocoileus virginianus).

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0095034

Alanine in HI: a silent mutation cries out!

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4045579

Translational selection and molecular evolution

27 September 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0095034

Measuring codon usage bias

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0095034

Differential GC Content between Exons and Introns Establishes Distinct Strategies of Splice-Site Recognition

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4045579

Purifying selection on silent sites -- a constraint from splicing regulation?

15 November 2018

1 reference

12 December 2020

Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes

1 reference

12 December 2020

Evidence for purifying selection acting on silent sites in BRCA1

1 reference

12 December 2020

Monoallelic expression and tissue specificity are associated with high crossover rates

1 reference

12 December 2020

The price of silent mutations

1 reference

12 December 2020

Comparative evolutionary rates of introns and exons in murine rodents

1 reference

12 December 2020

Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution

1 reference

12 December 2020

The sounds of silence: synonymous mutations affect function

1 reference

12 December 2020

10.1371/JOURNAL.PONE.0095034

Identifiers

DOI

1 reference

7 August 2017

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1 reference

7 August 2017

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