(Q36637572)

15 August 2017

Differential requirements for mRNA folding partially explain why highly expressed proteins evolve slowly (English)

1 reference

15 August 2017

0 references

Chungoo Park

1 reference

15 August 2017

Xiaoshu Chen

series ordinal

1 reference

15 August 2017

Jian-Rong Yang

series ordinal

1 reference

15 August 2017

Jianzhi Zhang

series ordinal

1 reference

15 August 2017

language of work or name

English

0 references

publication date

4 February 2013

1 reference

Proceedings of the National Academy of Sciences of the United States of America

15 August 2017

1 reference

15 August 2017

110

1 reference

15 August 2017

1 reference

15 August 2017

E678-86

1 reference

Balanced codon usage optimizes eukaryotic translational efficiency

15 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3581962

Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3581962

High expression hampers horizontal gene transfer

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3581962

Protein misinteraction avoidance causes highly expressed proteins to evolve slowly

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3581962

Global or local? Predicting secondary structure and accessibility in mRNAs

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3581962

The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3581962

The evolution of gene expression levels in mammalian organs

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3581962

The ribosome uses two active mechanisms to unwind messenger RNA during translation

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3581962

Misfolded proteins impose a dosage-dependent fitness cost and trigger a cytosolic unfolded protein response in yeast

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3581962

The developmental transcriptome of Drosophila melanogaster

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3581962

Impact of translational error‐induced and error‐free misfolding on the rate of protein evolution

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3581962

Expression Level, Evolutionary Rate, and the Cost of Expression

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3581962

Genome-wide measurement of RNA secondary structure in yeast

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3581962

The relationship among gene expression, the evolution of gene dosage, and the rate of protein evolution

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3581962

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3581962

Universal distribution of protein evolution rates as a consequence of protein folding physics

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3581962

Translation efficiency is determined by both codon bias and folding energy

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3581962

The integrated microbial genomes system: an expanding comparative analysis resource

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3581962

Architecture and secondary structure of an entire HIV-1 RNA genome

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3581962

Coding-sequence determinants of gene expression in Escherichia coli

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3581962

Population genomics of domestic and wild yeasts

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3581962

Why is the correlation between gene importance and gene evolutionary rate so weak?

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3581962

Conflicting selection pressures on synonymous codon use in yeast suggest selection on mRNA secondary structures

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3581962

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3581962

The transcriptional landscape of the yeast genome defined by RNA sequencing

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3581962

Following translation by single ribosomes one codon at a time.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3581962

RNA structure: experimental analysis

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3581962

PAML 4: phylogenetic analysis by maximum likelihood

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3581962

High guanine and cytosine content increases mRNA levels in mammalian cells

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3581962

Evidence for selection on synonymous mutations affecting stability of mRNA secondary structure in mammals

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3581962

Gene expression intensity shapes evolutionary rates of the proteins encoded by the vertebrate genome

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3581962

Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure prediction

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3581962

MUSCLE: multiple sequence alignment with high accuracy and high throughput

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3581962

Widespread selection for local RNA secondary structure in coding regions of bacterial genes

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3581962

Translational selection and yeast proteome evolution

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3581962

Evolutionary rate in the protein interaction network

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3581962

Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3581962

Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3581962

mRNAs have greater negative folding free energies than shuffled or codon choice randomized sequences

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3581962

Comparative analyses of the secondary structures of synthetic and intracellular yeast MFA2 mRNAs

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3581962

Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3581962

Evolutionary Rate at the Molecular Level

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3581962

On Some Principles Governing Molecular Evolution

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3581962

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3581962

Long-range base pairing in Drosophila and human mRNA sequences

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3581962

Do essential genes evolve slowly?

28 June 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1218066110

Significant impact of protein dispensability on the instantaneous rate of protein evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1218066110

Impacts of gene essentiality, expression pattern, and gene compactness on the evolutionary rate of mammalian proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1218066110

Mammalian housekeeping genes evolve more slowly than tissue-specific genes

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1218066110

A single determinant dominates the rate of yeast protein evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1218066110

Protein dispensability and rate of evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1218066110

An analysis of determinants of amino acids substitution rates in bacterial proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1218066110

Impact of extracellularity on the evolutionary rate of mammalian proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1218066110

Calculating nucleic acid secondary structure

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1218066110

Fast folding and comparison of RNA secondary structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1218066110

Highly expressed genes in yeast evolve slowly.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3581962

Unifying measures of gene function and evolution

20 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23382244

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Model for folding and aggregation in RNA secondary structures

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23382244

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1073/PNAS.1218066110

1 reference

15 August 2017

0 references

1 reference

15 August 2017

PubMed publication ID

23382244

1 reference