(Q28645761)

title

Determinants of the rate of protein sequence evolution (English)

0 references

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2

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26055156%20AND%20SRC:MED&resulttype=core&format=json

13 June 2020

author name string

Jianzhi Zhang

series ordinal

1

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26055156%20AND%20SRC:MED&resulttype=core&format=json

13 June 2020

language of work or name

English

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publication date

July 2015

0 references

published in

Nature Reviews Genetics

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26055156%20AND%20SRC:MED&resulttype=core&format=json

13 June 2020

volume

16

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26055156%20AND%20SRC:MED&resulttype=core&format=json

13 June 2020

issue

7

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26055156%20AND%20SRC:MED&resulttype=core&format=json

13 June 2020

page(s)

409-420

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26055156%20AND%20SRC:MED&resulttype=core&format=json

Ribosome profiling reveals pervasive and regulated stop codon readthrough in Drosophila melanogaster

13 June 2020

cites work

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

17 March 2017

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17 March 2017

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17 March 2017

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17 March 2017

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An integrated view of protein evolution

17 March 2017

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Molecular clocks: four decades of evolution

17 March 2017

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17 March 2017

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17 March 2017

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17 March 2017

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17 March 2017

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17 March 2017

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Correlation between the substitution rate and rate variation among sites in protein evolution

17 March 2017

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17 March 2017

Non-Darwinian Evolution

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Evolutionary Rate at the Molecular Level

17 March 2017

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On Some Principles Governing Molecular Evolution

17 March 2017

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Chromosomal location and evolutionary rate variation in enterobacterial genes

17 March 2017

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TimeTree: a public knowledge-base of divergence times among organisms

17 March 2017

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Among-site rate variation and its impact on phylogenetic analyses

7 April 2017

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Functional roles for noise in genetic circuits

7 April 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4523088

Transcription-coupled DNA repair: two decades of progress and surprises

7 April 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4523088

In vivo enhancer analysis of human conserved non-coding sequences

7 April 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4523088

Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection

7 April 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4523088

Evolutionary rate in the protein interaction network

7 April 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4523088

7 April 2017

Biochemical evolution

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Protein evolution. Pervasive degeneracy and epistasis in a protein-protein interface.

7 April 2017

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Yeast mutation accumulation experiment supports elevated mutation rates at highly transcribed sites

3 June 2018

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Codon-by-codon modulation of translational speed and accuracy via mRNA folding.

3 June 2018

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Somatic mosaicism and disease.

3 June 2018

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Impacts of pretranscriptional DNA methylation, transcriptional transcription factor, and posttranscriptional microRNA regulations on protein evolutionary rate

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4523088

Integrating multiple genomic data to predict disease-causing nonsynonymous single nucleotide variants in exome sequencing studies

3 June 2018

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Human coding RNA editing is generally nonadaptive

3 June 2018

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From single-cell to cell-pool transcriptomes: stochasticity in gene expression and RNA splicing.

3 June 2018

1 reference

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Site-specific structural constraints on protein sequence evolutionary divergence: local packing density versus solvent exposure.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4523088

The hourglass and the early conservation models--co-existing patterns of developmental constraints in vertebrates

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4523088

No gene-specific optimization of mutation rate in Escherichia coli

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4523088

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4523088

Cellular crowding imposes global constraints on the chemistry and evolution of proteomes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4523088

Genomic evidence for elevated mutation rates in highly expressed genes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4523088

High expression hampers horizontal gene transfer

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4523088

Protein misinteraction avoidance causes highly expressed proteins to evolve slowly

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4523088

Insights into the regulation of protein abundance from proteomic and transcriptomic analyses

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4523088

Transcription as a source of genome instability

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4523088

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4523088

Negative correlation between expression level and evolutionary rate of long intergenic noncoding RNAs

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4523088

Testing hypotheses on the rate of molecular evolution in relation to gene expression using microRNAs

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4523088

Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4523088

Impact of gene expression noise on organismal fitness and the efficacy of natural selection

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4523088

The relationships among microRNA regulation, intrinsically disordered regions, and other indicators of protein evolutionary rate

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4523088

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4523088

Evolutionary rates and gene dispensability associate with replication timing in the archaeon Sulfolobus islandicus

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4523088

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4523088

Expression level, evolutionary rate, and the cost of expression

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4523088

Chaperonin-dependent accelerated substitution rates in prokaryotes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4523088

Mutant p53 gain-of-function in cancer

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4523088

Highly expressed and slowly evolving proteins share compositional properties with thermophilic proteins

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4523088

The evolutionary consequences of erroneous protein synthesis.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4523088

The relationship between the evolution of microRNA targets and the length of their UTRs

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4523088

Positive selection for elevated gene expression noise in yeast

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4523088

Integrated assessment of genomic correlates of protein evolutionary rate

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4523088

Evolutionary rates and centrality in the yeast gene regulatory network

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4523088

Transcription-associated recombination in eukaryotes: link between transcription, replication and recombination

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4523088

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4523088

Whole-genome mutational biases in bacteria

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4523088

Comparable contributions of structural-functional constraints and expression level to the rate of protein sequence evolution.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4523088

Constraints imposed by non-functional protein-protein interactions on gene expression and proteome size

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4523088

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4523088

Relating three-dimensional structures to protein networks provides evolutionary insights

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4523088

Structural determinants of the rate of protein evolution in yeast.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4523088

Protein misfolding and human disease

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4523088

Toward a molecular understanding of pleiotropy

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4523088

Influence of metabolic network structure and function on enzyme evolution

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4523088

Why highly expressed proteins evolve slowly

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4523088

Functional genomic analysis of the rates of protein evolution

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4523088

Aberrant mRNA translation in cancer pathogenesis: an old concept revisited comes finally of age.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4523088

Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4523088

Essential genes are more evolutionarily conserved than are nonessential genes in bacteria

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4523088

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4523088

SNPs, protein structure, and disease.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4523088

Residue depth: a novel parameter for the analysis of protein structure and stability.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4523088

Synonymous codon usage in Drosophila melanogaster: natural selection and translational accuracy.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4523088

Positive selection is a general phenomenon in the evolution of abalone sperm lysin

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4523088

Do essential genes evolve slowly?

3 June 2018

1 reference

Protein dispensability and rate of evolution

21 January 2018

1 reference

Genomic function (communication arising): Rate of evolution and gene dispensability

21 January 2018

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

A single determinant dominates the rate of yeast protein evolution

21 January 2018

1 reference

Intrinsic protein disorder and interaction promiscuity are widely associated with dosage sensitivity.

21 January 2018

1 reference

Evolvability as a function of purifying selection in TEM-1 β-lactamase.

21 January 2018

1 reference

Mammalian housekeeping genes evolve more slowly than tissue-specific genes.

21 January 2018

1 reference

Impact of extracellularity on the evolutionary rate of mammalian proteins

21 January 2018

1 reference

Biogeochemical forces shape the composition and physiology of polymicrobial communities in the cystic fibrosis lung.

21 January 2018

1 reference

Determinants of protein evolutionary rates in light of ENCODE functional genomics

21 January 2018

1 reference

Evolutionary rate heterogeneity in proteins with long disordered regions.

21 January 2018

1 reference

Protein conformational diversity correlates with evolutionary rate.

21 January 2018

1 reference

Essential Genes Are More Evolutionarily Conserved Than Are Nonessential Genes in Bacteria

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4523088

Highly expressed genes in yeast evolve slowly.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4523088

Error prevention and mitigation as forces in the evolution of genes and genomes

27 November 2018

1 reference

Evolutionary Divergence and Convergence in Proteins

21 January 2018

1 reference

Unifying measures of gene function and evolution

31 March 2020

1 reference

Structural determinants of protein evolution are context-sensitive at the residue level

31 March 2020

1 reference

Assessing determinants of exonic evolutionary rates in mammals

31 March 2020

1 reference

Low rates of expression profile divergence in highly expressed genes and tissue-specific genes during mammalian evolution

31 March 2020

1 reference

Coupling between protein level selection and codon usage optimization in the evolution of bacteria and archaea

31 March 2020

1 reference

Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks

31 March 2020

1 reference

31 March 2020

Identifiers

DOI

10.1038/NRG3950

2 references

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26055156%20AND%20SRC:MED&resulttype=core&format=json

Dimensions Publication ID

13 June 2020

1034056750

0 references

1 reference

2 references

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26055156%20AND%20SRC:MED&resulttype=core&format=json

13 June 2020

2 references