Similar compositional biases are caused by very different mutational effects. (Q39983675)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17068325%20AND%20SRC:MED&resulttype=core&format=json

21 December 2019

title

Similar compositional biases are caused by very different mutational effects (English)

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21 December 2019

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21 December 2019

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21 December 2019

Edward J Feil

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21 December 2019

publication date

26 October 2006

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21 December 2019

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21 December 2019

volume

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21 December 2019

issue

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21 December 2019

page(s)

1537-1547

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DNA primase acts as a molecular brake in DNA replication

21 December 2019

cites work

1 reference

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Origin of replication in circular prokaryotic chromosomes

22 September 2017

1 reference

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Identification of oligonucleotide sequences that direct the movement of the Escherichia coli FtsK translocase

22 September 2017

1 reference

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Comparisons of dN/dS are time dependent for closely related bacterial genomes

22 September 2017

1 reference

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KOPS: DNA motifs that control E. coli chromosome segregation by orienting the FtsK translocase

22 September 2017

1 reference

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Environments shape the nucleotide composition of genomes

22 September 2017

1 reference

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Why highly expressed proteins evolve slowly

22 September 2017

1 reference

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Opinion: Re-evaluating prokaryotic species

22 September 2017

1 reference

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Comparative and evolutionary analysis of the bacterial homologous recombination systems

22 September 2017

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Replication-associated strand asymmetries in mammalian genomes: toward detection of replication origins

22 September 2017

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Codon usage bias from tRNA's point of view: redundancy, specialization, and efficient decoding for translation optimization

22 September 2017

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Chemical specificity of nucleic acids and mechanism of their enzymatic degradation

22 September 2017

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Where does bacterial replication start? Rules for predicting the oriC region

22 September 2017

1 reference

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The replication-related organization of bacterial genomes.

22 September 2017

1 reference

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On the genetic basis of variation and heterogeneity of DNA base composition

22 September 2017

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Transcription increases multiple spontaneous point mutations in Salmonella enterica

22 September 2017

1 reference

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Mutation patterns of mitochondrial H- and L-strand DNA in closely related Cyprinid fishes.

22 September 2017

1 reference

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Vanishing GC-rich isochores in mammalian genomes.

22 September 2017

1 reference

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Asymmetric directional mutation pressures in bacteria

22 September 2017

1 reference

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Is there a role for replication fork asymmetry in the distribution of genes in bacterial genomes?

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665637

Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2)

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665637

Heterotachy, an important process of protein evolution

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665637

Ongoing evolution of strand composition in bacterial genomes

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665637

Initial sequencing and analysis of the human genome

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665637

Replication orientation affects the rate and direction of bacterial gene evolution

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665637

Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665637

Asymmetric substitution patterns: a review of possible underlying mutational or selective mechanisms

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665637

How does replication-associated mutational pressure influence amino acid composition of proteins?

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665637

Nucleotide substitution rate of mammalian mitochondrial genomes

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665637

Proteome composition and codon usage in spirochaetes: species-specific and DNA strand-specific mutational biases

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665637

Base composition skews, replication orientation, and gene orientation in 12 prokaryote genomes

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665637

Replicational and transcriptional selection on codon usage in Borrelia burgdorferi

22 September 2017

1 reference

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Unequal fidelity of leading strand and lagging strand DNA replication on the Escherichia coli chromosome

22 September 2017

1 reference

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DNA replication: one strand may be more equal.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665637

Analyzing genomes with cumulative skew diagrams

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665637

Strand compositional asymmetry in bacterial and large viral genomes

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665637

Initiation and Velocity of Chromosome Replication in Escherichia coli B/r and K-12

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665637

Asymmetric substitution patterns in the two DNA strands of bacteria

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665637

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665637

Codon catalog usage is a genome strategy modulated for gene expressivity

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665637

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665637

The guanine and cytosine content of genomic DNA and bacterial evolution

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665637

Determinants of DNA sequence divergence between Escherichia coli and Salmonella typhimurium: codon usage, map position, and concerted evolution

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665637

Rickettsia rickettsii induces superoxide radical and superoxide dismutase in human endothelial cells

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665637

Molecular basis of base substitution hotspots in Escherichia coli

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665637

An appraisal of the potential for illegitimate recombination in bacterial genomes and its consequences: from duplications to genome reduction

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665637

Strand-specific compositional asymmetries in double-stranded DNA viruses.

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665637

Strand asymmetries in DNA evolution

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665637

Evidence that discontinuous DNA replication in Escherichia coli is primed by approximately 10 to 12 residues of RNA starting with a purine

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665637

Strong asymmetric mutation bias in endosymbiont genomes coincide with loss of genes for replication restart pathways

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665637

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

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665637

Essentiality, not expressiveness, drives gene-strand bias in bacteria.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665637

Aerobiosis increases the genomic guanine plus cytosine content (GC%) in prokaryotes

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665637

Base composition bias might result from competition for metabolic resources.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665637

Asymmetry of frameshift mutagenesis during leading and lagging-strand replication in Escherichia coli.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665637

Composition strand asymmetries in prokaryotic genomes: mutational bias and biased gene orientation.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665637

Evolutionary implications of the frequent horizontal transfer of mismatch repair genes

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665637

Bacterial DNA strand compositional asymmetry.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665637

Skewed oligomers and origins of replication.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665637

Asymmetrical directional mutation pressure in the mitochondrial genome of mammals.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665637

Asymmetries generated by transcription-coupled repair in enterobacterial genes

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665637

An extreme codon preference strategy: codon reassignment.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665637

High divergence rate of sequences located on different DNA strands in closely related bacterial genomes

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665637

Evolution rates of genes on leading and lagging DNA strands

4 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665637

Characteristics of Chi distribution on different bacterial genomes

4 November 2018

1 reference

12 December 2020

Correlations between genomic GC levels and optimal growth temperatures in prokaryotes

1 reference

12 December 2020

The contributions of replication orientation, gene direction, and signal sequences to base-composition asymmetries in bacterial genomes

1 reference

12 December 2020

Problems with Parsimony in Sequences of Biased Base Composition

1 reference

12 December 2020

Universal replication biases in bacteria

1 reference

12 December 2020

Identification of putative chromosomal origins of replication in Archaea

1 reference

12 December 2020

Patterns of nucleotide substitution in pseudogenes and functional genes

1 reference

12 December 2020

Identifiers

DOI

10.1101/GR.5525106

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17068325%20AND%20SRC:MED&resulttype=core&format=json

21 December 2019

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17068325%20AND%20SRC:MED&resulttype=core&format=json

21 December 2019

PubMed publication ID

17068325

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17068325%20AND%20SRC:MED&resulttype=core&format=json