(Q36295354)

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Synonymous Genetic Variation in Natural Isolates of Escherichia coli Does Not Predict Where Synonymous Substitutions Occur in a Long-Term Experiment

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scholarly article

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Europe PubMed Central

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13 August 2017

Synonymous Genetic Variation in Natural Isolates of Escherichia coli Does Not Predict Where Synonymous Substitutions Occur in a Long-Term Experiment (English)

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Europe PubMed Central

PMC publication ID

13 August 2017

Escherichia coli

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based on heuristic

inferred from title

6

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Europe PubMed Central

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13 August 2017

Claudine Médigue

4

object named as

Claudine Médigue

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Jeffrey E Barrick

5

object named as

Jeffrey E Barrick

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Europe PubMed Central

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13 August 2017

author name string

Rohan Maddamsetti

1

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Europe PubMed Central

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13 August 2017

Philip J Hatcher

2

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Europe PubMed Central

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13 August 2017

Stéphane Cruveiller

3

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13 August 2017

publication date

20 July 2015

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13 August 2017

Molecular Biology and Evolution

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13 August 2017

32

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Europe PubMed Central

PMC publication ID

13 August 2017

11

1 reference

Europe PubMed Central

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13 August 2017

2897-2904

1 reference

Europe PubMed Central

PMC publication ID

13 August 2017

Recombinant transfer in the basic genome of Escherichia coli.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4651231

30 September 2017

Adaptation, Clonal Interference, and Frequency-Dependent Interactions in a Long-Term Evolution Experiment with Escherichia coli

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4651231

30 September 2017

Quantitative evolutionary dynamics using high-resolution lineage tracking

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4651231

30 September 2017

Mutation rate, spectrum, topology, and context-dependency in the DNA mismatch repair-deficient Pseudomonas fluorescens ATCC948.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4651231

30 September 2017

Bacterial phylogenetic reconstruction from whole genomes is robust to recombination but demographic inference is not.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4651231

30 September 2017

Large chromosomal rearrangements during a long-term evolution experiment with Escherichia coli

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4651231

30 September 2017

Genome dynamics during experimental evolution

1 reference

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Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations

1 reference

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30 September 2017

Mutation rates, spectra, and genome-wide distribution of spontaneous mutations in mismatch repair deficient yeast

1 reference

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30 September 2017

Mycobacterium tuberculosis mutation rate estimates from different lineages predict substantial differences in the emergence of drug-resistant tuberculosis

1 reference

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Strong purifying selection at synonymous sites in D. melanogaster

1 reference

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30 September 2017

No gene-specific optimization of mutation rate in Escherichia coli

1 reference

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30 September 2017

On the mutational topology of the bacterial genome

1 reference

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30 September 2017

Nucleoid-associated proteins affect mutation dynamics in E. coli in a growth phase-specific manner

1 reference

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30 September 2017

Mutation rate dynamics in a bacterial population reflect tension between adaptation and genetic load

1 reference

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30 September 2017

Good codons, bad transcript: large reductions in gene expression and fitness arising from synonymous mutations in a key enzyme

1 reference

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30 September 2017

Recombination modulates how selection affects linked sites in Drosophila

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4651231

30 September 2017

Genomic evidence for elevated mutation rates in highly expressed genes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4651231

30 September 2017

Drift-barrier hypothesis and mutation-rate evolution.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4651231

30 September 2017

Genomic analysis of a key innovation in an experimental Escherichia coli population

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4651231

30 September 2017

Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4651231

30 September 2017

High expression hampers horizontal gene transfer

1 reference

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30 September 2017

Patterns of gene flow define species of thermophilic Archaea

1 reference

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30 September 2017

Mutation Rate Inferred From Synonymous Substitutions in a Long-Term Evolution Experiment With Escherichia coli

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4651231

30 September 2017

Quantifying the variation in the effective population size within a genome.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4651231

30 September 2017

Mutation rates across budding yeast chromosome VI are correlated with replication timing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4651231

30 September 2017

Second-order selection for evolvability in a large Escherichia coli population

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4651231

30 September 2017

Evidence that mutation is universally biased towards AT in bacteria

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4651231

30 September 2017

Evidence of selection upon genomic GC-content in bacteria

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4651231

30 September 2017

Mutational patterns cannot explain genome composition: Are there any neutral sites in the genomes of bacteria?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4651231

30 September 2017

Why genes evolve faster on secondary chromosomes in bacteria

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4651231

30 September 2017

The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana

1 reference

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Genome evolution and adaptation in a long-term experiment with Escherichia coli

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4651231

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Tracing ancestors and relatives of Escherichia coli B, and the derivation of B strains REL606 and BL21(DE3).

1 reference

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30 September 2017

dUTP incorporation into genomic DNA is linked to transcription in yeast

1 reference

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30 September 2017

Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths

1 reference

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30 September 2017

Toward a selection theory of molecular evolution

1 reference

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30 September 2017

Estimating the per-base-pair mutation rate in the yeast Saccharomyces cerevisiae

1 reference

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Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans

1 reference

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Mutations of Bacteria from Virus Sensitivity to Virus Resistance

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Estimating diversifying selection and functional constraint in the presence of recombination

1 reference

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Parallel changes in gene expression after 20,000 generations of evolution in Escherichiacoli

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30 September 2017

Mutators and sex in bacteria: conflict between adaptive strategies

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4651231

30 September 2017

Evolution of high mutation rates in experimental populations of E. coli

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4651231

30 September 2017

Dynamics of adaptation and diversification: a 10,000-generation experiment with bacterial populations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4651231

30 September 2017

Evolutionary Rate at the Molecular Level

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4651231

30 September 2017

Chromosomal location and evolutionary rate variation in enterobacterial genes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4651231

30 September 2017

Accelerated gene evolution through replication-transcription conflicts

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4651231

29 June 2018

Levels of naturally occurring DNA polymorphism correlate with recombination rates in D. melanogaster

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4651231

29 June 2018

Adaptive synonymous mutations in an experimentally evolved Pseudomonas fluorescens population

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4651231

22 September 2018

Long-term dynamics of adaptation in asexual populations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4651231

22 September 2018

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1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4651231

22 September 2018

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1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4651231

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1 reference

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22 September 2018

Genome sequences of Escherichia coli B strains REL606 and BL21(DE3).

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4651231

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1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4651231

22 September 2018

Evolutionary implications of the frequent horizontal transfer of mismatch repair genes.

1 reference

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1 reference

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Structured coalescent processes on different time scales.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4651231

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Clonal divergence in Escherichia coli as a result of recombination, not mutation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4651231

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Synonymous substitutions are clustered in enterobacterial genes.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4651231

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Correlated asymmetry of sequence and functional divergence between duplicate proteins of Saccharomyces cerevisiae

1 reference

https://pubmed.ncbi.nlm.nih.gov/26199375

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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10.1093/MOLBEV/MSV161

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Europe PubMed Central

PMC publication ID

13 August 2017

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

13 August 2017

PubMed publication ID

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Europe PubMed Central

PMC publication ID

13 August 2017

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