(Q35811484)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21856647%20AND%20SRC:MED&resulttype=core&format=json

11 February 2020

title

Reduced efficacy of natural selection on codon usage bias in selfing Arabidopsis and Capsella species (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21856647%20AND%20SRC:MED&resulttype=core&format=json

11 February 2020

1 reference

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21856647%20AND%20SRC:MED&resulttype=core&format=json

11 February 2020

Stephen I Wright

series ordinal

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21856647%20AND%20SRC:MED&resulttype=core&format=json

11 February 2020

5

Deborah Charlesworth

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21856647%20AND%20SRC:MED&resulttype=core&format=json

11 February 2020

author name string

Suo Qiu

series ordinal

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21856647%20AND%20SRC:MED&resulttype=core&format=json

11 February 2020

Kai Zeng

series ordinal

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21856647%20AND%20SRC:MED&resulttype=core&format=json

11 February 2020

publication date

18 August 2011

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21856647%20AND%20SRC:MED&resulttype=core&format=json

Genome Biology and Evolution

11 February 2020

published in

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21856647%20AND%20SRC:MED&resulttype=core&format=json

11 February 2020

volume

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21856647%20AND%20SRC:MED&resulttype=core&format=json

11 February 2020

page(s)

868-880

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21856647%20AND%20SRC:MED&resulttype=core&format=json

The effects of demography and linkage on the estimation of selection and mutation parameters

11 February 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296465

Evolution of self-compatibility in Arabidopsis by a mutation in the male specificity gene

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296465

Establishing, maintaining and modifying DNA methylation patterns in plants and animals

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296465

A simple multiallele model and its application to identifying preferred-unpreferred codons using polymorphism data

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296465

The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296465

Studying patterns of recent evolution at synonymous sites and intronic sites in Drosophila melanogaster

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296465

Estimating selection intensity on synonymous codon usage in a nonequilibrium population

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296465

Estimating the rate of adaptive molecular evolution in the presence of slightly deleterious mutations and population size change

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296465

Recent speciation of Capsella rubella from Capsella grandiflora, associated with loss of self-incompatibility and an extreme bottleneck

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296465

Recent speciation associated with the evolution of selfing in Capsella.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296465

Hotspots of biased nucleotide substitutions in human genes

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296465

Estimating translational selection in eukaryotic genomes

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296465

The effects of deleterious mutations on evolution in non-recombining genomes.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296465

GC-biased gene conversion promotes the fixation of deleterious amino acid changes in primates.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296465

27 July 2018

Selection on Codon Bias

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296465

Patterns of polymorphism and demographic history in natural populations of Arabidopsis lyrata

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296465

High DNA sequence diversity in pericentromeric genes of the plant Arabidopsis lyrata

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296465

Selection on amino acid substitutions in Arabidopsis

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296465

Adaptive genic evolution in the Drosophila genomes

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296465

Maximum likelihood estimation of ancestral codon usage bias parameters in Drosophila.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296465

Inferring the demographic history and rate of adaptive substitution in Drosophila

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296465

Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296465

The pattern of polymorphism in Arabidopsis thaliana

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296465

Simultaneous inference of selection and population growth from patterns of variation in the human genome

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296465

Patterns of polymorphism and divergence from noncoding sequences of Drosophila melanogaster and D. simulans: evidence for nonequilibrium processes

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296465

Recombination and base composition: the case of the highly self-fertilizing plant Arabidopsis thaliana

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296465

Multilocus analysis of variation and speciation in the closely related species Arabidopsis halleri and A. lyrata

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296465

Biased gene conversion: implications for genome and sex evolution

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296465

Requirements for intron-mediated enhancement of gene expression in Arabidopsis.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296465

The extent of linkage disequilibrium in Arabidopsis thaliana

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296465

Gene genealogies in a metapopulation

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296465

Effects of metapopulation processes on measures of genetic diversity

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296465

Comparative evolutionary analysis of chalcone synthase and alcohol dehydrogenase loci in Arabidopsis, Arabis, and related genera (Brassicaceae)

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296465

On the average coefficient of dominance of deleterious spontaneous mutations

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296465

Nonequilibrium migration in human history

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296465

High recombination rate in natural populations of Plasmodium falciparum

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296465

Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296465

Codon usage and gene function are related in sequences of Arabidopsis thaliana

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296465

The coalescent process with selfing

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296465

Evolution of a finite population under gene conversion

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296465

The hitch-hiking effect of a favourable gene

27 July 2018

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296465

27 July 2018

12 December 2020

On the theory of partially inbreeding finite populations. I. Partial selfing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296465

Models of nearly neutral mutations with particular implications for nonrandom usage of synonymous codons.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296465

The selection-mutation-drift theory of synonymous codon usage

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296465

GC-biased gene conversion and selection affect GC content in the Oryza genus (rice).

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296465

Determinants of synonymous and nonsynonymous variability in three species of Drosophila

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296465

Dated molecular phylogenies indicate a Miocene origin for Arabidopsis thaliana

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296465

Patterns of codon usage bias in Silene latifolia.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296465

Genome-wide evidence for efficient positive and purifying selection in Capsella grandiflora, a plant species with a large effective population size

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296465

Analysis of the genome sequences of three Drosophila melanogaster spontaneous mutation accumulation lines

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296465

Native range genetic variation in Arabidopsis thaliana is strongly geographically structured and reflects Pleistocene glacial dynamics.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296465

Joint inference of the distribution of fitness effects of deleterious mutations and population demography based on nucleotide polymorphism frequencies

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296465

Neutral evolution of synonymous base composition in the Brassicaceae.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296465

Testing for effects of recombination rate on nucleotide diversity in natural populations of Arabidopsis lyrata.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296465

The transition to self-compatibility in Arabidopsis thaliana and evolution within S-haplotypes over 10 Myr.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296465

Adaptive evolution of non-coding DNA in Drosophila

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296465

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

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296465

Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296465

A metapopulation perspective on genetic diversity and differentiation in partially self-fertilizing plants

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296465

Inferring parameters of mutation, selection and demography from patterns of synonymous site evolution in Drosophila

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296465

Genetic isolation by distance in Arabidopsis thaliana: biogeography and postglacial colonization of Europe

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296465

Inference of population structure using multilocus genotype data

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296465

Linkage disequilibrium, gene trees and selfing: an ancestral recombination graph with partial self-fertilization

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296465

U-richness is a defining feature of plant introns and may function as an intron recognition signal in maize.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296465

The effect of deleterious mutations on neutral molecular variation

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296465

Monte Carlo sampling methods using Markov chains and their applications

24 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FGBE%2FEVR085

Equation of State Calculations by Fast Computing Machines

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FGBE%2FEVR085

Arabidopsis MPSS. An online resource for quantitative expression analysis

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FGBE%2FEVR085

Restricted wobble rules for eukaryotic genomes

21 January 2018

1 reference

12 December 2020

Subdivision and haplotype structure in natural populations of Arabidopsis lyrata

1 reference

12 December 2020

Rates and patterns of molecular evolution in inbred and outbred Arabidopsis

1 reference

12 December 2020

DNA METHYLATION IN PLANTS

1 reference

12 December 2020

Identifiers

DOI

10.1093/GBE/EVR085

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21856647%20AND%20SRC:MED&resulttype=core&format=json

11 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21856647%20AND%20SRC:MED&resulttype=core&format=json

11 February 2020

PubMed publication ID

21856647

1 reference