(Q35441451)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25414349%20AND%20SRC:MED&resulttype=core&format=json

23 February 2020

title

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25414349%20AND%20SRC:MED&resulttype=core&format=json

23 February 2020

1 reference

whole genome sequencing

1 reference

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25414349%20AND%20SRC:MED&resulttype=core&format=json

23 February 2020

Nicholas J Croucher

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25414349%20AND%20SRC:MED&resulttype=core&format=json

23 February 2020

Andrew J. Page

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25414349%20AND%20SRC:MED&resulttype=core&format=json

23 February 2020

Aidan J Delaney

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25414349%20AND%20SRC:MED&resulttype=core&format=json

23 February 2020

Jacqueline A Keane

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25414349%20AND%20SRC:MED&resulttype=core&format=json

23 February 2020

7

Julian Parkhill

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25414349%20AND%20SRC:MED&resulttype=core&format=json

23 February 2020

6

Stephen D Bentley

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25414349%20AND%20SRC:MED&resulttype=core&format=json

23 February 2020

8

Simon R Harris

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25414349%20AND%20SRC:MED&resulttype=core&format=json

23 February 2020

language of work or name

English

0 references

publication date

20 November 2014

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25414349%20AND%20SRC:MED&resulttype=core&format=json

23 February 2020

published in

Nucleic Acids Research

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25414349%20AND%20SRC:MED&resulttype=core&format=json

23 February 2020

volume

43

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25414349%20AND%20SRC:MED&resulttype=core&format=json

23 February 2020

issue

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25414349%20AND%20SRC:MED&resulttype=core&format=json

23 February 2020

page(s)

e15

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25414349%20AND%20SRC:MED&resulttype=core&format=json

Creative Commons Attribution 4.0 International

23 February 2020

copyright license

start time

7 November 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Variable recombination dynamics during the emergence, transmission and 'disarming' of a multidrug-resistant pneumococcal clone

1 reference

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Evidence for soft selective sweeps in the evolution of pneumococcal multidrug resistance and vaccine escape

27 July 2018

1 reference

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Heterogeneity in the frequency and characteristics of homologous recombination in pneumococcal 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=4330336

Evolutionary pathway to increased virulence and epidemic group A Streptococcus disease derived from 3,615 genome sequences

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330336

Dense genomic sampling identifies highways of pneumococcal recombination

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330336

Genomic characterisation of invasive non-typhoidal Salmonella enterica Subspecies enterica Serovar Bovismorbificans isolates from Malawi

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330336

Dominant role of nucleotide substitution in the diversification of serotype 3 pneumococci over decades and during a single infection

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330336

Distinguishable epidemics of multidrug-resistant Salmonella Typhimurium DT104 in different hosts

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330336

Population genomics of post-vaccine changes in pneumococcal epidemiology.

27 July 2018

1 reference

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Whole-genome sequencing to identify transmission of Mycobacterium abscessus between patients with cystic fibrosis: a retrospective cohort study

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330336

Chromosome painting in silico in a bacterial species reveals fine population structure

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330336

Bacterial genomes in epidemiology--present and future.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330336

Comparative genomics of recent Shiga toxin-producing Escherichia coli O104:H4: short-term evolution of an emerging pathogen

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330336

Phylogeographic variation in recombination rates within a global clone of methicillin-resistant Staphylococcus aureus

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330336

Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330336

A high-resolution view of genome-wide pneumococcal transformation

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330336

FastML: a web server for probabilistic reconstruction of ancestral sequences

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330336

RAxML-Light: a tool for computing terabyte phylogenies

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330336

Whole-genome analysis of diverse Chlamydia trachomatis strains identifies phylogenetic relationships masked by current clinical typing

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330336

Detection of recombination events in bacterial genomes from large population samples

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330336

Evidence for several waves of global transmission in the seventh cholera pandemic

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330336

Recombination and population structure in Salmonella enterica.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330336

Analysing recombination in nucleotide sequences

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330336

Rapid pneumococcal evolution in response to clinical interventions

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330336

Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330336

Inference of homologous recombination in bacteria using whole-genome sequences

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330336

RDP3: a flexible and fast computer program for analyzing recombination

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330336

Evolution of MRSA during hospital transmission and intercontinental spread

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330336

Genome sequence of a recently emerged, highly transmissible, multi-antibiotic- and antiseptic-resistant variant of methicillin-resistant Staphylococcus aureus, sequence type 239 (TW).

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330336

Role of conjugative elements in the evolution of the multidrug-resistant pandemic clone Streptococcus pneumoniaeSpain23F ST81

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330336

Evolution, population structure, and phylogeography of genetically monomorphic bacterial pathogens

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330336

High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330336

Methods for handling multiple testing

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330336

Inference of bacterial microevolution using multilocus sequence 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=4330336

cBrother: relaxing parental tree assumptions for Bayesian recombination detection

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330336

A simple and robust statistical test for detecting the presence of recombination

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330336

Evolution of Staphylococcus aureus by large chromosomal replacements.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330336

How clonal is Staphylococcus aureus?

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330336

Allelic variation in the highly polymorphic locus pspC of Streptococcus pneumoniae.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330336

27 July 2018

DNA uptake in bacteria

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330336

27 July 2018

How clonal are bacteria?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330336

Molecular evolution of the Escherichia coli chromosome. IV. Sequence comparisons

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330336

Statistical methods of DNA sequence analysis: detection of intragenic recombination or 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=4330336

Analyzing the mosaic structure of 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=4330336

Genomic epidemiology of Neisseria gonorrhoeae with reduced susceptibility to cefixime in the USA: a retrospective observational study

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330336

progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330336

FastTree 2--approximately maximum-likelihood trees for large alignments

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330336

A comparison of homologous recombination rates in bacteria and archaea.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330336

GARD: a genetic algorithm for recombination detection

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330336

A bimodal pattern of relatedness between the Salmonella Paratyphi A and Typhi genomes: convergence or divergence by homologous recombination?

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330336

Discriminating between rate heterogeneity and interspecific recombination in DNA sequence alignments with phylogenetic factorial hidden Markov models

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330336

Effect of chromosome location on bacterial mutation rates.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330336

Statistical tests for detecting gene conversion.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330336

Localized sex in bacteria

26 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25414349

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Detecting recombination from gene trees

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25414349

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/NAR/GKU1196

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25414349%20AND%20SRC:MED&resulttype=core&format=json

23 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25414349%20AND%20SRC:MED&resulttype=core&format=json

23 February 2020

PubMed publication ID

25414349

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25414349%20AND%20SRC:MED&resulttype=core&format=json