(Q37057250)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27363362%20AND%20SRC:MED&resulttype=core&format=json

17 March 2020

title

Alignment-free microbial phylogenomics under scenarios of sequence divergence, genome rearrangement and lateral genetic transfer (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27363362%20AND%20SRC:MED&resulttype=core&format=json

17 March 2020

1 reference

1 reference

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27363362%20AND%20SRC:MED&resulttype=core&format=json

17 March 2020

Mark A. Ragan

series ordinal

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27363362%20AND%20SRC:MED&resulttype=core&format=json

17 March 2020

author name string

Guillaume Bernard

series ordinal

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27363362%20AND%20SRC:MED&resulttype=core&format=json

17 March 2020

language of work or name

English

0 references

publication date

1 July 2016

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27363362%20AND%20SRC:MED&resulttype=core&format=json

17 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27363362%20AND%20SRC:MED&resulttype=core&format=json

17 March 2020

volume

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27363362%20AND%20SRC:MED&resulttype=core&format=json

17 March 2020

page(s)

28970

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27363362%20AND%20SRC:MED&resulttype=core&format=json

Creative Commons Attribution 4.0 International

17 March 2020

copyright license

start time

1 July 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

exact match

https://scigraph.springernature.com/pub.10.1038/srep28970

0 references

cites work

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Inference of Markovian properties of molecular sequences from NGS data and applications to comparative genomics.

29 September 2017

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Whole-genome analyses resolve early branches in the tree of life of modern birds

29 September 2017

1 reference

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Genome sequencing defines phylogeny and spread of methicillin-resistant Staphylococcus aureus in a high transmission setting

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4929450

Inferring phylogenies of evolving sequences without multiple sequence alignment.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4929450

Kmacs: the k-mismatch average common substring approach to alignment-free sequence comparison

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4929450

Molecular phylogenetics before sequences: oligonucleotide catalogs as k-mer spectra

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4929450

Alignment-free phylogenetics and population genetics

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4929450

Alignment-free genetic sequence comparisons: a review of recent approaches by word analysis

29 September 2017

1 reference

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Alignment-free sequence comparison based on next-generation sequencing reads

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4929450

Next-generation phylogenomics

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4929450

Co-phylog: an assembly-free phylogenomic approach for closely related organisms

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4929450

Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing

29 September 2017

1 reference

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A pilot study of rapid benchtop sequencing of Staphylococcus aureus and Clostridium difficile for outbreak detection and surveillance

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4929450

ALF--a simulation framework for genome evolution

29 September 2017

1 reference

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Within-species lateral genetic transfer and the evolution of transcriptional regulation in Escherichia coli and Shigella.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4929450

Experimental design and statistical rigor in phylogenomics of horizontal and endosymbiotic gene transfer

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4929450

Beyond the bacterium: planctomycetes challenge our concepts of microbial structure and function.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4929450

Whole-genome phylogeny of Escherichia coli/Shigella group by feature frequency profiles (FFPs)

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4929450

A grammar-based distance metric enables fast and accurate clustering of large sets of 16S sequences

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4929450

Accuracy of phylogeny reconstruction methods combining overlapping gene data sets

29 September 2017

1 reference

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The tree and net components of prokaryote evolution

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4929450

Using jackknife to assess the quality of gene order phylogenies

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4929450

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4929450

Whole-proteome phylogeny of prokaryotes by feature frequency profiles: An alignment-free method with optimal feature resolution

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4929450

Estimating mutation distances from unaligned genomes

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4929450

A fungal phylogeny based on 82 complete genomes using the composition vector method

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4929450

Alignment-free genome comparison with feature frequency profiles (FFP) and optimal resolutions

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4929450

Dynamics of genome rearrangement in bacterial populations

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4929450

Broad phylogenomic sampling improves resolution of the animal tree of life

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4929450

The average common substring approach to phylogenomic reconstruction

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4929450

Highways of gene sharing in prokaryotes

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4929450

Alignment-free sequence comparison-a review

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4929450

Bayesian inference of phylogeny and its impact on evolutionary biology

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4929450

MRBAYES: Bayesian inference of phylogenetic trees

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4929450

Escherichia coli molecular phylogeny using the incongruence length difference test

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4929450

Evolutionary trees from DNA sequences: A maximum likelihood approach

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4929450

Standard reference strains of Escherichia coli from natural populations

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4929450

Phylogenetic structure of the prokaryotic domain: The primary kingdoms

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4929450

Spaced words and kmacs: fast alignment-free sequence comparison based on inexact word matches

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4929450

Alignment-free sequence comparison (II): theoretical power of comparison statistics

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4929450

Alignment uncertainty and genomic analysis

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4929450

Extraction of high quality k-words for alignment-free sequence comparison.

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4929450

Fast alignment-free sequence comparison using spaced-word frequencies.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4929450

Computing the distribution of a tree metric.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4929450

Assigning Escherichia coli strains to phylogenetic groups: multi-locus sequence typing versus the PCR triplex method.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4929450

Phylogenetic inference based on matrix representation of trees

4 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1038%2FSREP28970

The impact of reticulate evolution on genome phylogeny

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/27363362

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

A simulation test bed for hypotheses of genome evolution

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/27363362

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1038/SREP28970

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27363362%20AND%20SRC:MED&resulttype=core&format=json

17 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27363362%20AND%20SRC:MED&resulttype=core&format=json

17 March 2020

PubMed publication ID

27363362

1 reference