(Q30582508)

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Mycobacterial phylogenomics: an enhanced method for gene turnover analysis reveals uneven levels of gene gain and loss among species and gene families

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Europe PubMed Central

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24904011%20AND%20SRC:MED&resulttype=core&format=json

20 March 2020

Mycobacterial phylogenomics: an enhanced method for gene turnover analysis reveals uneven levels of gene gain and loss among species and gene families (English)

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Europe PubMed Central

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24904011%20AND%20SRC:MED&resulttype=core&format=json

20 March 2020

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24904011%20AND%20SRC:MED&resulttype=core&format=json

20 March 2020

1

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24904011%20AND%20SRC:MED&resulttype=core&format=json

20 March 2020

Alejandro Sánchez-Gracia

3

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Europe PubMed Central

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24904011%20AND%20SRC:MED&resulttype=core&format=json

20 March 2020

Sergios-Orestis Kolokotronis

4

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Europe PubMed Central

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24904011%20AND%20SRC:MED&resulttype=core&format=json

20 March 2020

Filipe G. Vieira

2

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Filipe G Vieira

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Europe PubMed Central

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20 March 2020

publication date

5 June 2014

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20 March 2020

Genome Biology and Evolution

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24904011%20AND%20SRC:MED&resulttype=core&format=json

20 March 2020

6

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Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24904011%20AND%20SRC:MED&resulttype=core&format=json

20 March 2020

6

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24904011%20AND%20SRC:MED&resulttype=core&format=json

20 March 2020

1454-1465

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24904011%20AND%20SRC:MED&resulttype=core&format=json

20 March 2020

New approaches to target the mycolic acid biosynthesis pathway for the development of tuberculosis therapeutics

1 reference

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Identification of new drug targets and resistance mechanisms in Mycobacterium tuberculosis

1 reference

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20 June 2018

Comparative phylogenomics of pathogenic and non-pathogenic mycobacterium

1 reference

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20 June 2018

Disruption of mycobactin biosynthesis leads to attenuation of Mycobacterium tuberculosis for growth and virulence

1 reference

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20 June 2018

Identification of a small molecule with activity against drug-resistant and persistent tuberculosis

1 reference

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20 June 2018

The variability of the 16S rRNA gene in bacterial genomes and its consequences for bacterial community analyses

1 reference

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20 June 2018

Comparative genomic and phylogenetic approaches to characterize the role of genetic recombination in mycobacterial evolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079203

20 June 2018

Virulence factors of the Mycobacterium tuberculosis complex

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079203

20 June 2018

T-REX: a web server for inferring, validating and visualizing phylogenetic trees and networks

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079203

20 June 2018

Comparative analysis of Mycobacterium and related Actinomycetes yields insight into the evolution of Mycobacterium tuberculosis pathogenesis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079203

20 June 2018

Role of glycans and glycoproteins in disease development by Mycobacterium tuberculosis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079203

20 June 2018

The PE and PPE proteins of Mycobacterium tuberculosis.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079203

20 June 2018

Development of new antituberculous drugs based on bacterial virulence factors interfering with host cytokine networks

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079203

20 June 2018

Anchor-based whole genome phylogeny (ABWGP): a tool for inferring evolutionary relationship among closely related microorganisms [corrected].

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079203

20 June 2018

Mycobacterium africanum--review of an important cause of human tuberculosis in West Africa

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079203

20 June 2018

Human T cell epitopes of Mycobacterium tuberculosis are evolutionarily hyperconserved

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079203

20 June 2018

DendroPy: a Python library for phylogenetic computing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079203

20 June 2018

Identification of virulence determinants of Mycobacterium avium that impact on the ability to resist host killing mechanisms

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079203

20 June 2018

Application of 'next-generation' sequencing technologies to microbial genetics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079203

20 June 2018

Efficient computation of the phylogenetic likelihood function on multi-gene alignments and multi-core architectures

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079203

20 June 2018

Ontologizer 2.0--a multifunctional tool for GO term enrichment analysis and data exploration

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079203

20 June 2018

Insights from the complete genome sequence of Mycobacterium marinum on the evolution of Mycobacterium tuberculosis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079203

20 June 2018

An improved general amino acid replacement matrix

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079203

20 June 2018

Nutrient acquisition by mycobacteria

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079203

20 June 2018

Comparative genomic analysis of the odorant-binding protein family in 12 Drosophila genomes: purifying selection and birth-and-death evolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079203

20 June 2018

Tuberculosis as a zoonosis from a veterinary perspective

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079203

20 June 2018

16S rRNA gene sequencing for bacterial identification in the diagnostic laboratory: pluses, perils, and pitfalls

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079203

20 June 2018

Reconstructing the ancestor of Mycobacterium leprae: the dynamics of gene loss and genome reduction.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079203

20 June 2018

A genomic view of sugar transport in Mycobacterium smegmatis and Mycobacterium tuberculosis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079203

20 June 2018

PAML 4: phylogenetic analysis by maximum likelihood

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079203

20 June 2018

Evolution of Mycobacterium ulcerans and other mycolactone-producing mycobacteria from a common Mycobacterium marinum progenitor

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079203

20 June 2018

RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079203

20 June 2018

Bottlenecks and broomsticks: the molecular evolution of Mycobacterium bovis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079203

20 June 2018

Control of iron metabolism in Mycobacterium tuberculosis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079203

20 June 2018

Concerted and birth-and-death evolution of multigene families

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079203

20 June 2018

Application of phylogenetic networks in evolutionary studies

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079203

20 June 2018

Hidden likelihood support in genomic data: can forty-five wrongs make a right?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079203

20 June 2018

Contribution of the Mycobacterium tuberculosis MmpL protein family to virulence and drug resistance

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079203

20 June 2018

MAFFT version 5: improvement in accuracy of multiple sequence alignment

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079203

20 June 2018

Integr8 and Genome Reviews: integrated views of complete genomes and proteomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079203

20 June 2018

Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079203

20 June 2018

Impact of Genotypic Studies on Mycobacterial Taxonomy: the New Mycobacteria of the 1990s

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079203

20 June 2018

An efficient algorithm for large-scale detection of protein families

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079203

20 June 2018

Mycobacterium leprae and leprosy: a compendium

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079203

20 June 2018

Bacterial fatty acid biosynthesis: targets for antibacterial drug discovery

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079203

20 June 2018

A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079203

20 June 2018

The rapidly growing mycobacteria: saprophytes and parasites.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079203

20 June 2018

Mycobacterium ulcerans infection.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079203

20 June 2018

Identification of a Mycobacterium tuberculosis gene cluster encoding the biosynthetic enzymes for assembly of the virulence-conferring siderophore mycobactin

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079203

20 June 2018

BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079203

20 June 2018

Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079203

20 June 2018

The epidemiology of Mycobacterium bovis infections in animals and man: A review

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079203

20 June 2018

A new method for calculating evolutionary substitution rates

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079203

20 June 2018

The rapid generation of mutation data matrices from protein sequences

1 reference

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20 June 2018

A new look at the statistical model identification

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVU117

21 January 2018

Estimating gene gain and loss rates in the presence of error in genome assembly and annotation using CAFE 3.

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVU117

21 January 2018

BadiRate: estimating family turnover rates by likelihood-based methods.

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVU117

21 January 2018

Inferring ancient divergences requires genes with strong phylogenetic signals.

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVU117

21 January 2018

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1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVU117

21 January 2018

Automatic genome-wide reconstruction of phylogenetic gene trees.

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVU117

21 January 2018

Global epidemiology of tuberculosis. Morbidity and mortality of a worldwide epidemic

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079203

26 November 2018

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1 reference

https://pubmed.ncbi.nlm.nih.gov/24904011

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Confidence Limits on Phylogenies: an Approach using the Bootstrap

1 reference

https://pubmed.ncbi.nlm.nih.gov/24904011

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1093/GBE/EVU117

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24904011%20AND%20SRC:MED&resulttype=core&format=json

20 March 2020

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24904011%20AND%20SRC:MED&resulttype=core&format=json

20 March 2020

PubMed publication ID

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24904011%20AND%20SRC:MED&resulttype=core&format=json

20 March 2020

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