Comparative genomic and phylogenetic approaches to characterize the role of genetic recombination in mycobacterial evolution (Q34493970)

2 August 2017

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

1 reference

2 August 2017

1 reference

Silvia E Smith

1

1 reference

2 August 2017

Patrice Showers-Corneli

2

1 reference

2 August 2017

Caitlin N Dardenne

3

1 reference

2 August 2017

Henry H Harpending

4

1 reference

2 August 2017

Darren P Martin

5

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2 August 2017

Robert G Beiko

6

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2 August 2017

language of work or name

English

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publication date

26 November 2012

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2 August 2017

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2 August 2017

7

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2 August 2017

11

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2 August 2017

e50070

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Creative Commons Attribution 4.0 International

2 August 2017

start time

26 November 2012

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

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cites work

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After the bottleneck: Genome-wide diversification of the Mycobacterium tuberculosis complex by mutation, recombination, and natural selection

6 July 2018

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Complete genome sequences of 138 mycobacteriophages

6 July 2018

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6 July 2018

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The Public Goods Hypothesis for the evolution of life on Earth

6 July 2018

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Telling the whole story in a 10,000-genome world

6 July 2018

1 reference

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Origins of bacterial diversity through horizontal genetic transfer and adaptation to new ecological niches

6 July 2018

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HMMER web server: interactive sequence similarity searching

6 July 2018

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Comparative genomics of cell envelope components in mycobacteria

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506542

Horizontal gene transfer (HGT) as a mechanism of disseminating RDX-degrading activity among Actinomycete bacteria.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506542

Complete genome sequence of Segniliparus rotundus type strain (CDC 1076)

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506542

Expanding the diversity of mycobacteriophages: insights into genome architecture and evolution

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506542

RDP3: a flexible and fast computer program for analyzing recombination

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506542

Search and clustering orders of magnitude faster than BLAST

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506542

DendroPy: a Python library for phylogenetic computing

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506542

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506542

Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506542

Non mycobacterial virulence genes in the genome of the emerging pathogen Mycobacterium abscessus

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506542

Genomic islands link secondary metabolism to functional adaptation in marine Actinobacteria

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506542

Identifying recombinants in human and primate immunodeficiency virus sequence alignments using quartet scanning

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506542

A rapid bootstrap algorithm for the RAxML Web servers

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506542

IS6110, a Mycobacterium tuberculosis complex-specific insertion sequence, is also present in the genome of Mycobacterium smegmatis, suggestive of lateral gene transfer among mycobacterial species

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506542

An exact nonparametric method for inferring mosaic structure in sequence triplets

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506542

The role of laterally transferred genes in adaptive evolution

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506542

Insights into the evolutionary history of tubercle bacilli as disclosed by genetic rearrangements within a PE_PGRS duplicated gene pair

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506542

Evolution and expansion of the Mycobacterium tuberculosis PE and PPE multigene families and their association with the duplication of the ESAT-6 (esx) gene cluster regions

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506542

Comparative genomics of metabolic pathways in Mycobacterium species: gene duplication, gene decay and lateral gene transfer

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506542

Evidence for recombination in Mycobacterium tuberculosis

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506542

Detecting recombination in evolving nucleotide sequences

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506542

A new GntR family transcriptional regulator in streptomyces coelicolor is required for morphogenesis and antibiotic production and controls transcription of an ABC transporter in response to carbon source

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506542

Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506542

Whole-genome plasticity among Mycobacterium avium subspecies: insights from comparative genomic hybridizations

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506542

Horizontal gene transfer, genome innovation and evolution

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506542

The TetR family of transcriptional repressors.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506542

MUSCLE: multiple sequence alignment with high accuracy and high throughput

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506542

A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506542

Origins of highly mosaic mycobacteriophage genomes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506542

Prokaryotic evolution in light of gene transfer

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506542

Recombination in evolutionary genomics

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506542

An approximately unbiased test of phylogenetic tree selection

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506542

TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506542

The effect of recombination on the accuracy of phylogeny estimation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506542

CONSEL: for assessing the confidence of phylogenetic tree selection

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506542

Evaluation of methods for detecting recombination from DNA sequences: computer simulations

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506542

Genomic sequence and transcriptional analysis of a 23-kilobase mycobacterial linear plasmid: evidence for horizontal transfer and identification of plasmid maintenance systems

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506542

Sister-scanning: a Monte Carlo procedure for assessing signals in recombinant sequences

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506542

Consequences of recombination on traditional phylogenetic analysis.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506542

Interpreting the universal phylogenetic tree

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506542

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506542

New insertion sequences and a novel repeated sequence in the genome of Mycobacterium tuberculosis H37Rv

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506542

MODELTEST: testing the model of DNA substitution

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506542

Molecular keys to speciation: DNA polymorphism and the control of genetic exchange in enterobacteria

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506542

The evolutionary advantage of recombination

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506542

The general stochastic model of nucleotide substitution

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506542

Basic local alignment search tool

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506542

Analyzing the mosaic structure of genes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3506542

Widespread homologous recombination within and between Streptomyces species

6 July 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0050070

Simultaneous infection with multiple strains of Mycobacterium tuberculosis

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0050070

Choosing BLAST options for better detection of orthologs as reciprocal best hits.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0050070

RDP: detection of recombination amongst aligned sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0050070

A Modified Bootscan Algorithm for Automated Identification of Recombinant Sequences and Recombination Breakpoints

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0050070

Lateral gene transfer in Mycobacterium avium subspecies paratuberculosis

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0050070

Plasmids -- potential tool for the investigation of gene transfer in Mycobacterium tuberculosis

21 January 2018

1 reference

12 December 2020

Recombination and the molecular clock

1 reference

12 December 2020

Integration and excision of the Mycobacterium tuberculosis prophage-like element, phiRv1

1 reference

12 December 2020

Clinical features of pulmonary disease caused by rapidly growing mycobacteria. An analysis of 154 patients

1 reference

12 December 2020

Simultaneous infection with multiple strains of Mycobacterium tuberculosis identified by restriction fragment length polymorphism analysis

1 reference

12 December 2020

Of clades and clans: terms for phylogenetic relationships in unrooted trees

1 reference

12 December 2020

Mycobacteriophage L5 infection of Mycobacterium bovis BCG: implications for phage genetics in the slow-growing mycobacteria

1 reference

12 December 2020

Contribution of horizontally acquired genomic islands to the evolution of the tubercle bacilli

1 reference

12 December 2020

Possible emergence of new geminiviruses by frequent recombination

1 reference

12 December 2020

Isolation of plasmids from Mycobacterium avium-intracellulare complex (MAC) strains from India

1 reference

12 December 2020

10.1371/JOURNAL.PONE.0050070

Identifiers

DOI

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2 August 2017

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2 August 2017

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