Regulation of genetic flux between bacteria by restriction-modification systems (Q36930940)

17 August 2017

Regulation of genetic flux between bacteria by restriction-modification systems (English)

1 reference

17 August 2017

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27140615%20AND%20SRC:MED&resulttype=core&format=json

5 June 2020

Marie Touchon

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27140615%20AND%20SRC:MED&resulttype=core&format=json

5 June 2020

Eduardo Rocha

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27140615%20AND%20SRC:MED&resulttype=core&format=json

5 June 2020

author name string

Pedro H Oliveira

1

1 reference

17 August 2017

Marie Touchon

2

1 reference

17 August 2017

Eduardo P C Rocha

3

1 reference

17 August 2017

language of work or name

English

0 references

publication date

2 May 2016

1 reference

Proceedings of the National Academy of Sciences of the United States of America

17 August 2017

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27140615%20AND%20SRC:MED&resulttype=core&format=json

5 June 2020

volume

113

1 reference

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5 June 2020

issue

20

1 reference

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5 June 2020

page(s)

5658-5663

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27140615%20AND%20SRC:MED&resulttype=core&format=json

ClonalFrameML: efficient inference of recombination in whole bacterial genomes

5 June 2020

cites work

1 reference

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Diversification of bacterial genome content through distinct mechanisms over different timescales.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878467

The interplay of restriction-modification systems with mobile genetic elements and their prokaryotic hosts

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878467

Type II restriction endonucleases--a historical perspective and more

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878467

PopGenome: an efficient Swiss army knife for population genomic analyses in R

29 September 2017

1 reference

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Bacterial transformation: distribution, shared mechanisms and divergent control

29 September 2017

1 reference

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RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

29 September 2017

1 reference

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To be or not to be: regulation of restriction-modification systems and other toxin-antitoxin systems

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878467

Impact of target site distribution for Type I restriction enzymes on the evolution of methicillin-resistant Staphylococcus aureus (MRSA) 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=4878467

Mobility of DNA sequence recognition domains in DNA methyltransferases suggests epigenetics-driven adaptive 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=4878467

Diverse functions of restriction-modification systems in addition to cellular defense

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878467

Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal 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=4878467

Context-dependent conservation of DNA methyltransferases in bacteria

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878467

Promiscuous restriction is a cellular defense strategy that confers fitness advantage to bacteria

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878467

The repertoire of ICE in prokaryotes underscores the unity, diversity, and ubiquity of conjugation

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878467

Recombination and population structure in Salmonella enterica.

29 September 2017

1 reference

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HMMER web server: interactive sequence similarity searching

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878467

Ultra-fast sequence clustering from similarity networks with SiLiX.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878467

Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878467

Neisseria meningitidis is structured in clades associated with restriction modification systems that modulate homologous recombination

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878467

Horizontal transfer, not duplication, drives the expansion of protein families 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=4878467

Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among 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=4878467

Lateral genetic transfer and the construction of genetic exchange communities

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878467

phangorn: phylogenetic analysis in R

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878467

Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878467

A type III-like restriction endonuclease functions as a major barrier to horizontal gene transfer in clinical Staphylococcus aureus strains

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878467

New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878467

Bacteriophage resistance mechanisms

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878467

Network analyses structure genetic diversity in independent genetic worlds

29 September 2017

1 reference

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The impact of long-distance horizontal gene transfer on prokaryotic genome size

29 September 2017

1 reference

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SeaView version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building

29 September 2017

1 reference

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REBASE--a database for DNA restriction and modification: enzymes, genes and genomes

29 September 2017

1 reference

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Inference and characterization of horizontally transferred gene families using stochastic mapping

29 September 2017

1 reference

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Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths

29 September 2017

1 reference

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Recombination and the nature of bacterial speciation

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878467

Inference of bacterial microevolution using multilocus sequence data

29 September 2017

1 reference

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NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878467

Detecting recombination in evolving nucleotide 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=4878467

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878467

Mobile genetic elements: the agents of open source 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=4878467

Mechanisms of, and barriers to, horizontal gene transfer between bacteria

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878467

Comparative and evolutionary analysis of the bacterial homologous recombination systems

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878467

MUSCLE: a multiple sequence alignment method with reduced time and space complexity

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878467

APE: Analyses of Phylogenetics and Evolution in R language

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878467

An efficient algorithm for large-scale detection of protein families

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878467

Behavior of restriction-modification systems as selfish mobile elements and their impact on genome 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=4878467

Identification of type II restriction and modification systems in Helicobacter pylori reveals their substantial diversity among strains

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878467

Genetic variation: molecular mechanisms and impact on microbial 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=4878467

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878467

Horizontal gene transfer contributes to the wide distribution and evolution of type II restriction-modification systems

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878467

Restriction-modification systems as genomic parasites in competition for specific 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=4878467

Analyzing the mosaic structure of genes

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878467

The adaptation of temperate bacteriophages to their host 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=4878467

A program for calculating and displaying compatibility matrices as an aid in determining reticulate evolution in molecular sequences.

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878467

Widespread homologous recombination within and between Streptomyces species

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878467

Causes of insertion sequences abundance in prokaryotic genomes

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878467

Statistical tests for detecting gene conversion.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878467

PHAGE-MEDIATED SELECTION AND THE EVOLUTION AND MAINTENANCE OF RESTRICTION-MODIFICATION.

4 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1073%2FPNAS.1603257113

MAFFT: iterative refinement and additional methods

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/27140615

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Sensitivity of naturally occurring coliphages to type I and type II restriction and modification

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/27140615

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1073/PNAS.1603257113

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27140615%20AND%20SRC:MED&resulttype=core&format=json

5 June 2020

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27140615%20AND%20SRC:MED&resulttype=core&format=json

5 June 2020

PubMed publication ID

27140615

1 reference