(Q34509703)

2 August 2017

title

An automated approach for the identification of horizontal gene transfers from complete genomes reveals the rhizome of Rickettsiales (English)

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2 August 2017

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7

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2 August 2017

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Phuong Thi Le

1

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2 August 2017

Hemalatha Golaconda Ramulu

2

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2 August 2017

Laurent Guijarro

3

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2 August 2017

Julien Paganini

4

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2 August 2017

Philippe Gouret

5

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2 August 2017

Olivier Chabrol

6

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2 August 2017

Pierre Pontarotti

8

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2 August 2017

publication date

12 December 2012

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2 August 2017

published in

BMC Evolutionary Biology

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2 August 2017

volume

12

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2 August 2017

page(s)

243

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https://scigraph.springernature.com/pub.10.1186/1471-2148-12-243

2 August 2017

exact match

0 references

cites work

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7 July 2018

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The rhizome of life: the sympatric Rickettsia felis paradigm demonstrates the random transfer of DNA sequences

7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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Gene gain and loss events in Rickettsia and Orientia species

7 July 2018

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7 July 2018

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Networks of gene sharing among 329 proteobacterial genomes reveal differences in lateral gene transfer frequency at different phylogenetic depths

7 July 2018

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7 July 2018

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Rickettsial evolution in the light of comparative genomics

7 July 2018

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Phagocytosis ofCryptococcus neoformansby, and Nonlytic Exocytosis from,Acanthamoeba castellanii

7 July 2018

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The contribution of mobile genetic elements to the evolution and ecology of Vibrios

7 July 2018

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Unprecedented levels of horizontal gene transfer among spatially co-occurring Shewanella bacteria from the Baltic Sea.

7 July 2018

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Amoebae as genitors and reservoirs of giant viruses

7 July 2018

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Amoeba/amoebal symbiont genetic transfers: lessons from giant virus neighbours

7 July 2018

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Shewanella spp. genomic evolution for a cold marine lifestyle and in-situ explosive biodegradation

7 July 2018

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Genome analysis of microorganisms living in amoebae reveals a melting pot of evolution

7 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3575314

Giant Marseillevirus highlights the role of amoebae as a melting pot in emergence of chimeric microorganisms

7 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3575314

ACLAME: a CLAssification of Mobile genetic Elements, update 2010

7 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3575314

PhyloPattern: regular expressions to identify complex patterns in phylogenetic trees

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3575314

PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3575314

A hidden reservoir of integrative elements is the major source of recently acquired foreign genes and ORFans in archaeal and bacterial genomes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3575314

Massive comparative genomic analysis reveals convergent evolution of specialized bacteria

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3575314

Horizontal gene transfer between Wolbachia and the mosquito Aedes aegypti

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3575314

Massive Horizontal Gene Transfer in Bdelloid Rotifers

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3575314

Wolbachia genome integrated in an insect chromosome: evolution and fate of laterally transferred endosymbiont genes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3575314

Lateral gene transfer between obligate intracellular bacteria: evidence from the Rickettsia massiliae genome

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3575314

A robust species tree for the alphaproteobacteria

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3575314

Phylogenetic analyses of cyanobacterial genomes: quantification of horizontal gene transfer events

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3575314

Genome sequence of Rickettsia bellii illuminates the role of amoebae in gene exchanges between intracellular pathogens

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3575314

The Gene Ontology (GO) project in 2006

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3575314

Mobile genetic elements: the agents of open source evolution

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3575314

Genome Streamlining in a Cosmopolitan Oceanic Bacterium

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3575314

FIGENIX: intelligent automation of genomic annotation: expertise integration in a new software platform

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3575314

GeneInfoViz: constructing and visualizing gene relation networks.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3575314

Detection and characterization of horizontal transfers in prokaryotes using genomic signature

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3575314

Some lessons from Rickettsia genomics

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3575314

Computational inference of scenarios for alpha-proteobacterial genome evolution

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3575314

Phylogenetic analysis of the Francisella-like endosymbionts of Dermacentor ticks

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3575314

MUSCLE: multiple sequence alignment with high accuracy and high throughput

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3575314

Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elements

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3575314

A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3575314

Visualization of the phylogenetic content of five genomes using dekapentagonal maps

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3575314

History of the ADP/ATP-translocase-encoding gene, a parasitism gene transferred from a Chlamydiales ancestor to plants 1 billion years ago

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3575314

OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3575314

The source of laterally transferred genes in bacterial genomes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3575314

7 July 2018

A giant virus in amoebae

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3575314

An approximately unbiased test of phylogenetic tree selection

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3575314

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3575314

Detection of genes with atypical nucleotide sequence in microbial genomes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3575314

Wolbachia: evolutionary novelty in a rickettsial bacteria

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3575314

Horizontal gene transfer in prokaryotes: quantification and classification

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3575314

Orientia tsutsugamushi infection: overview and immune responses

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3575314

The COG database: new developments in phylogenetic classification of proteins from complete genomes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3575314

Distribution and evolution of bacteriophage WO in Wolbachia, the endosymbiont causing sexual alterations in arthropods

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3575314

Lateral gene transfer and the nature of bacterial innovation

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3575314

Gene ontology: tool for the unification of biology

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3575314

The COG database: a tool for genome-scale analysis of protein functions and evolution

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3575314

Obligate intracellular parasites: Rickettsia prowazekii and Chlamydia trachomatis

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3575314

Rickettsiae and Chlamydiae: evidence of horizontal gene transfer and gene exchange

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3575314

Profile hidden Markov models

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3575314

Genome phylogeny based on gene content

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3575314

The genome sequence of Rickettsia prowazekii and the origin of mitochondria

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3575314

Genome Sequence of an Obligate Intracellular Pathogen of Humans: Chlamydia trachomatis

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3575314

Molecular archaeology of the Escherichia coli genome

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3575314

Rickettsioses as paradigms of new or emerging infectious diseases

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3575314

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3575314

Classification of Rickettsia tsutsugamushi in a new genus, Orientia gen. nov., as Orientia tsutsugamushi comb. nov

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3575314

Identification of a granulocytotropic Ehrlichia species as the etiologic agent of human disease.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3575314

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3575314

Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3575314

The tribe Ehrlichieae and ehrlichial diseases

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3575314

Ehrlichia chaffeensis, a new species associated with human ehrlichiosis

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3575314

Isolation and characterization of an Ehrlichia sp. from a patient diagnosed with human ehrlichiosis

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3575314

Horizontal gene transfer accelerates genome innovation and evolution.

7 July 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2148-12-243

Bacteriophage WO and virus-like particles in Wolbachia, an endosymbiont of arthropods

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2148-12-243

The post-Darwinist rhizome of life

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2148-12-243

The genomic code: inferring Vibrionaceae niche specialization

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3575314

Genomes in Flux: The Evolution of Archaeal and Proteobacterial Gene Content

27 October 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2148-12-243

21 January 2018

1 reference

https://pubmed.ncbi.nlm.nih.gov/23234643

12 December 2020

inferred from PubMed ID database lookup

Tsutsugamushi Disease (Scrub Typhus) in World War II

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23234643

12 December 2020

inferred from PubMed ID database lookup

Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23234643

12 December 2020

inferred from PubMed ID database lookup

Identifiers

DOI

10.1186/1471-2148-12-243

1 reference

Dimensions Publication ID

2 August 2017

1036330320

0 references

Fatcat ID

release_kqwpzheym5c5ffaln7k44zr64u

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/kqwpzheym5c5ffaln7k44zr64u

24 November 2022

mapped directly with Wikidata item

PMC publication ID

3575314

1 reference

2 August 2017

1 reference