Assembling networks of microbial genomes using linear programming (Q33751901)

29 July 2017

title

Assembling networks of microbial genomes using linear programming (English)

1 reference

29 July 2017

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Catherine Holloway

1

1 reference

29 July 2017

Robert G Beiko

series ordinal

2

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29 July 2017

publication date

20 November 2010

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29 July 2017

published in

BMC Evolutionary Biology

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29 July 2017

volume

10

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29 July 2017

page(s)

360

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describes a project that uses

29 July 2017

Cytoscape

object named as

Cytoscape

2 references

9 June 2022

https://europepmc.org/search?query=(METHODS:'Cytoscape')

inferred from PubMed Central ID database lookup

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

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Ancestral genome sizes specify the minimum rate of lateral gene transfer during prokaryote evolution.

21 June 2018

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21 June 2018

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The fate of laterally transferred genes: life in the fast lane to adaptation or death

21 June 2018

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21 June 2018

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21 June 2018

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21 June 2018

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21 June 2018

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Evolutionary origins of genomic repertoires in bacteria

21 June 2018

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21 June 2018

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21 June 2018

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21 June 2018

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21 June 2018

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Signature sequences in diverse proteins provide evidence for the late divergence of the Order Aquificales.

21 June 2018

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Archaeal phylogeny based on proteins of the transcription and translation machineries: tackling the Methanopyrus kandleri paradox

21 June 2018

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21 June 2018

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21 June 2018

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Imbroglios of viral taxonomy: genetic exchange and failings of phenetic approaches

21 June 2018

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The effect of recombination on the accuracy of phylogeny estimation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224671

Horizontal gene transfer in prokaryotes: quantification and classification

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224671

The causes of Pseudomonas diversity

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224671

Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224671

Phylogenetic classification and the universal tree

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224671

Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224671

Constructing multigenome views of whole microbial genomes.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224671

rpoB sequence analysis as a novel basis for bacterial identification

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224671

A genomic perspective on protein families

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224671

Horizontal transfer of ATPase genes--the tree of life becomes a net of life

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224671

Genetic transfer and bacterial taxonomy

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224671

Hyper-recombination, diversity, and antibiotic resistance in pneumococcus.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224671

Filtered Z-closure supernetworks for extracting and visualizing recurrent signal from incongruent gene trees.

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224671

Reticulate representation of evolutionary and functional relationships between phage genomes

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224671

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

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224671

Phylogenetic super-networks from partial trees.

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224671

Adaptive evolution of bacterial metabolic networks by horizontal gene transfer.

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224671

Does a tree-like phylogeny only exist at the tips in the prokaryotes?

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224671

RNA polymerase beta-subunit-based phylogeny of Ehrlichia spp., Anaplasma spp., Neorickettsia spp. and Wolbachia pipientis

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1 reference

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Do genealogical patterns in purple photosynthetic bacteria reflect interspecific gene transfer?

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The impact of reticulate evolution on genome phylogeny

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Frequent recombination in a saltern population of Halorubrum

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Identifiers

DOI

10.1186/1471-2148-10-360

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Dimensions Publication ID

29 July 2017

0 references

1 reference

29 July 2017

1 reference