(Q33751901)

29 July 2017

title

Assembling networks of microbial genomes using linear programming (English)

1 reference

29 July 2017

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A21092133

30 August 2024

author

Claire M. B. Holloway

series ordinal

1

object named as

Catherine Holloway

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A21092133

30 August 2024

author name string

Robert G. Beiko

series ordinal

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A21092133

30 August 2024

language of work or name

English

1 reference

National Center for Biotechnology Information

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=21092133

30 August 2024

publication date

20 November 2010

1 reference

full work available at URL

29 July 2017

https://bmcecolevol.biomedcentral.com/counter/pdf/10.1186/1471-2148-10-360

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A21092133

http://www.biomedcentral.com/content/pdf/1471-2148-10-360.pdf

30 August 2024

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A21092133

https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21092133/pdf/?tool=EBI

30 August 2024

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A21092133

https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21092133/?tool=EBI

30 August 2024

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A21092133

http://www.biomedcentral.com/1471-2148/10/360

30 August 2024

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A21092133

http://www.biomedcentral.com/1471-2148/10/360/abstract

30 August 2024

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A21092133

https://europepmc.org/articles/PMC3224671

30 August 2024

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A21092133

https://europepmc.org/articles/PMC3224671?pdf=render

30 August 2024

content deliverer

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A21092133

30 August 2024

published in

BMC Evolutionary Biology

1 reference

29 July 2017

volume

10

1 reference

29 July 2017

page(s)

360

1 reference

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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21 June 2018

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21 June 2018

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21 June 2018

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Search for a 'Tree of Life' in the thicket of the phylogenetic forest

21 June 2018

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21 June 2018

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Computing galled networks from real data

21 June 2018

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The genome sequence of the psychrophilic archaeon, Methanococcoides burtonii: the role of genome evolution in cold adaptation

21 June 2018

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On the chimeric nature, thermophilic origin, and phylogenetic placement of the Thermotogales

21 June 2018

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Ancient gene transfer as a tool in phylogenetic reconstruction

21 June 2018

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Newly introduced genomic prophage islands are critical determinants of in vivo competitiveness in the Liverpool Epidemic Strain of Pseudomonas aeruginosa

21 June 2018

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21 June 2018

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Accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of aquificales in the phylogeny of Bacteria

21 June 2018

1 reference

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Dendroscope: An interactive viewer for large phylogenetic trees

21 June 2018

1 reference

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Widespread lateral gene transfer from intracellular bacteria to multicellular eukaryotes

21 June 2018

1 reference

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Widespread distribution of archaeal reverse gyrase in thermophilic bacteria suggests a complex history of vertical inheritance and lateral gene transfers

21 June 2018

1 reference

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Phylogenetic signal and functional categories in Proteobacteria genomes

21 June 2018

1 reference

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

21 June 2018

1 reference

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Rooting the tree of life by transition analyses

21 June 2018

1 reference

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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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Toward Automatic Reconstruction of a Highly Resolved Tree of Life

21 June 2018

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Visualizing and assessing phylogenetic congruence of core gene sets: a case study of the gamma-proteobacteria

21 June 2018

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Ancient lateral gene transfer in the evolution of Bdellovibrio bacteriovorus.

21 June 2018

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The genome of Salinibacter ruber: convergence and gene exchange among hyperhalophilic bacteria and archaea

21 June 2018

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Highways of gene sharing in prokaryotes

21 June 2018

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The net of life: reconstructing the microbial phylogenetic network

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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Transmission of Creutzfeldt-Jakob disease from man to the guinea pig

21 June 2018

1 reference

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RAPTOR: optimal protein threading by linear programming

21 June 2018

1 reference

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Biased biological functions of horizontally transferred genes in prokaryotic genomes

21 June 2018

1 reference

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

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

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

21 June 2018

1 reference

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Neighbor-net: an agglomerative method for the construction of phylogenetic networks

21 June 2018

1 reference

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Cytoscape: a software environment for integrated models of biomolecular interaction networks

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

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

21 June 2018

1 reference

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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

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

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

30 October 2018

1 reference

12 December 2020

The impact of reticulate evolution on genome phylogeny

1 reference

12 December 2020

A simulation test bed for hypotheses of genome evolution

1 reference

12 December 2020

Frequent recombination in a saltern population of Halorubrum

1 reference

12 December 2020

Identifiers

DOI

10.1186/1471-2148-10-360

1 reference

Dimensions Publication ID

29 July 2017

0 references

1 reference

29 July 2017

1 reference