Toward an efficient method of identifying core genes for evolutionary and functional microbial phylogenies (Q34023960)

30 July 2017

Toward an efficient method of identifying core genes for evolutionary and functional microbial phylogenies (English)

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30 July 2017

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1

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30 July 2017

Curtis Huttenhower

2

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language of work or name

English

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publication date

12 September 2011

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30 July 2017

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30 July 2017

6

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30 July 2017

9

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30 July 2017

e24704

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Creative Commons Attribution 4.0 International

30 July 2017

start time

12 September 2011

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April 2022 Public Data File from Crossref

copyright status

copyrighted

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cites work

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5 July 2018

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5 July 2018

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5 July 2018

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5 July 2018

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High frequency of hotspot mutations in core genes of Escherichia coli due to short-term positive selection.

5 July 2018

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5 July 2018

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5 July 2018

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The evolution of modularity in bacterial metabolic networks.

5 July 2018

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Functional metagenomic profiling of nine biomes

5 July 2018

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Genome evolution in cyanobacteria: the stable core and the variable shell

5 July 2018

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SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB

5 July 2018

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5 July 2018

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Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: a comprehensive assessment

5 July 2018

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Toward a more robust assessment of intraspecies diversity, using fewer genetic markers

5 July 2018

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The origin and evolution of Archaea: a state of the art

5 July 2018

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Toward Automatic Reconstruction of a Highly Resolved Tree of Life

5 July 2018

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

5 July 2018

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Computational identification of strain-, species- and genus-specific proteins

5 July 2018

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Highways of gene sharing in prokaryotes

5 July 2018

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Towards a genome-based taxonomy for prokaryotes

5 July 2018

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Evolutionary and functional genomics of the Archaea

5 July 2018

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An emerging phylogenetic core of Archaea: phylogenies of transcription and translation machineries converge following addition of new genome sequences

5 July 2018

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Computing prokaryotic gene ubiquity: rescuing the core from extinction

5 July 2018

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Determination of the core of a minimal bacterial gene set

5 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=3171473

Detection of evolutionarily stable fragments of cellular pathways by hierarchical clustering of phyletic patterns

5 July 2018

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Comparative genomics, minimal gene-sets and the last universal common ancestor

5 July 2018

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Community structure and metabolism through reconstruction of microbial genomes from the environment

5 July 2018

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From gene trees to organismal phylogeny in prokaryotes: the case of the gamma-Proteobacteria

5 July 2018

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The genetic core of the universal ancestor

5 July 2018

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STRING: a database of predicted functional associations between proteins

5 July 2018

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Escherichia coli in disguise: molecular origins of Shigella

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3171473

Genome trees and the tree of life

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3171473

A phylogenomic approach to bacterial phylogeny: evidence of a core of genes sharing a common history

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3171473

CoreGenes: a computational tool for identifying and cataloging "core" genes in a set of small genomes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3171473

Extreme genome reduction in Buchnera spp.: toward the minimal genome needed for symbiotic life

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3171473

Genome trees constructed using five different approaches suggest new major bacterial clades

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3171473

Universal trees based on large combined protein sequence data sets.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3171473

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3171473

Multiple independent origins of Shigella clones of Escherichia coli and convergent evolution of many of their characteristics

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3171473

Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3171473

Genome phylogeny based on gene content

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3171473

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3171473

fastDNAmL: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3171473

Comparative genomic analysis of the family Iridoviridae: re-annotating and defining the core set of iridovirus genes

5 July 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0024704

A multigene approach to phylogenetic analysis using the genus Mycobacterium as a model

21 January 2018

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https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0024704

Identification of functional links between genes using phylogenetic profiles.

21 January 2018

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https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0024704

The rate of adaptive evolution in enteric bacteria.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0024704

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0024704

10.1371/JOURNAL.PONE.0024704

21 January 2018

Identifiers

DOI

1 reference

30 July 2017

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30 July 2017

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PubMed ID

21931822