Phylogenomics and systematics in Pseudomonas. (Q35659660)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26074881%20AND%20SRC:MED&resulttype=core&format=json

17 February 2020

title

Phylogenomics and systematics in Pseudomonas (English)

1 reference

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17 February 2020

1 reference

1

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17 February 2020

Jorge Lalucat

4

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17 February 2020

Elena García-Valdés

5

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author name string

Arantxa Peña

2

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Magdalena Mulet

3

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17 February 2020

publication date

18 March 2015

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26074881%20AND%20SRC:MED&resulttype=core&format=json

Frontiers in Microbiology

17 February 2020

published in

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volume

6

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page(s)

214

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describes a project that uses

17 February 2020

MUMmer

object named as

MUMmer

1 reference

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

cites work

Bioinformatic genome comparisons for taxonomic and phylogenetic assignments using Aeromonas as a test case

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447124

The relationship of the whole genome sequence identity to DNA hybridization varies between genera of prokaryotes

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447124

Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447124

The Complete Genome Sequence of Pseudomonas putida NBRC 14164T Confirms High Intraspecies Variation

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447124

Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447124

LPSN--list of prokaryotic names with standing in nomenclature

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447124

Pseudomonas aestusnigri sp. nov., isolated from crude oil-contaminated intertidal sand samples after the Prestige oil spill

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447124

The complete genome sequence of the plant growth-promoting bacterium Pseudomonas sp. UW4

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447124

Draft Genome of Pseudomonas stutzeri Strain NF13, a Nitrogen Fixer Isolated from the Galapagos Rift Hydrothermal Vent

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447124

Genome sequence-based species delimitation with confidence intervals and improved distance functions

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447124

Concordance between whole-cell matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry and multilocus sequence analysis approaches in species discrimination within the genus Pseudomonas.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447124

Taxonomic characterisation of Pseudomonas strain L48 and formal proposal of Pseudomonas entomophila sp. nov.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447124

Pseudomonas protegens sp. nov., widespread plant-protecting bacteria producing the biocontrol compounds 2,4-diacetylphloroglucinol and pyoluteorin

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447124

Ssg, a putative glycosyltransferase, functions in lipo- and exopolysaccharide biosynthesis and cell surface-related properties in Pseudomonas alkylphenolia

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447124

Complete genome sequence of the multiresistant taxonomic outlier Pseudomonas aeruginosa PA7.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447124

Shifting the genomic gold standard for the prokaryotic species definition

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447124

Comparative systems biology across an evolutionary gradient within the Shewanella genus.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447124

Historical evolution and current status of the taxonomy of genus Pseudomonas.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447124

Comparative phylogenies of Burkholderia, Ralstonia, Comamonas, Brevundimonas and related organisms derived from rpoB, gyrB and rrs gene sequences

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447124

DNA-DNA hybridization values and their relationship to whole-genome sequence similarities

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447124

Biology of Pseudomonas stutzeri

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447124

Towards a genome-based taxonomy for prokaryotes

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447124

Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447124

Towards a prokaryotic genomic taxonomy

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447124

Genomic insights that advance the species definition for prokaryotes

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447124

PermutMatrix: a graphical environment to arrange gene expression profiles in optimal linear order

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447124

Application of tetranucleotide frequencies for the assignment of genomic fragments

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447124

Versatile and open software for comparing large genomes

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447124

Pedigree and taxonomic credentials of Pseudomonas putida strain KT2440.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447124

Phylogenetic affiliation of the pseudomonads based on 16S rRNA sequence

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447124

Phylogenetic relationships of Pseudomonas putida strains deduced from the nucleotide sequences of gyrB, rpoD and 16S rRNA genes

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447124

The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447124

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447124

TreeView: an application to display phylogenetic trees on personal computers

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447124

Evolutionary trees from DNA sequences: A maximum likelihood approach

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447124

The aerobic pseudomonads: a taxonomic study

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447124

Definition of Plant-Pathogenic Pseudomonas Genomospecies of the Pseudomonas syringae Complex Through Multiple Comparative Approaches.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447124

Phylogenetic affiliation of Pseudomonas putida biovar A and B strains

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447124

DNA sequence-based analysis of the Pseudomonas species

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447124

Pseudomonas oleovorans subsp. lubricantis subsp. nov., and reclassification of Pseudomonas pseudoalcaligenes ATCC 17440T as later synonym of Pseudomonas oleovorans ATCC 8062 T.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447124

Molecular phylogeny of the genus Pseudomonas based on rpoB sequences and application for the identification of isolates

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447124

Towards a prokaryotic genomic taxonomy

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447124

Improved resolution on the phylogenetic relationships among Pseudomonas by the combined analysis of atp D, car A, rec A and 16S rDNA.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447124

Phylogeny of the genus Pseudomonas: intrageneric structure reconstructed from the nucleotide sequences of gyrB and rpoD genes.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447124

Intra- and Intergeneric Similarities of Pseudomonas and Xanthomonas Ribosomal Ribonucleic Acid Cistrons

25 September 2018

1 reference

https://api.crossref.org/works/10.3389%2FFMICB.2015.00214

Ribosomal Ribonucleic Acid Cistron Similarities of Phytopathogenic Pseudomonas Species

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFMICB.2015.00214

Genotypic Relationships and Taxonomic Localization of Unclassified Pseudomonas and Pseudomonas-Like Strains by Deoxyribonucleic Acid:Ribosomal Ribonucleic Acid Hybridizations

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFMICB.2015.00214

Approved Lists of Bacterial Names

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFMICB.2015.00214

Report of the Ad Hoc Committee on Reconciliation of Approaches to Bacterial Systematics

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFMICB.2015.00214

The Determination and Comparison of the 16S rRNA Gene Sequences of Species of the Genus Pseudomonas (sensu stricto and Estimation of the Natural Intrageneric Relationships

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFMICB.2015.00214

21 January 2018

Identifiers

DOI

10.3389/FMICB.2015.00214

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26074881%20AND%20SRC:MED&resulttype=core&format=json

17 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26074881%20AND%20SRC:MED&resulttype=core&format=json

17 February 2020

PubMed publication ID

26074881

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26074881%20AND%20SRC:MED&resulttype=core&format=json