In-silico Taxonomic Classification of 373 Genomes Reveals Species Misidentification and New Genospecies within the Genus Pseudomonas

Correspondence: Spontaneous secondary mutations confound analysis of the essential two-component system WalKR in Staphylococcus aureus

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Insect pathogenicity in plant-beneficial pseudomonads: phylogenetic distribution and comparative genomics

(2016) Pascale Flury et al.   ISME Journal

PGAdb-builder: A web service tool for creating pan-genome allele database for molecular fine typing

(2016) Yen-Yi Liu et al.   Scientific Reports

Diversity of Pseudomonas Genomes, Including Populus-Associated Isolates, as Revealed by Comparative Genome Analysis

(2015) Se-Ran Jun et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

Expression profiling of the bloom-forming cyanobacterium Nodularia CCY9414 under light and oxidative stress conditions

(2015) Matthias Kopf et al.   ISME Journal

Functional overlap of the Arabidopsis leaf and root microbiota

(2015) Yang Bai et al.   NATURE

Phylogenomics and systematics in Pseudomonas

(2015) Margarita Gomila et al.   Frontiers in Microbiology

Sequencing and Analysis of the Pseudomonas fluorescens GcM5-1A Genome: A Pathogen Living in the Surface Coat of Bursaphelenchus xylophilus

(2015) Kai Feng et al.   PLoS One

Induced Systemic Resistance by Beneficial Microbes

(2014) Corné M.J. Pieterse et al.   Annual Review of Phytopathology

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Complete Genome Sequence of the Plant Growth-Promoting Bacterium Pseudomonas sp. UW4

(2013) Jin Duan et al.   PLoS One

Phylogenetic affiliation of Pseudomonas putida biovar A and B strains

(2013) Magdalena Mulet et al.   RESEARCH IN MICROBIOLOGY

PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes

(2013) Nicola Segata et al.   Nature Communications

Getting the ecology into interactions between plants and the plant growth-promoting bacterium Pseudomonas fluorescens

(2013) W. H. Gera Hol et al.   Frontiers in Plant Science

BIGSdb: Scalable analysis of bacterial genome variation at the population level

(2011) Keith A Jolley et al.   BMC BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison

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Shifting the genomic gold standard for the prokaryotic species definition

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