Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens

The complete genome sequence of Dickeya zeae EC1 reveals substantial divergence from other Dickeya strains and species

(2015) Jianuan Zhou et al.   BMC GENOMICS

Detection of Pantoea stewartii from sweet corn leaves by loop-mediated isothermal amplification (LAMP)

(2015) Hiroshi Uematsu et al.   JOURNAL OF GENERAL PLANT PATHOLOGY

Microbial species delineation using whole genome sequences

(2015) Neha J. Varghese et al.   NUCLEIC ACIDS RESEARCH

Plant pathogenic bacteria in open irrigation systems: what risk for crop health?

(2015) J. R. Lamichhane et al.   PLANT PATHOLOGY

Finding Our Way through Phenotypes

(2015) Andrew R. Deans et al.   PLOS BIOLOGY

Characterisation ofPectobacterium wasabiaeandPectobacterium carotovorumsubsp.carotovorumisolates from diseased potato plants in Finland

(2015) M. Pasanen et al.   ANNALS OF APPLIED BIOLOGY

Detection, identification and differentiation ofPectobacteriumandDickeyaspecies causing potato blackleg and tuber soft rot: a review

(2014) R. Czajkowski et al.   ANNALS OF APPLIED BIOLOGY

Simultaneous detection of major blackleg and soft rot bacterial pathogens in potato by multiplex polymerase chain reaction

(2014) M. Potrykus et al.   ANNALS OF APPLIED BIOLOGY

SplitMEM: a graphical algorithm for pan-genome analysis with suffix skips

(2014) Shoshana Marcus et al.   BIOINFORMATICS

Epidemiology of Dickeya dianthicola and Dickeya solani in ornamental hosts and potato studied using variable number tandem repeat analysis

(2014) Neil Parkinson et al.   EUROPEAN JOURNAL OF PLANT PATHOLOGY

Construction of a genome-scale metabolic network of the plant pathogenPectobacterium carotovorumprovides new strategies for bactericide discovery

(2014) Cheng Wang et al.   FEBS LETTERS

Genomic overview of the phytopathogen Pectobacterium wasabiae strain RNS 08.42.1A suggests horizontal acquisition of quorum-sensing genes

(2014) Slimane Khayi et al.   GENETICA

Genetic Diversity of Pectobacterium carotovorum subsp. brasiliensis Isolated in Korea

(2014) Dong Hwan Lee et al.   Plant Pathology Journal

Bacterial pectate lyases, structural and functional diversity

(2014) Nicole Hugouvieux-Cotte-Pattat et al.   Environmental Microbiology Reports

Seeking the source ofPseudomonas aeruginosainfections in a recently opened hospital: an observational study using whole-genome sequencing

(2014) Joshua Quick et al.   BMJ Open

Genotype-phenotype matching analysis of 38 Lactococcus lactis strains using random forest methods

(2013) Jumamurat R Bayjanov et al.   BMC MICROBIOLOGY

Non-phenotypic tests to detect and characterize antibiotic resistance mechanisms in Enterobacteriaceae

(2013) Agnese Lupo et al.   DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE

Dickeya solani sp. nov., a pectinolytic plant-pathogenic bacterium isolated from potato (Solanum tuberosum)

(2013) J. M. van der Wolf et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Phylogeny and classification of Dickeya based on multilocus sequence analysis

(2013) G. Marrero et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

(2013) Morgan G I Langille et al.   NATURE BIOTECHNOLOGY

MetaRef: a pan-genomic database for comparative and community microbial genomics

(2013) Katherine Huang et al.   NUCLEIC ACIDS RESEARCH

Pathogenicity of and plant immunity to soft rot pectobacteria

(2013) Pär R. Davidsson et al.   Frontiers in Plant Science

Characterisation of pectobacterium wasabiae causing blackleg and soft rot diseases in South Africa

(2012) Lucy N. Moleleki et al.   EUROPEAN JOURNAL OF PLANT PATHOLOGY

Phylogenetic conservatism of functional traits in microorganisms

(2012) Adam C Martiny et al.   ISME Journal

Top 10 plant pathogenic bacteria in molecular plant pathology

(2012) JOHN MANSFIELD et al.   MOLECULAR PLANT PATHOLOGY

Detection of phytopathogens of the genusDickeyausing a PCR primer prediction pipeline for draft bacterial genome sequences

(2012) L. Pritchard et al.   PLANT PATHOLOGY

Alignment-Free Design of Highly Discriminatory Diagnostic Primer Sets for Escherichia coli O104:H4 Outbreak Strains

(2012) Leighton Pritchard et al.   PLoS One

Revised Phylogeny and Novel Horizontally Acquired Virulence Determinants of the Model Soft Rot Phytopathogen Pectobacterium wasabiae SCC3193

(2012) Johanna Nykyri et al.   PLoS Pathogens

PGAP: pan-genomes analysis pipeline

(2011) Yongbing Zhao et al.   BIOINFORMATICS

The evolution of metabolic networks of E. coli

(2011) David J Baumler et al.   BMC Systems Biology

Open-Source Genomic Analysis of Shiga-Toxin–ProducingE. coliO104:H4

(2011) Holger Rohde et al.   NEW ENGLAND JOURNAL OF MEDICINE

Dickeya species: an emerging problem for potato production in Europe

(2011) I. K. Toth et al.   PLANT PATHOLOGY

Genome-scale diversity and niche adaptation analysis of Lactococcus lactis by comparative genome hybridization using multi-strain arrays

(2011) Roland J. Siezen et al.   Microbial Biotechnology

Characterization of Pectobacterium species from Iran using biochemical and molecular methods

(2010) Sareh Baghaee-Ravari et al.   EUROPEAN JOURNAL OF PLANT PATHOLOGY

The Tree and Net Components of Prokaryote Evolution

(2010) Pere Puigbò et al.   Genome Biology and Evolution

Evolutionary Dynamics of Complete Campylobacter Pan-Genomes and the Bacterial Species Concept

(2010) Tristan Lefébure et al.   Genome Biology and Evolution

Phylogeny of Gammaproteobacteria

(2010) K. P. Williams et al.   JOURNAL OF BACTERIOLOGY

Harvesting Evolutionary Signals in a Forest of Prokaryotic Gene Trees

(2010) K. Schliep et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer

(2009) Talima Pearson et al.   BMC BIOLOGY

Bacterial Evolution by Genomic Island Transfer Occurs via DNA Transformation In Planta

(2009) Helen C. Lovell et al.   CURRENT BIOLOGY

Sequencing the species pan-genome

(2009) Stephen Bentley   NATURE REVIEWS MICROBIOLOGY

Shifting the genomic gold standard for the prokaryotic species definition

(2009) Michael Richter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Biochemical and genetic diversity of pectolytic enterobacteria causing soft rot disease of potatoes in New Zealand

(2008) Andrew R. Pitman et al.   AUSTRALASIAN PLANT PATHOLOGY

Comparative genomics: the bacterial pan-genome

(2008) Hervé Tettelin et al.   CURRENT OPINION IN MICROBIOLOGY

The Pangenome Structure of Escherichia coli: Comparative Genomic Analysis of E. coli Commensal and Pathogenic Isolates

(2008) D. A. Rasko et al.   JOURNAL OF BACTERIOLOGY

Horizontal gene transfer: sustaining pathogenicity and optimizing host-pathogen interactions

(2008) CLARENCE I. KADO   MOLECULAR PLANT PATHOLOGY

Quorum Sensing Coordinates Brute Force and Stealth Modes of Infection in the Plant Pathogen Pectobacterium atrosepticum

(2008) Hui Liu et al.   PLoS Pathogens