Horizontal Gene Acquisitions, Mobile Element Proliferation, and Genome Decay in the Host-Restricted Plant PathogenErwinia Tracheiphila

Taking the pseudo out of pseudogenes

(2015) Ian Goodhead et al.   CURRENT OPINION IN MICROBIOLOGY

One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly

(2015) Sergey Koren et al.   CURRENT OPINION IN MICROBIOLOGY

Bacterial Wilt of Cucurbits: Resurrecting a Classic Pathosystem

(2015) Erika Saalau Rojas et al.   PLANT DISEASE

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Expanded microbial genome coverage and improved protein family annotation in the COG database

(2014) Michael Y. Galperin et al.   NUCLEIC ACIDS RESEARCH

Dynamics of short- and long-term association between a bacterial plant pathogen and its arthropod vector

(2014) L. R. Shapiro et al.   Scientific Reports

Large-Scale Genomic Analysis Suggests a Neutral Punctuated Dynamics of Transposable Elements in Bacterial Genomes

(2014) Jaime Iranzo et al.   PLoS Computational Biology

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

(2013) Chen-Shan Chin et al.   NATURE METHODS

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Genetic and Virulence Variability AmongErwinia tracheiphilaStrains Recovered from Different Cucurbit Hosts

(2013) E. Saalau Rojas et al.   PHYTOPATHOLOGY

Genomic Analysis of the Kiwifruit Pathogen Pseudomonas syringae pv. actinidiae Provides Insight into the Origins of an Emergent Plant Disease

(2013) Honour C. McCann et al.   PLoS Pathogens

Fire Blight: Applied Genomic Insights of the Pathogen and Host

(2012) Mickael Malnoy et al.   Annual Review of Phytopathology

The Bacterium Pantoea stewartii Uses Two Different Type III Secretion Systems To Colonize Its Plant Host and Insect Vector

(2012) Valdir R. Correa et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Genomic insights into strategies used by Xanthomonas albilineans with its reduced artillery to spread within sugarcane xylem vessels

(2012) Isabelle Pieretti et al.   BMC GENOMICS

Pathogen effects on vegetative and floral odours mediate vector attraction and host exposure in a complex pathosystem

(2012) Lori Shapiro et al.   ECOLOGY LETTERS

Hybrid error correction and de novo assembly of single-molecule sequencing reads

(2012) Sergey Koren et al.   NATURE BIOTECHNOLOGY

A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs

(2012) Martin T Swain et al.   Nature Protocols

Insights from genomic comparisons of genetically monomorphic bacterial pathogens

(2012) M. Achtman   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Lateral gene transfer

(2011) Olga Zhaxybayeva et al.   CURRENT BIOLOGY

Massive Genomic Decay in Serratia symbiotica, a Recently Evolved Symbiont of Aphids

(2011) Gaelen R. Burke et al.   Genome Biology and Evolution

Erwinia typographi sp. nov., isolated from bark beetle (Ips typographus) gut

(2011) V. Skrodenyte-Arbaciauskiene et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

PHAST: A Fast Phage Search Tool

(2011) Y. Zhou et al.   NUCLEIC ACIDS RESEARCH

The Plant Pathogen Pseudomonas syringae pv. tomato Is Genetically Monomorphic and under Strong Selection to Evade Tomato Immunity

(2011) Rongman Cai et al.   PLoS Pathogens

Citrobacter rodentium is an Unstable Pathogen Showing Evidence of Significant Genomic Flux

(2011) Nicola K. Petty et al.   PLoS Pathogens

DendroPy: a Python library for phylogenetic computing

(2010) J. Sukumaran et al.   BIOINFORMATICS

Complete genome sequence of the fire blight pathogen Erwinia pyrifoliae DSM 12163T and comparative genomic insights into plant pathogenicity

(2010) Theo HM Smits et al.   BMC GENOMICS

Genome comparison of the epiphytic bacteria Erwinia billingiae and E. tasmaniensis with the pear pathogen E. pyrifoliae

(2010) Michael Kube et al.   BMC GENOMICS

Metalloprotease type III effectors that specifically cleave JNK and NF-κB

(2010) Kobi Baruch et al.   EMBO JOURNAL

Floral Transmission ofErwinia tracheiphilaby Cucumber Beetles in a WildCucurbita pepo

(2010) M. A. Sasu et al.   ENVIRONMENTAL ENTOMOLOGY

Intensive Farming: Evolutionary Implications for Parasites and Pathogens

(2010) Adèle Mennerat et al.   Evolutionary Biology

Complete Genome Sequence of the Fire Blight PathogenErwinia amylovoraCFBP 1430 and Comparison to OtherErwiniaspp.

(2010) Theo H. M. Smits et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes

(2010) Amrita Pati et al.   NATURE METHODS

Genome Evolution Following Host Jumps in the Irish Potato Famine Pathogen Lineage

(2010) S. Raffaele et al.   SCIENCE

CRISPR/Cas, the Immune System of Bacteria and Archaea

(2010) P. Horvath et al.   SCIENCE

The Extinction Dynamics of Bacterial Pseudogenes

(2010) Chih-Horng Kuo et al.   PLoS Genetics

Transposable elements: powerful facilitators of evolution

(2009) Keith R. Oliver et al.   BIOESSAYS

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Pseudogene accumulation in the evolutionary histories of Salmonella enterica serovars Paratyphi A and Typhi

(2009) Kathryn E Holt et al.   BMC GENOMICS

Evolution, Population Structure, and Phylogeography of Genetically Monomorphic Bacterial Pathogens

(2008) Mark Achtman   Annual Review of Microbiology

The Origins of Plant Pathogens in Agro-Ecosystems

(2008) Eva H. Stukenbrock et al.   Annual Review of Phytopathology

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH