Multiple Recombination Events Drive the Current Genetic Structure of Xanthomonas perforans in Florida

ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R

(2018) Emmanuel Paradis et al.   BIOINFORMATICS

The type III effector AvrBsT enhances Xanthomonas perforans fitness in field-grown tomato

(2018) Peter Abrahamian et al.   PHYTOPATHOLOGY

Genomic Inference of Recombination-Mediated Evolution in Xanthomonas euvesicatoria and X. perforans

(2018) Mustafa O. Jibrin et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Core Genome Multilocus Sequence Typing: a Standardized Approach for Molecular Typing of Mycoplasma gallisepticum

(2017) Mostafa Ghanem et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Impact of Recombination on the Base Composition of Bacteria and Archaea

(2017) Louis-Marie Bobay et al.   MOLECULAR BIOLOGY AND EVOLUTION

Efficient Inference of Recent and Ancestral Recombination within Bacterial Populations

(2017) Rafal Mostowy et al.   MOLECULAR BIOLOGY AND EVOLUTION

Population analysis of clinical and environmental Vibrio parahaemolyticus isolated from eastern provinces in China by removing the recombinant SNPs in the MLST loci

(2016) Xin Lu et al.   INFECTION GENETICS AND EVOLUTION

Phylogenomic networks reveal limited phylogenetic range of lateral gene transfer by transduction

(2016) Ovidiu Popa et al.   ISME Journal

Population and Functional Genomics of Neisseria Revealed with Gene-by-Gene Approaches

(2016) Martin C. J. Maiden et al.   JOURNAL OF CLINICAL MICROBIOLOGY

ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data

(2016) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Analysis of Sequenced Genomes ofXanthomonas perforansIdentifies Candidate Targets for Resistance Breeding in Tomato

(2016) Sujan Timilsina et al.   PHYTOPATHOLOGY

Combined Analysis of Variation in Core, Accessory and Regulatory Genome Regions Provides a Super-Resolution View into the Evolution of Bacterial Populations

(2016) Alan McNally et al.   PLoS Genetics

Whole genome-based population biology and epidemiological surveillance of Listeria monocytogenes

(2016) Alexandra Moura et al.   Nature Microbiology

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

micropan: an R-package for microbial pan-genomics

(2015) Lars Snipen et al.   BMC BIOINFORMATICS

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Measurably evolving pathogens in the genomic era

(2015) Roman Biek et al.   TRENDS IN ECOLOGY & EVOLUTION

ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes

(2015) Xavier Didelot et al.   PLoS Computational Biology

Phylogenomics of Xanthomonas field strains infecting pepper and tomato reveals diversity in effector repertoires and identifies determinants of host specificity

(2015) Allison R. Schwartz et al.   Frontiers in Microbiology

Multilocus Sequence Analysis of Xanthomonads Causing Bacterial Spot of Tomato and Pepper Plants Reveals Strains Generated by Recombination among Species and Recent Global Spread of Xanthomonas gardneri

(2014) Sujan Timilsina et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

(2014) Nicholas J. Croucher et al.   NUCLEIC ACIDS RESEARCH

A Reference Pan-Genome Approach to Comparative Bacterial Genomics: Identification of Novel Epidemiological Markers in Pathogenic Campylobacter

(2014) Guillaume Méric et al.   PLoS One

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Applying evolutionary biology to address global challenges

(2014) S. P. Carroll et al.   SCIENCE

GET_HOMOLOGUES, a Versatile Software Package for Scalable and Robust Microbial Pangenome Analysis

(2013) Bruno Contreras-Moreira et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

MLST revisited: the gene-by-gene approach to bacterial genomics

(2013) Martin C. J. Maiden et al.   NATURE REVIEWS MICROBIOLOGY

IMG 4 version of the integrated microbial genomes comparative analysis system

(2013) Victor M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Transgenic Resistance Confers Effective Field Level Control of Bacterial Spot Disease in Tomato

(2012) Diana M. Horvath et al.   PLoS One

Routine Use of Microbial Whole Genome Sequencing in Diagnostic and Public Health Microbiology

(2012) Claudio U. Köser et al.   PLoS Pathogens

Comparative genomics reveals diversity among xanthomonads infecting tomato and pepper

(2011) Neha Potnis et al.   BMC GENOMICS

BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons

(2011) Nabil-Fareed Alikhan et al.   BMC GENOMICS

Contrasting recombination patterns and demographic histories of the plant pathogen Ralstonia solanacearum inferred from MLSA

(2011) Emmanuel Wicker et al.   ISME Journal

SequenceMatrix: concatenation software for the fast assembly of multi-gene datasets with character set and codon information

(2010) Gaurav Vaidya et al.   CLADISTICS

Suppression of the AvrBs1-specific hypersensitive response by the YopJ effector homolog AvrBsT from Xanthomonas depends on a SNF1-related kinase

(2010) Robert Szczesny et al.   NEW PHYTOLOGIST

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

How Xanthomonas type III effectors manipulate the host plant

(2009) Sabine Kay et al.   CURRENT OPINION IN MICROBIOLOGY

The type III effectors ofXanthomonas

(2009) FRANK F. WHITE et al.   MOLECULAR PLANT PATHOLOGY

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

Genomic islands are dynamic, ancient integrative elements in bacterial evolution

(2009) E. Fidelma Boyd et al.   TRENDS IN MICROBIOLOGY

Role of Recombination in the Evolution of the Model Plant Pathogen Pseudomonas syringae pv. tomato DC3000, a Very Atypical Tomato Strain

(2008) S. Yan et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Comparative genomics: the bacterial pan-genome

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

Virulence evolution and the trade-off hypothesis: history, current state of affairs and the future

(2008) S. ALIZON et al.   JOURNAL OF EVOLUTIONARY BIOLOGY