The Green Revolution shaped the population structure of the rice pathogen Xanthomonas oryzae pv. oryzae

Genome-Wide Detection of Genes Under Positive Selection in Worldwide Populations of the Barley Scald Pathogen

(2018) Norfarhan Mohd-Assaad et al.   Genome Biology and Evolution

Genome-wide evidence for divergent selection between populations of a major agricultural pathogen

(2018) Fanny E. Hartmann et al.   MOLECULAR ECOLOGY

IR64: a high-quality and high-yielding mega variety

(2018) David J. Mackill et al.   Rice

A phylogenetic method to perform genome-wide association studies in microbes that accounts for population structure and recombination

(2018) Caitlin Collins et al.   PLoS Computational Biology

Piggy: a rapid, large-scale pan-genome analysis tool for intergenic regions in bacteria

(2018) Harry A Thorpe et al.   GigaScience

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

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

Genomic variation in 3,010 diverse accessions of Asian cultivated rice

(2018) Wensheng Wang et al.   NATURE

Natural variations in the promoter of OsSWEET13 and OsSWEET14 expand the range of resistance against Xanthomonas oryzae pv. oryzae

(2018) Abha Zaka et al.   PLoS One

A Strain of an Emerging Indian Xanthomonas oryzae pv. oryzae Pathotype Defeats the Rice Bacterial Blight Resistance Gene xa13 Without Inducing a Clade III SWEET Gene and Is Nearly Identical to a Recent Thai Isolate

(2018) Sara C. D. Carpenter et al.   Frontiers in Microbiology

Evolution of Transcription Activator-Like Effectors in Xanthomonas oryzae

(2017) Annett Erkes et al.   Genome Biology and Evolution

Population genomic insights into variation and evolution of Xanthomonas oryzae pv. oryzae

(2017) Samriti Midha et al.   Scientific Reports

Plant-Pathogen Effectors: Cellular Probes Interfering with Plant Defenses in Spatial and Temporal Manners

(2016) Tania Y. Toruño et al.   Annual Review of Phytopathology

ggtree: anrpackage for visualization and annotation of phylogenetic trees with their covariates and other associated data

(2016) Guangchuang Yu et al.   Methods in Ecology and Evolution

AnnoTALE: bioinformatics tools for identification, annotation and nomenclature of TALEs from Xanthomonas genomic sequences

(2016) Jan Grau et al.   Scientific Reports

Effector Diversification Contributes to Xanthomonas oryzae pv. oryzae Phenotypic Adaptation in a Semi-Isolated Environment

(2016) Ian Lorenzo Quibod et al.   Scientific Reports

IonGAP: integrative bacterial genome analysis for Ion Torrent sequence data

(2015) Adrian Baez-Ortega et al.   BIOINFORMATICS

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

Fusarium Wilt of Banana

(2015) Randy C. Ploetz   PHYTOPATHOLOGY

ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes

(2015) Xavier Didelot et al.   PLoS Computational Biology

New Multilocus Variable-Number Tandem-Repeat Analysis Tool for Surveillance and Local Epidemiology of Bacterial Leaf Blight and Bacterial Leaf Streak of Rice Caused by Xanthomonas oryzae

(2014) L. Poulin et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Durable resistance: A key to sustainable management of pathogens and pests

(2014) Christopher C. Mundt   INFECTION GENETICS AND EVOLUTION

PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses in R

(2014) Bastian Pfeifer et al.   MOLECULAR BIOLOGY AND EVOLUTION

SNP-Seek database of SNPs derived from 3000 rice genomes

(2014) Nickolai Alexandrov et al.   NUCLEIC ACIDS RESEARCH

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Diverse Functions of Restriction-Modification Systems in Addition to Cellular Defense

(2013) K. Vasu et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

FUBAR: A Fast, Unconstrained Bayesian AppRoximation for Inferring Selection

(2013) B. Murrell et al.   MOLECULAR BIOLOGY AND EVOLUTION

Hierarchical and Spatially Explicit Clustering of DNA Sequences with BAPS Software

(2013) L. Cheng et al.   MOLECULAR BIOLOGY AND EVOLUTION

The evolution of plant pathogens in response to host resistance: Factors affecting the gain from deployment of qualitative and quantitative resistance

(2012) Giovanni Lo Iacono et al.   JOURNAL OF THEORETICAL BIOLOGY

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

(2012) Alexei J. Drummond et al.   MOLECULAR BIOLOGY AND EVOLUTION

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

The Emergence of Ug99 Races of the Stem Rust Fungus is a Threat to World Wheat Production

(2011) Ravi P. Singh et al.   Annual Review of Phytopathology

HrpG and HrpX Play Global Roles in Coordinating Different Virulence Traits ofXanthomonas axonopodispv.citri

(2011) Yinping Guo et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Spatial variation in disease resistance: from molecules to metapopulations

(2010) Anna-Liisa Laine et al.   JOURNAL OF ECOLOGY

ABACAS: algorithm-based automatic contiguation of assembled sequences

(2009) S. Assefa et al.   BIOINFORMATICS

High-throughput functional annotation and data mining with the Blast2GO suite

(2008) S. Gotz et al.   NUCLEIC ACIDS RESEARCH