Hybridization of powdery mildew strains gives rise to pathogens on novel agricultural crop species

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Sequencing of Chloroplast Genomes from Wheat, Barley, Rye and Their Relatives Provides a Detailed Insight into the Evolution of the Triticeae Tribe

(2014) Christopher P. Middleton et al.   PLoS One

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

The wheat powdery mildew genome shows the unique evolution of an obligate biotroph

(2013) Thomas Wicker et al.   NATURE GENETICS

Evaluation of Resistance to Powdery Mildew in Triticale Seedlings and Adult Plants

(2013) V. Troch et al.   PLANT DISEASE

Mosaic genome structure of the barley powdery mildew pathogen and conservation of transcriptional programs in divergent hosts

(2013) S. Hacquard et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

GAPIT: genome association and prediction integrated tool

(2012) Alexander E. Lipka et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Phylogeography and virulence structure of the powdery mildew population on its 'new' host triticale

(2012) Veronique Troch et al.   BMC EVOLUTIONARY BIOLOGY

Genome Evolution Due to Allopolyploidization in Wheat

(2012) M. Feldman et al.   GENETICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Fusion of two divergent fungal individuals led to the recent emergence of a unique widespread pathogen species

(2012) E. H. Stukenbrock et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

The Probability of a Gene Tree Topology within a Phylogenetic Network with Applications to Hybridization Detection

(2012) Yun Yu et al.   PLoS Genetics

A major invasion of transposable elements accounts for the large size of the Blumeria graminis f.sp. tritici genome

(2011) Francis Parlange et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

The Plant Pathogen Phytophthora andina Emerged via Hybridization of an Unknown Phytophthora Species and the Irish Potato Famine Pathogen, P. infestans

(2011) Erica M. Goss et al.   PLoS One

Multiple emergences of genetically diverse amphibian-infecting chytrids include a globalized hypervirulent recombinant lineage

(2011) R. A. Farrer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Coalescent Histories on Phylogenetic Networks and Detection of Hybridization Despite Incomplete Lineage Sorting

(2011) Yun Yu et al.   SYSTEMATIC BIOLOGY

The Newick utilities: high-throughput phylogenetic tree processing in the UNIX shell

(2010) T. Junier et al.   BIOINFORMATICS

Fast and SNP-tolerant detection of complex variants and splicing in short reads

(2010) T. D. Wu et al.   BIOINFORMATICS

TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations

(2010) Federico Abascal et al.   NUCLEIC ACIDS RESEARCH

Evidence of host-range expansion from new powdery mildew (Blumeria graminis) infections of triticale (×Triticosecale) in France

(2010) A. S. Walker et al.   PLANT PATHOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Rapid emergence of hybrids between the two subspecies ofOphiostoma novo-ulmiwith a high level of pathogenic fitness

(2009) C. M. Brasier et al.   PLANT PATHOLOGY

PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships

(2008) Cuong Than et al.   BMC BIOINFORMATICS

Oomycete RXLR effectors: delivery, functional redundancy and durable disease resistance

(2008) Paul RJ Birch et al.   CURRENT OPINION IN PLANT BIOLOGY