Expression Profiling of the Wheat Pathogen Zymoseptoria tritici Reveals Genomic Patterns of Transcription and Host-Specific Regulatory Programs

Coevolution and Life Cycle Specialization of Plant Cell Wall Degrading Enzymes in a Hemibiotrophic Pathogen

(2013) Patrick C. Brunner et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Bdtf1 Gene in Alternaria brassicicola Is Important in Detoxifying Brassinin and Maintaining Virulence on Brassica Species

(2013) Akhil Srivastava et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Transcriptional Reprogramming of Wheat and the Hemibiotrophic Pathogen Septoria tritici during Two Phases of the Compatible Interaction

(2013) Fen Yang et al.   PLoS One

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

Genome Wide Association Identifies Novel Loci Involved in Fungal Communication

(2013) Javier Palma-Guerrero et al.   PLoS Genetics

Breakage-fusion-bridge Cycles and Large Insertions Contribute to the Rapid Evolution of Accessory Chromosomes in a Fungal Pathogen

(2013) Daniel Croll et al.   PLoS Genetics

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Analysis of the bread wheat genome using whole-genome shotgun sequencing

(2012) Rachel Brenchley et al.   NATURE

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH

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

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

NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data

(2012) Ravi K. Patel et al.   PLoS One

Defining the Predicted Protein Secretome of the Fungal Wheat Leaf Pathogen Mycosphaerella graminicola

(2012) Alexandre Morais do Amaral et al.   PLoS One

Tomato immune receptor Ve1 recognizes effector of multiple fungal pathogens uncovered by genome and RNA sequencing

(2012) R. de Jonge et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes Fungi

(2012) Robin A. Ohm et al.   PLoS Pathogens

Ultra-fast sequence clustering from similarity networks with SiLiX

(2011) Vincent Miele et al.   BMC BIOINFORMATICS

The making of a new pathogen: Insights from comparative population genomics of the domesticated wheat pathogen Mycosphaerella graminicola and its wild sister species

(2011) E. H. Stukenbrock et al.   GENOME RESEARCH

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations

(2011) Thierry Rouxel et al.   Nature Communications

Finished Genome of the Fungal Wheat Pathogen Mycosphaerella graminicola Reveals Dispensome Structure, Chromosome Plasticity, and Stealth Pathogenesis

(2011) Stephen B. Goodwin et al.   PLoS Genetics

An ABC Transporter and a Cytochrome P450 ofNectria haematococcaMPVI Are Virulence Factors on Pea and Are the Major Tolerance Mechanisms to the Phytoalexin Pisatin

(2010) Jeffrey J. Coleman et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium

(2010) Li-Jun Ma et al.   NATURE

Genome sequencing and analysis of the model grass Brachypodium distachyon

(2010) John P. Vogel et al.   NATURE

Maize Tumors Caused by Ustilago maydis Require Organ-Specific Genes in Host and Pathogen

(2010) D. S. Skibbe et al.   SCIENCE

Linking the emergence of fungal plant diseases with ecological speciation

(2010) Tatiana Giraud et al.   TRENDS IN ECOLOGY & EVOLUTION

Whole-Genome and Chromosome Evolution Associated with Host Adaptation and Speciation of the Wheat Pathogen Mycosphaerella graminicola

(2010) Eva H. Stukenbrock et al.   PLoS Genetics

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Fungal Effector Proteins

(2009) Ioannis Stergiopoulos et al.   Annual Review of Phytopathology

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Meiosis Drives Extraordinary Genome Plasticity in the Haploid Fungal Plant Pathogen Mycosphaerella graminicola

(2009) Alexander H. J. Wittenberg et al.   PLoS One

The Genome of Nectria haematococca: Contribution of Supernumerary Chromosomes to Gene Expansion

(2009) Jeffrey J. Coleman et al.   PLoS Genetics

Phylogeny.fr: robust phylogenetic analysis for the non-specialist

(2008) A. Dereeper et al.   NUCLEIC ACIDS RESEARCH

SMART 6: recent updates and new developments

(2008) I. Letunic et al.   NUCLEIC ACIDS RESEARCH

A Rapid Bootstrap Algorithm for the RAxML Web Servers

(2008) Alexandros Stamatakis et al.   SYSTEMATIC BIOLOGY

Genomic Islands in the Pathogenic Filamentous Fungus Aspergillus fumigatus

(2008) Natalie D. Fedorova et al.   PLoS Genetics