Adaptive genomic structural variation in the grape powdery mildew pathogen, Erysiphe necator

Exploring genome characteristics and sequence quality without a reference

(2014) Jared T. Simpson   BIOINFORMATICS

Genome analyses of the wheat yellow (stripe) rust pathogen Puccinia striiformis f. sp. tritici reveal polymorphic and haustorial expressed secreted proteins as candidate effectors

(2013) Dario Cantu et al.   BMC GENOMICS

Host-Induced Gene Silencing in Barley Powdery Mildew Reveals a Class of Ribonuclease-Like Effectors

(2013) Clara Pliego et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

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

(2013) Thomas Wicker et al.   NATURE GENETICS

Induced overexpression of cytochrome P450 sterol 14α-demethylase gene (CYP51) correlates with sensitivity to demethylation inhibitors (DMIs) inSclerotinia homoeocarpa

(2013) Bangya Ma et al.   PEST MANAGEMENT SCIENCE

Comparative Studies of Copy Number Variation Detection Methods for Next-Generation Sequencing Technologies

(2013) Junbo Duan 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

Aluminum tolerance in maize is associated with higher MATE1 gene copy number

(2013) L. G. Maron et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

(2013) Keith R Bradnam et al.   GigaScience

The Genomics of Obligate (and Nonobligate) Biotrophs

(2012) Pietro D. Spanu   Annual Review of Phytopathology

Overexpression ofShCYP51BandShatrDin Sclerotinia homoeocarpa Isolates Exhibiting Practical Field Resistance to a Demethylation Inhibitor Fungicide

(2012) Jon Hulvey et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Fungal cytochrome P450 sterol 14α-demethylase (CYP51) and azole resistance in plant and human pathogens

(2012) Rayko Becher et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Structure and evolution of barley powdery mildew effector candidates

(2012) Carsten Pedersen et al.   BMC GENOMICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Dual RNA-seq of pathogen and host

(2012) Alexander J. Westermann et al.   NATURE REVIEWS MICROBIOLOGY

Using Hierarchical Clustering of Secreted Protein Families to Classify and Rank Candidate Effectors of Rust Fungi

(2012) Diane G. O. Saunders et al.   PLoS One

Copy Number Variation of Multiple Genes at Rhg1 Mediates Nematode Resistance in Soybean

(2012) D. E. Cook et al.   SCIENCE

Wheat TILLING Mutants Show That the Vernalization Gene VRN1 Down-Regulates the Flowering Repressor VRN2 in Leaves but Is Not Essential for Flowering

(2012) Andrew Chen et al.   PLoS Genetics

Human Copy Number Variation and Complex Genetic Disease

(2011) Santhosh Girirajan et al.   Annual Review of Genetics

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Grapevine powdery mildew (Erysiphe necator): a fascinating system for the study of the biology, ecology and epidemiology of an obligate biotroph

(2011) DAVID M. GADOURY et al.   MOLECULAR PLANT PATHOLOGY

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

Genome structural variation discovery and genotyping

(2011) Can Alkan et al.   NATURE REVIEWS GENETICS

Molecular Modelling of the Emergence of Azole Resistance in Mycosphaerella graminicola

(2011) Jonathan G. L. Mullins et al.   PLoS One

Transformations, transport, and potential unintended consequences of high sulfur inputs to Napa Valley vineyards

(2011) E.-L. S. Hinckley et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Obligate biotrophy features unraveled by the genomic analysis of rust fungi

(2011) S. Duplessis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gene Gain and Loss during Evolution of Obligate Parasitism in the White Rust Pathogen of Arabidopsis thaliana

(2011) Eric Kemen et al.   PLOS BIOLOGY

Phylogeography and population structure of the grape powdery mildew fungus, Erysiphe necator, from diverse Vitis species

(2010) Marin TALBOT Brewer et al.   BMC EVOLUTIONARY BIOLOGY

Powdery mildew fungal effector candidates share N-terminal Y/F/WxC-motif

(2010) Dale Godfrey et al.   BMC GENOMICS

Genomics of biotrophy in fungi and oomycetes—emerging patterns

(2010) Pietro Spanu et al.   CURRENT OPINION IN PLANT BIOLOGY

Copy Number Variation Shapes Genome Diversity in Arabidopsis Over Immediate Family Generational Scales

(2010) Seth DeBolt   Genome Biology and Evolution

Copy number variation modifies expression time courses

(2010) E. Chaignat et al.   GENOME RESEARCH

Population resequencing reveals local adaptation of Arabidopsis lyrata to serpentine soils

(2010) Thomas L Turner et al.   NATURE GENETICS

Signatures of Adaptation to Obligate Biotrophy in the Hyaloperonospora arabidopsidis Genome

(2010) L. Baxter et al.   SCIENCE

Genome Expansion and Gene Loss in Powdery Mildew Fungi Reveal Tradeoffs in Extreme Parasitism

(2010) P. D. Spanu et al.   SCIENCE

Copy Number Variation and Transposable Elements Feature in Recent, Ongoing Adaptation at the Cyp6g1 Locus

(2010) Joshua M. Schmidt et al.   PLoS Genetics

Towards a comprehensive structural variation map of an individual human genome

(2010) Andy W Pang et al.   GENOME BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

CNV-seq, a new method to detect copy number variation using high-throughput sequencing

(2009) Chao Xie et al.   BMC BIOINFORMATICS

Mechanisms of change in gene copy number

(2009) P. J. Hastings et al.   NATURE REVIEWS GENETICS

Copy Number Variation and Transcriptional Polymorphisms of Phytophthora sojae RXLR Effector Genes Avr1a and Avr3a

(2009) Dinah Qutob et al.   PLoS One

Coevolution between a Family of Parasite Virulence Effectors and a Class of LINE-1 Retrotransposons

(2009) Soledad Sacristán et al.   PLoS One

A Novel Mechanism of Transposon-Mediated Gene Activation

(2009) Zhongge Zhang et al.   PLoS Genetics

Evolution of prokaryotic and eukaryotic virulence effectors

(2008) Wenbo Ma et al.   CURRENT OPINION IN PLANT BIOLOGY

Assessing the gene space in draft genomes

(2008) Genis Parra et al.   NUCLEIC ACIDS RESEARCH