Integrated Analysis of Gene Expression, SNP, InDel, and CNV Identifies Candidate Avirulence Genes in Australian Isolates of the Wheat Leaf Rust Pathogen Puccinia triticina

Whole-genome sequencing of Puccinia striiformis f. sp. tritici mutant isolates identifies avirulence gene candidates

(2020) Yuxiang Li et al.   BMC GENOMICS

Long-Read–Based de novo Genome Assembly and Comparative Genomics of the Wheat Leaf Rust Pathogen Puccinia triticina Identifies Candidates for Three Avirulence Genes

(2020) Jing Qin Wu et al.   Frontiers in Genetics

The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads

(2019) Yang Liao et al.   NUCLEIC ACIDS RESEARCH

The global burden of pathogens and pests on major food crops

(2019) Serge Savary et al.   Nature Ecology & Evolution

Rust pathogen effectors: perspectives in resistance breeding

(2019) Pramod Prasad et al.   PLANTA

The AvrPm3-Pm3 effector-NLR interactions control both race-specific resistance and host-specificity of cereal mildews on wheat

(2019) Salim Bourras et al.   Nature Communications

De Novo Genome Assembly and Comparative Genomics of the Barley Leaf Rust Pathogen Puccinia hordei Identifies Candidates for Three Avirulence Genes

(2019) Jiapeng Chen et al.   G3-Genes Genomes Genetics

Improved prediction of fungal effector proteins from secretomes with EffectorP 2.0

(2018) Jana Sperschneider et al.   MOLECULAR PLANT PATHOLOGY

Copy Number Variation in Fungi and Its Implications for Wine Yeast Genetic Diversity and Adaptation

(2018) Jacob L. Steenwyk et al.   Frontiers in Microbiology

Two Methods for Mapping and Visualizing Associated Data on Phylogeny Using Ggtree

(2018) Guangchuang Yu et al.   MOLECULAR BIOLOGY AND EVOLUTION

Advances in understanding obligate biotrophy in rust fungi

(2018) Cécile Lorrain et al.   NEW PHYTOLOGIST

Distinct Trajectories of Massive Recent Gene Gains and Losses in Populations of a Microbial Eukaryotic Pathogen

(2017) Fanny E. Hartmann et al.   MOLECULAR BIOLOGY AND EVOLUTION

ApoplastP : prediction of effectors and plant proteins in the apoplast using machine learning

(2017) Jana Sperschneider et al.   NEW PHYTOLOGIST

Variation in theAvrSr35gene determinesSr35resistance against wheat stem rust race Ug99

(2017) Andres Salcedo et al.   SCIENCE

Loss ofAvrSr50by somatic exchange in stem rust leads to virulence forSr50resistance in wheat

(2017) Jiapeng Chen et al.   SCIENCE

Extensive Copy Number Variation in Fermentation-Related Genes Among Saccharomyces cerevisiae Wine Strains

(2017) Jacob Steenwyk et al.   G3-Genes Genomes Genetics

Comparative Genomics Integrated with Association Analysis Identifies Candidate Effector Genes Corresponding to Lr20 in Phenotype-Paired Puccinia triticina Isolates from Australia

(2017) Jing Qin Wu et al.   Frontiers in Plant Science

Dissection of genomic features and variations of three pathotypes of Puccinia striiformis through whole genome sequencing

(2017) Kanti Kiran et al.   Scientific Reports

LOCALIZER: subcellular localization prediction of both plant and effector proteins in the plant cell

(2017) Jana Sperschneider et al.   Scientific Reports

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

Copy number variation contributes to cryptic genetic variation in outbreak lineages of Cryptococcus gattii from the North American Pacific Northwest

(2016) Jacob L. Steenwyk et al.   BMC GENOMICS

Physiologic Specialization of Puccinia triticina on Wheat in the United States in 2014

(2016) J. A. Kolmer et al.   PLANT DISEASE

Comparative Analysis Highlights Variable Genome Content of Wheat Rusts and Divergence of the Mating Loci

(2016) Christina A. Cuomo et al.   G3-Genes Genomes Genetics

The 100-genomes strains, anS. cerevisiaeresource that illuminates its natural phenotypic and genotypic variation and emergence as an opportunistic pathogen

(2015) Pooja K. Strope et al.   GENOME RESEARCH

Comparative genomics of Australian isolates of the wheat stem rust pathogen Puccinia graminis f. sp. tritici reveals extensive polymorphism in candidate effector genes

(2015) Narayana M. Upadhyaya et al.   Frontiers in Plant Science

VariantAnnotation: a Bioconductor package for exploration and annotation of genetic variants

(2014) V. Obenchain et al.   BIOINFORMATICS

circlize implements and enhances circular visualization in R

(2014) Zuguang Gu et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

SNPhylo: a pipeline to construct a phylogenetic tree from huge SNP data

(2014) Tae-Ho Lee et al.   BMC GENOMICS

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

(2014) Dinah Qutob et al.   PLoS One

Using transcription of six Puccinia triticina races to identify the effective secretome during infection of wheat

(2014) Myron Bruce et al.   Frontiers in Plant Science

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

Leaf Rust of Wheat: Pathogen Biology, Variation and Host Resistance

(2013) James Kolmer   Forests

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

Chromosomal Copy Number Variation, Selection and Uneven Rates of Recombination Reveal Cryptic Genome Diversity Linked to Pathogenicity

(2013) Rhys A. Farrer et al.   PLoS Genetics

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

cn.MOPS: mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate

(2012) Günter Klambauer et al.   NUCLEIC ACIDS RESEARCH

Proteinortho: Detection of (Co-)orthologs in large-scale analysis

(2011) Marcus Lechner et al.   BMC BIOINFORMATICS

Variation in chromosome copy number influences the virulence of Cryptococcus neoformans and occurs in isolates from AIDS patients

(2011) Guanggan Hu et al.   BMC GENOMICS

Global status of wheat leaf rust caused by Puccinia triticina

(2011) J. Huerta-Espino et al.   EUPHYTICA

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

rtracklayer: an R package for interfacing with genome browsers

(2009) M. Lawrence et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Wheat leaf rust caused byPuccinia triticina

(2008) MELVIN D. BOLTON et al.   MOLECULAR PLANT PATHOLOGY

Breeding cereals for rust resistance in Australia

(2008) R. F. Park   PLANT PATHOLOGY