De Novo Assembly and Phasing of Dikaryotic Genomes from Two Isolates of Puccinia coronata f. sp. avenae, the Causal Agent of Oat Crown Rust

Puccinia coronata f. sp. avenae : a threat to global oat production

(2017) Eric S. Nazareno et al.   MOLECULAR PLANT PATHOLOGY

Phylogenomic evolutionary surveys of subtilase superfamily genes in fungi

(2017) Juan Li et al.   Scientific Reports

An overview of genetic rust resistance: From broad to specific mechanisms

(2017) Sambasivam Periyannan et al.   PLoS Pathogens

Regulation of proteinaceous effector expression in phytopathogenic fungi

(2017) Kar-Chun Tan et al.   PLoS Pathogens

Transcription Factors in Fungi: TFome Dynamics, Three Major Families, and Dual-Specificity TFs

(2017) Ekaterina Shelest   Frontiers in Genetics

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

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

Assemblytics: a web analytics tool for the detection of variants from an assembly

(2016) Maria Nattestad et al.   BIOINFORMATICS

Genome analysis and avirulence gene cloning using a high-density RADseq linkage map of the flax rust fungus, Melampsora lini

(2016) Claire Anderson et al.   BMC GENOMICS

OcculterCut: A Comprehensive Survey of AT-Rich Regions in Fungal Genomes

(2016) Alison C. Testa et al.   Genome Biology and Evolution

Phased diploid genome assembly with single-molecule real-time sequencing

(2016) Chen-Shan Chin et al.   NATURE METHODS

The Hemileia vastatrix effector HvEC-016 suppresses bacterial blight symptoms in coffee genotypes with the S H 1 rust resistance gene

(2016) Thiago Maia et al.   NEW PHYTOLOGIST

KEGG: new perspectives on genomes, pathways, diseases and drugs

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes

(2016) Todd M. Lowe et al.   NUCLEIC ACIDS RESEARCH

Putative Rust Fungal Effector Proteins in Infected Bean and Soybean Leaves

(2016) Bret Cooper et al.   PHYTOPATHOLOGY

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

Kingdom-Wide Analysis of Fungal Small Secreted Proteins (SSPs) Reveals their Potential Role in Host Association

(2016) Ki-Tae Kim et al.   Frontiers in Plant Science

BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS: Table 1.

(2015) Katharina J. Hoff et al.   BIOINFORMATICS

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

The two-speed genomes of filamentous pathogens: waltz with plants

(2015) Suomeng Dong et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Effector P: predicting fungal effector proteins from secretomes using machine learning

(2015) Jana Sperschneider et al.   NEW PHYTOLOGIST

Twenty years of theMEROPSdatabase of proteolytic enzymes, their substrates and inhibitors

(2015) Neil D. Rawlings et al.   NUCLEIC ACIDS RESEARCH

Comparative genomic and transcriptional analyses of the carbohydrate-active enzymes and secretomes of phytopathogenic fungi reveal their significant roles during infection and development

(2015) Xueliang Lyu et al.   Scientific Reports

Advances and Challenges in Computational Prediction of Effectors from Plant Pathogenic Fungi

(2015) Jana Sperschneider et al.   PLoS Pathogens

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

Evaluation of Secretion Prediction Highlights Differing Approaches Needed for Oomycete and Fungal Effectors

(2015) Jana Sperschneider et al.   Frontiers in Plant Science

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Reconstructing complex regions of genomes using long-read sequencing technology

(2014) J. Huddleston et al.   GENOME RESEARCH

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

The Ins and Outs of Rust Haustoria

(2014) Diana P. Garnica et al.   PLoS Pathogens

On the current status of Phakopsora pachyrhizi genome sequencing

(2014) Marco Loehrer   Frontiers in Plant Science

Genome size analyses of Pucciniales reveal the largest fungal genomes

(2014) Sílvia Tavares et al.   Frontiers in Plant Science

The genome sequence and effector complement of the flax rust pathogen Melampsora lini

(2014) Adnane Nemri et al.   Frontiers in Plant Science

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

(2013) Y. Liao et al.   BIOINFORMATICS

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Comparative analysis of fungal genomes reveals different plant cell wall degrading capacity in fungi

(2013) Zhongtao Zhao et al.   BMC GENOMICS

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

Fungal plant cell wall-degrading enzyme database: a platform for comparative and evolutionary genomics in fungi and Oomycetes

(2013) Jaeyoung Choi et al.   BMC GENOMICS

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

The carbohydrate-active enzymes database (CAZy) in 2013

(2013) Vincent Lombard et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

High genome heterozygosity and endemic genetic recombination in the wheat stripe rust fungus

(2013) Wenming Zheng et al.   Nature Communications

Comparative Genomics of a Plant-Pathogenic Fungus, Pyrenophora tritici-repentis , Reveals Transduplication and the Impact of Repeat Elements on Pathogenicity and Population Divergence

(2013) Viola A. Manning et al.   G3-Genes Genomes Genetics

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

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

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

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

Exploring Massive, Genome Scale Datasets with the GenometriCorr Package

(2012) Alexander Favorov et al.   PLoS Computational Biology

Somatic Hybridization in the Uredinales

(2011) Robert F. Park et al.   Annual Review of Phytopathology

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

(2011) Marcus Lechner et al.   BMC BIOINFORMATICS

Virulence in Oat Crown Rust (Puccinia coronata f. sp. avenae) in the United States from 2006 through 2009

(2011) M. L. Carson   PLANT DISEASE

Next Generation Sequencing Provides Rapid Access to the Genome of Puccinia striiformis f. sp. tritici, the Causal Agent of Wheat Stripe Rust

(2011) Dario Cantu et al.   PLoS One

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

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Co-evolutionary interactions between host resistance and pathogen effector genes in flax rust disease

(2010) MICHAEL RAVENSDALE et al.   MOLECULAR PLANT PATHOLOGY

Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium

(2010) Li-Jun Ma et al.   NATURE

Plant immunity: towards an integrated view of plant–pathogen interactions

(2010) Peter N. Dodds et al.   NATURE REVIEWS GENETICS

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

The Origins of Plant Pathogens in Agro-Ecosystems

(2008) Eva H. Stukenbrock et al.   Annual Review of Phytopathology

The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics

(2008) B. L. Cantarel et al.   NUCLEIC ACIDS RESEARCH

Breeding cereals for rust resistance in Australia

(2008) R. F. Park   PLANT PATHOLOGY

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

(2008) Brian J Haas et al.   GENOME BIOLOGY

A Rapid Method for Detecting and Quantifying Bacterial DNA in Rust Fungal DNA Samples

(2007) C. W. Barnes et al.   PHYTOPATHOLOGY