A chromosome-level, fully phased genome assembly of the oat crown rust fungus Puccinia coronata f. sp. avenae: a resource to enable comparative genomics in the cereal rusts

Galaxy HiCExplorer 3: a web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization

(2020) Joachim Wolff et al.   NUCLEIC ACIDS RESEARCH

RepeatModeler2 for automated genomic discovery of transposable element families

(2020) Jullien M. Flynn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolution of virulence in rust fungi — multiple solutions to one problem

(2020) Melania Figueroa et al.   CURRENT OPINION IN PLANT BIOLOGY

Victorin, the host-selective cyclic peptide toxin from the oat pathogen Cochliobolus victoriae, is ribosomally encoded

(2020) Simon C. Kessler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Increased virulence of Puccinia coronata f. sp.avenae populations through allele frequency changes at multiple putative Avr loci

(2020) Marisa E. Miller et al.   PLoS Genetics

Integrating Hi-C links with assembly graphs for chromosome-scale assembly

(2019) Jay Ghurye et al.   PLoS Computational Biology

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

OUP accepted manuscript

(2018)   BIOINFORMATICS

Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization

(2018) Joachim Wolff et al.   NUCLEIC ACIDS RESEARCH

Detection of race-specific resistance against Puccinia coronata f. sp. avenae in Brachypodium species

(2018) Vahid Omidvar et al.   PHYTOPATHOLOGY

Deconstructing the evolutionary complexity between rust fungi ( Pucciniales ) and their plant hosts

(2018) M.C. Aime et al.   STUDIES IN MYCOLOGY

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

(2018) Marisa E. Miller et al.   mBio

D-GENIES: dot plot large genomes in an interactive, efficient and simple way

(2018) Floréal Cabanettes et al.   PeerJ

Repeat elements organise 3D genome structure and mediate transcription in the filamentous fungus Epichloë festucae

(2018) David J. Winter et al.   PLoS Genetics

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics

(2017) Robert M Waterhouse et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

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

Changing the Game: Using Integrative Genomics to Probe Virulence Mechanisms of the Stem Rust Pathogen Puccinia graminis f. sp. tritici

(2016) Melania Figueroa et al.   Frontiers in Plant Science

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

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

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

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

The rise and fall of the Phytophthora infestans lineage that triggered the Irish potato famine

(2013) Kentaro Yoshida et al.   eLife

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

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

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

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

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS