MARPLE, a point-of-care, strain-level disease diagnostics and surveillance tool for complex fungal pathogens

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Nextstrain: real-time tracking of pathogen evolution

(2018) James Hadfield et al.   BIOINFORMATICS

Nanopore Sequencing as a Surveillance Tool for Plant Pathogens in Plant and Insect Tissues

(2018) Aline Bronzato Badial et al.   PLANT DISEASE

A Near-Complete Haplotype-Phased Genome of the Dikaryotic Wheat Stripe Rust Fungus Puccinia striiformis f. sp. tritici Reveals High Interhaplotype Diversity

(2018) Benjamin Schwessinger et al.   mBio

Pathogenomic Analysis of Wheat Yellow Rust Lineages Detects Seasonal Variation and Host Specificity

(2017) Vanessa Bueno-Sancho et al.   Genome Biology and Evolution

Next-generation sequencing (NGS) in the microbiological world: How to make the most of your money

(2017) Antony T. Vincent et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Yellow Rust Epidemics Worldwide Were Caused by Pathogen Races from Divergent Genetic Lineages

(2017) Sajid Ali et al.   Frontiers in Plant Science

Advanced DNA-Based Point-of-Care Diagnostic Methods for Plant Diseases Detection

(2017) Han Yih Lau et al.   Frontiers in Plant Science

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Real-time, portable genome sequencing for Ebola surveillance

(2016) Joshua Quick et al.   NATURE

Molecular markers for tracking the origin and worldwide distribution of invasive strains ofPuccinia striiformis

(2016) Stephanie Walter et al.   Ecology and Evolution

Crop-destroying fungal and oomycete pathogens challenge food security

(2015) Daniel P. Bebber et al.   FUNGAL GENETICS AND BIOLOGY

Next-Generation Sequencing for Infectious Disease Diagnosis and Management

(2015) Martina I. Lefterova et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Race-Specific Adult-Plant Resistance in Winter Wheat to Stripe Rust and Characterization of Pathogen Virulence Patterns

(2015) Eugene A. Milus et al.   PHYTOPATHOLOGY

Replacement of the European wheat yellow rust population by new races from the centre of diversity in the near-Himalayan region

(2015) M. S. Hovmøller et al.   PLANT PATHOLOGY

Field pathogenomics reveals the emergence of a diverse wheat yellow rust population

(2015) Amelia Hubbard et al.   GENOME BIOLOGY

Research investment implications of shifts in the global geography of wheat stripe rust

(2015) Jason M. Beddow et al.   Nature Plants

Advanced methods of plant disease detection. A review

(2014) Federico Martinelli et al.   Agronomy for Sustainable Development

A reassessment of the risk of rust fungi developing resistance to fungicides

(2014) Richard P Oliver   PEST MANAGEMENT SCIENCE

Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data

(2014) Thibaut Jombart et al.   PLoS Computational Biology

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

Dendroscope 3: An Interactive Tool for Rooted Phylogenetic Trees and Networks

(2012) Daniel H. Huson et al.   SYSTEMATIC BIOLOGY

ggplot2: Elegant Graphics for Data Analysis

(2011) Cedric Ginestet   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES A-STATISTICS IN SOCIETY

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

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

Discriminant analysis of principal components: a new method for the analysis of genetically structured populations

(2010) Thibaut Jombart et al.   BMC GENETICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

A Rapid Bootstrap Algorithm for the RAxML Web Servers

(2008) Alexandros Stamatakis et al.   SYSTEMATIC BIOLOGY