Niklaus J. Grünwald

This study shows that k-mer-based whole-genome similarity can rapidly and accurately classify fungal taxa from genus to intraspecies variants, outperforming traditional methods in speed and efficiency.

PathogenSurveillance automates population genomic analyses of WGS data to enable rapid pathogen identification and biosurveillance.

Krisp designs CRISPR and amplification-based diagnostic assays from whole genome data to differentiate pathogen groups, validated with Phytophthora ramorum data.

This paper investigates the genomic variation in Phytophthora fragariae to identify pathogenicity-associated genes and finds that transcriptional variation, not sequence polymorphisms, is linked to race-specific avirulence.

The paper uses GBS to analyze genetic variation in three Alternaria species from tomato and potato, revealing population structure and linkage disequilibrium.

effectR predicts candidate effectors in oomycete genomes using regular expressions and hidden Markov models, validated on published genomes.

The paper reports draft genome sequences of Phytophthora rubi and P. fragariae to study genomic processes underlying host adaptation in these plant pathogens.

Metacoder is an R package that enables parsing, manipulation, and visualization of hierarchical community taxonomic data through flexible plotting and analysis functions.

VcfR is an R package that manipulates and visualizes VCF data, offering tools for quality control and integration with other genetic data formats.