Fungal Pathogen Genomics

Application deadline – 7 Feb 2019

The kingdom of Fungi includes a biologically diverse group of organisms adapted to diverse environmental niches, playing important roles in ecosystems and human/animal/plant health. Fusarium, Magnaporthe, Ustilago, Puccinia, and Zymoseptoria species threaten agricultural ecosystems and food security worldwide, while Aspergillus, Candida, Coccidioides, Cryptococcus, Histoplasma, Pneumocystis, Batrachochytrium and other human and animal fungal pathogens cause allergies, serious illnesses, and sometimes life-threatening infections that are of great concern for veterinary and medical professionals arounds the world. Furthermore, fungi are also important model systems for basic and applied research and workhorses in biotechnology, food, pharmaceutical, and biofuel industries.

Advancements in high throughput ‘omics’ data generation technologies enable researchers to carry out large-scale analyses to investigate genomes, transcriptomes, proteomes, and metabolomes of numerous fungal organisms to address questions about pathogenicity, host-pathogen interactions, and identify new drug targets. To facilitate accessibility and analysis, a number of online fungal bioinformatic resources have been developed.
This week-long course is a collaborative teaching effort between the web-based fungal data mining resources:

• FungiDB
• EnsemblFungi
• PomBase
• SGD/CGD
• MycoCosm
• JGI

The Fungal Pathogen Genomics course provides hands-on training on how to take advantage of unique tools offered by each database; develop testable hypotheses, and investigate transcriptomics, proteomics and genomics datasets across multiple databases and different user interfaces.

Daily activities at the workshop will include individual and group hands-on training exercises, supplementary lectures on bioinformatic techniques and tools used by various databases, and presentations by distinguished guest speakers. For example, you will learn how to:

• Perform RNA-seq and SNP analysis and visualization via EuPathDB Galaxy workspace in FungiDB
• Identify secondary metabolite clusters in MycoCosm
• Find virulence genes and annotation in Ensembl
• Access genetic interactions in CGD/SGD
• Discover taxonomic conservation or phenotypes in PomBase