Fungal Pathogen Genomics 

The kingdom of Fungi encompasses a diverse range of organisms adapted to various environmental niches, playing crucial roles in ecosystems, human/animal/plant health, and global food security. Species like Fusarium, Pyricularia, Ustilago, Puccinia, and Zymoseptoria, etc. threaten agricultural ecosystems and food security worldwide. Fungal pathogens such as Aspergillus, Candida, Mucor, Cryptococcus, Histoplasma, Coccidioides, Batrachochytrium, and others are of great concern for medical and veterinary professionals due to their potential to cause allergies, illnesses, and life-threatening infections. Furthermore, fungi serve as essential model systems in basic and applied research and play pivotal roles in biotechnology, food production, biomedical and pharmaceutical research and the biofuel industry.

High-throughput ‘omics’ data technologies empower scientists to conduct extensive analyses of the genomes, transcriptomes, proteomes, genetic variance data of a wide array of fungal and oomycete organisms. These analyses are essential for inquiries regarding pathogenicity, host-pathogen interactions, and the discovery of novel drug targets. To enhance accessibility and re-use of data, and facilitate analysis of different types of data, several web-based bioinformatic resources have been developed.

This week-long course represents a collaborative teaching effort involving the following resources dedicated to supporting research on fungal and oomycete species:

• FungiDB/VEuPathDB 
• Ensembl Fungi/EBI
• SGD/CGD 
• MycoCosm/JGI

The Fungal Pathogen Genomics course offers hands-on training on how to use unique, web-based tools provided by individual resources and apply them to both public and private datasets. Participants will learn to formulate testable hypotheses and explore genomes, functional omics datasets (transcriptomics, SNP, proteomics, etc.) and other data types across multiple databases.

Target audience

This course is aimed at graduate students, postdocs, clinical scientists, clinicians/healthcare professionals or lab heads working on fungal pathogens.

Daily activities will encompass both individual and group training exercises, complemented by supplementary lectures focusing on bioinformatics techniques and tools utilized by various databases. For example, the learning materials will address the following topics:

• Navigating gene record pages and genome browsers.
• Identification of orthologs and orthology-based inference.
• Comparative genomics, gene trees, whole-genome alignment.
• Creating in-silico experiments in FungiDB by employing search queries and public omics datasets, and performing enrichment analysis on search results. 
• Omics data analysis and visualization in VEuPathDB Galaxy, including RNA-Seq and Variant calling analysis (with Ensembl Variant Effect Predictor tool).
• Identifying genetic interactions, virulence genes, secondary metabolites.
• Introduction to manual genome curation using Apollo, a web-based platform for structural and functional genome annotation.

The programme also features talks by globally renowned guest speakers and provides occasions for engaging in scientific discussions and networking within a friendly environment.

Learning outcomes

After attending this course, participants will be able to:

• Navigate each database and answer research questions by creating custom queries across multiple bioinformatics resources.
• Utilize built-in web-based bioinformatics tools to mine omics data, including:
  • finding genes
  • identifying orthologs in other species via orthologous transformations,
  • determining trends through GO and metabolic pathway enrichment analysis,
  • visualizing genomics, proteomics, and transcriptomics data,
• Perform RNA-Seq and Variant calling analysis in VEuPathDB Galaxy, exporting and sharing analysis results, and more.
• Gain an understanding of the practical advantages and limitations of the tools used in bioinformatics, ensuring that the skills acquired are pertinent to their research and future endeavors.
• Develop skills and knowledge necessary to actively contribute to community genome curation and annotation efforts.
• Apply their newfound skills in web-based bioinformatic resources in their research projects. 

Training Team

Evelina Basenko
University of Liverpool, UK

David Roos
University of Pennsylvania, USA

Nishadi De Silva
EMBL-EBI, UK

Jodi Lew-Smith
Stanford University, USA

Steven Ahrendt
US DOE Joint Genome Institute, USA

Kathryn Crouch
University of Glasgow

Manuel Carbajo Martinez
EMBL-EBI

Stuart Brown
University of Pennsylvania, USA

Guest Speakers

Jane Usher
MRC Centre for Medical Mycology, Universtiy of Exeter, UK

Jason Rudd
Rothamsted Research, UK

Prerequisites
Applicants should graduate students, postdocs, clinical scientists, clinicians/healthcare professionals or lab heads working on fungal pathogens.

How to Apply
Please click the Apply button above to begin the online application process. Places are limited and will be awarded on merit. If you have any problems with the online application process, please contact us.

Please note: Applications must be supported by a recommendation from a scientific or clinical sponsor (e.g. supervisor, line manager or head of department). A request for a supporting statement will be sent to your nominated sponsor automatically during the application process. Applicants must ensure that their sponsor provides this supporting statement by the application deadline. Applications without a supporting statement cannot be considered.

*The course fee is subsidised by Wellcome Connecting Science and applies to non-commercial applicants. Please contact us for the commercial fee.

Bursaries

Limited bursaries are available (up to 50% reduction on the course fee) and are awarded on merit. If you would like to apply for a bursary, please complete the bursary section of the online application form.

Where there are many bursary applications, the selection committee may issue smaller amounts.

Bursaries can be applied for as part of the course application form. Applicants will be notified of a bursary award along with their place on the course, usually within one month of the application deadline. The decision of the selection committee is final.

Please note that both the applicant and sponsor are required to provide a justification for the bursary as part of the application.

Additional funding opportunities
Visit our support page for additional financial support currently available.

Accommodation services phishing scam – please be vigilant. More information.

Feedback from the 2023 course:

“The people I met were fantastic and getting opinions and perspectives from others on my research was great. The organization was amazing and the amount of time on each database and technique. The amount of time set aside to get to know other people was also very helpful and I made many new friends.”

“The course exceeded my expectations in that a bigger chunk of the material covered will be useful to me in my thesis research than I initially expected. It had me thinking about new avenues to take with my research.”

“The course provided an excellent guide to accessing and using a range of tools from multiple databases, as well as facilitating meeting and meaningful interactions with the other participants and instructors.”