Fungal Pathogen Genomics (Virtual)

Please note: The 2026 Fungal Pathogen Genomics course will be delivered in a virtual format.

Fungi play critical roles in ecosystems, health, and food security. Agricultural pathogens like Fusarium, Pyricularia, and Puccinia threaten crops worldwide, while medical pathogens such as Aspergillus, Candida, and Cryptococcus cause serious infections in humans and animals. Fungi also serve as valuable model organisms in research and have important applications in biotechnology, pharmaceuticals, and biofuel production.

Modern genomic technologies enable comprehensive analysis of fungal genomes, transcriptomes, proteomes, and genetic variation. These tools are essential for understanding pathogenicity, host-pathogen interactions, and identifying potential drug targets.

This course is a collaborative effort between leading fungal genomics resources:

• FungiDB/VEuPathDB
• Ensembl Fungi (EMBL-EBI)
• SGD/CGD
• MycoCosm/JGI

By the end of this course, participants will be able to:

• Navigate multiple fungal genomics databases and formulate custom queries
• Use bioinformatics tools to mine omics data effectively
• Find genes, identify orthologues, and visualise genomic data
• Perform enrichment analyses to identify biological trends
• Understand the strengths and limitations of different bioinformatics approaches
• Contribute to community genome annotation efforts
• Apply these skills directly to their own research projects

Participants will gain hands-on experience using web-based bioinformatics tools to analyse public and private datasets. The course covers:

• Navigating gene pages and genome browsers
• Finding orthologues and performing comparative genomics
• Analysing gene expression data
• Creating custom search strategies in FungiDB using omics datasets
• Predicting variant effects with Ensembl tools
• Identifying virulence genes, genetic interactions, and secondary metabolites
• Manual genome annotation using Apollo
• Performing GO and pathway enrichment analysis

Schedule

Daily Format: Approximately 4 hours of live instruction plus 1–2 hours of independent work
Dates: Monday, June 1 through Friday, June 5. The course will start in the afternoons, BST.

This course includes a homework component that must be completed prior to the workshop’s start. During the course, each day includes individual and group exercises, lectures on bioinformatics techniques, guest presentations from leading researchers, and opportunities for networking and scientific discussion. Instructors will be available for questions beyond scheduled hours.

Training Team

Evelina Basenko
University of Liverpool, UK

David Roos
University of Pennsylvania, USA

Manuel Carbajo Martinez
EMBL-EBI, UK

Jorge Batista da Rocha
EMBL-EBI, UK

Jodi Lew-Smith
Stanford University, USA

Kathryn Crouch
University of Glasgow, UK

Stuart Brown
University of Pennsylvania, USA

Richard Hayes
US DOE Joint Genome Institute, USA

Wellcome Connecting Science - Learning and Training

Alice Matimba
Head of Training and Global Capacity

Martin Aslett
Informatics Manager

Vaishnavi Vikas Gangadhar
Informatics Technical Officer

Monica Abrudan
Education Developer

Karon Chappell
Event Organiser

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

How to Apply

1. Start the application
   • Click on the “Apply” button above to start your application. Please note that places are limited and will be awarded based on merit.
2. Demonstrate the course’s relevance to your project/role
   • Our courses are highly subscribed, so it is essential to clearly show how the skills you will learn in the course will be directly applicable and beneficial to your current role/project and how do you plan to disseminate the knowledge after the course.
   • Preference will be given to applicants who are currently working on related projects or soon will be.
3. Letter of recommendation
   
   • Applications must be supported by a recommendation from a scientific or clinical sponsor (e.g., supervisor, line manager, or head of department). Ensure that your sponsor provides a tailored supporting statement by the application deadline. This statement must be uploaded as a PDF document to the registration system within your application. Applications without a supporting statement will not be considered.
4. Need help?
   • If you encounter any problems with the online application process, please contact us at courses@wellcomeconnectingscience.org for assistance.

Application deadline: 16 March 2026

*The course fee is subsidised by Wellcome Connecting Science. Contact us at courses@wellcomeconnectingscience.org for the commercial rate.

The fee will be requested once acceptance is confirmed.

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, explaining why you would benefit from funding.

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.

Deadline: 16 March 2026

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

Feedback from 2025 course:

“I was very impressed with both the structure and content of the course.”

“I was expecting an intensive course where most of the available tools would be explained to us, and that’s exactly what it was, with clear examples of how to apply them in our day-to-day work”

“Extremely helpful in providing guidance to various web sources and to demonstrate the possibilities”