Wellcome Connecting Science Course Run Website
[Course Time Table 2025](coming soon)
[Course Informatics Guide](Add link here)
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
- 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.
After attending this course, participants will be able to:
- Navigate each database and answer research questions by creating custom queries across multiple bioinformatics resources.
- Utilise 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
- 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.
Course organisers
- David Roos, University of Pennsylvania, USA
- Nishadi De Silva, EMBL-EBI, UK
- Evelina Basenko, University of Liverpool, UK
Course Instructors
- Jodi Lew-Smith, Stanford University, USA
- Richard Hayes, US DOE Joint Genome Institute, USA
- Kathryn Crouch, University of Glasgow, UK
- Manuel Carbajo Martinez, EMBL-EBI, UK
- Stuart Brown, University of Pennsylvania, USA
- Louisse Mirabueno, EMBL-EBI, UK
Wellcome Connecting Science Team
- Martin Aslett, Informatics Manager
- Vaishnavi Vikas Gangadhar, Informatics Technical Officer
- Karon Chapell, Events Organiser
The course data are free to reuse and adapt with appropriate attribution. All course data in these repositories are licensed under the Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0).
Each course landing page is assigned a DOI via Zenodo, providing a stable and citable reference. These DOIs can be found on the respective course landing pages and can be included in CVs or research publications, offering a professional record of the course contributions.
Take a look at what courses are coming up at Wellcome Connecting Science Courses & Conference Website.
For more information or queries, feel free to contact us via the Wellcome Connecting Science website.
Find us on socials Wellcome Connecting Science Linktr