Hands-on training in web-based data-mining resources for fungal genomes
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
- David Roos, University of Pennsylvania, USA
- Nishadi De Silva, EMBL-EBI, UK
- Evelina Basenko, University of Liverpool, UK
- David Roos, University of Pennsylvania, USA
- Nishadi De Silva, EMBL-EBI, UK
- Evelina Basenko, University of Liverpool, UK
- Jodi Lew-Smith, Stanford University, USA
- Steven Ahrendt, US DOE Joint Genome Institute, USA
- Kathryn Crouch, University of Glasgow, UK
- Nishadi De Silva, EMBL-EBI, UK
- Manuel Carbajo Martinez, EMBL-EBI, UK
- Stuart Brown, University of Pennsylvania, USA
- Louisse Mirabueno, EMBL-EBI, UK
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Any reuse of the course materials, data or code is encouraged with due acknowledgement.
This work is licensed under a Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0).
