Fungal Pathogen Genomics
Date: 2 - 7 June 2024
Timezone: London
Duration: 6 days
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.
Keywords: fungal, fungi, pathogen genomics, Bioinformatic databases, Bioinformatic analysis, RNAseq, transcriptomics, SNPs, Genomics, mycology, FungiDB, JGI MycoCosm, Ensembl, Candida genome database, Saccharomyces genome database
City: HInxton
Prerequisites:
none
Learning objectives:
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.
Organizer: Wellcome Connecting Science
Eligibility:
- By invitation
Target audience: This course is aimed at graduate students, postdocs, clinical scientists, clinicians/healthcare professionals or lab heads working on fungal pathogens.
Event types:
- Workshops and courses
Activity log
