Fungal Pathogen Genomics (Virtual)

Please note: Due to the ongoing Covid-19 pandemic, the 2021 Fungal Pathogen Genomics course will be delivered in a virtual format.

The kingdom of Fungi includes a biologically diverse group of organisms adapted to diverse environmental niches, playing important roles in ecosystems and human/animal/plant health. Fusarium , Magnaporthe , Ustilago , Puccinia , and Zymoseptoria species threaten agricultural ecosystems and food security worldwide, while Aspergillus , Candida , Coccidioides , Cryptococcus , Histoplasma , Pneumocystis , Batrachochytrium and other human and animal fungal pathogens cause allergies, serious illnesses, and sometimes life-threatening infections that are of great concern for veterinary and medical professionals around the world.

Furthermore, fungi are also important model systems for basic and applied research and workhorses in biotechnology, food, pharmaceutical, and biofuel industries.

Advancements in high throughput ‘omics’ data generation technologies enable researchers to carry out large-scale analyses to investigate genomes, transcriptomes, proteomes, and metabolomes of numerous fungal organisms to address questions about pathogenicity, host-pathogen interactions, and identify new drug targets. To facilitate accessibility and analysis, a number of online fungal bioinformatic resources have been developed.

This week-long course is a collaborative teaching effort between the following web-based fungal data mining resources:

● FungiDB/VEuPathDB
● EnsemblFungi
● SGD/CGD
● MycoCosm/JGI

The Fungal Pathogen Genomics course provides hands-on training on how to take advantage of unique tools offered by each database; develop testable hypotheses, and investigate transcriptomics, proteomics and genomics datasets across multiple databases and different user interfaces.

Daily activities will include individual and group training exercises, supplementary lectures on bioinformatics techniques and tools used by various databases, and presentations by distinguished guest speakers.

For our virtual courses, we use video conferencing (Zoom) and instant messaging (Slack) applications along with other online and virtual machine (VM) teaching resources to deliver the different elements of the course as interactively as possible.

The course will run approximately 11:00-19:00 (BST) daily. Some teaching materials may be pre-recorded but participants must be available to attend live, interactive sessions online between these times.

The programme will include virtual lectures, discussions and hands-on, interactive sessions covering the following topics:

• Comparative genomics, gene trees, whole-genome alignment
• Identification of orthologs and orthology-based inference
• Genome browsers and gene pages
• RNA-Seq analysis and visualization in VEuPathDB Galaxy
• Variant calling analysis and Ensembl Variant Effect Predictor (VEP) tool
• Development of advanced biologically relevant queries using FungiDB ‘search strategies’ and mining integrated datasets (proteomics, transcriptomics, phenotypes, etc.)
• Genetic interactions, virulence genes, secondary metabolites
• Overview of ontology structure, evidence, available tools, slimming and enrichment
• Introduction to annotation and curation of fungal genomes (e.g. Apollo in EnsemblFungi, FungiDB, and MycoCosm/JGI)

What’s not covered:
This course provides intensive training in web-based fungal resources using public datasets. The course does not include training in command-line data manipulation or analysis.

Learning outcomes
After attending this course, participants should be able to:

• Navigate effectively within each database and answer biologically-related research questions by creating custom queries across multiple fungal resources
• Use built-in web-based bioinformatics tools to mine data (e.g. find DNA motifs using regular expressions, identify orthologs in other species via orthologous transformations, determine trends via GO and metabolic pathways enrichment analysis, visualize genomics, proteomics, transcriptomics data and NGS (RNA-Seq and variant calling) analysis results, export and share analysis results, and more
• Contribute to community annotation and curatorial efforts
• Understand the advantages and limitations of the tools used

Course instructors

David Roos
University of Pennsylvania, USA

Nishadi De Silva
EMBL-EBI, UK

Omar Harb
University of Pennsylvania, USA

Evelina Basenko
University of Liverpool, UK

Marek Skrzypek
Stanford University, USA

Kathryn Crouch
University of Glasgow, UK

Michal Szpak
EMBL-EBI, UK

Stephen Mondo
University of California, USA

Guest speakers

Lynne Boddy
Cardiff University, UK

Jo Dicks
Quadram Institute, UK

Johanna Rhodes
Imperial College London, UK

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

Please note that due to the virtual format for this course, participants will require minimum computer specifications and internet access to fully benefit. A guide to these requirements can be found here (PDF).

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 Genome Campus Advanced Courses and Scientific Conferences 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.

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Feedback from the 2019 course:

“Thank you for offering this course. I greatly appreciate the time spent organizing and coordinating the activities and people. The experience was invaluable to me and I am grateful for the opportunity to participate.”

“It was a great learning experience. The interactions with other participants and tutors were very fruitful. I really felt I would particularly like to mention that the instructors were always willing to attend to our queries.”

“Would highly recommend this course! Instructors are lovely and highly approachable, very willing to help and explain any queries. I am genuinely happy to be selected for this course and have learnt a great deal about data mining. Coursemates are an excellent mix of students, PIs, and other professionals. Thank you, instructors!”

“Thank you for a fantastic course!”

“Thank you for offering this great course! These databases are important resources that many researchers could benefit from learning to use. I particularly appreciated the instructors’ enthusiasm and openness to discussion. It was obvious that they worked very hard to prepare the exercises and facilitate participants’ understanding of the material.”

“Its a very engaging, brilliant course on Fungal Pathogen Genomics. I learnt a couple of existing tools and how easily one can use it for analysis of Fungal models. The instructors are always there to help and also give a free hand to try your own datasets. A highly recommended course if you would like to learn more about Fungal Pathogens.”