Fungal Pathogen Genomics

The kingdom of Fungi includes a biologically diverse group of organisms
adapted to a wide range of environments. While numerous fungal species
are a food source and/or natural recyclers of plant biomass others are
targets of industrial, agricultural, and biomedical research due to their
important roles in biofuel production and pathogenesis. Many fungal plant
pathogens including but not limited to Fusarium, Magnaporthe,
Ustilago, and Zymoseptoria species threaten agricultural
ecosystems and food security worldwide. 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
arounds the world.

Advancements in high throughput ‘omics’ data generation technologies
enable researchers to carry out high- 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 resources have been developed. As
the complexity of the integrated data increases, so do the resources!

• FungiDB
• Ensembl/PhytoPathDB
• PHI-Base
• PomBase
• SGD/CGD
• MycoCosm
• JGI

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

Daily activities at the workshop will include individual
and group
hands-on training exercises, supplementary lectures on
bioinformatic
techniques and tools used by various databases, and
presentations by
distinguished guest speakers. For example, you will learn how to:

• perform RNA-seq and SNP analysis and
  visualization via EuPathDB Galaxy workspace in FungiDB
• find secondary
  metabolite clusters in MycoCosm
• find virulence genes and annotation in
  Ensembl/PhytoPathDB/PHI-Base
• access genetic interactions in CGD/SGD.

Feedback from the 2017 course

“Excellent course.”
“You have done an exellent job, keep on going.”
“This was really a great course. I hope more people have the change to do
it. I think the supervisors of the course were highly motivated, prepared
to discuss all different aspects, and were able to answer all different
questions that we asked. The contribution of them made the course really
valuable. Thank you very much!”
“would like to congratulate the organizers of the course for their great
work.”

The programme will include lectures, discussions and practical,
computer-based sessions covering the following topics:

• Comparative genomics and browsers: Gbrowse, Jbrowse, ACT, Artemis, Ensembl
• Use of Web Apollo annotation tools for fungal genomes
• Web-based resources for fungal genomic data including: FungiDB, Ensembl/PhytoPathDB, PHI-Base, PomBase, SGD/CGD, MycoCosm, JGI, etc.
• Identification of orthologs, and orthology-based inference (using OrthoMCL, Compara, etc.)
• Analysis of genome annotation (using Companion)
• RNA sequence analysis and visualization
• Next generation sequence analysis, including variant calling
• Developing advanced biologically relevant queries, using FungiDB ‘search strategies’
• Best
  practices using ontologies to generate hypotheses and analyse data
  (ontology structure, evidence, available tools, slimming and enrichment,
  etc.)

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, and transcriptomics data and NGS analysis results from EuPathDB Galaxy in a genome browser, export and share analysis results, and more).
• Contribute to community annotation and curatorial efforts
• Understand the advantages and limitations of the tools used

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.

Lead Instructors
David
Roos University of Pennsylvania, USA
Paul
Kersey EMBL-EBI, UK
Omar
Harb University of Pennsylvania, USA
Evelina
Basenko University of Liverpool, UK

Guest Speakers
Elaine Bignell The University of Manchester,
UK
Regine Kahmann Max Planck Institute for Terrestrial Microbiology,
Germany
Tammi Camila Vesth Technical University of Denmark

Prerequisites
The course is aimed at graduate students, postdocs, clinicians and lab
heads working on fungal organisms.

Applications
Applications can be submitted online. 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 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.

Deadlines
Deadline for Applications: Closed

Travel visas (delete for overseas courses)
Please contact the
event organiser if you require a letter to support a travel visa
application. Note that letters will be provided to confirmed attendees.

Non-European Economic Area or Swiss nationals may be required to have a
visa to enter the UK.
Early application is strongly advised, as this process can take 6-8 weeks
or longer.

Please visit the following websites for further information:
UK Border Agency website and information for general visitors and business
visitors.

Cost
The course is subsidised by the Wellcome Genome Campus Advanced Courses
and Scientific Conferences Programme. This is a residential course and
the fee is £625, including all accommodation and meals.
This subsidised fee is available to all non-commercial applicants. Please
contact us
for the commercial fee.

Bursaries
Advanced Courses are subsidised for non-commercial
applicants from anywhere in the world. Additional, limited bursaries are
available (up to a 50% reduction of 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.

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 Funding webpage for additional funding opportunities currently
available.

Bursary terms and conditions

UK Courses (held at the Wellcome Genome Campus, Hinxton,
Cambridge)
A
limited number of bursaries are available for each course. These are
awarded by the selection committee according to merit. The bursary
covers a maximum of 50% of the course fee, though in exceptional
circumstances an application for the total course fee may be considered.
Where there are many bursary applications, the selection committee may
issue smaller amounts. We cannot assist with travel costs to attend UK
courses.