Fungal Pathogen Genomics

Numerous fungal species are important pathogens, affecting humans both
directly (e.g. Aspergillus, Candida, Cryptococcus, Histoplasma,
Pneumocystis) and indirectly through crop destruction (e.g.
Fusarium, Magneporthe, Ustilago). The increasing availability and
decreasing cost of sequencing technologies and other omics-scale
approaches have made hundreds (and soon thousands) of fungal genomes and
functional genomics datasets available for analysis. These resources will
play a pivotal role in addressing and mitigating the heavy disease burden
of fungal pathogens.

This exciting new week-long course aims to provide experimental
biologists working on fungal organisms with hands-on experience in
genomic-scale data analysis; including genome browsers and comparison
tools, data mining using resources such as FungiDB, Ensembl/PhytoPathDB, PomBase, SGD/CGD, MycoCosm,
analysis of genome annotation, and next generation sequence analysis and
visualization (including RNA sequence analysis and variant calling). An
important aim is that the participants should
understand the origin of
data available in public resources and how to
analyse it in conjunction
with their own.

The course is taught as a collaborative effort between available fungal
informatics resources. The majority of this intensive course will be
based on hands-on exercises, supplemented by lectures on genomics and
bioinformatics techniques and keynote presentations by distinguished
guest speakers.

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

• Interrogate large-scale genomic and functional genomic databases to answer biologically-related research questions and develop testable hypotheses
• Use software and web-based services to browse genomes, visualize next generation data and display genome comparisons
• Contribute to community annotation and curation efforts
• Use ontologies in analysis, and be aware of problems and pitfalls

The programme will include lecture 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, PomBase, SGD/CGD, MycoCosm, 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)

The programme will also feature keynote research seminars by distiguished
guest speakers.

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

• Interrogate
  large-scale genomic and functional genomic databases to answer
  biologically-related research questions and develop testable hypotheses
• Use software and web-based services to browse genomes, visualize next generation data and display genome comparisons
• Contribute to community annotation and curation efforts
• Use ontologies in analysis, and be aware of problems and pitfalls

Lead Instructors
Omar
Harb University of Pennsylvania, USA
Christiane
Hertz-Fowler University of Liverpool, UK
Paul
Kersey EMBL-EBI, UK
David
Roos University of
Pennsylvania, USA

The programme will also feature keynote seminars by distiguished guest
speakers (TBA shortly).

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

Cost
The
course is subsidised by the Wellcome Genome Campus Advanced Courses
and Scientific Conferences Programme. This is a residential
course and
there is a fee of £610 towards board and lodging for
non-commercial applicants. Please contact us for the commercial fee.

Additional limited bursaries are available (up to 50%
of the course fee)
and are awarded on merit. Please see the “Bursaries”
tab for details.

Applications
Applications for this course can be completed online. 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
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
there is a fee of £610 towards board and lodging for
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 50% 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.

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.

Overseas Courses (held outside of the UK)
A
limited number of bursaries are available for each course. These are
awarded on merit to cover travel, accommodation and sustenance. The
maximum award for travel (economy class) will be £750.

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.