NewThis course type is computational

Fungal Pathogen Genomics

11 - 16 May 2017Wellcome Genome Campus, Hinxton, UK
Deadlines (at 23:59 UTC):
  • Application Deadline Closed

  • Summary

    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
  • Programme

    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
  • Instructors / Speakers

    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).

  • How to Apply

    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 / Bursaries

    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.