This course type is computational

Fungal Pathogen Genomics

13 - 18 May 2018Wellcome Genome Campus, Hinxton, UK
Deadlines (at 23:59 UTC):
  • Application Deadline Closed

  • Summary

    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!

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

    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.”

  • Programme

    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
    .

  • Instructors / Speakers

    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

  • How to Apply

    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 / Bursaries

    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.