Section outline

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    Proteogenomics and Immunopeptidomics


    29 November - 1 December 2017

    University of Lausanne, Genopode building, room 2020

    This page is addressed to registered participants. To access the course description and the application form, please click here.

    For any assistance, please contact training@sib.swiss.

  • Schedule

    29 November

    09:00 - 10:00
    A short introduction to proteomics techniques and workflows (Dr. Manfredo Quadroni, Head Protein Analysis Facility, UNIL
    10:00 - 11:00
    Introduction to computational proteomics and proteogenomics (Dr. Markus Mueller, Vital-IT, SIB Swiss Institute of Bioinformatics)
    11:00 - 11:30
    Coffee break
    11:30 - 12:30
    Variant discovery by deep sequencing (Dr. Sylvain Pradervand, Head Bioinformatics Unit, Genomic Technologies Faculty, UNIL)
    14:00 - 15:30
    A novel, integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomics (Dr. Christian Ahrens, head Bioinformatics and Proteogenomics group, Agroscope / SIB Swiss Institute of Bioinformatics)
    15:30 - 16:00
    Coffee break
    16:00 - 17:00
    (Christian Ahrens)
       

    30 November

    09:00 - 10:30
    Introduction to the MaxQuant software (Prof. Jürgen Cox, group leader Computational Systems Biochemistry, Max Planck Institute of Biochemistry)
    10:30 - 11:00
    Coffee break
    11:00 - 12:30
    Introduction to the Perseus software (Prof. Jürgen Cox)
    14:00 - 15:30
    Hands-on exercises (Prof. Jürgen Cox)
    15:30 - 16:00
    Coffee break
    16:00 - 17:00
    Hands-on exercises (Prof. Jürgen Cox)

    1 December

    09:00 - 10:00
    Putting variant information in context: the UniProtKB/Swiss-Prot reference and other resources (Dr. Lionel Breuza, Swiss-Prot group, SIB Swiss Institute of Bioinformatics)
    10:00 - 10:30
    Coffee break
    10:30 - 12:00
    MS-based immunopeptidomics - Accelerating the development of personalized cancer immunotherapy (Dr. Michal Bassani, group leader Human integrated tumor immunology discovery engine (Hi-TIDe), Department of Oncology, University Hospital of Lausanne)
    14:00 - 15:00
    Deciphering HLA-I motifs across HLA peptidomes (Prof. David Gfeller, group leader Computational Cancer Biology Group, SIB Swiss Institute of Bioinformatics / Ludwig Centre for Cancer Research of the University of Lausanne)
    15:00 - 16:00
    De novo peptide sequencing (Dr. Roman Mylonas, Protein Analysis Facility, UNIL / Vital-IT, SIB Swiss Institute of Bioinformatics)

  • Prerequisites & course Material

    Knowledge / skills:
    Basic knowledge of immunology (HLA, T-cell, etc) and basic computer skills (program install, but no programming) are required. Previous experience in proteomics is a plus.

    Material / software:

    • Participants should bring their own laptop with a Wifi connection.
    • PEAK and MaxQuant software installation (compatible with Windows only)
    • other install
    Course material