Section outline

  • 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)