What we do

In the Computational Cancer Biology Group, our aim is to study interactions between cancer and immune cells. We are focusing on molecular and cellular aspects of cancer immune cell interactions. At the molecular level, we have developed tools to predict (neo-)antigen presentation from HLA peptidomics datasets and are currently working on TCR-peptide-HLA interaction predictions. At the cellular level, we are developing novel approaches to characterizing immune infiltrations and the different states of immune cells from (single-cell) gene expression data.

All our tools are available at https://github.com/GfellerLab

Highlights 2018

  • Characterization of C-terminal extensions in HLA-I ligands
  • Peptide length distribution and multiple specificity of HLA-I molecule
  • Annotation of tumor infiltrating CD8 T cells from single-cell RNA-Seq data

Find out more about the Group’s activities

Main publications 2018

  • Guillaume P et al.
    The C-terminal extension landscape of naturally presented HLA-I ligands.
    PNAS, doi: 10.1073/pnas.1717277115
  • Gfeller D et al.
    The length distribution and multiple specificity of naturally presented HLA-I ligands.
    J Immunol, doi: 10.4049/jimmunol.1800914
  • Dib L et al.
    Polymorphic sites preferentially avoid co-evolving residues in MHC class I proteins.
    PLoS Comp Bio, doi: 10.1371/journal.pcbi.1006188

Members

epfl

David Gfeller
Computational Cancer Biology Group
University of Lausanne
Group Webpage

Domains of activity:

  • Proteins and proteomes
  • Immunology
  • Oncology
  • Protein interactions

Domains of application:

  • Basic research

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