What we do

The Cancer Systems Immunology lab focuses on understanding how the immune system responds to cancer. We aim to define cancer-associated immune cell states, to identify the genetic programs that drive their differentiation, to reveal how immune cells are impacted by cancer immunotherapies and what is their role in immunotherapies resistance. Our vision is that improved cancer immunotherapies will derive from innovative systems biology approaches that can exploit the vast amounts of single-cell omics data that are being generated. We develop novel computational methods, conduct meta-analyses of public data and generate hypotheses that are tested by our experimental collaborators.

Read "Fast and automated interpretation of single-cell RNA-seq data” - an interview with Santiago Carmona about his in silico talk

Find out about the Group’s activities

Main publications 2021

  • Massimo Andreatta, Fabrice P.A. David, Christian Iseli, Nicolas Guex, Santiago J.Carmona. SPICA: Swiss Portal for Immune Cell Analysis. Nucleic Acids Research (in press)
    web resource URL: https://spica.unil.ch/
  • Andreatta M and Carmona SJ. UCell: Robust and scalable single-cell gene signature scoring. Computational and Structural Biotechnology Journal, 19:3796-3798 (2021)
  • M Andreatta, JC Osorio, S Muller, R Cubas, G Coukos, SJ Carmona. Interpretation of T cell states from single-cell transcriptomics data using reference atlases
    Nature Communications (2021) 12, 2965
  • Andreatta M & Carmona SJ. STACAS: Sub-Type Anchoring Correction for Alignment in Seurat. Bioinformatics (2021)


epfl lausanne

Santiago Carmona
Cancer Systems Immunology
University of Lausanne
Group Webpage

Domain(s) of activity:

  • Systems biology
  • Data mining
  • Immunology
  • Infectious diseases
  • Machine learning
  • Oncology
  • Personalised medicine
  • Single-cell biology
  • Transcriptomics

Domain(s) of application:

  • Basic research
  • Medicine and health