Carmona lab

Working at the crossroads of data science, single-cell multi-omics, and cancer immunology, our lab develops and applies computational methods to understand how our immune system responds to cancer and to identify new therapeutic targets and biomarkers. Our group is part of the Department of Oncology and the Ludwig Institute for Cancer Research of the University of Lausanne, and affiliated to the Swiss Institute of Bioinformatics. ...

Research projects

Innovative bioinformatics tools for single-cell data science

Recent advances in single-cell sequencing technologies have opened a unique opportunity to explore biological systems at a resolution and scale that seemed inconceivable only ten years ago. However, interpretation of the vast and complex data generated by these technologies remains a major challenge in the field. Our team develops open-source computational tools tackling some key challenges in single-cell data science. These include reference-based approaches to interpret single-cell omics data, data integration, gene signature scoring, cell type purification and web resources for single-cell data analysis (

Dissecting the tumor immune microenvironment by single-cell omics data mining

We mine single-cell omics data to dissect the diversity of immune cells in the tumor microenvironment. Our approach is based on the use of “reference atlases” which summarize current knowledge of immune cell diversity, and serve as stable, curated systems of coordinates for the interpretation of unknown data, such as from a cancer patient biopsy (Interpretation of T cell states from single-cell transcriptomics data using reference atlases | Nature Communications). We conduct large-scale meta-analysis of single-cell omics data to investigate how the immunological status of a patient, at the single-cell level, relates to its likelihood to respond to a specific therapy. 

A meta-analysis of T-cell states in cancer and infection

Single-cell omics data including transcriptome, chromatin accessibility, T cell receptor and antigen specificity allows exploring the interplay between transcriptional and epigenetic programs, T cell affinity and clonotype. The aim of this project is to exploit single-cell multi-omics data from multiple timepoints and tissues to reconstruct T cell differentiation pathways in cancer and infection models. In collaboration with our experimental partners, we use CRISPR-based screenings to study the effect of targeting gene regulators on reprogramming T cell fate in vivo


Santiago Carmona

PhD SNF Ambizione Fellow, Group Leader, Cancer systems immunology, SIB, Department of Oncology UNIL & CHUV CarmonaLab

Other members

Massimo Andreatta

Postdoctoral Fellow, SIB, UNIL & CHUV

Paul Gueguen

Postodoctoral Fellow, SIB, UNIL & CHUV

Selected Publications

scGate: marker-based purification of cell types from heterogeneous single-cell RNA-seq datasets.

Andreatta M, Berenstein AJ, Carmona SJ

Bioinformatics (Oxford, England) – 2022 Mar 8

SPICA: Swiss portal for immune cell analysis.

Andreatta M, David FPA, Iseli C, Guex N, Carmona SJ

Nucleic acids research – 2022 Jan 7

A single-cell reference atlas delineates CD4+ T cell subtype-specific adaptation during acute and chronic viral infections

Massimo Andreatta, Zachary Sherman, Ariel Tjitropranoto, (...), Michael C. Kelly, View ORCID ProfileThomas Ciucci, View ORCID ProfileSantiago J. Carmona

Biorxiv – 2021 September 20

UCell: Robust and scalable single-cell gene signature scoring.

Andreatta M, Carmona SJ

Computational and structural biotechnology journal – 2021 Jun 30

Interpretation of T cell states from single-cell transcriptomics data using reference atlases.

Andreatta M, Corria-Osorio J, Müller S, (...), Cubas R, Coukos G, Carmona SJ

Nature communications – 2021 May 20

STACAS: Sub-Type Anchor Correction for Alignment in Seurat to integrate single-cell RNA-seq data.

Andreatta M, Carmona SJ

Bioinformatics (Oxford, England) – 2021 May 5

Enhanced Phenotype Definition for Precision Isolation of Precursor Exhausted Tumor-Infiltrating CD8 T Cells.

Martinez-Usatorre A, Carmona SJ, Godfroid C, (...), Yacoub Maroun C, Labiano S, Romero P

Frontiers in immunology – 2020 Feb 27

MicroRNA-155 Expression Is Enhanced by T-cell Receptor Stimulation Strength and Correlates with Improved Tumor Control in Melanoma.

Martinez-Usatorre A, Sempere LF, Carmona SJ, (...), Zehn D, Jandus C, Romero P

Cancer immunology research – 2019 May 1

Intratumoral Tcf1+PD-1+CD8+ T Cells with Stem-like Properties Promote Tumor Control in Response to Vaccination and Checkpoint Blockade Immunotherapy.

Siddiqui I, Schaeuble K, Chennupati V, (...), Luther SA, Speiser DE, Held W

Immunity – 2019 Jan 8

Single-cell transcriptome analysis of fish immune cells provides insight into the evolution of vertebrate immune cell types.

Carmona SJ, Teichmann SA, Ferreira L, (...), Stubbington MJ, Cvejic A, Gfeller D

Genome research – 2017 Jan 13

Towards High-throughput Immunomics for Infectious Diseases: Use of Next-generation Peptide Microarrays for Rapid Discovery and Mapping of Antigenic Determinants.

Carmona SJ, Nielsen M, Schafer-Nielsen C, (...), Campetella O, Buscaglia CA, Agüero F

Molecular & cellular proteomics : MCP – 2015 Apr 28