Carmona Lab members

Research interest 

My current research focus is on the development of computational methods for single-cell biology. We are constructing high-resolution maps for several immune cell types, and analytical tools to study the transcriptomic and epigenetic phenotype of immune cells in cancer and infection.

Background

After obtaining my PhD from the Technical University of Denmark with Pr Ole Lund, I worked in Pr Stephen Smale’s lab at the City University of Hong Kong and did a postdoc with Pr Morten Nielsen at UNSAM in Argentina. Throughout my research experience, I contributed to the development of bioinformatics tools for peptide-MHC binding prediction (NetMHC, NNAlign), immunopeptidome characterization (GibbsCluster, MS-Rescue), to the toolkit of the Immune Epitope Database (IEDB), and more recently in single-cell data analysis (STACAS, UCell, ProjecTILs). I joined the Carmona Lab in October 2019.  

Research interest 

I joined the Carmona lab in April 2022 to further our current understanding of T cell phenotypes in the context of cancer and infections. My postdoctoral work focuses on immune cell single-cell data integration, annotation, and mapping. My interest lies in understanding how to best construct and leverage such single-cell references. Ultimately, the ambition is to use these well-curated maps to understand immune cells in a wide range of contexts. Thanks to ongoing collaborations, we will focus on tumor-specific CD4+ T cell function and T cell metabolism in cancer.

Background

I have a PhD in immunology from l'Institut Curie in Paris where I tackled immune-related questions using bioinformatics, especially using scRNA-seq and scTCR-seq data. During this time, I focused mainly on CD8+ T cell differentiation paths when these cells infiltrate tumors. I defended my PhD in March 2021 and then took up a position as research engineer at Mnemo Therapeutics, working on epigenetically modified CAR-T cells, until March 2022. 

Research interest 

My current interest is to use omics methods to advance basic understanding of human disease, especially cancer, improving diagnostic capabilities for doctors and finally resulting in better treatment for patients. This could be strongly leveraged by exploiting the already existing and exponentially growing amount of data. Combining these would allow for deeper and statistically more significant and unbiased system-wide insights into the pan-cancer landscape across patients and cohorts. However, currently there is an unmet need for simplified and standardized data analysis workflows prohibiting such large-scale meta-analyses which have proven invaluable in other fields. This is the basic foundation that needs to be established to understand complex biological entities in health and disease in a wholistic system-wide approach in the future.

Background

During my MSc at ETH Zurich in molecular health sciences I worked as a bioinformatician in the proteomics group of Ruedi Aebersold. In the course of a multi-omics study, the characterization of the mitochondrial proteome across different organs and diverse mouse genetic reference strains helped to better understand the links between genotype, phenotype and metabotype, for example in obesity and diabetes (Williams and Wu et al. Mol Cell Proteomics, 2018). Further projects included a molecular cell biology study on tendon fibrosis at the Snedeker group at ETHZ/Uniklinik Balgrist and a proteomics project at Biozentrum Basel, investigating nucleo-cytoplasmic transport. After that I worked at Solvias AG, a biopharmaceutical CRO, as an R&D scientist and head bioinformatician in the Large Molecule Bio-MS division, working mainly on anti-cancer drugs, before joining the Carmona Lab as a PhD student in 2022.