Bassani-Sternberg Lab members

Bioinformatician CONTACT ME

Research interest

Background

Bioinformatician CONTACT ME

Research interest

I focus my work on the identification of clinically relevant cancer specific Human Leukocyte Antigen (HLA) ligands that will guide the development of personalized cancer immunotherapy.In this regard, I am developing pipelines and tools for the analysis of next-generation sequencing (WGS, WES and RNAseq) and proteomics (MS/MS) data analysis.

Background

I obtained my Master’s in Molecular and Structural Biology (focusing on cancer research) at the University of Geneva. Passionate about biology and informatics, I decided to combine both. I initiated my bioinformatics skills at Vital-IT (Swiss Institute of Bioinformatics) where I worked on diverse projects ranging from next-generation sequencing to data visualization. 

Laboratory technician CONTACT ME

Research interest

The immunopeptidomics laboratory is involved in the development of personalized cancer immunotherapy through the detection by mass spectrometry of naturally HLA presented epitopes and by the prediction and the prioritization of mutated antigens. I have the great opportunity to contribute everyday to the conduct of clinical trials applying this innovating therapeutic strategy by being involved in the sample processing of patients included in those studies and coordinating the clinical activities of our group.

Background

I obtained my Master’s in Biomedical Sciences at the Université Libre de Bruxelles in 2010. My master's thesis was on the re-expression of the NIS transporter for the treatment of dedifferentitated thyroid cancers. Following my studies, I worked three years as a biologist then project coordinator in a Belgian company focused on the development of cellular therapies for bone diseases. After some experience in the quality fields, I had the pleasure of returning to the research environment by joining the Hi-TIDe in 2016.

Research associate CONTACT ME

Research interest

My field of expertise is computational analysis of mass spectrometry data and machine learning. In my research within the Hi-TIDe, I use statistical and machine learning methods to improve the identification and prioritization of cancer specific antigens and neoantigens. This research includes several aspects: first we try to increase the breadth of potential antigens by searching large proteogenomics databases containing non-canonical sequences, which requires statistical methods for stratified error control and improved MS/MS-peptide matching. Second, we mine large datasets of HLA binding peptides in order to find patterns of HLA presentation that are complementary to binding affinity and mRNA expression. We then use these patterns and other features to train machine learning algorithms on datasets that provide immunogenicity measurements of antigens in various cancer tissues in order to improve the antigen ranking for cancer immunotherapy.

Background

I studied theoretical physics at ETHZ. After 2 years of research, I went to industry where I worked as a software engineer. Back in academia, I did a PhD in Bioinformatics at the University of Geneva and then worked in several research positions at the University of Geneva, ETHZ and SIB Swiss Institute of Bioinformatics (SIB). I currently work 80% as a Senior scientist within the Hi-TIDe, and 20% as Principal scientist at Vital-IT, SIB. 

Research associate CONTACT ME

Research interest 

My main interest is the analysis of HLA peptides by Liquid Chromatography hyphenated to mass spectrometry (LC-MS) using multiomics approaches (immunopeptidomics, proteomics and bioinformatics). I am also interested in R&D of LC-MS methods: optimization/improvement of existing methods and implementation of new methods.

Background 

After my Degree in Proteomics and Bioinformatics, I worked as Research assistant at the University of Geneva's Proteomics core facility. There, I obtained my PhD in Pharmaceutical Sciences and developed and implemented data-independent ion sampling methods and an algorithm to process such a data. I am currently working as Research supervisor in LC-MS within the Hi-TIDe.

PhD student CONTACT ME

Background

Before joining Lausanne, I obtained a Bachelor's and a Master's in Biomedicine from the University of Zurich (UZH). For my master's thesis, I spent a year in the lab of Pr Thomas Krämer in the Department of forensic pharmacology and toxicology, developing analytical methods for the pharmacokinetic profiling of small molecules  in mouse section by means of MALDI-MSI and LC-MS. After graduating from UZH, I had the chance to work in industry for a year, focusing on MS-based proteomics, immunopeptidomics, and method development. Following my time in industry, I started my PhD studies by joining the Hi-TIDe in September 2021.

Senior bioinformatician (SIB) CONTACT ME

Research interest 

I create computational pipelines to analyse data produced by my colleagues in the lab. One example is the prediction of somatic mutations in patient tumors, an essential part in the development of personalized immunotherapy. Pipeline construction involves identifying useful programmatic tools that are available in the academic environment, and then writing computer code to glue them together into productive workflows. If no tools are available for the task in hand, I write customized code to analyse research data. High-throughput data analysis has become an key part of modern genome-wide "omics" techniques, including NGS exome and RNAseq. 

Background 

I studied undergraduate biochemistry at the University of Glasgow and obtained a PhD in Molecular Genetics from the University of Lausanne in 1987, working at the ISREC in Epalinges. After postdoctoral research on signal transduction and cell biology in the yeast Saccharomyces cerevisiae at the University of Oregon, I joined Novartis AG as a bioinformatics specialist. Continuing in bioinformatics, I returned to academia in 1999 as part of the recently created OIT group of the Ludwig Institute for Cancer Research in Lausanne (LICR), and was subsequently appointed Associate investigator in the LICR Computational Genomics Group. I joined the Swiss Institute of Bioinformatics (SIB) Vital-IT group as a Senior scientist in 2011, and have been working within the Coukos research environment since 2012, collaborating with the Hi-TIDe since 2016, becoming an integrated lab member in 2019.

Technician CONTACT ME

Research interest 

Passionate about immunology and oncology, I joined the Hi-TIDe in 2021, as a technician. I have the great opportunity to work on clinical trials including the development of personalized cancer immunotherapy through the detection by mass spectrometry of HLA binding peptides and the prediction of mutated antigens.

Background 

I obtained my Master’s in Biology at the Université de Bourgogne (France) in 2020.

Bioinformatician CONTACT ME

Research interest

Background

PhD student CONTACT ME

Research interest

Background