Aebersold lab, Proteomics, Computational mass spectrometry and Immunology
Two bioinformatics projects available
The collection of peptides presented to the cell surface by class I and class II major histocompatibility complex (MHC) molecules are referred to as the immunopeptidome and are of great importance for basic and translational science. For basic science, the comprehensive analysis of the immunopeptidome is a critical component for understanding the immune system; for translational science, exact knowledge of the immunopeptidome can directly fuel and guide the development of next-generation vaccines and immunotherapies against autoimmunity, infectious diseases and cancers (1).
We are looking for two highly motivated and focussed MSc students with skills in bioinformatics. A strong background in programming skills (R, Python and similar) is required.
The first 6-month project aims at automating a computational workflow for the analysis of immunopeptidomic data generated by mass spectrometry. The workflow will be useful to organize large immunopeptidomic datasets generated by the community, as well as for the analysis of SWATH MS data.
The second 6-month project aims at analyzing a tissue-based map of the mouse immunopeptidome. Integration of multiple –omic datasets will be the main task in this project.
Both MSc students are expected to show a high level of independence. The work will be published in a scientific journal and the students will be involved in writing the manuscript.
Please send your C.V. and a motivation letter to Dr. Etienne Caron
Reference:
1. Gubin MM, Zhang X, Schuster H, Caron E, Noguchi T, Ward JP, Ivanova Y, Hundal J, Arthur CD, Krebber WJ, Mulder GE, Vesely MD, Lam SSK, Korman AJ, Allison JP, Freeman GJ, Sharpe AH, Pearce EL, Aebersold R, Rammensee HG, Melief CJM, Mardis ER, Gillanders WE, Artyomov MN, Schreiber RD. Checkpoint blockade cancer immunotherapy targets tumour-specific mutant antigens. Nature. 2014, 515:577-581.