Similar to genomics, mass spectrometry-based proteomics generates large amounts of data and thus heavily relies on bioinformatics and computational methods for data analysis and interpretation. Due to the complex nature of proteomic data, a large variety of computational, mathematical and statistical methods are necessary to generate lists of proteins for data interpretation as well as other informative visualizations.
For example, tandem mass spectra are interpreted by proteomic search engines which assign peptide sequences by either database searching (i.e. indexing and signal processing) or de novo peptide identification (i.e. graph theory and dynamic programming). The list of identified spectra subsequently requires false discovery rate (FDR) control which is commonly done by the target-decoy strategy (i.e. mathematical modeling, statistics and machine learning). Peptides are then aggregated into proteins (i.e. graph theory and bayesian statistics) and FDR controlled. These lists of identified and quantified peptides and proteins are then interpreted in light of the experimental design (i.e. modeling, statistics and data visualization). Last but not least, the final results are then made publicly available (i.e. databases).
The bioinformatics group at the Chair of Proteomics and Bioanalytics is embedded in a rich environment of biologists, biochemists, chemists and mass spectrometrists and thus provides direct access to primary data. The large variety of experiments performed at the chair requires tool, method and algorithm development in areas such as data visualization, machine learning and databases with applications ranging from basic research to clinical setups. For this, we make use of our own IT infrastructure consisting of more than 20 Windows and Linux CPU and GPU servers.
Current group members
Matthew The – Group Leader
Firas Hamood – PhD Student
Cecilia Jensen – PhD Student
Julian Müller – PhD Student
Amirhossein Sakhteman – Post-Doc
We are always looking for candidates interested in joining our bioinformatics team, please contact Matthew The for more information.
A list of open PostDoc/PhD/Scientist positions can be found here.
A list of available internship/BSc/MSc projects in bioinformatics can be found here.