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Research Projects

The dark interactome – methods for discovering novel protein-nucleic acid interactions from complex samples

[call for this position closed]

Supervision

Timo Sachsenberg
EKUT, 1st Supervisor

Sven Degroeve
VIB, 2nd Supervisor

Objectives

Development of Algorithms and tools for statistical valid identification and quantification of protein-nucleic acid cross-links with a focus on novel cross-linking strategies and protocols. Visualization of cross-linking results in a graphical user interface (GUI).

Methodology

Development will be performed as part of OpenMS the major C++ open-source framework for computational proteomics. Improved algorithms will be wrapped in C# to provide them as Proteome Discoverer nodes.

Required skills

Good software engineering skills. Ideally knowledge of the C++ and C# programming language.
Git-based version control system. If available, please provide a link to e.g. your GitHub account and/or link to past projects in your application.
Ideally, a background in machine learning.
Ideally, knowledge of (computational) mass spectrometry.
Strong command of English.

Expected Results

Validated algorithms and user-friendly user interfaces for the large-scale analysis of cross-linking data for RNA and DNA with proteins and the application to biologically relevant data sets.

Planned Secondments

Host: THERMO (B. Delanghe), Duration: 1 Month; When: Year 2; Goal: Practical programming and translation to industry.

Host: VIB (S. Degroeve), Duration: 1 Month; When: Year 2; Goal: Learn modifications open-search algorithms.

Enrolment in doctoral programs

Ph.D. from the Faculty of Mathematics and Science at Eberhard Karls Universität Tübingen.

References

1. Kramer, K., Sachsenberg, T., Beckmann, B. M., Qamar, S., Boon, K.-L., Hentze, M. W., Kohlbacher, O., & Urlaub, H. (2014). Photo-cross-linking and high-resolution mass spectrometry for assignment of RNA-binding sites in RNA-binding proteins. Nature Methods, 11(10), 1064–1070. https://doi.org/10.1038/nmeth.3092

2. Stützer, A., Welp, L. M., Raabe, M., Sachsenberg, T., Kappert, C., Wulf, A., Lau, A. M., David, S.-S., Chernev, A., Kramer, K., Politis, A., Kohlbacher, O., Fischle, W., & Urlaub, H. (2020). Analysis of protein-DNA interactions in chromatin by UV induced cross-linking and mass spectrometry. Nature Communications, 11(1), 1–12. https://doi.org/10.1038/s41467-020-19047-7