supervised by Prof. Kohlbacher and Dr. Timo Sachsenberg – starting ASAP.

This PhD position will be part of PROTrEIN (www.protrein.eu), a European Innovative Training Network (ITN) composed of 11 beneficiaries, and 6 partner organizations, from the academic and non-academic sectors (including two SMEs and two large companies).

The ITN’s mission is to train a new generation of computational proteomics researchers by providing them an inter-sectoral and interdisciplinary set of skills to tackle the main challenges in the field and improve their future employability.

Important: The mobility criteria of the ITN states that PhD-students must not have resided or carried out their main activity (work, studies, etc.) in Germany for more than 12 months in the 3 years immediately before the recruitment date.

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

As part of this PhD, you will learn the ins and outs of computational proteomics, improve algorithms, and develop machine learning methods for identification and quantification of protein-nucleic acid cross-links. In two secondments you will collaborate with an industry partner (Thermo Fisher Scientific) and experts in the field of machine learning (Ghent University).

Expected Results: Improved algorithms for identification and quantification of cross-links. A user-friendly interface for large-scale analysis of cross-linking data in collaboration with Thermo Scientific. Application of developed methods to biologically relevant data sets.

Enrolment in doctoral programs: Ph.D. from the Faculty of Science at Eberhard Karls Universität Tübingen.

Responsibilities include

• Writing scientific papers and attending relevant conferences.
• Active participation in the open-source project OpenMS.
• Mentoring of bachelor and master students.

Requirements

• Mobility criteria of ITN must be fulfilled.
• A master’s degree in Bioinformatics, Computer science, or a related field.
• Strong command of English.
• Strong programming skills.
• Experience with machine learning is beneficial.

Your application

Salary will be according to the German public service (TV-L E13) (See https://academicpositions.be/career-advice/phd-postdoc-and-professor-salaries-in-germany for details). Initially, the position is limited to 36 months but may be extended further. The University seeks to raise the number of women in research and teaching and therefore urges qualified women academics to apply for these positions. Equally qualified applicants with disabilities will be given preference. The employment will be carried out by the central administration of the University of Tübingen.

An application is solely possible via the PROTrEIN application form: http://protrein.eu/call-for-applicants/. When applying, select “The dark interactome – methods for discovering novel protein-nucleic acid interactions from complex samples” as your primary project.

Applications arriving before April 30, 2021 will receive full consideration, and applications arriving after April 30, 2021 will be considered until the position is filled.

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