Faculty of Science



PhD position in Computational Biology/Bioinformatics (m/f/d; TV-L E13, 3 years)

Faculty of Science, Center for Bioinformatics

Application deadline : 28.02.2021

The Chair for Applied Bioinformatics (Prof. Oliver Kohlbacher), Center for Bioinformatics at Eberhard Karls University Tübingen, one of eleven German universities distinguished as excellent under the German government’s initiative, is currently offering a 

PhD position in Computational Biology/Bioinformatics (m/f/d; TV-L E13, 3 years)

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 Ph.D., you will develop algorithms, machine learning methods, and tools for statistical valid identification and quantification of protein-nucleic acid cross-links with a focus on novel cross-linking strategies and protocols.


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.

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.
Enrolment in doctoral programs: PhD from the Faculty of Mathematics and 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.


  • Mobility criteria of ITN must be fulfilled.
  • A master’s degree in Bioinformatics, Computer science, or a related field.
  • Strong command of English.
  • 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.

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 February 28, 2021 will receive full consideration, and applications arriving after February 28, 2021 will be considered until the position is filled.


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