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Marie-Sklodowska Curie PROTrEIN-ITN Early Stage Researcher (PhD student) position: The dark interactome – methods for discovering novel protein-nucleic acid interactions from complex samples (EKUT, Tuebingen, Germany)

Gene Regulation, Stem Cells and Cancer

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Barcelona Spain Bioinformatics Data Analysis Computer Science Software Engineering

About the Project

PROTrEIN ( is a European Innovative Training Network composed of 11 beneficiaries, and 6 partner organizations, from the academic and non-academic sectors (including two SMEs and two large companies).

The network’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.


Subproject 11: (Host: Eberhard Karls Universitaet Tübingen - EKUT, Tuebingen, Germany)

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

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 FISHER (Germany), Duration: 1 Month; When: Year 2; Goal: Practical programming and translation to industry.

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

Enrolment in doctoral programs: PhD from the Faculty of Mathematics and Science at Eberhard Karls Universität Tübingen

Application Procedure: 

An application is solely possible via the PROTrEIN application form:

Applications must be in English. Applicants may indicate 3 ESR Projects which they would like to work on, ranking them in order to preference. Uploading reference letters is not mandatory, but applicants should be aware that referees will be automatically contacted after submission and receive a questionnaire. Candidates must provide all information before the deadline. Candidates should ensure that referees answer the questionnaire.

Application deadline: 28 February 2021


About Eberhard Karls Universitaet Tuebingen:

The Eberhard Karls Universitaet Tuebingen (EKUT), founded in 1477, is one of the leading German research universities. It is one of eleven German universities distinguished as excellent under the German government’s initiative. The Institute for Bioinformatics and Medical Informatics (IBMI) was founded in 2000 as one of the five nationwide centers of excellence in bioinformatics funded by the German Science Foundation and recently expanded into medical informatics. EKUT established the first bioinformatics curriculum in Germany in 1998 and has one of the broadest Ph.D. programs in bioinformatics/computational biology in Germany (currently about 70 Ph.D. students enrolled).

Funding Notes

The position is fully funded for 36 months by the European Commission under the H2020 Marie Curie Innovative Training Network Programme.
Marie Curie ITNs provide a highly competitive salary to the ESR, including a competitive monthly living and mobility allowance and (if eligible) a monthly family allowance.
The eligibility criteria dictated by the European Commission under the H2020 Marie Curie Innovative Training Network Programme must be fulfilled.


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.
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.

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