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. Kyowon Jeong – 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.

Improved algorithms and tools for the identification of novel proteoforms using top-down proteomics.

As part of this Ph.D., you will implement sensitive and specific protein species identification and characterization methods for targeted and untargeted proteomics study by leveraging recently introduced mass deconvolution algorithms. You will also be involved in various applications of the developed methods to reveal novel proteoforms.


Both algorithmic and machine learning-based approaches will be applied for an efficient and sensitive proteoform identification method. The developed algorithm will be used in a stand-alone tool as well as in an interactive visualization tool. The algorithm also could be embedded in instruments for better data acquisition. The development will be performed as part of OpenMS the major C++ open-source framework for computational proteomics.

Expected Results:

Tools implementing millisecond order of runtime per spectrum and increased proteoform identification rates at a given false-discovery rate. Application of these tools to large-scale proteomics data to identify novel proteoforms.

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.
  • A strong background in algorithm
  • 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 statistics.
  • 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 “Identification of novel proteoforms using top-down proteomics” as your primary project.

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


1. Jeong, K., Kim, J., Gaikwad, M., Hidayah, S. N., Heikaus, L., Schlüter, H., & Kohlbacher, O. (2020). FLASHDeconv: Ultrafast, High-Quality Feature Deconvolution for Top-Down Proteomics. Cell Systems, 10(2), 213-218.e6. https://doi.org/10.1016/j.cels.2020.01.003 2. Chen, B., Brown, K. A., Lin, Z., & Ge, Y. (2017). Top-Down Proteomics: Ready for Prime Time? Analytical Chemistry, 90(1), 110–127. https://doi.org/10.1021/acs.analchem.7b04747 
2. 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