Job Offers

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 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 February 28, 2021 will receive full consideration, and applications arriving after February 28, 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
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 develop sensitive and specific protein species (proteoform) identification and characterization algorithms using algorithmic and/or machine learning-based techniques. The application of the developed algorithms is not limited to the analysis of biological data sets but is extended to the control of mass spectrometers for better data acquisition. In two secondments you will have chance to collaborate with experts in computational proteomics and mass spectrometry instrumentation (in CNRS-IPBS and University of Southern Denmark).

 

Expected Results: Efficient algorithms enabling accurate and sensitive identification of proteoforms. Application of the developed algorithms to large-scale proteomics data to identify novel proteoforms.

Enrolment in doctoral programs: PhD 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 in machine learning and/or algorithm 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 “Identification of novel proteoforms using top-down proteomics” 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.

 

References

  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

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