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Benjamin Schubert
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Benjamin Schubert

Eberhard Karls Universität Tübingen
Center for Bioinformatics
Applied Bioinformatics Group
Room C321, Sand 14

Tübingen D-72076
Work: +49-7071-29-70460


2007 Abitur at Freie Waldorfschule Heidelberg
2007-2010 BSc in Bioinformatics at University Tübingen
2011-2013 MSc in Bioinformatics at University Tübingen
2012-2013 Exchange student at CBS -Technical University Denmark
Since 2013 PhD Student at Applied Bioinformatics Group 


B. Schubert. Transferlernen in der Immunoinformatik. Bachelor Thesis. University Tübingen. 2010
B. Schubert. Evaluation of Peptide Selection Approaches for Epitope-based Vaccine Design. Master Thesis. University Tübingen/Technical University Denmark. 2013

Research Interests

Applications of Machine Learning and Combinatorial Optimization in:
  • Computational Immunomics and Computer aided Vaccine Design
  • Structural Bioinformatics with focus on deimmunization of therapeutic proteins


Feldhahn, M., Dönnes, P., Schubert, B., Schilbach, K., Rammensee, H.-G. and Kohlbacher, O. (2012) miHA-Match: Computational detection of tissue-specific minor histocompatibility antigens. Journal of Immunological Methods.

Schubert, B., Lund, O. and Nielsen, M. (2013) Evaluation of peptide selection approaches for epitope‐based vaccine design. Tissue antigens, 82, 243-251.

Szolek, A.*, Schubert, B.*, Mohr, C.*, Sturm, M., Feldhahn, M., & Kohlbacher, O. (2014). OptiType: precision HLA typing from next-generation sequencing dataBioinformatics30(23), 3310-3316.

Schubert, B., Brachvogel, H., Jürges, C., and Kohlbacher, O. (2015) EpiToolKit – A Web-based Workbench for Vaccine Design. Bioinformatics, 31(13):2211-2213
Schubert, B., and Kohlbacher, O. (2016) Designing string-of-beads vaccines with optimal spacers. Genome Medicine, 8(9). 
Schubert, B., Walzer, M., Brachvogel, H., Mohr, C., Szolek, A., and Kohlbacher, O. (accepted). FRED2 – An Immunoinformatics Framework for Python. Bioinformatics.

Book Chapters

Olabarriaga, S. D., Benabdelkader, A., Caan, M. W., Jaghoori, M. M., Krüger, J., de la Garza, L., Mohr, C., Schubert B., Danezi, A., & Kiss, T. (2014). WS-PGRADE/gUSE-Based Science Gateways in Teaching. In Science Gateways for Distributed Computing Infrastructures (pp. 223-234). Springer International Publishing.