Applied Bioinformatics Group

A   A   A
Home > People > Benjamin Schubert

Skip to content. | Skip to navigation

Benjamin Schubert
Document Actions

Benjamin Schubert

Harvard Medical School
Departments of Cell and Systems Biology,
Boston, USA


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
2013-2016 PhD Student at Applied Bioinformatics Group
Since 2016 Postdoctoral Fellow in Debora Marks and Chris Sander Labs at Harvard Medical School, USA 


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
B. Schubert. Advanced Immunoinformatics Approaches for Precision Medicine. PhD Thesis. University Tübingen. 2017

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.
Schubert, BAdvanced Immunoinformatics Approaches for Precision Medicine. PhD Thesis. University Tübingen. 2017
Schubert, B., de la Garza, L., Mohr, C., Walzer, M., & Kohlbacher, O. (2017). ImmunoNodes–graphical development of complex immunoinformatics workflowsBMC bioinformatics18(1), 242.

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.