Scientists of the University of Tübingen publish a framework to improve the design of novel cancer vaccines

Epitope-based vaccines has emerged as a promising approach to treat not only infectious diseases but also to promote the battle against cancer by a patient’s own immune system. Actually, the prediction and assembly of viable epitopes and spacers in a string-of-beads like polypeptide remain one of the challenges. The design of the spacers between the epitopes and order of the epitopes thereby seem to affect crucially the probability that the selected peptides will be fully recovered and subsequently presented by patient´s HLA molecules and that risk is reduced, that adverse neoepitopes are generated within this process.

Benjamin Schubert and Oliver Kohlbacher from the University of Tübingen proposed in their work, which recently was published in Genome Medicine, a mathematical model to design spacer sequences of optimal design. First results are promising, as they showed indeed higher recovery rates and lower neoepitope generation using the proposed framework.

Together with partners, the researchers of Tübingen are going to validate the model in experimental tests within the project APERIM. Results will show if this approach helps to improve and accelerate epitope vaccine development.


Schubert B, Kohlbacher O: Designing string-of-beads vaccines with optimal spacers, Genome Medicine 2016, 8:9  full text

Benjamin Schubert; Mathias Walzer; Hans-Philipp Brachvogel; Andras Szolek; Christopher Mohr; Oliver Kohlbacher: FRED 2 – An Immunoinformatics Framework for Python. Bioinformatics 2016; doi: 10.1093/bioinformatics/btw113  full text


Further information:
Benjamin Schubert
Eberhard Karls University Tübingen
Applied Bioinformatics Group
Sand 14, D-72076 Tübingen
schubert (at)