I am currently working as a software architect/developer at DB Systel where I’m supporting the digitalization of the German railway system. Previously, I completed my PhD at the Max Planck Institute for Informatics where I researched computational methods for improving treatment and prevention of viral infections.
PhD (Bioinformatics), 2019
Max Planck Institute for Informatics
MSc (Bioinformatics), 2014
BSc (Computational Molecular Biology), 2011
During my PhD, I worked as a researcher at the department of Computational Biology & Applied algorithmics at the Max Planck Institute for Informatics. As a member of the Statistical Learning in Computational Group, the focus of my work was on the development of machine learning methods that can assist the fight against viral infections such as HIV.
In my work, I was involved in evaluating two clinical studies. For the EucoHIV project, which studies the efficacy of maraviroc treatment in Europe, I computed descriptive statistics and visualizations of quantities of interest such as CD4 cell counts, viral loads, and treatment success. To report the current status of the analysis, I created several comprehensive summaries of the results using Latex. For an epidemiological study on HCV, I was responsible for the statistical analyses of the data using log-linear models.
Having attended a meeting of the HIV-2EU study group, I became aware of the problem of HIV-2 coreceptor prediction. After I had collected pairs of viral sequences and tropism assay measurements, I began developing a support vector machine for predicting HIV-2 coreceptor usage. Using R, I processed the data, engineered relevant features, performed model selection, and deployed the model (C++/PHP) in terms of the geno2pheno[coreceptor-hiv2] web service.
Finally, I developed openPrimeR, a new multiplex primer design tool that is suitable for the amplification of highly mutated antibodies against HIV-1, which evolved through close collaboration with Florian Klein’s group. The work resulted in two R packages that were released at Bioconductor, the openPrimeR package as well as the openPrimeRui package, which provides a frontend using the Shiny framework.
I’m frequently writing posts on datascienceblog.net, a blog about everything related to data science and programming.