Experience

 
 
 
 
 
February 2019 – Present
Frankfurt/Main

Software Architect

DB Systel

I am currently working on a project that aims at optimizing the usage of the German railroad infrastructure.
 
 
 
 
 
September 2014 – January 2019
Saarbrücken

Researcher in Bioinformatics

Max Planck Institute for Informatics

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.

My responsibilities also included calling drug resistance mutations using next-generation sequencing (NGS) data. For this purpose, I maintained and extended an NGS pipeline (Python/R) for the determination of HBV/HCV resistance mutations. Based on this experience, I developed the geno2pheno[ngs-freq] web server (C++/JavaScript), which can be used to identify minor resistance variants in HIV-1 and HCV using the algorithms of geno2pheno[resistance] and geno2pheno[hcv], respectively. The development of the tool was guided by the experts in the field, particularly those from the Institute of Virology in Cologne.

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.

In summary:

  • Using machine learning, I developed two treatment decision support systems, which are used in clinical practice
  • I developed a new tool for multiplex primer design with which novel antibodies against HIV-1 were identified
  • I was involved in the statistical analysis for two clinical studies
  • I maintained and extended a NGS processing pipeline for identifying drug resistance mutations
 
 
 
 
 
April 2014 – September 2018
Saarbrücken

Fitness Trainer

Uni-Fit

As a trainer at the university’s gym, my responsibilities included supervision of introductory courses and personal training.
 
 
 
 
 
October 2012 – July 2012
Saarbrücken

Mentor

Saarland University

As a mentor, I was responsibe for assisting new Bioinformatics students arriving at university.
 
 
 
 
 
June 2012 – September 2012
Menlo Park (California)

Software Development Intern

Miaplaza

As a software development intern, I worked on an e-learning platform using C# and was involved in game development using ImpactJS.
 
 
 
 
 
October 2011 – December 2012
Saarbrücken

Scientific Assistant

Max Planck Institute for Informatics

As a scientific assistant I was responsible for deploying a naive-Bayes model for genotyping HBV using PHP.
 
 
 
 
 
April 2011 – July 2011
Saarbrücken

Teaching Assistant

Saarland University

As a teaching assistant for the lecture Software Tools for Bioinformatics, I assisted during the tutorials where we taught students how to use current bioinformatic tools (e.g. Copasi and Cytoscape) and databases (e.g. NCBI and UniProt).
 
 
 
 
 
March 2011 – June 2011
Saarbrücken

Scientific Assistant

Max Planck Institute for Informatics

In my role as a scientific assistant, I was responsible for documenting the GISAID EpiFlu database using HTML resources.
 
 
 
 
 
April 2010 – January 2011
Saarbrücken

Scientific Assistant

Max Planck Institute for Informatics

In my role as a scientific assistant, I was responsible for creating a summary of the Bioinformatics 2 lecture. This involved transcribing audios from the lectures, researching bioinformatic methods, and creating a Latex document.

Selected Publications

geno2pheno [ngs-freq]: a genotypic interpretation system for identifying viral drug resistance using next-generation sequencing data

PDF Project Poster

A genotypic method for determining HIV-2 coreceptor usage enables epidemiological studies and clinical decision support

PDF Poster

Projects

openPrimeR

An R tool for multiplex PCR primer design.

geno2pheno[ngs-freq]

A web service for interpreting viral drug resistance using next-generation sequencing data.

geno2pheno[coreceptor-hiv2]

A web service for the identifiation of HIV-2 coreceptor usage.