I am a bioinformatician in the Hildebrand Group based at the Quadram Institute, with a strong interest in metagenomics, k-mer and alignment based analysis of metagenomes, C++ tool development all aimed towards improving metagenomic analysis and pushing the taxonomic resolution beyond species/subspecies level.

I have both a bachelor’s and master’s degree in bioinformatics from the University of Tuebingen. After I focused on immunomics in my bachelors, I developed an interest for metagenomics during my masters. As a result, my masters thesis is about k-mer based taxonomic profiling using protein reference. In order to follow this passion for metagenomics, I joined Falk Hildebrand’s group as a PhD student.

In my PhD I focus on k-mer and alignment-based methods for taxonomic and strain-level profiling as well as investigating methods to improve the taxonomic resolution. To achieve this, I use C++ for high performance tool development, data structures such as specialised hash maps for efficient data storage as well as Python and R for scripting and statistical analysis, respectively.

Key Publications

Özkurt, E., Fritscher, J., Soranzo, N. et al. LotuS2: an ultrafast and highly accurate tool for amplicon sequencing analysis. Microbiome 10, 176 (2022). https://doi.org/10.1186/s40168-022-01365-1