Hi! I’m Alex, a bioinformatician working in the context of liver cancer analysis at the Quantitative Biology Center Tuebingen and formerly for paleogenetics at the Max-Planck-Institute for the Science of Human History in Jena/Germany and the Eberhard-Karls-Universität in Tübingen/Germany. My work centers around developing novel methods for the scalable and reproducible analysis of multi-omics liver cancer data.
Formerly, I worked on developing novel methods for the analysis and handling of ancient DNA (aDNA), with a specific focus on making my methods more user-friendly and thus suitable for archaeologists and biologists. My main PhD project was about making state of the art methods available to a larger (and growing!) community that wants to leverage aDNA to gain insights into evolutionary events all over the globe.
Another aspect of my work is to make my research reproducible: Making use of projects such as Docker, NextFlow and other tools to “sandbox” genomics applications to make them portable between different types of infrastructure, such as cloud instances, local workstations and HPC environments. My ancient DNA pipeline EAGER has been one of the first available genomics pipelines obtaining a licence for bundling the Genome Analysis Toolkit (GATK) officially in such a Docker container, making it possible for researchers to genotype their genomic data without having to install anything else than Docker - and my container. In general user-friendly applications for genomics can be seen as one of the thriving aspects of my work. I also made some smaller tools e.g. in R/Shiny to help users in choosing better parameters for their DNA mapping analysis with BWA-Mismatches.
I received my BSc and MSc degrees in Bioinformatics both from the Eberhard-Karls-Universität Tübingen, while also studying abroad at the San Francisco State University, CA (USA) for half a year during my Master’s.
Check out my GitHub page if you’re looking for some of my tools and methods. Most of them are open source and licenced under GPLv3 and I’m very happy to receive feedback or pull requests.