I am a bioinformatician working in pathogen genomics. I am heading a small group that provides bioinformatics support for a medical microbiology department of an academic hospital. In short, we design, write and maintain pipelines and databases, carry out or advise on analysis of high-throughput sequencing data and provide bioinformatics education and consultation.
My own research interest is to find patterns in DNA sequencing data and to apply this knowledge to the genomic epidemiology of organisms causing infectious diseases. These patterns translated to sequence differences corresponding to transmission of Mycobacterium tuberculosis strains during my phD; or to distinct physical entities, such as the identification and reconstruction of viruses from metagenome data. Recently, I am interested in the reconstruction of plasmids from bacterial whole genome short read sequencing data.
I am passionate about teaching and supervising, because I like to share my enthousiasm for bioinformatics, open science and reproducible research as a way to do difficult tasks better, faster, stronger. I teach university courses and Carpentries workshops as an instructor and trainer, and contribute to lesson development as a lesson maintainer for the Data Carpentry Genomics lesson.