I am a postdoctoral researcher at the University of Antwerp working on Microbial genomics, and metagenomics, and I am gradually expanding my work into entrepreneurship. You can find more about my research interests in bioinformatics, computational biology and microbiology throughout this page. Beyond science, I enjoy building websites, exploring productivity systems, playing music, hiking and staying active.
After completing my Master’s degree in Biology (Cell and Systems Biology) at the University of Antwerp, I started a PhD in January 2018 with support from an FWO-SB fellowship. This joint project between the University of Antwerp and the Institute of Tropical Medicine Antwerp focused on the genomics of Salmonella. I worked on Salmonella Concord, performing culture-based work, short- and long-read sequencing (Illumina, PacBio and Nanopore) and antimicrobial susceptibility testing. Through this work, I developed broad expertise in microbiology, bacterial genomics and bioinformatics pipeline design. A large part of my PhD work was published in Nature Communications (manuscript link).
During my PhD, I also specialised in antimicrobial resistance, which led to one of my most-cited papers in Microbial Genomics (manuscript link). Additionally, I examined differences in gene co-expression between two Salmonella Typhimurium strains. This led to the development of the R package gccR (https://github.com/Cuypers-Wim/gccR), which was one of my larger coding projects of my PhD.
I defended my PhD thesis, Genomic adaptation of Salmonella to antimicrobials and the human host, in June 2023.
After completing my PhD fellowship, I have worked at the Adrem Data Lab on LeapSEQ, a project focused on enabling rapid, mobile pathogen monitoring using Nanopore sequencing. To launch this work, I first established a fully functional sequencing laboratory, an exciting first for a research group within the Department of Computer Science! Our first paper on Nanopore adaptive sampling, published in mBio (manuscript link), was possible due to this lab.
Through LeapSEQ, I recognised the need for better datasets and benchmarks for microbial Nanopore sequencing. This led me to develop SquiDBase with the team, a platform for sharing microbial Nanopore raw signal data, and helped shape SquiDBench, a benchmarking framework being developed by my PhD student Laura.
A central goal in my career is to help make near–real-time pathogen detection accessible, particularly in settings where this can provide meaningful value for low- and middle-income countries. This drive led me to wastewater metagenomics as a way to monitor antimicrobial resistance and pathogens. The field combines scientific discovery with a clear practical purpose, which aligns well with my growing interest in entrepreneurship. Recent publications I co-authored in this field are about best practices, and sequencing the wastewater virome.
Equitable access to innovative technologies and bioinformatics training motivates much of my work. This commitment led me to join the ISCB Student Council and to co-develop and teach pathogen bioinformatics courses in Addis Ababa, Ethiopia, alongside colleagues from AHRI and ITM (latest course notes). Working with dedicated and motivated participants has deepened my understanding of the challenges researchers face in settings with limited resources and strengthened my commitment to accessible training and long-term collaboration.
Alongside my academic work, I enjoy advising start-ups on genomics and sequencing strategy. This consulting activity is something I plan to expand, as it allows me to translate scientific expertise into practical, real-world applications. I also intend to develop a university spin-off that builds on the technologies and insights emerging from my research.
Outside the lab, basketball has played a major role in my life for more than 15 years. I have played for Oxaco BBC Boechout, Antwerp Giants and Mercurius Berchem. The teamwork and group spirit that define the sport influence how I approach scientific and collaborative projects. I also enjoy playing acoustic guitar, mainly Blues, Country and Bluegrass, but I recently started taking classical guitar classes. Another one of my favourite free time activities is hiking or backpacking.