Introduction
What I Do
There is an old saying, attributed to Galileo, that the laws of Nature are written in the language of mathematics. After 10+ years in quantitative research, I can only confirm: he was right. I am trained as a theoretical and computational physicist but over my career I have had the opportunity to apply mathematics across multiple fields of research, including quantum computing, engineering, biology, and medicine. Currently, I work in computational cancer biology, where I take on multiple roles. First, I provide statistical consulting and data analysis for pre-clinical and clinical research projects, and together with wet-lab researchers, I help interpret the data. Second, I develop novel machine learning–based approaches to uncover dynamical patterns in biological data, with the potential to predict cell fate under drug perturbations. And third, I am interested in biotech business development, as I want to better understand how research can be translated into real-world impact.
These are the research groups and institutions where I am currently active:
The lab of Momo Bentires-Alj at the Department of Biomedicine at the University Hospital and University of Basel. Main goal of the lab is to understand mechanisms of resistance in breast cancer.
The group of Robert Ivanek within the Swiss Institute of Bioinformatics. This group is a bioinformatics core group at the Department of Biomedicine. I have also close collaborations with the group of Michael Stadler at Friedrich Miescher Institute (Novartis).
RXcel, a pre-seed start-up which I co-founded with the aim of designing “smart” therapeutic RNAs to target aggressive solid tumors.
Next to the world of math, biology and data, there is another one that completely immerses me from time to time, and that’s music. You can listen to some of my production on Soundcloud.
My Interests
There are the main areas I am currently particularly interested in:
What can we learn about cell-cell interactions in single-cell data how can we overlay multiple modalities, mainly with spatially-resolved data.
How dynamical pattens in intracellular signalling determine cell fate or how precisely we can model transcriptional regulation from sparse time-resolved sequencing or qPCR data.
How “smart” RNA design allows to control optimal delivery profile of the effector protein.
My Journey
I studied Physics at Charles University in Prague. My field of study was Nuclear and Subnuclear Physics. For my PhD I joined the group of Prof. Pavel Cejnar where I specialized in Computational Quantum Physics of Many-Body Systems. After my PhD I was a visiting scientist at Technical University in Berlin with Dr. Gernot Schaller and then I moved to Basel in 2019. I started as a post-doc in the group of Prof. Christoph Bruder where we worked on optimal control with machine learning. In 2021, I made a career shift towards biomedicine and joined the lab of Prof. Momo Bentires-Alj. In 2023, I co-founded RXcel.
What Can Be Found Here
Reason for these web pages is to communicate results, thoughts and my experience that not always end in papers. I can imagine it will be constantly under construction, but already now you can check the Projects section where I give quick description about some recently finished or running projects. Some of the talks I have given are in section Talks. Some are purely technical notes on my experience with various bioinformatics tools. I believe they could be valuable to share with the community, but they are the kind of insights that would never be published on their own. If time allows, I will add more “blog posts” about these topics in the future, and not just the pdf slides.