Karel Břinda on research at Harvard and working with bacteria as if they were books

What does it take to build a scientific career across continents, disciplines, and research cultures? Karel Břinda sheds light on how curiosity, mobility, and interdisciplinarity can shape a modern researcher’s path in a world where science increasingly transcends borders. Exploring his personal experience with the Ivy League, as well as his current work on genomic data sequencing and antibiotic resistance, he explains how seemingly abstract computational techniques can evolve into real-world impact.

You have built an international career that spans Prague, Paris, Boston, Rennes… How would you describe that academic journey so far?

“I think that in my heart, I'm a computer scientist. I originally studied at the Czech Technical University at the faculty of nuclear sciences and physical engineering, where I started in the math department. Later, I was considering going abroad to Western Europe because I wanted to pursue a research career in the future, and I somehow felt that it was very important to get this international experience. So, I moved to Paris. I got this PhD position with Gregory Kucherov, who is a well-known scientist in bioinformatics, and this is actually how I moved from pure mathematics more to the biology world. After my PhD, I wanted to do a post-doc abroad, and I ended up in Boston at Harvard University. And after five years in Boston, I wanted to get back to Europe, because in my heart I'm definitely European, I'm not American. And I got a permanent researcher position in France, in Rennes.”

Could you maybe describe to us a little bit the differences in the research environments between the Czech Republic, USA, and here in France?

“From my point of view, the biggest difference that I could see there is the interdisciplinarity. In Europe, I was used to departments being separated by individual topics. In the US, I experienced something completely different. It was really like a melting pot of all the disciplines together, like biology, computer science, medicine, and epidemiology. I really internalized this sense of interdisciplinarity in the US, and this is something that I'm actually trying to bring back to Europe.”

So just to follow up on that a little bit, to a non-professional, how would you explain exactly what it is that you do?

“In short, my research focuses on the development of algorithms for the so-called sequencing of data. DNA sequencing is one of the major technological advances in the last several decades. A bacterial genome can be imagined as a book, and now imagine that we put it into a paper shredder. And now I will ask you: “What is the original genome?” My research focuses on developing faster methods that would be able to give the information to the patient about resistance, ideally within a day.”

You mentioned the term phylogenetic compression. Can you tell us a bit more about that and what that process entails?

“When we think of bacteria, in some sense, we can think of books. If you imagine that you put all the printed bacterial genomes one next to each other on a single bookshelf, this bookshelf would go approximately from Prague to Pilsen. We proposed to pre-order the books, bacteria, in an intelligent way. Essentially, sort them according to evolutionary history. And then they become instantly very compressible, because the two books that contain the same phrase now will be very close to each other.”

What would your message be to Czech students who dream big of joining institutions like Harvard or INRIA?

“First would definitely be: be ambitious and don't get discouraged. Oftentimes, I see in the Czech environment a lot of discouragement coming from the higher levels of academia. Second, you need to have some data on your CV. Really start early on, and try to develop a CV so that later, when you really want to make this transition, you can somehow simplify it to the people. I would like to highlight that, really, for me, the transition to Harvard was actually the simplest one from all the transitions I've made.”

Watch the video for the full interview

This interview was produced within a joint project by Radio Prague International, the Czech Centre in Paris, and the Czexpats in Science initiative. The Science Without Borders series with young successful Czech scientists working in various fields in France was recorded in Paris. It is a follow-up to the first series of ten interviews from Vienna.