Bioinformatics career story: Thomas Bersez
We are proud to present the talents in our team and the unique stories behind them. Our Scientific Project Manager, Thomas Bersez, joined a video call in the middle of a busy morning in Helsinki to share his career story.
Discovering bioinformatics
Thomas Bersez’s path to becoming Genevia’s Scientific Project Manager started in Southern France, at the University of Bordeaux, where he completed his Bachelor’s in Biology. During the heavily lab-oriented program, Thomas realized that his interests were broader: rather than focusing solely on biology, he wanted to continue learning more about mathematics, physics, and chemistry as well.
– During the last year of my Bachelor’s, we spent a lot of time in a wet lab, putting reagents in tubes and waiting for the results, and doing dissections on rats, for example. I started to feel like this was not something I wanted to do as a profession, and, to be honest, I felt like I wasn’t really good at the lab work, he explains.
Thomas began to direct his studies toward biostatistics and molecular biology and says that this is when he discovered bioinformatics. After his Bachelor’s, he moved to the southern suburbs of Paris to study computer science for life sciences at Paris-Saclay University. His first contact with Genevia Technologies took place towards the end of his studies.
– In France, every student has to do an internship of six months. When the time came for me, I basically just went to Google and searched for biotech companies in Europe. I found out that there’s this interesting company in Finland called Genevia Technologies and emailed their CEO, Antti Ylipää. He told me that unfortunately, they were not able to take interns, but encouraged me to apply again once I got my diploma, and that’s what I did, says Thomas.
Entrepreneurial venture in precision medicine
Thomas joined Genevia’s R&D team in 2019, working on the EU’s Marie Skłodowska-Curie Actions (MSCA) program. He stayed for three years until he decided to move back to Paris to found a precision medicine startup with his former classmates. Thomas still sounds excited when talking about their business idea:
– I can even give you our pitch, he says, laughing.
He explains that when a person has a kidney graft, due to cancer, for example, a physician needs to take a biopsy from the kidney from time to time to check that the graft is not being rejected. The problem with that is, of course, that it can’t be done too often, or, as Thomas describes it, the kidney will turn into Swiss cheese with holes everywhere. The idea of Thomas and his friends was to try and find signs of graft degradation by the immune system in blood and urine.
To do that, they relied on what’s called circulating DNA: when the immune system attacks the kidney, the kidney cells start to pop, releasing their DNA into the bloodstream. The DNA molecules can then be isolated one by one by digital PCR—PCR in small oil droplets. The origin of the isolated DNA molecules can be deduced from different markers, and their abundance indicates whether the kidney is healthy or not.
– In that context, I was taking care of the computational part: the algorithm to analyze the data and the machine learning models to predict the outcome and make recommendations for physicians. Technically, everything was working, but unfortunately, we didn’t get enough funding, says Thomas. He rejoined the Genevia team in December 2023, welcomed by a growing company and a bunch of new colleagues.
Current role at Genevia Technologies
Thomas describes his scientific interests as computationally oriented. In his role at Genevia, half of his time is dedicated to developing and maintaining the company’s data analysis pipelines and internal web applications, and the other half to client projects with specific computational needs.
– I like anything machine learning related the most. For me, it’s not really about the biological context; I am interested in oncology, for example, but what inspires me more are the methods, tools, and the reasoning you can have around the data.
He gives an example of a client project he’s found especially interesting, and during which he’s felt he’s in his strong area:
– Right now, I’m working on a web application project for a clinical oncologist. He’s interested in survival rates in different kinds of cancers and wants to build a machine learning system to examine patients with a lot of data and records such as age, weight, previous treatments, and so on. He wants a model to predict who is going to survive the longest and how the survival rate is going to evolve over time, for example. My colleague, Reija Hieta, built the model, and it was working very well, so the client wanted to be able to try the model with some data sets himself. For that, he needed a web application, and that’s where I came in. I built the web framework and the platform so he can just upload the data sets to the cloud to get a model and prediction with nice graphs and all. I also improved the algorithm a bit, so that it’s doing some things automatically now, like defining the risk groups and picking the time point at which the risk groups should be found, etc. Working on this has been really interesting; a bit of machine learning and a bit of web development. Those kinds of projects are my specialty.
Among the skills he’s learned during his time at Genevia, communication is the one Thomas values the most. He notes that the mindset and scientific thinking of a biologist or a clinical doctor and a bioinformatician can be very different, and that sometimes the client may not understand anything about computers in general; he’s had to learn how to explain what he’s doing in a very simple manner to ensure the client understands.
Hobbies help Thomas maintain work-life balance: he has played bass for over ten years and likes to do a lot of sports too, especially Thai-boxing. He also enjoys the flexibility brought about by the possibility of remote work:
– It is very nice to know that if I someday get bored of Finland—which is absolutely not the case right now—it is possible for me to go back to France and still keep my job, he says with a smile.
Thomas thinks that the most important thing to consider when pursuing a career in bioinformatics is whether you are actually interested in what you’re doing. In addition, he highlights the importance of patience and a willingness to keep learning.
– At the end of the day, you’re going to spend most of your time in a chair behind the computer, so if you’re bored, those are going to be some really long days at work. You need to be interested in what you’re doing and you need to be curious and willing to invest time in developing every day: you’re not going to work on the same project twice, and there are new technologies and concepts to learn each time, he reflects.
When asked what he enjoys the most about his current job, he proves to be practicing what he preaches:
– I would say what I enjoy the most about my job is that it’s just interesting in general. I go into this mode where I’m all focused on my code and don’t even realize that the clock is running until I suddenly look up and realize that hours have passed. It’s a very nice feeling when you don’t get bored at work: you just do your job, the time goes by, and at the end of the day you feel like you’ve done something super interesting.
Our d’Artagnan of the pipelines
