Jan Oppelt

You lead the Bioinformatics Core Facility at the St. Anna Children’s Cancer Research Institute (St. Anna CCRI) in Vienna. How does someone from Brno end up in such a position?

My path was a bit longer. After completing my PhD, I wanted to focus more on independent research, so I went to the United States for a four-year postdoctoral position. For personal reasons, I later decided to return closer to home.

My first position after returning was at a software company, where I continued working in bioinformatics but focused more on software development and less on research. After some time, however, I realized I lacked the motivation to go to work every day.

Personally, I need to see that my work has meaning—that its results will help someone and that my skills contribute to improving society with a tangible impact. I wasn’t able to find that in my previous role, so I started looking for something new.

When the position in the Bioinformatics Core Facility at St. Anna CCRI opened up, it was an obvious choice for me.

How would you describe the practical outcomes of your work in lay terms?

We help researchers and clinicians understand the genetic background of different types of cancer. Our institute focuses heavily on rare cancers, so whatever we discover, we share with partner institutes and hospitals worldwide.

The goal is to help pediatric patients who are not “fortunate” enough to have a common type of cancer that pharmaceutical companies typically focus on. In children, cancer is generally more challenging because it behaves differently than in adults and often progresses more rapidly. You need experts from multiple disciplines with extensive experience, and diagnostics must be performed very quickly.

When we succeed in identifying a mutation, a signaling pathway, or an overall mechanism that is crucial for a specific cancer type, it can lead to improved diagnostics or to identifying suitable targeted therapies.

In rare pediatric cancers, every new finding is valuable because data are scarce and patients even more so.

We work closely with the St. Anna Children’s Hospital, so our work directly contributes to diagnosing pediatric patients. Our work is not always about saying, “Here is the cure,” but rather, “Here is the direction worth pursuing.”

That said, we also have a number of projects that combine research and diagnostics, where research findings are directly implemented into clinical diagnostics within a short time frame literally in the hospital next door.

Your role is both managerial and scientific. What does your typical workday look like?

I handle several things at once. About one-third of my time is dedicated to team management. This includes capacity planning, setting the strategic direction of the team, defining standard processes and best practices, mentoring team members, and resolving interpersonal issues. It involves both managing what’s happening today and planning for what will happen a year from now.

Communication with senior management is also part of my role in both directions. I have to ensure that information flows from leadership to the team and from the team back to leadership. Essentially, I need to make sure everyone is satisfied. It often involves negotiation and finding a middle ground between the expectations of different stakeholders.

Another part of management involves coordinating bioinformatics at the institute-wide level. This includes planning computational infrastructure together with IT, as well as communicating with scientists and physicians about their needs, which I then have to “translate” and synchronize with other departments.

Communication and explanation take up a lot of time. I interact with bioinformaticians, IT staff, other managers, group leaders, biologists, physicians, and the institute’s leadership. Everyone understands their own field, and my role is to build bridges between them to translate information in a way that others can understand.

And what do you focus on when you’re not communicating with others?

The remaining time I dedicate to bioinformatics analyses, building pipelines, and consulting on projects and grant proposals.

We do not run our own independent research projects; we primarily collaborate with research groups on theirs. Some collaborations involve standard analyses, while others are purely scientific research.

We also develop algorithms. Additionally, we are involved in several large-scale projects, both at the institute level and in collaboration with leading international institutes. A small part of the practical work includes administering computational resources, user accounts, and data management.

Continuing hands-on work was one of my conditions for accepting this position. For now, I wouldn’t want a purely managerial role. I still enjoy solving practical problems and keeping my brain engaged.

If a student approached you today wanting to join your team, what should they know?

The field is called bioinformatics, so you need to understand both biology and informatics.

In our group, it’s important to have a foundation in molecular biology, genetics, cancer biology, and sometimes biochemistry. We also use a great deal of statistics.

On the informatics side, it’s beneficial to have programming skills (Python or R), experience with Linux, and most importantly a willingness to learn.

We do not restrict the tools used within the team. We aim to develop code based on best practices so that it can be easily shared and understood by others within a reasonable time. Since we work on highly diverse projects, most of the code we produce is quite specialized.

However, the most important skill is the ability to understand a biological problem and think about it from a data-driven perspective. It is also crucial to know what questions to ask and how to ask them. It’s not about knowing every tool or detail—those can be learned. Logical thinking, precision, and communication skills are more important.

Communication is often underestimated. You can have the best results in the world, but if you cannot communicate them to collaborators at the appropriate level of detail, they are useless.

Given the diversity of projects, independence and responsibility are also important within our team. Of course, this has limits, and it’s important not to be afraid to ask questions.

One advantage of an international and interdisciplinary environment is that there is always an expert nearby who can provide guidance. There is no need to reinvent the wheel.

Why did you choose to study bioinformatics?

I always enjoyed biology and wanted to pursue it. However, when I looked into career prospects as a biology graduate, they were not exactly what I had envisioned.

I also considered studying medicine, but once I realized how demanding the program is and how long it takes to become a physician, I decided against it.

I was looking for something that would allow me to study biology and medicine while offering broader career opportunities. In the year I started my bachelor’s degree, the program in Chemoinformatics and Bioinformatics opened at Masaryk University. It combined exactly what I enjoyed and added informatics. Informatics is the component that now allows me broader career prospects.

This field represents an ideal intersection while remaining highly practical.

What advice would you give to high school students considering bioinformatics but unsure whether it’s the right path?

If you enjoy both biology and informatics and don’t want to give up either, bioinformatics is an excellent choice.

It’s a field that requires combining multiple disciplines, forming hypotheses, designing ways to test them, and identifying the correct answers in the results. No AI can yet perform this entire cycle and it will likely remain that way for some time.

You don’t need to be a genius in every field. Curiosity and a willingness to solve problems are far more important. The rest can be learned over time.

Bioinformatics has a broad reach, and the expertise can take you anywhere in the world. It offers opportunities in academia, healthcare, and the private sector alike