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Academic Life Issue 9 PI Presenting Alumni

Fran Supek: “I always try to cook up new ideas, otherwise it gets boring!”

🕒 16 min

Today, it is my pleasure to present an interview with a long-standing alumnus – Fran Supek. Fran was part of S3 for several years, as a project leader and as organizer of the School, and is now an aspiring group leader researching genome biology in Barcelona. So, let’s get to know our S3 PI!

Where does your passion for science come from? Was it something you developed during high school, or were there even earlier signs of a love for science?

Fran Supek
Group Leader
IRB Barcelona

2011 S3++ project leader
2010 S3++ project leader
2009 S3++ organizer
2008 S3++ project leader
2007 S3++ project leader

I was always intrigued by how things worked and why nature is the way it is. I was fortunate to have a supportive environment, including my family (particularly my grandfather, who was key in getting me interested in the natural sciences), as well as some fellow geeks among my friends and schoolmates with whom I had shared interests.

Education and career

Great support is very important, especially a good school where teachers transmit their passion. But unfortunately, not all schools have the necessary funds or enthusiastic personnel. Can you tell us a bit more about your high school?

My high school was quite cool in one particular way: there were not many other schools where you could feel fine (or even cool!) by being a geek among many other geeks. Essentially, I was surrounded by many like-minded students who were, e.g. eager to take part in science competitions, or to participate in ‘hobby groups’ where we studied additional aspects of specific subjects like math. Notably, these groups were led by some of our teachers, who noticed our hunger for knowledge and volunteered their time to teach us a bit more than the curriculum. I am grateful for all their enthusiasm and the time they invested in us.

As a person who went through a natural science-oriented grammar school myself, I wonder how easy it was for you to decide on a particular university? Did you immediately know you wanted to study biology?

Definitely not! I was interested in how the world works, and so I found an interest in, say, sociology, as well as in computer science or biology. I was deciding between the Faculty of Electrical Engineering and Computing and the Faculty of Science, up until the last minute. I went with the latter because I was more interested in research, which was less of a focus at the other faculties I considered. However, I always had a thought in the back of my mind that this decision might, in a matter of speaking, also change later. That is, even if I chose one over the other, I felt I might ultimately end up studying or working on other things as well. This is kind of what happened in the end: my background is in molecular biology, but I am working in bioinformatics and genomics (which are very computationally oriented; in some ways, they are more computer science than biology).

How did you like your biology studies, was it all you’d hoped for?

It was a phenomenal experience. We had plenty of dedicated professors, and I had great colleagues. We learnt a lot – we studied biology quite broadly, covering many vastly different fields. That was mandatory, most of our subjects were not elective, in fact. At the time, I wondered a bit if it made sense to spend all this time learning something that you were (almost) sure you wouldn’t work on. However, one never knows. That may well be an advantage of this approach to organizing the curriculum, as it gave us the chance to get a taste of many fields and to better find our niche. Furthermore, there was a growing need among biology students to have their own society, which resulted in the formation of BIUS student association, which I took part in.

How did you get to know about bioinformatics?

I did not take bioinformatics as a course during my undergraduate studies (because this did not exist at my university back then), but I managed to find a master’s lab where I could work on genomics, which was very fulfilling. Later, I got so interested in it that I would come and join genomics lectures at the university with younger students, while I was working on a PhD in the field.

Tell us a bit about your PhD experience, then!

It was fantastic! Driven by my new interest in computational biology, I decided to join the Laboratory for Information Systems at the Ruder Boskovic Institute (RBI) in Zagreb. My research topic was how to apply artificial intelligence to genomics and evolutionary biology. In specific terms, we studied (relatively simple) bacterial genome sequences – the only ones available at the time. I was the only biologist in a group of computer scientists, which made it a very enriching experience. I learned a lot about machine learning algorithms and their applications to biomedicine, which the group specialized in. Since I was the go-to life scientist in a group where many of the projects were in applied biomedicine, I got a lot of opportunities to collaborate with others and contribute to many other projects.

When you look back at those days, as the experienced scientist you are now, was there something you would do differently?

If I try to look back objectively on the progress of my PhD, it could perhaps have been done in less time, with similar results. I think I was not self-disciplined enough to focus better and to avoid taking on cool little side-projects (which did, however, teach me a lot, so there are some benefits to my lack of focus). For example, I participated in many very diverse collaborations, which I liked a lot, but many of these projects were so far from my topic that they did not make it into my thesis.

A thing I missed a bit at my PhD institution back in Croatia – which is otherwise a fantastic, supportive environment – was a bit more interaction with the international research community. We could have benefitted from more talks from international speakers, followed by discussions to share ideas, thus perhaps sparking some international collaborations. This would enable students to connect and learn about opportunities for interesting positions abroad. More lively interactions with people from across the globe help scientific communities thrive and generate new ideas.

After your PhD, you decided to leave Croatia and do an international postdoc. Can you tell us how that happened?

I started looking into labs around Europe that were doing research in genomics. I stumbled upon this amazing institute, CRG in Barcelona, which was right at the beachfront! I did some extra research on the CRG institute and liked what I saw. The process was relatively straightforward: I had to apply for a postdoc call by writing up a project proposal. After that I had to defend my proposal in front of a committee, which seemed quite critical of it. At least that was my impression at the time. I felt overwhelmed and thought that the whole thing did not go too well. But they liked my idea, and I got the position. I spent six years there, working in two different labs. I studied the evolution of microbial genomes and of human cancer genomes by developing new statistical methods to learn how they evolve and why these genomes are the way they are.

What would you say were the most valuable lessons you learned during your postdoc?

When deciding what to do after your PhD, if you consider a postdoc in academia, you should ask yourself if you are ready to invest five or so years into working with remarkably high focus and dedication, with the goal of training and building up your track record to the level required to get an independent position in academic research centers or universities. It is a bit of an emotional decision – if you really “feel the pull” towards basic science and an academic career (with all its upsides and downsides), then you should go for it. Otherwise, there is a variety of cool jobs you can go for with your newly minted PhD, which might fit you better.

What does it mean for you to become a group leader? How hard was that process?

It is a demanding but very fulfilling job. The job market is tough and there may not be many openings locally, and so geographical mobility is often a must. Depending on your situation, this is not always the easiest to pull off. Furthermore, once you start at an independent position, you will typically be greeted with very high expectations, e.g. publishing groundbreaking papers, getting a big grant (or two or three), being a good mentor to students. In the beginning, it can be quite overwhelming. It bears mentioning that a good chunk of your time (perhaps a third) will be used for administration: participating in different committees, managing budgets, filing different documents to run your lab smoothly, like reports for ongoing projects and such.

When it comes to the process of finding a position – in my case, I applied to several places in Europe, some of them also in Spain. I was quite happy when an offer from IRB Barcelona came in, because it had a very good reputation for being among the best institutions in Spain by quality of research, and is also recognized globally.

What is your group working on?

We are working mostly in the field of cancer genomics. Our current topic of interest is mutagenesis; we are trying to understand how and when mutations occur, as well as which cellular mechanisms are responsible for avoiding or generating them. With the advent of whole-genome analyses in the last decade, it has been shown that the probability of a mutation occurring is unevenly distributed across the human genome. This is additionally complicated by differently regulated and expressed genes, which can affect mutation rates in all kinds of ways. Upon the occurrence of a mutation, our cells are able to direct their limited capacity for DNA repair to the genome locations which are most precious – where the most highly expressed genes reside. There are several overlapping mechanisms of DNA repair and each of them is ‘guided’ differently, so the story gets beautifully complicated. More things for us to explore!

And can you tell me a bit about the people in your group?

My group, the Genome Data Science laboratory, consists of 13 people – quite a lot for a 4 year-old group. I was fortunate with getting funding from the European Union, which allowed the group to grow quickly. Plus, the interest among prospective students was quite strong. There are now six PhD students, plus several postdocs and engineers. It’s a mixed group, but with the majority of people being from Spain. In jest, I often say that we are quite an international group as some of us are from Catalonia, while others are from Asturias or from Andalucía (which are all different parts of Spain). But we do have people from France, Germany, Russia – and Croatia of course. Our official language is English so that nobody feels left out. In terms of interests, we are a mostly computational group, but we have three experimental people, who mostly work with human cell cultures to investigate quality-control mechanisms in cancer cells. Although I am certainly not impartial, I think the people in my group are a fantastic bunch! They are dedicated and talented and collegial. I enjoy the collaborative spirit and the scientific discussions within the lab.

How does it feel to be a group leader?

Probably the closest to the truth is to say that it is quite chaotic due to the amount of different tasks you need to juggle. At certain times, there is a manageable amount of things that require attention and hence regular working hours are fine, but sometimes you are working towards a deadline, e.g. to submit a grant, or write a paper revision. Then it may not exactly be the 40-hour work week. So, some stamina may be required. As mentioned, there is lots of admin work involved, which is not necessarily very fulfilling. However, the scientific discussions that I have with my group members and the joy of discovery more than make up for it. Unfortunately, I do not find as much time to write code or analyze data myself, but I do try to be there for my students or collaborators as much as needed (some emails may go unanswered…). I often have to switch my attention from one project to another, while also staying focused on the most important things and not getting easily distracted by details. This can be quite challenging in the beginning, as you really need to learn how to juggle your time and mental energy.

What kind of supervision style do you practice with your students?

I like the title “advisor” much better than “supervisor” – I think that describes my approach. I try to keep it very informal, as well as to make time for a chat every week (or more, if needed), so we can discuss about what matters at any given time – organizing work, planning, looking at the results of their experiments, interesting papers that came out recently, writing up manuscripts etc. At IRB, the students must present their progress in front of a committee on a yearly basis, which puts quite a bit of pressure on them, and so we also practice these talks and help them organize their results. As a rule of thumb, for every student in the lab, our aim is to publish at least two first-author computational papers during their four years of PhD, or one in the case of experimental projects. This helps them (and me!) to focus and, as an added benefit, they can submit their PhD thesis as a collection of papers instead of having to write a full thesis. I do not necessarily put a strong focus on publishing in high impact journals; my thinking is, do your research on important and interesting topics and it will probably get picked up by the editors and reviewers of a nice journal.

What does the future hold for you? Can you give us a sneak peak?

I always try to cook up new ideas, otherwise it gets boring! I can share some of the exciting new research we started – for instance, we are studying the mechanisms of mRNA quality control (so-called NMD) in human cells, which can degrade transcripts in case a stop codon occurs in the wrong place. We have some evidence that this mechanism, usually seen as protective, is actually involved in aggravating many genetic diseases (including cancer). This finding really surprised us, and it implies that NMD inhibitory drugs could be used for alleviating the symptoms of many different genetic diseases. Furthermore, a particular patient’s genome data could predict if they can be treated successfully or not. Now we’re working with a few hypotheses on how to connect NMD inhibition to fighting cancer by potentiating the effects of immunotherapy.

It sounds very interesting, especially the possibility of treating genetic diseases! Thank you so much for sharing these interesting points.

Summer School of Science

Now I would love for you to go back in time by a decade or so and remind us of your S3 experience. How did you get in touch with S3?

I was approached by Martina Mijuskovic in 2007, who asked me to lead a project. I liked the idea, so I organized a computational project. I still remember how surprised I was by the conditions at the S3 school in Visnjan at the time, which were, shall we say, quite basic. However, I was immediately won over by the enthusiasm, spirit and atmosphere. I was often impressed by these naïve, but very to-the-point questions that the students would sometimes ask – they were quick to see the big picture and spot the unknowns in the field. These and many other reasons kept me coming back for several years to come.

If you could turn back time, would you want to take part as a participant?

Absolutely! Whenever I was there, I kept on thinking how I would love to have been that high school student who could attend S3. When I was in high school, there were no such initiatives back home. I really think that there should exist more of these types of programs in Croatia. For example, here in Barcelona high school students have the opportunity to join the “Crazy about Biomedicine” program that is run over weekends at my institution, the IRB.

Did you stay in touch with some of your S3 colleagues and/or participants?

I still keep in touch with some of the old gang, such as Anamarija Stafa. Other than that, I really love joining reunions, as they tend to happen over the holidays, when I am visiting Croatia. It’s nice to reminisce on the good old times. I didn’t join the digital reunion this year, as I got distracted by other things, but I do hope that in the future we can have both digital reunions and the in-person one.

As we are getting to the end of our interview, let me ask you a seemingly easy question – after all your experiences, which advice would you give your younger self?

Easy question you say? Not quite! I think I would not change much, but maybe I would advise myself to be more focused, meaning to do fewer things, but do them well. (However, too much focus may not be good for creativity either. So perhaps I am not too good at this advice-giving business after all!)

I would perhaps suggest one thing to young people just starting their professional life. Each of us has a certain set of ideas and visions of how life should play out, professionally. For many people, this vision tends to prioritize security and predictability. This, however, has a way of becoming a bit of a trap. Essentially, you might be holding yourself hostage by avoiding choices that seem risky but could potentially be rewarding and allow you to advance and grow. Don’t be a prisoner to comfort. Be brave. Fail. Don’t get caught up in calculating risks too much – there is so much uncertainty ahead anyhow that you cannot control it all. Just follow good opportunities, give it your best, and work hard – and things will work out eventually.

Very nicely said – see, it wasn’t that hard after all! And for the final question – what are your hobbies? How do you relax when you have the time for it?

Nothing out of the ordinary to report here. Things changed so much during this past year, so during this pandemic-ridden time I enjoy watching TV shows, lately a lot of sci-fi. Hanging out with friends – well, mostly over Skype and Zoom. Such are the times. Before the pandemic, we would often go restaurants for dinner, but now I guess it’s a good opportunity to work on some cooking skills!

Thank you, Fran, for such a nice conversation! We wish you good luck working at the frontiers of science and hope to see you at least as a speaker in some of the S3 camps to come.

How did you like this interview? Would you like to ask Fran any extra questions? Let us know in the comments section!

By Petra Gerber

Computational biologist focused on single cell data. Board game enthusiast and passionate about talking with our alumni.

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