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Meet Our Expert: Frans-Paul Ruzius

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6 min read

In Meet Our Expert you will get to meet the talented people behind Cergentis' success on a personal level. In this interview, Frans-Paul recounts his educational and professional journey. With a naturally inquisitive mind, find out what motivated him to pursue bioinformatics and how an interesting string of interconnected career events has landed him a spot at Cergentis. Besides, Frans-Paul describes our work culture and shares some of his most serious hobbies!

Can you tell us about your childhood?

Yes, so I was born at a very young age [laughs]. More seriously, I was born in Groningen, a province in the North of the Netherlands. I come from a very small village called Meeden, where I attended primary school. At some point, of course, I needed to look for a study. I was always interested in computers but did not want to pursue IT nor major in informatics/computer science. Since I was not bad at biology, I decided to give bioinformatics a try. And basically, I never left the field!

What drew you to science?

You often hear that kids have a “why” phase. That they ask “why” a lot. I never grew out of that [laughs]. I had it until I was 16! Always trying to find more details, figuring out why things work the way they do and not simply assuming nor accepting something just because someone told me. Basically, I always worked with the scientific method even before I knew what it was.

From what I understand, you were keen to study an interdisciplinary field. Was it then a difficult decision or was bioinformatics an obvious choice from the outset?

What I sometimes do, when dealing with difficult decisions, is to not overthink it. Your first impression is usually the best one. Whenever a choice sounds good, I don’t look further. Because otherwise, you will never stop looking! So, bioinformatics was just the first one that sounded very interesting to me. “Researching with a computer”, that’s how they advertised it. It turned out to be a very nice study!

Was bioinformatics popular back then?

Not at all. My cohort belonged to one of the first three I think. In fact, I believe we were the third generation of graduates from that bachelor study. So, I was one of the first trained bioinformatician!

At the time, most were either fully trained as informaticians or biologists that had learned programming skills on-the-job afterwards.

My study included general biology and lab work at the beginning. It’s nice to read about PCR but you of course also need to know how it works and what to do practically. The program then went straight into genetics because that’s where most of the bioinformatics is needed. I also had the chance to get exposed to immunology. The subsequent years were more about programming.

What did you do once you graduated?

I first applied for an internship in Patrick Kemmeren’s lab, at the University Medical Center of Utrecht. Back then, I brought my report on RNA sequencing and he was the one who suggested me to contact prof. dr. Edwin Cuppen (since his research was also focused on RNA). Long story short, he had a spot available. At the end of my internship, dr. Elzo de Wit (co-founder & former Head of Bioinformatics at Cergentis) was my supervisor: my first connection to Cergentis. A year later, Edwin offered me a job and Marieke Simonis (former Head of Bioinformatics at Cergentis) also joined the team. My second link to Cergentis [laughs].

Were you actively involved in the development of the Targeted Locus Amplification (TLA) technology?

Back then, my job was to do the primary mapping of all the sequencing data in Cuppen’s lab. Essentially, I performed the first analysis and Marieke took over for the more detailed inspection. Sometimes, we needed to work together to dive into some details in order to determine whether some things needed to be more standardized. Which was what I was responsible for. In other words, I wrote the pipeline.

What made you decide to crossover to industry?

After working at the Hubrecht Institute, I contacted GenDx because I was looking for a job. They were interested in NGS, and I had quite some experience with it. My programming skills and sequencing knowledge helped me differentiate from other candidates. They ended up hiring me.

During my time at GenDx, I truly learned the difference between making scripts (a.k.a “fixing a problem” or “answering a question”) and building a software that you can actually sell. They are worlds apart. It’s like drawing a cartoon on a napkin and actually making a painting. That’s how big the difference is!

Overall, it was a nice start-up job and I ended staying there for 8 years.

Why did you decide to join Cergentis?

After 8 years, I wanted to start something new. At GenDx, I wasn’t just a software developer. I was also their system administrator. And I personally just wanted to program more.

I always kept an interest in Cergentis because spin-off plans [for TLA] started right after I had left Hubrecht Institute. Also, Petra Klous (Operational & Customer Contact Manager) is a friend of mine and I kept in contact with Marieke Simonis. I also knew Elzo de Wit, and Erik Splinter (CTO). So, I knew what was happening at Cergentis.

How did you experience our rapid growth?

Well, I was used to it because GenDx was always constantly growing. But it’s nice that, in this case, the Bioinformatics team gets to grow with it too!

Shortly after I joined Cergentis, Vera Boersma also made the decision to fully transition to the bioinformatics side. Mario Cangiano (Bioinformatics Scientist) was then hired, and Georgios Georgiou replaced Marieke as Head of Bioinformatics & Software Development. More recently, Hector Ordonez (Full-stack Developer) also joined us. In a way, it all happened very gradually.

Besides company-related meetings, does the Bioinformatics team meet up for fun and team bonding activities on the side?

Actually, we are trying to organize something because we do want to hang out more! There was this idea to play board games together every now and then, during lunch breaks for example. However, with the latest COVID restrictions it makes it difficult. We might have to wait a bit longer before this can happen.

Can you describe our work culture?

Cergentis has very clear objectives and does not hide what its short or long-term plans are. It is nice to get such transparency from the Management Team (MT)!

We also have the freedom, within our own team, to fulfill and achieve these goals as we see fit. It helps to have a Head of Bioinformatics like George, who can “defend us”. However, that’s rarely necessary! Often, it is all fine because the expectations set by the MT are realistic. So, it’s a very good working environment!

What are your current responsibilities?

Officially, my title is now Bioinformatician/Full-stack developer. That means that I am responsible for developing software (TLApp), with the goal of making it accessible to our customers who opt for our in-house solutions. With that said, my job also involves maintaining the software, QCing it and developing new features for the TLApp. Next to this, I also help others with any bioinformatics sub-tasks/related activities.

For those who are currently considering adopting our new and fully integrated in-house solution for CHO clone selection (CHOice), can you help explain what they can expect from the TLApp?

By distributing our new TLApp, our customers can immediately analyze their own TLA-based data as soon as they generate it. It’s also scalable! So, if they want to analyze many samples, it can handle it. With these advantages, the turnaround time will even be shorter for our customers!

Are there any other exciting developments in the bioinformatics pipeline?

Given that CHOice is our newest release, we want to make sure that as soon as we make any new changes, that those will be quickly introduced and made available to our customers.

Internally, we also aim to further automate our analyses, to further decrease the turnaround time of our TLA-based services for our customers. All the while increasing throughput of course!

Besides work, what are some of your favorite pastimes?

I really like photography! Especially nature photography. Therefore, hiking and biking are part of my hobbies too. Essentially, any activity that allows me to bring my camera. Besides that, I also enjoy watching movies, reading, and gaming of course!


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