“We had to rethink everything: the samples, the systems, the scale”
The 25-year journey from Microarray Facility to cutting-edge Nucleomics Core
In two weeks, we celebrate a key milestone: the VIB Nucleomics Core's 25th anniversary (you are invited!). What began as the institute’s first institutional core facility has grown into a cornerstone of its research infrastructure. Along the way, it has quietly played a central role in shaping how technologies are integrated, scaled, and shared, not only within VIB, but increasingly across the broader scientific ecosystem.
The early days: microarrays
The story of the Nucleomics Core started in 1999, with the founding of the MicroArray Facility or MAF. At the time, VIB leadership saw a shift coming: research was becoming more data-driven and technologically complex. Techniques like PCR and microscopy were widely adopted, but microarrays required more infrastructure, more training, and more consistency.
“Microarrays were not trivial,” says Geert Van Minnebruggen, VIB’s Technology Director. “They required infrastructure, standardization, and specialized handling. Centralizing that expertise was essential if we wanted to make it broadly accessible.”
The model proved effective. The facility supported research across life science domains, from neuro to cancer to plant biology. More than a technical solution, founding the MAF was also a statement of intent. Technology would not be an afterthought. It would be embedded, professionalized, and available to all.
Kizi Coeck, now lab manager, was a student working at the KU Leuven Center for Human Genetics at the time. In those early days, she was intrigued by this up-and-coming service lab.
“I always had to collect arrays from the MAF for our lab. Whenever I went up there, I always thought, ‘This place seems exciting.’ There was something about it—the machines, the process—that made me want to be part of it.”
She joined the MAF in 2005, and her first task was to operate the newly acquired microarray spotter, placing DNA fragments on glass slides for hybridization. It was her first experience working hands-on, developing the arrays she had previously only picked up as a student, and it gave her a new appreciation for the complexity behind them. “I realized how much precision and effort went into creating an array from start to finish,” she says. “It was a real eye-opener.”
The dynamic nature of the work, coupled with the evolving technology, made it an exciting place to grow. Much of that energy, she adds, came from Paul Van Hummelen, the facility’s first head: “Paul created a great atmosphere. He was approachable, respected, and truly invested in both the science and the people. Everyone who worked with him felt that.”
A technology transformed
The late 2000s brought a wave of change that would permanently reshape the MicroArray Facility.
In the early days, the facility worked with a mix of in-house spotted arrays and commercially available ones. These internally developed arrays were highly adaptable and well-suited to the diverse needs of the VIB research community. But as commercial providers improved the quality and customization of their offerings, the need for in-house array production diminished. By 2008, the decision was made to stop producing custom arrays internally.
Around the same time, sequencing technologies started to mature. But it was far from clear which platform would ultimately dominate. Multiple players were vying for relevance, including Roche, Applied Biosystems, and a still relatively young company called Illumina.
“We were in a kind of transitional phase,” says Geert. “The science was moving fast, but there was still a lot of uncertainty. We knew sequencing would be key, but nobody knew yet what the standard would be.”
The team began offering services in short-read sequencing and, over time, expanded into long-read platforms. To reflect this expanded scope, the facility was renamed the VIB Nucleomics Core. The new name captured both the technological transformation and the growing importance of analysis across the full spectrum of DNA and RNA-based research.
Geert Van Minnebruggen: “We made a conscious decision to not focus on one single platform and keep our offering broad, not just to keep up with the field, but to create something that could truly support where research was heading.”
Bigger and bigger
The Core’s first sequencer was Illumina’s MiSeq. “It was a benchtop sequencer, but it already felt huge at the time,” says Kizi. “Everything had to change: the protocols, the lab setup, the way we handled samples…”
That shift brought not only new workflows but also new realities. Unlike the relatively low-cost, small-scale microarray projects, sequencing introduced a steep increase in reagent and equipment costs. “I remember looking at the purchase orders for flow cells and thinking ‘wow, we are really spending a lot of money’,” Kizi recalls.
As sequencing matured, project sizes grew and high-throughput became the new standard. Workflows that had once managed a few dozen samples began routinely handling hundreds, with far more data, and far greater expectations.
The arrival of the NovaSeq pushed those boundaries even further. “Our first run was exciting but also nerve-racking,” says Kizi. “The data output was enormous, and we knew the stakes were high. Now we run NovaSeqs every week. Easy peasy!”
Behind the scenes, the operational model had to evolve too. In 2015, Stefaan Derveaux took over as head of the core at a time when both the technology and the service model were under pressure. “We needed a different cost structure, a new approach to data handling, and more robust internal infrastructure,” he recalls. Together with Geert Van Minnebruggen and the team, Stefaan guided a course of renewal, strengthening the bioinformatics pipeline, revamping internal processes, and bringing in a dedicated system administrator to manage data backups and streamline data flow.
“We were producing more data than ever before, but we lacked the infrastructure to support it,” he says. “There was no centralized Data Core yet, so we had to build it ourselves, piece by piece. It was a steep climb, but it laid the foundation for everything we do now.”
A new era of automation
The next transformation came not from sequencing itself, but from how the core managed sample volume. With project sizes increasing and researcher expectations rising, manual processing began to show its limits.
A key turning point came through a collaboration with the Jeroen Raes lab on a project involving more than 15,000 samples. It provided both the urgency and the opportunity to rethink how workflows were structured and to make the core’s first significant investments in automation.
“That project gave us the push we needed,” says Stefaan. “We started with one robot, then added more. Now we have five.”
The automation strategy was deliberately modular. Rather than locking into one large system, the team introduced smaller, interoperable platforms that could be adapted and reconfigured as needed. As technologies like single-cell and spatial omics continue to evolve, the team is well-positioned to integrate new workflows without overhauling existing infrastructure.
“Our technicians now learn Python,” Kizi says. “They program the robots themselves. It makes the work more engaging. And we can scale more confidently because the systems are in our hands.”
A model for technology integration
Over its 25-year journey, the Nucleomics Core helped define what a core facility can be, and what role it should play in a research organization.
“Our Cores are not side projects,” says Geert. “They are dedicated platforms for discovery. The Nucleomics Core helped prove that model, not just once, but continuously, by evolving with the science.”
The Nucleomics Core was the very first core but also unique in that it was launched centrally from VIB headquarters, rather than emerging from within an individual research group. “It was a bit of an experiment at first,” Geert recalls. “But it proved that a centralized, professional core, not tied to any single PI, could deliver value across domains and scale as needed. That changed how we approached all the cores that came after, and has influenced how we approach cross-core collaboration today.”
Instead of consolidating everything under one roof, VIB has opted to build strong individual cores and link them through shared pipelines and strategic alignment. This enabled cross-cutting initiatives in areas like single-cell and spatial technologies. The approach has also allowed VIB to remain flexible as the landscape changes, testing and introducing new platforms as needed, while keeping operations coherent and user-focused.
“Installing a new platform is only one part of the challenge,” says Stefaan. “What really matters is building the right system around it—technically, financially, and organizationally—so that it continues to support researchers as their needs evolve.”
Future-focused
Today, the Nucleomics Core remains firmly future-focused. Illumina’s long-standing dominance in sequencing is being challenged, as new players are entering the market. Recently for example, the core was the first in Europe to adopt Element’s new AVITI system, underscoring its continued commitment to early technology evaluation and platform innovation.
“We are not here to chase every shiny new thing,” clarifies Stefaan. “We want to be early, but also realistic. If something has the potential to improve science, we test it. And when it’s ready, we scale.”
As sequencing becomes increasingly intertwined with spatial omics, proteomics, and imaging, the core is preparing for a more connected and integrated technological landscape, one where data generation is just one part of a much broader pipeline.
“We are heading into a new era,” says Geert. “Sequencing is no longer a standalone capability. It becomes a readout method, embedded in larger systems, tied to biological context, and integrated with complementary data types.”
Powered by people
Throughout all the shifts in tools and technology, one thing has remained remarkably consistent: the way the people behind the core approach their work.
From the start, the lab attracted individuals who were curious, collaborative, and committed to quality. That remains true today. Whether designing a pipeline, optimizing a protocol, or supporting a new user, the team is known for its openness, professionalism, and drive.
“We are ten people,” says Kizi, “but no two are alike. We all have very different personalities, backgrounds, and working styles. But that is what makes it work. We learn from each other, and we make each other better.”
She credits both past and present leadership for helping maintain that team spirit. “Paul set the tone in the early days. He was approachable, respected, and present. Stefaan has carried that forward. He is steady, supportive, and makes it easy for us to keep doing our best work.”
Geert agrees:
“You can buy the same machines anywhere. What makes the difference is the mindset: the culture you build, the people you attract, and how you keep moving forward together.”
“I never imagined we would go from spotting arrays to programming robots,” Kizi says, laughing. “But here we are.”
She adds, more seriously, “I think we’re all proud of what we’ve built here. The work we do is cutting-edge, and we’re eager to show it.”
Come celebrate 25 years VIB Nucleomics Core
The VIB Nucleomics Core team invites you to mark this milestone with them on 19 May 2025. The day will feature:
> Scientific sessions with internal and external speakers
> Lab tours offering a behind-the-scenes look at the core
> Networking reception to reconnect, reflect, and raise a glass to the future
VIB Nucleomics Core, Gasthuisberg Campus, Leuven
Register now
Liesbeth Aerts
