Ulrike Boenisch

Sometimes the path to sciences unfolded on its own

Read more about Ulrike Bönisch's story. Discover her diverse responsibilities as the head of our deep sequencing unit - from quality control and troubleshooting to the introduction of new technologies. Learn how she, as a career changer, has managed to advance from the daughter of a farmer to a technically adept scientist. Also, find out how essential it is to keep pace with technological progress through collaboration in order to successfully navigate a highly specialized research unit through the dynamic research landscape of genomics.

Could you just give us an idea what your role is as the head of the deep sequencing facility? What are your main responsibilities?

I’ll start with a little disclaimer. Everything we’re doing is a real team effort, alongside my team and the bioinformatics group. As for my role, it’s multifaceted. It begins with ensuring our facility is in top shape, making sure we have everything we need. We focus on providing access to our sequencing service. We address relevant questions and technologies with tailored workflows in a service-oriented approach. One of the challenges is delivering highly accurate results. Over the years, we’ve developed a comprehensive net of quality control measures that act as an alert system, quickly detecting any issues. This brings me to another crucial aspect of my work: troubleshooting. We delve deep into issues, layer by layer, whether it’s related to data, hardware, software, workflows, or samples. It keeps us busy, but each problem we solve teaches us something new, making us. Another significant aspect is the constant interaction and dialogue with researchers. We’re always asking: What do you need now? What about in the future? This leads us to strategic discussions like: ‘Which technologies should we invest in?’ We’re committed to staying at the forefront, ensuring we have the latest tools to generate the best datasets. However, implementing new technology is a rigorous process, especially in compliance with regulations. It’s time-consuming; despite our desire for speed and competitiveness, navigating grant approvals, procurement, financing, and installation typically takes about a year. Balancing agility with bureaucratic processes is a challenge, particularly in the public sector. Managing these tasks consumes a significant portion of my time, constantly juggling these key responsibilities.

Can you outline a typical workflow you offer at the facility?

It seems straightforward at first glance – a classic input-output scenario. But truth be told, it is often a more nuanced sequential process, especially when we’re tackling big-picture biological questions. We’re not just churning out data; we’re tailoring it to fit specific research queries. So, picture this: there’s a biological question, and we dive into this collaborative dance between researchers, deep sequencing team, and bioinformaticians. We’re figuring out the best dataset we should produce to answer the question. Then we get, let’s say, a DNA sample, but before we can run it through our analyzers, there’s a whole quality control routine to ensure it’s prepped just right. We’ve got to finesse it to match the technical specs of our instruments, hitting that sweet spot in terms of length or quantity. Once it’s analyzed and digitized, it’s packaged up and sent off via servers, undergoing yet another round of quality checks before reaching the end user. Sometimes they can already find their answers in the data; other times, they’ll need to send us more samples for further analysis. And that’s pretty the way we are operating.

Can you describe how you became head of the sequencing facility. You specialized in genomics and this eventually led you to the position you are in today.

You know, looking back, I sort of stumbled into this role. Genomics wasn’t my specialty; I kind of learned on the fly. My background was more in a technology, not in this specific branch of biology back then. This was around 15 years ago when the whole sequencing and genomics scene was just taking off. Back then, during my PhD, I was doing microarray work in a collaboration project between the University Hospital and the then Institute of Microsystem Engineering in Freiburg. This technology of making microarrays was back then the technology to do transcriptomics or genomics, but nobody talks anymore about microarrays now. After my PhD, I found myself at a pivotal moment when Thomas Jenuwein arrived at the MPI with plans to kickstart a bioinformatics and a sequencing facility. He needed someone who knew their way around the tech, and well, I fit the bill, sort of. So, we started from scratch. I mean, there was literally nothing here and we built the facility up from the ground. I grew into the genomics field as we went along, learning as we progressed. Thinking about it now, I don’t think it would happen the same way today. You’d probably need a more solid background in genomics from the get-go. But hey, back then it was still possible to start such a position as lateral career mover.

There’s a lot of technological advancements in the field how do you keep pace?

It's tough. But I am not navigating this alone; it's a collaborative effort, especially when it comes to acquiring sequencing equipment. Given the limited number of providers in the market, there's considerable interaction and support available. That makes it all a bit easier. Moreover, there's a network of academic facility heads across Tübingen, Berlin or at EMBL in Heidelberg. We exchange information and experiences, comparing investments and strategies. This collegial approach helps us gauge our standing and make informed decisions. And I can compare if we are at the same level and I can see what they invest into and why. Additionally, within our own group, Bioinformatics and DeepSeq, we benefit from a wealth of insights and perspectives. We're also plugged into the wider research community, where discussions often drive innovation. For instance, as the field transitioned from short-read to long-read sequencing, we followed quick to ensure we can offer comprehensive analyses. But in some case, we also align with the interests and initiatives of specific research groups. We're committed to maintaining a cutting-edge facility, even if it means continually evolving and adapting to changing trends.

Was it always clear to you that you would like to become a scientist or somebody who’s using state-of-the-art technology for doing research?

I don't come from an academic family; both sides were farmers. Instead of following in those footsteps, I joint the gymnasium and later dived into studying nutrition science. But it was the science part of nutrition science that really captured my attention, not so much the applied nutrition side of things. I was fascinated by biology and biochemistry. Eventually, I decided to go for a PhD, but I steered away from nutrition and into the realm of basic molecular biology and technology, right here in Freiburg. There was something about the technical side of things that really appealed to me more than the big scientific questions. I was all about getting those precise answers, using technology, and producing results. And this whole science adventure in my career? Definitely not something my parents had mapped out for me, given our family background. It kind of just happened, step by step. I often find it interesting when I chat with others who've always had a clear vision of what they wanted to do. That wasn't me; my path sort of just unfolded on its own. However, it feels like it was meant to be, especially being here at the Institute because the whole package here fits extremely well. I can't imagine being anywhere else or doing anything different.

If you would go back and if you could give some sort of advice to your younger self at some point is there anything where you would say?

Reflecting on my own experiences and observing the young IMPRS students, I often think, "You've made a smart choice by opting for a structured PhD program." Unlike my journey, where I frequently found myself stumbling into situations without clear direction, leading to a prolonged PhD of six years due to the lack of structured support and mentorship. In contrast, these students have chosen a path that offers organized mentorship and collaboration, set within a timeline. This structured approach not only facilitates their academic journey but also ensures they're not navigating the challenges alone. Seeing this, I can't help but wish I had been more discerning about the opportunities I pursued, looking for programs that offered more than just a position but also mentorship, peer support, and a definitive end point. It's crucial to ensure that you are gaining valuable experiences and not overstaying in your doctoral studies without clear progress. If I could give advice to my younger self, it would be to seek out environments that offer mutual growth, ensuring that while you contribute, you're also receiving something enriching in return, avoiding the trap of an extended stay without advancement.

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