Conversations with experts: applied bioinformatics in life (sciences)

In anticipation of the upcoming Applied Bioinformatics in Life Sciences conference, we had the pleasure of sitting down with two experts. The first is Alex Botzki, head of the Technology Training unit at VIB and driving force behind the conference. The second is Amelie Stein, an invited speaker who leads a lab at the University of Copenhagen. Both share insights into their work, hot topics in the field, collaboration, and their vision for the future of bioinformatics.

Alexander Botzki (left) and Amelie Stein (right)
Alexander Botzki (left) and Amelie Stein (right)

Could you tell us a bit about your work in applied bioinformatics?

Amelie: “Certainly. I work in protein modeling, and my focus is on the consequences of mutations on proteins. Each person's genome has approximately 10,000 sequence changes. Most of these changes are well-tolerated without any major effects, but some can have severe consequences. In my lab, we use AI-supported modeling methods and sequence analysis to understand the impact of changes in protein structure and function. We also do high-throughput experiments to test those consequences experimentally for a few proteins.”

Alex: “I don’t do research as such, but I have a service role in technology and bioinformatics training at VIB. I lead the VIB Technology Training unit. Our unit collaborates with colleagues from VIB Technologies to co-create training courses that cover the entire service offering, from experimental design to data analysis and reporting. Our ultimate goal is to provide a comprehensive curriculum that includes all available technologies. I think it's a noble cause to train people, and I'm proud to be a part of it. Our scope has broadened over time, and bioinformaticians have become a larger fraction of our target audience. In fact, that’s why I suggested the topic for this conference ten years ago.”

Speaking of the conference, why do you think applied bioinformatics is such a hot topic right now?

Amelie: “In the life sciences and industry, we see an avalanche of data being generated. This sparks a great interest in finding ways to tackle it. Additionally, I feel like the field is rapidly expanding. Compared to demand, there is still a lack in bioinformatics education. At the University of Copenhagen, where I work, we have now established an official bachelor's program in bioinformatics to address this.”

Alex: “It’s fantastic to see the educational landscape evolving to meet the growing demand. And, let's address the elephant in the room: the AI boom. Although Machine Learning has been around for ages, the recent surge, especially in generative AI, is mind-blowing. The challenge ahead is connecting these methods to tackle biological questions, and that's what makes the conference theme so spot-on.”

Is there any specific topic or speaker you’re excited about?

Alex: “Definitely! can't wait for Sergey Ovchinnikov's session. His accessible notebooks on structure prediction are game-changers. Plus, his commitment to open science is something I deeply admire. I’m also looking forward to Amelie’s talk! She also built some accessible applications and will also give a training session on one of them before the conference. ”

Amelie: [laughs] “Thanks! I’m actually really excited for Sergey, as well! His work at the intersection of structure modeling and machine learning, particularly from a smaller independent lab, adds a unique perspective to the field.”

How do you collaborate with others in your field?

Amelie: “Collaboration is vital in bioinformatics, especially with those who conduct experiments. We also work with other bioinformatics labs to exchange different methods. However, it is essential to validate models experimentally, as otherwise it just becomes an academic exercise. I think conferences, in a way, are a collaborative space, too! I'm particularly excited to restart the international conference experience for my PhD students who missed out due to COVID.”

Alex: “Collaboration has been a game-changer for us within Elixir, the European Bioinformatics infrastructure. We’ve really built a great network of like-minded people. I think it’s important to get insights from other EU institutions, learn from each other’s approaches, and give back to the community. We have already created a curation framework for e-learning content and are working on extending tools like TeSS for a one-stop-shop European training experience.”

Where do you personally think the next breakthrough lies in this field?

Alex: “I don’t have a crystal ball, but I think we’re moving fast toward predicting entire organisms from molecular data. I think the combination of different AI methodologies and robotics holds a lot of potential. In general, I think we’re heading towards a future where humans could work less. However, to achieve this, we will have to continue to promote lifelong learning and utilize training to reskill people.”

Amelie: “I'm keeping a close eye on the intersection of image analysis and bioinformatics, especially the combination of microscopy images with library screening. And from a structural perspective, I think dynamics will be booming. Recent advancements like Alpha-Fold2 keep us all on our toes about what is coming next.”

As a child, could you have imagined doing this work?

Amelie: “When I was 14 years old, I saw a protein structure, and I was completely captivated. I found a bioinformatics education and never looked back – though I had to search a bit to find mentors who shared my interest in protein structures. While I envisioned a career in science, bioinformatics unfolded as I explored my interests. It’s been a fascinating journey.”

Alex: “Same here. I knew that science was going to be the path, though the journey took some unexpected turns. I transitioned from pure chemistry to a multidisciplinary field, which made me more of a generalist. Although it was never the plan, I found out I really love teaching!”

If you could ask an omniscient higher being one question, what would it be and why?

Alex: “I’d love to brainstorm ways to create a better life for more people around the world.”

Amelie: “I would ask how to achieve world peace or combat climate change.”

And finally, what’s your favorite book at the moment?

Alex: “I’m currently immersed in ‘War and Turpentine’ by Stefan Hertmans. It’s a fascinating historical novel with lots of analogies from which we can learn.”

Amelie: “Right now, I’m reading The Imperial Radch Trilogy. This sci-fi opera is my favorite series at the moment.”


Thank you both! Looking forward to seeing you at the conference.

India Jane Wise

India Jane Wise

Science Communications Expert, VIB


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