Building our ambition in bioinformatics

Giving scientists the support to carry out ambitious big-data projects is a key aim of our BHF Research Excellence Award, REA4. Central to that support is a new team of bioinformaticians: Donncha Dunican and his team members Christelle Robert and Nikolaos Giannakis. Together, they are establishing a Bioinformatics Core Facility, providing in-house expertise and bespoke assistance for REA4 scientists grappling with research data.

All members of the team have experience in industry as well as academia, and bring wide-ranging expertise in analysing and integrating multiple data types. “You’re going to get brilliant support from us, and you’re going to get it in a very tailored way,” says Donncha. “We want to be as accessible and open as possible.”

Finding a way in

The team have taken various routes into bioinformatics, but a fascination with biological systems and a love of maths or physics are among the things they have in common.

Donncha’s experience of programming began around the age of 10, when his father – a Professor of Microbiology at the University of Galway – brought home a Macintosh computer during the Christmas holidays, which gave Donncha and his brother an opportunity for some early experiments in writing code.

When it was time to apply to university, bioinformatics was still getting established as a field and there were no degree courses in the subject. Donncha thought about becoming a mathematician, but in the end a fascination with genetics led him to study biochemistry. His interest in programming revived during his PhD, when he was working on studies of cancer gene activity. At the time, Excel spreadsheets could hold a maximum of 16,384 rows, while Donncha’s data had around 80,000 rows, so an engineer friend showed him how to write a script in Perl to manage and analyse the data.

Donncha continued with wet-lab research, but the amount of programming he was doing steadily increased. It was the explosion of omics technologies in the 2010s, which generated huge amounts of data on the activity of genes and the presence of proteins and other molecules in cells, that finally determined his fate as a bioinformatician.

Today, one of the things Donncha enjoys most about bioinformatics is the way a single dataset can reveal a multitude of insights. “I love the idea that there’s so much data out there in resources like the ones held by the National Center for Biotechnology Information in the US, or the European Bioinformatics Institute, where you can take people’s datasets and look at them from a different angle with a different question,” he says. “They might have spent thousands of pounds making those datasets, and you can analyse them without that cost and maybe see the data in a completely different way. I like the right to repair and I like to recycle things, so for me that’s like another kind of recycling.”

Fundamental principles

Christelle’s pathway into bioinformatics was shaped by a deep curiosity about the fundamental principles underlying biological systems. With a master’s degree in physical chemistry, she wanted to understand not just what biological systems do, but the physical mechanisms behind them. A postgraduate specialisation in molecular biophysics enabled her to build skills in computational approaches, which she further developed during doctoral training in computational biology.

“I’d always enjoyed programming, and bioinformatics provided the opportunity to combine that with understanding biological systems at a deeper level,” she explains. “As I learned more about what it entails I thought, ‘This is what I’ve been looking for.’”

Christelle also values the multifaceted nature of working as a bioinformatician. Her work has involved supporting people with grant writing and planning research projects, and she emphasises collaboration and relationship building as other crucial aspects of the role. “A fascinating part of the job is building relationships with people studying a multitude of biological systems,” she says. “I look forward to working with REA4 researchers to address diverse, interdisciplinary research questions.”

Seeking the unknown

Nikolaos always loved mathematics at school, but it was not until he started his degree in molecular biology that he began considering bioinformatics as a career. “I had this amazing professor who was teaching us computational biology,” he says. “It was really like he opened a window that we can use programming or statistics to access all kinds of biological information. That’s when I started thinking that this could be a good direction for me.”

He recalls the challenges of learning programming in the early days, and asking for guidance from friends who had studied computer science. “I had not been exposed to that before, and until you understand that programming is a philosophy, it can be very difficult,” he says. “Even when you’re experienced, you always need to keep learning and seeking out the unknown.”

In his new role, Nikolaos is looking forward to doing exactly that, as he works with scientists on a diverse range of topics and learns more about their research. “We’ll talk to people, help them analyse their data, and identify the best way possible to find out what’s going on in the biological systems they’re studying,” he says, “and we’re here to do that in a very friendly and collaborative way.”

Sharing skills

Another quality the team have in common is an enthusiasm for sharing their knowledge with others. Nikolaos is teaching statistics and RStudio to third-year biomedical students, while Christelle has been involved in developing and delivering bioinformatics training for researchers in low- and middle-income countries. Donncha has worked on courses in conjunction with Ed-DaSH, the University’s data science training programme for health and biosciences. He’d also like to set up new courses to complement those currently on offer. “There may be a need within our centre to do slightly different courses, maybe for people working on metabolomics or proteomics or imaging,” he says. “We’re keen to hear what people would like to learn about.”

If you have ideas about new training courses, or would like help or advice from the team, you can find out more about their services and request support on the new BHF Bioinformatics Core webpages.

As the team’s work gets under way, Donncha is looking forward not only to helping solve research problems but also to building a community of scientists who feel more informed and confident in analysing their data. “I think this is the perfect role for me,” he says. “I can take my knowledge of biology and my knowledge of computational work, combine it with some of the best aspects of industry, and grow something organic from the ground up. It’s really exciting.”

Links

BHF Bioinformatics Core

Ed-DaSH data science training programme for health and biosciences