Fergal Martin – Eukaryotic Annotation Team Leader

Fergal Martin discusses the importance of open access data and his work in different biodiversity initiatives

Man leaning against a window with corridor in the background
Fergal Martin, Eukaryotic Annotation Team Leader at EMBL-EBI. Photo credit: Jeff Dowling/EMBL-EBI

Access to accurate genome annotations and comparative genomics resources – the locations of repeats and genes in a genome and how different genomes relate to one another – is a fundamental need for many researchers. Fergal Martin has stepped up to a new challenge as Eukaryotic Annotation Team Leader and, in this role, he will be responsible for prioritising the eukaryotic genome annotations produced by EMBL’s European Bioinformatics Institute (EMBL-EBI).

What is your professional background?

I started studying bioinformatics through a degree in Computational Biology and Bioinformatics and followed that with a PhD in comparative genomics and evolutionary biology, both at Maynooth University in Ireland. For my PhD, I focused on looking at how and why genes cluster in bacteria along with how well we can separate the evolutionary relationships between and within different bacterial groups.

After that, I did a postdoc at Trinity College Dublin looking at de novo gene formation in primates. This is the process by which random mutations occurring in ancestrally non-coding regions of the genome lead to the formation of open reading frames. I was trying to find examples of this; it’s a very rare occurrence and it’s hard to tell how biologically meaningful these things are.

I then had a brief stint at being an independent game developer. I spent a year building and releasing my own game for Android devices. It was a fantastic experience and so much fun to dedicate time to building something from scratch. It was also a great opportunity to practice programming in a highly resource constrained environment. At the time, smartphones were not very powerful and trying to build something that worked well across many different devices was a real challenge.

Finally, I joined Ensembl as part of the Genebuild team, initially at the Wellcome Sanger Institute. A year later, we moved to EMBL-EBI.

What does your role entail?

I oversee the eukaryotic annotation within Ensembl, so I’m navigating the strategic direction of the Comparative Genomics team and the Genebuild team.

The Genebuild team creates genome annotations from genome assemblies of different species. This information gets passed to the Comparative Genomics team who aligns the genome sequences with other species to figure out the links in their genomic alignments. This team also builds phylogenetic trees to show the relationship between genes across species.

I also help to balance this work not just with the needs of our individual users, but with large biodiversity initiatives like the Darwin Tree of Life (DToL) and the Earth BioGenome. One of the aspects I enjoy most about the job is getting to be part of all the different communities and consortia to help ensure all these high quality genome assemblies get decorated with genome annotations and comparative analyses, which really helps accelerate downstream research.

What motivated you to work at EMBL-EBI?

Since the early days of my university studies, I was aware of the work going on at EMBL-EBI. We had a book called ‘Introduction to Bioinformatics’ that included details on Ensembl and UniProt, and I used EMBL-EBI resources pretty much daily from my undergrad days right up to my time as a postdoc. So when I saw an opening in the Ensembl Genebuild team, I jumped at the chance to get to work with the people who developed these resources and participate in making a difference for the people using them.

The fact that EMBL-EBI data is open access has benefited my research enormously. The downstream achievements made possible by these open access data have a massive impact on many fields, including human health and food security. It makes me proud to be part of this whole process.

What are some of the challenges in your new job?

A big challenge for me is trying to balance expectations; we work on a lot of different projects and we constantly need to prioritise the data we are putting out. I try to find the best balance between the resources we have and to ensure that our users are getting the data they need quickly. Our work also spans many different consortia and large scale sequencing projects, so I need to think carefully about how best to allocate my team’s resources to work on all of these.

What is your approach as a manager?

I like to lead by example, so I can be quite hands-on with projects. I’m always really interested in the technical side of things and underlying biological questions, so I tend to get involved in steering the direction of our projects. I care greatly about the work that’s going on and I enjoy working with my team to find new solutions and motivating them to enjoy the work too.

What is one thing we couldn’t find out about you from an online search?

I love fencing; I’m a former national champion in Ireland and competed in the Irish national team when I was younger. I still train multiple times a week and enter competitions. I take it less seriously now, but it’s something I love doing and have done for a long time. It’s a very tactical and strategic sport but also incredibly quick; you need good reflexes. The combination of the physical and psychological aspects of fencing are what I really enjoy about it.

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