Interview: Nanopore sequencing: the mobile methylome

Adam Ewing leads the Translational Bioinformatics Group at the Mater Research Institute - University of Queensland in Australia, where he works to develop methods and software for analysing high throughput genome sequence data. Ahead of his upcoming webinar with Technology Networks, we talked to Adam about his research and how long-read sequencing is having an impact on our understanding of genomic regulation.

Adam will be presenting his webinar ‘Nanopore sequencing: the mobile methylome’ on Thursday 19th November at 4pm UK time, describing how long reads, combined with the ability to infer methylated CpG bases, greatly facilitates the study of transposable element genomics in particular and the methylome in general.

What are your current research interests?

Mutation, transposable element genomics, evolution and susceptibility to genetic disease, collaborative bioinformatics.

What first ignited your interest in genomics?

As an undergraduate in computer science, I think it was recognising the potential to use computational methods to explore questions in biology.

Can you tell us more about how long-read sequencing technology is changing your field? How has it benefited your work?

It seems like we’re on a track such that routine assembly of entire large genomes from long reads, coupled with methods from metagenomics, will fundamentally revolutionise genomics. Long reads enable better resolution of structural variants, including transposable elements which are challenging due to their high copy number.

Couple this with relative affordability and direct resolution of DNA methylation and it’s a game changer.

What impact could a greater understanding of the methylome have?

Speaking about transposable elements specifically, it will help us understand their (dys)regulation in various contexts e.g., differential methylation across tissues, developmental stages, and tumours. Speaking more generally, given the importance of methylation as a regulatory layer on the genome it’s difficult to overstate the impact of a comprehensive and accurate picture here.

What have been the main challenges in your research and how have you approached them?

As someone who does a lot of collaborative work, finding time for my own projects is a key challenge.

What is your advice for someone getting started?

In relation to bioinformatics specifically, build a solid foundation: statistics, algorithms, command-line skills. Try to find a research environment and a mentor that is supportive yet enables you to work on what interests you. Avoid being painted into a corner with your research topic.

Make sure you tune in on Thursday 19th November to hear the full story from Adam, in Nanopore sequencing: the mobile methylome’.