Barry Ryan on developing tools to integrate multiple genomic datasets

Tell us about the project you presented at the ENGOG Symposium and how your work involves genomics/makes use of genomic technologies

My research involves the integration of multiple genomic datasets for predicting patient outcomes. Our belief is that different disease signatures are captured in different genomic datasets. In order to capture all these signatures, we have to leverage all the genomic data available. Combining genomic data can be difficult due to missing patient data, the large scale of the datasets and different data types in each dataset. We have developed a tool called Multi-Omic Graph Diagnosis (MOGDx) which overcomes many of these challenges. MOGDx represents genomic data as a network by measuring the similarity between patients with a disease. We then use artificial intelligence to perform network integration and stratify patients into disease subtypes, gradings or other applications. So far, we have highlighted the effectiveness of this method on cancer datasets and in stratifying individuals with Parkinson’s disease.

Please summarise your previous work and career so far.

I completed a degree in Electrical and Electronic Engineering from University College Cork in Ireland. While there I completed a research internship in MIT in Boston and also a work internship in an engineering company called Qualcomm. Unfortunately, MIT weren’t hiring, and I ended up working as a Digital Design Engineer on the debug team for Qualcomm in Cork for 1 year. Qualcomm are responsible for making the processing chips for smart phones and my job involved ensuring that all the different components such as camera, Wi-Fi chip, screen etc, were able to communicate properly during testing. I applied and was accepted onto a master’s research program in Trinity College Dublin in Computer and Data Science. During this time, I developed more skills in the field of artificial intelligence and in particular the applications of it to biology. I completed my masters project predicting the risk of relapse in patients with the condition ANCA vasculitis. It was this experience that motivated me to join the Biomedical AI CDT programme in Edinburgh where I obtained a second master’s during my first year. This was my first real taste of genomic data, and I haven’t looked back since.

What inspired you to follow your career path?

I was never a child who knew exactly what they wanted to be when they grew up. My career path has largely been dictated by following my interests and exploring different opportunities. I always enjoyed math and science which led me to undertake a degree in electrical and electronic engineering. On completion of the degree, I had thought about further research, however, I ended up accepting a role in industry. Sometimes, understanding what you don’t like is important, and pretty quickly during this time, I knew I wanted to pursue a career path in science research. The freedom to experiment, explore different topics and add to the human knowledge domain are things that inspired me to make that switch and continue to inspire me throughout my research.

If you could have tea with anyone (alive or dead), who would it be? What would you talk about?

I’d like to have a cup of tea with David Goggins. David Goggins is a retired Navy Seal, an ultra-marathon runner and has been labelled ‘the toughest man alive’. He takes a brute force approach to life and outwardly believes that our biggest limitation is our own minds. I’d love to get his perspective on this and the role of genetics in being able to accomplish some of the crazy things he has done.  

What is the most unusual thing you have done during your career?

There aren’t many unusual things that can happen behind the safety of a computer screen. The most unusual thing that comes to mind is winning a water powered rocket competition in high school using a 2L plastic coke bottle, a carboard cereal box and one of my sisters High School Musical DVD’s (again, sorry Molly).

Do you have any advice for people wanting to pursue a research career? What do you like best about your job? What do you like the least?

My advice for anyone considering a research career would be to try it. A career in research provides the freedom to follow your instincts and explore areas that you are interested in. The research community is diverse, welcoming, and always happy to help. One aspect of the career, which I still struggle with, is the open-ended nature of the work. Rarely is there a clearly defined end goal. This is freeing in that you can experiment as much as you like but it can also be daunting and difficult to know when enough is enough.

How do you spend your time outside of research? Is there anything else you would like to tell us about?

Outside of research, I enjoy being active and playing sport. I play Gaelic Football (an Irish sport which is a cross between basketball and rugby) with the local men’s team in Edinburgh called Dunedin Connolly’s.  I love to watch and attend rugby games. I try to go to Murrayfield as often as I can. Otherwise, I love to run along all the different paths around Edinburgh such as union canal, water of leith and trinity path.

Recent preprint

Barry has recently published a preprint alongside his PhD supervisors Professor Ian Simpson and Professor Riccardo Marioni. In this preprint he introduces 'Multi-Omic Graph Diagnosis (MOGDx)', a bioinformatic tool for the integration of multi-omic data to perform classification tasks for heterogeneous diseases. 

Links

Biomedical Informatics Group

UKRI CDT in Biomedical AI