Neural networks researcher scoops Embark award

27 May 2004

A 22-year-old electronic and computer engineering graduate from Roscommon has won the inaugural Embark IEI Computer Science Achievement Award.

Shaun Mahony (pictured), a postgraduate researcher at NUI Galway, won the prize for his research project, Neural networks to identify functional patterns in DNA sequences, an advanced computer-based study of the interactions between DNA strands, the building blocks of life within the cell.

The Research Achievement Award is sponsored by the Institute of Engineers of Ireland and the Irish Research Council for Science, Engineering and Technology’s Embark Initiative – a major national research funding programme that supports researchers at masters, doctoral and post-doctoral level and encourages them to build their careers in Ireland.

Computer science deans of research throughout third-level institutes in Ireland nominated the 11 candidates shortlisted for the award.

Mahony is based at the National Centre for Biomedical Engineering and Science within NUI Galway, where he is one of 80 researchers deployed in bioinformatics research work. This has been a thriving area of research, particularly since the 2001 announcement of the unravelling of the human genome, which has led to new challenges and opportunities for researchers in the area of medical cures and therapies.

Mahony’s project involved using neural network algorithms – artificial intelligence tools – to identify common or repeated patterns within bacterial genomes. These textbook algorithms were written many years ago and are highly popular within the computer science community, but it is very unusual to apply them to the analysis of molecular biology as Mahony has done.

“The algorithms are like a recipe: it’s up to you as a researcher to apply them to different problems,” he remarks.

Mahony explains that his research has two elements. The first involves looking at gene predictions in harmful bacteria such as meningitis. The second attempts to find biological ‘switches’ – tiny fragments of DNA code – that turn genes on and off. “If you can see what’s going on in a cell, you can potentially shut off a gene,” Mahony observes.

As part of his studies, Mahony recently spent five months at the University of California at Berkeley, one of the top three bioinformatics institutes worldwide. Researchers at Berkeley and Galway’s National Centre for Biomedical Engineering and Science are currently working together on a project to develop software that can predict the location of certain types of DNA.

In addition to a special certificate, Mahony was awarded a €3,000 bursary to be spent on bioinformatics research, which he says he will possibly use to fund visits to other research laboratories in Europe.

As to the future, Mahony’s short-term goal is to complete his doctorate. Although it is likely he will spend some time abroad after that, he thinks there should be also plenty of scope for career development at home, both within science generally and within his own research discipline, thanks to the Government’s increased funding for the area.

“The Regenerative Medicine Institute [Remedi] that has just opened at NUI Galway is a great example. This will conduct research into stem cell research. This is an encouraging sign that the bioinformatics area has plenty of opportunities,” he adds.