ProfessorDenis Shields

Our group focuses on identifying functional regions of proteins and genes that impact on disease risk and therapy. This is focused on studying functional short fragments of proteins, termed peptides, and on studying polymorphism in disease.

GENETIC POLYMORPHISM AND DISEASE Genome wide association technology and sequencing technology are revolutionising the discovery of genetic associations. We are interested in human disease and in infectious microbe genomics. We have particular interests in gene combinations (epistasis or synergy) and in amino acid altering variants.

PEPTIDES We are particularly interested in computational means of discovering bioactive peptides, which may be generated from food hydrolysis or provided by chemical synthesis. These peptides may be used as tools to understand biology, or may be used for their therapeutic benefit. Our research has led to the development of a suite of software servers as well as downloadable software dedicated to identifying peptides and motifs of functional importance (http://bioware.ucd.ie).

FOODS WITH OPTIMAL BREAKDOWN OF PEPTIDES When we digest protein in foods, it is broken down into many sub-fragments before being degraded completely into the amino acid building blocks that are used to build new proteins in our own body. These fragments are called peptides, and many of them can exert health altering effects. We are studying how breaking down food proteins before eating them, and enriching for subsets of peptides, can be health protecting or promoting.

BACTERIAL GENE ANALYSIS We are working on developing methods to identify gene clusters in bacteria more efficiently. in particular, we are focussing on domain clustering. These methods can help researchers identify new clusters of genes of related function, thus helping to make sense of the vast amount of genetic information being generated on bacteria in many environments, including the gut, skin, soil and water.