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Full NameProfessor Denis Shields


Organisation:University College Dublin

Email Address:Email hidden; Javascript is required.

Research Fields
  • genetics, genomics and molecular biology
Postgrad Medical Specialties
  • Medicine
Medical Subspecialties
  • Cardiology
  • Clinical Trials
  • Dermatology
  • Gastroenterology
  • Haematology
  • Health Informatics
  • Hospice and palliative medicine
  • Infectious diseases
  • Immunology
  • Neonatology
  • Nephrology
  • Pharmacology
  • Rheumatology
  • Vascular Medicine
My Work

Bioinformatics is used in our group to characterise and discover patterns of associations of sequence related data to disease processes. We have interests in genetic sequence variation in disease, in collaboration with rheumatologists and cardiologists. We have been developing specialised software to make sense of protein and peptide data, with a particular interest in the role of protein breakdown into peptides and the roles of digestive and inflammatory proteases in gastrointestinal disorders. We are also interested in the development of beneficial nutritional products for medical needs, using software methods to predict design and analyse the compositions of peptides and other protein factors in the foods. Computing tools used include machine learning, with varied applications, sequence analysis, statistical modelling and visualisation.

A listing of publications is available at:

Potential Projects

The role of proteolysis in Inflammatory Bowel Disease (supervisor: Denis Shields (Professor of Clinical Bioinformatics, UCD Belfield), co-supervisor Glen Doherty (Consultant Gastroenterologist, UCD St Vincent's Hospital).

Inflammatory Bowel Disease (IBD) is mainly treated by anti-inflammatory approaches, but nutritional approaches provide some benefits. This project seeks to analyse existing information collected in a clinical trial, and other sample sets, regarding the distribution of proteins and peptides in stool samples from IBD patients, in order to further our understanding of how proteolysis by both digestive and inflammatory proteases may contribute to disease. The project will define shifts in proteolysis patterns in the gut, during disease progression and remission, in order to understand the changes in proteolysis during disease. The project will focus on analysis of clinical datasets, and would give the candidate extensive exposure to computational and statistical analysis methods to make sense of peptide and protein identifications derived from mass spectrometric analysis. The project will also provide opportunities for the candidate to get centrally involved in the design of a nutritional randomised intervention, aimed at reducing the negative aspects of protease activities in the bowel, to provide symptom relief and accelerating resolution of inflammatory flare-ups. There is an opportunity for a nutrition focussed project, working also with Dr Eileen Gibney, integrating dietary information with proteomic and peptidomic profiles, and for extension to consider the role of the microbiome in IBD. We are also interested in the potential for studying IBS in this context.

Other projects in the area of clinical bioinformatics are also possible, depending on speciality and I am very happy to discuss such possibilities further.