Clinical Bioinformatics Group

Group Overview

The Clinical Bioinformatics group focuses on basic computational research underlying peptide therapeutic development, and on clinically relevant genetic variation. Peptide development focuses on platelet, cancer, infection and food areas, while genetic studies include cardiovascular and autism genetics, with a particular focus on genetic combination effects.

We are physically located in the Complex and Adaptive Systems Laboratory, currently in Belfield Office Park, which has help drive collaborations with computer scientists (CLIQUE network analysis cluster; machine learning) and physicists (molecular modelling). We are a multidisciplinary group focussed on computational analysis and modelling of biological and clinical processes. See http://bioinfo-casl.ucd.ie/shields/ for more details of our members' backgrounds activities and interests.

More Information About UCD Clinical Bioinformatics Group

  1. We have expanded our cardiovascular genetics collaborations allowing us to pool resources with consortia of collaborators in Europe and US, so that genetic discoveries in the Anglo-Scandinavian Coronary Outcomes Trial (ASCOT) may be replicated elsewhere. Our genetic collaborations with various groups have advanced understanding of genetic factors in cardiovascular disease, renal transplant and autism, including ongoing collaborations with the UCD and TCD autism research groups of Sean Ennis and Louise Gallagher.
  2. We have been active in software development for the prediction of short protein and peptide motif regions likely to contribute to bioactivity. Further details of this publically available software may be accessed at our web server, http://bioware.ucd.ie. This software is used extensively by researchers worldwide.
  3. We completed a survey of novel protein motifs in man, and this published resource (Molecular Bio systems vol 8 pp282-295,2012) makes our findings available to the scientific research community interested in discovering new roles for short protein regions involved in controlling protein-protein interactions, signalling, and other processes. We continued researches into better understanding the role of disordered regions in proteins.
  4. We continued to investigate experimentally the role of peptides predicted from our computational predictions, in collaboration with Niamh Moran, RCSI. A particular focus is on the integrin and cadherin adhesion complexes, which play key roles in thrombosis, cancer and other processes.
  5. Our involvement in the Food for Health Ireland (FHI) collaboration with industry and academia partners in Ireland has helped to characterise and prioritise particular food hydrolysates for further investigation, based on analysis of their peptide content by mass spectrometry, in parallel with computational prediction and testing of active synthetic peptides.
  6. We initiated the ICON Newman Genomics Fellowship funded by ICON plc. The fellow is exploring the role of genetic factors in complex disease. The results of our findings were presented at international conferences and in the peer-reviewed literature.

Research Team

Prof Denis Shields
Professor of Clinical Bioinformatics

Dr Anthony Chubb
Bioinformatics PhD Programme Manager

National & International Collaborators

Prof Des Higgins, UCD Conway Institute Dr Ger Cagney, UCD Conway Institute
Prof Finian Martin, UCD Conway Institute Dr Gianluca Pollastri, UCD Complex & Adaptive Systems
Dr Sean Ennis, UCD School of Medicine & Medical Science Dr Seamas Donnelly, UCD School of Medicine & Medical Science
Dr Glen Doherty, St Vincent’s University Hospital Dr Louise Gallagher, Trinity College Psychiatric Genetics
Dr Niamh Moran, Royal College of Surgeons in Ireland, Platelet biology Dr Marc Devocelle, Royal College of Surgeons in Ireland, Peptide synthesis
Dr Gianpiero Cavelleri/Prof Peter Conlon, Royal College of Surgeons in Ireland Dr Alice Stanton, Royal College of Surgeons in Ireland, Cardiovascular Genetics
Dr Ronen Zaidel Bar, Integrin/cadherin Biology, National University of Singapore Mrs Alessandra Bianchin, PhD

Director Biography

Denis has a genetics PhD (Trinity College Dublin) and has worked in universities (Ireland & UK) and in industry. He is currently Professor of Clinical Bioinformatics, UCD. He is director of the graduate education programme: Bioinformatics and Systems Biology PhD programme.