Professor Ken Wolfe joined UCD in 2013.  He is a world-leading expert in the field of molecular evolution. In particular he has advanced the field of fungal molecular genetics through his research. This includes revealing the origin of many genes in brewer’s yeast from an ancient genome duplication, and the discovery (Eukaryotic Cell 2009) that many fungal genomes harbour genes captured from viruses. He is a holder of a European Research Council (ERC) Advanced Grant award on the subject of ‘Programmed and unprogrammed genomic rearrangements during the evolution of yeast species’.

Professor Denis Shields joined UCD in 2005. He established the Irish Research Council funded Bioinformatics and Systems Biology PhD Programme, and is Deputy Director of the Wellcome Trust Computational Infection Biology PhD programme. He works on the computational discovery of bioactive peptides modulating protein-protein interactions. He is also interested in genetic epidemiology, in particular of synergistic combination effects. He also studies peptides in complex mixtures of food hydrolysates, as part of Food Health Ireland.

Assoc Professor Peadar O’Gaora joined UCD in 2004. He combines a background in microbiology and pathogen molecular biology with bioinformatics expertise. He is a participant in the Wellcome Trust Computational Infection Biology PhD programme. His research interests focus on high throughput genomics and transcriptomics data analysis in many fields including microbial pathogen genomics and gene expression in cancer progression.

Assoc Professor Gianluca Pollastri joined UCD in 2003. He is a leading expert in the application of machine learning to predict protein secondary structure. His particular expertise is in bidirectional recursive neural networks, which are particularly well suited to sequence analysis.

Professor Catherine Mooney joined UCD School of Computer Science as Assistant Professor in 2016. She has created a distinct niche in the biomarker field tackling important challenges including how to combine cutting-edge computational and biomedical techniques to efficiently integrate multiple data types into a single biomarker.  In 2013 she completed a four-year postdoctoral research fellowship in clinical bioinformatics with Prof Denis Shields where she developed web servers for short linear motif and peptide property prediction (bioware.ucd.ie). (more)

The UCD Bioinformatics Centre has three independently funded early-career research fellows (Assoc Professor Colm Ryan, Henry Wellcome fellowship from the Wellcome Trust; Dr Norman Davey ,SIRG award from Science Foundation Ireland; Dr Simon Furney Marie Curie Fellowship).  Dr Ryan’s research focusses on the progression of cancer treatments through the identification of genetic vulnerabilities in cancer cells. Dr Furney is working on prioritising non-coding somatic mutations in cancer, while Dr Davey is working on decoding the regulatory landscape of the intrinsically disordered proteome (many proteins are partly disordered, and discovering the functional consequences of this disorder is an area of active research).

The UCD Bioinformatics Centre actively supports collaboration. Supported in part by our PhD programmes, a large network of collaborations already exists around bioinformatics. A number of research groups at UCD are primarily focussed on genomic analyses, which are critically dependent on bioinformatics. Accordingly, they have bioinformatics researchers integrated within their research teams, who will benefit from association with the Centre. The research teams are as follows:

Professor Brendan Loftus is an expert in genomics applied to both bacterial and eukaryotic systems.  Professor David MacHugh works on animal genomics in relation to veterinary applications. Professor Geraldine Butler works on fungal pathogen genomics, and is also the Director of the Wellcome Trust Computational Infection Biology PhD programme. Professor Emma Teeling works on the genomics of bats, as a model system to understand ageing. 

The Statistics section of the School of Mathematical Sciences has had a close relationship with the Bioinformatics and Systems Biology PhD programme, with Professor Claire Gormley, Professor Brendan Murphy and Professor Andrew Parnell acting as primary supervisors of students, leading the development of statistical methodologies applied to bioinformatic problems in the areas of proteomics and glycomics. They have been joined by Anastasios Markitsis who has experience in analysis of RNA data.

Assoc Prof Vio Buchete (Physics) leads a research team in the UCD CASL (Complex and Adaptive Systems Biology) in the structural modelling of proteins. Assoc Prof Ricardo Segurado is based in CSTAR, in the School of Public Health, Physiotherapy and Sports Science, and has expertise in genetic epidemiology. Professor Jeremy Simpson applies high-throughput imaging technologies to study protein trafficking in cells, and develops novel software tools for image analysis. In Systems Biology Ireland, Professor Boris Kholodenko leads the mathematical modelling, and Professor Walter Kolch  leads experimental analysis. The UCD Bioinformatics Centre supports them in analysis of high-throughput datasets. 

Computational                               

 Experimental

We have hosted many researchers from different parts of the world, and EU Marie Curie funding provides one mechanism to support postdoctoral researchers to work here. We support many academic and industrial collaborations. Contact: denis.shields@ucd.ie

Group Websites 

Bioinformatics PhD Programmes

We currently offer two PhD programmes that are centred on bioinformatics training. The Bioinformatics and Systems Biology PhD programme supports students funded from a variety of sources, including students affiliated with Systems Biology Ireland. The Computational Infection Biology PhD programme is funded by the Wellcome Trust.

Bioinformatics Seminar Series

The Bioinformatics Seminar Series meets on Mondays at 1pm (usually UCD Conway seminar rooms 1 or 2). Usually we have coffee first at 12:30 in the interactive hub.