Centre for Bioinformatics

Centre Overview

There is an amazing diversity and quantity of information (with increasingly complex linkages) emerging in the biological and medical sciences. Bioinformatics is the use of computational approaches to make sense of biology, especially to analyse molecular sequences of DNA, RNA and protein.

The UCD Bioinformatics Centre is focused on advancing the quality of bioinformatics science.  It supports academic researchers working in the areas of bioinformatics, genomics and molecular evolution.  It encourages interdisciplinary collaborations inside and outside UCD through PhD programmes, teaching and software provision.  Key areas include sequence alignment, molecular evolution, short peptides, protein structure prediction, cancer, pathogens. 

Core Academic Staff

Professor Des Higgins joined UCD in 2003. Hehas an international reputation in bioinformatics as an innovator, a leader, and a practical provider of working solutions to key problems. Since 2007, Higgins has been cited over 94,000 times, and has 10 papers with over 1,000 citations. This includes his famous CLUSTAL paper, which is the 10th most cited paper of all time. His research interests include developing multiple sequence alignment, and multivariate analysis of genomics related data. . Recent highlights include his finding that very large multiple alignments of many sequences may be accelerated by use of simpler guide trees (Proc Natl Acad Sci USA 2014).  These findings are relevant to making sense of the very large sequence datasets emerging from high throughput modern sequencing methods.

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.

Dr 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.

Dr 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. 

Early Career Independent Investigators

The UCD Bioinformatics Centre has three independently funded early-career research fellows (Dr 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).

 

Affiliated Academic Staff

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 associated with the Centre. The research teams are as follows:

Brendan Loftus is an expert in genomics applied to both bacterial and eukaryotic systems.  David MacHugh works on animal genomics in relation to veterinary applications. Geraldine Butler works on fungal pathogen genomics, and is also the Director of the Wellcome Trust Computational Infection Biology PhD programme. 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 Gormley, Murphy and 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.

Vio Buchete (Physics) leads a research team in the UCD CASL (Complex and Adaptive Systems Biology) in the structural modelling of proteins. Ricardo Segurado is based in CSTAR, in the School of Public Health, Physiotherapy and Population Science, and has expertise in genetic epidemiology. 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, Boris Kholodenko leads the mathematical modelling, and Walter Kolch  leads experimental analysis. The UCD Bioinformatics Centre supports them in analysis of high-throughput datasets. 

Computational                               

Brendan Murphy Statistics (SMS) 
Claire Gormley Statistics (SMS) 
Andrew Parnell Statistics (SMS) 
Anastasios Markitsis Statistics (SMS)
Vio Buchete School of Physics
Boris Kholodenko SMMS
Ricardo Segurado SSTAR (SPHPPS)

 Experimental

Geraldine Butler SBBS
Brendan Loftus SBBS
Jeremy Simpson SBES
Walter Kolch SMMS
Gerard Cagney SBBS
Emma Teeling SBES
David MacHugh SAFS

Interested in Visiting, Collaborating or Working with Us?

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

Further Information

Group Websites 

Group leaderGroup websiteUCD Research Profile
Des Higgins  click  Available here
Gianluca Pollastri click Available here
Ken Wolfe click Available here
Denis Shields click Available here
Peadar O'Gaora   Availabel here

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.