What is Bioinformatics?Course AimsWhere Is It?Who Is It For?
Who Are We?2010 Available Projects2009 Projects2008 ProjectsHow To ApplyCoursesResearch Supervisors and Research Teams
The programme has the following bioinformatics and computational biomedicine staff (TCD and RCSI indicates based at Trinity College Dublin and the Royal College of Surgeons in Ireland, otherwise UCD).
- Prof Denis Shields - bioactive oligopeptides (Nat Chem Biol. 2007; Nature, 1997; PNAS, 1992; PNAS, 1991; Science, 1989)
- Prof Des Higgins is the developer of the CLUSTAL sequence alignment package, and has over 35,000 citations of this work in the scientific literature (PNAS, 2005; PNAS, 1991)
- Prof Brendan Loftus - microbial pathogen genomes (Science, 2007; Science. 2005; Nature, 2005; Science, 2002; PNAS, 2002; Science, 2001; Nature, 1997a; Nature, 1997b)
- Dr Gianluca Pollastri - inferring protein structure from sequence
- Prof Padraig Cunningham - Support Vector Machines, for gene expression and ChIP-on-chip
- Dr Jens Nielsen - structural bioinformatics and protein engineering - enzyme.ucd.ie
- Dr Mike O'Neill - Genetic programming and grammatical evolution
- Dr Zoltan Neufeld - Modelling of biological systems, biological fluid dynamics (PNAS, 2009)
- Dr Ted Cox - Applied Dymanical Systems, nonlinear waves, computational science
- Dr Peadar O'Gaora - bioinformatics, including gene expression data analysis (Nat Med, 2001; Nature, 2001; PNAS, 1994)
- Dr Claire Gormley and Prof Brendan Murphy - statistics: Bayesian, mixture models and latent variable models
- Prof Nial Friel - MCMC, image analysis, spatial statistics, stochastic processes
- Prof Ken Wolfe (TCD) - molecular evolution of yeasts (PNAS, 2008; Nature, 2007; PNAS, 2007; Nature, 2006; Nature Genet, 2005a; Nature Genet, 2005b; PNAS, 2004a; PNAS, 2004b; Nature Genet, 2003; PNAS, 2002; Nature Genet, 2002; Nat Rev Gen, 2001; Nature, 2001; PNAS, 2000; Science, 2000; PNAS, 1998; PNAS, 1998; Nature, 1987; PNAS, 1992; PNAS, 1991; Science, 1989; Nature, 1989; PNAS, 1989; PNAS, 1987).
- Dr Andrew Parnell - applied Bayesian statistics
- Prof Walter Kolch - Systems Biology (Nat Cell Biol, 2009; Nat Cell Biol, 2006; Nat Rev Mol Cell Biol, 2005; Science, 2004; Nature, 1999; Nature, 1993; Nature, 1991)
- Prof Boris Kolodenko - Systems Biology (Nat Cell Biol, 2007; PNAS, 2002; PNAS, 1998)
- Dr Anthony Chubb - Chemoinformatics and Drug Discovery (MMG)
- Prof Cathal Seoighe (NUIG) - bioinformatics (PNAS, 2007; PNAS, 2000; PNAS 1998)
- Dr Aaron Golden (NUIG) - machine learning (PNAS, 2009)
- Dr Derek Greene - machine learning
This PhD programme currently draws on the following co-supervisors from experimental and clinical biology research teams:
- Prof Pauline Rudd - glycans/glycotechnology (CV/résumé).
- Prof Bill Watson - Prostate cancer, proteomics and metabolomics
- Prof Geraldine Butler - Genomic analysis of pathogenic yeasts (Nature, 2009; PNAS, 2006)
- Prof Cormac Taylor - Hypoxia signalling: systems analysis
- Dr Jean Marc Jacque - HIV molecular biology (Nature, 2006; Nature, 2003; Nature, 2002)
- Prof Finian Martin - The role of adhesion proteins in breast cancer tumourogenesis
- Prof Liam Gallagher - Cancer genomics and proteomics (PNAS, 2008; PNAS, 2003)
- Dr Patrick Mallon - HIV treatment in patients
- Dr Lorraine Brennan - metabolomics (CV/résumé)
- Dr Sean Ennis - autism genetics and genotyping (Nat Genet, 2006)
- Dr Breandan Kennedy - Zebrafish circadian rhythms (Nat Genet, 1997)
- Prof Niamh Moran (RCSI) - platelets in thrombosis (Nat Chem Bio, 2007)
- Prof Alice Stanton (RCSI) - hypertension genetics
- Dr Louise Gallagher (TCD) - autism genetics (Nature, 2009; Nat Genet, 2009)
- Dr Frank Wellmer (TCD) - plant development (PNAS, 2009; Nature, 2004; Nat Genet, 2004)
- Dr Gavin Davey (TCD) - systems biology of islet cells
- Dr Philip Newsholme - systems biology of islet cells (CV/résumé)
- Dr Chandralal Hewage - NMR spectroscopy and molecular modelling (Proteins, 2007, 68, 92-99) (CV/résumé)
- Dr Gianpiero Cavalleri (RCSI) - epidemiology, genetics (Nature, 2005; PNAS, 2005)
- Dr Peter Conlon (RCSI) - Consultant Nephrologist/Renal Transplant Physician
- Dr Jim O'Gara - microbiology, biofilms
- Prof Laurence Egan (NUIG) - Clinical pharmacology and Gastroenterology (PNAS, 2004)
- Prof Brian McStay (NUIG) - Nuclear Structure and Gene expression
- Prof Jeremy Simpson - eukaryotic membrane traffic pathways (Nat Cell Bio, 1999)
- Prof Stephen Pennington - mammalian cell cycle, proteomics (Nature, 1987)
- Prof Robert Woods (NUIG) - carbohydrate recognition (PNAS, 2006; PNAS, 2001; Nat Struct Biol, 1994)
- Dr Gerard Cagney - proteomics (Nat Biotech, 2008; Nature, 2006; Nat Biotech, 2002; Nat Biotech, 2000; Nature, 2000)
- Prof Helen Roche - nutrigenomics
- Dr Emma Teeling - bats (PNAS, 2009; Science, 2005; PNAS, 2002; PNAS, 2001; Nature, 2000)
- Dr Angus Bell - malaria (Nat Rev Drug Disc, 2004)
Scientific Advisory Board
| Michael Stumpf | Systems Biology, Imperial College London |
| Andy Brass | Bioinformatics, University of Manchester |
| Kevin Karplus | Graduate Director of Bioinformatics, University of California, Santa Cruz |
| Joseph Lehar | Combinatorx Inc, Boston |
Steering Committee
| Denis Shields | Bioinformatics |
| Ted Cox | Mathematics |
| Des Higgins | Bioinformatics |
| Padraig Cunningham | Computer Science |
| Cathal Seoighe (NUIG) | Bioinformatics |
| Emer Cunningham | Graduate Studies |
| Boris Kholodenko | Systems Biology |
Students
| Student | Project Title | Supervisors |
| Kate Byrne | Chemotaxis, polarisation and GTPase cascades in cell motility | Zoltan Neufeld, Boris Kholodenko, Walter Kolch |
| Aimee Carmody | Spatiotemporal dynamics of cell signalling | Zoltan Neufeld, Boris Kholodenko |
| Fergal Duffy | Computational modeling of structurally constrained peptides as peptide mimetics | Denis Shields, Marc Devocelle (RCSI) |
| Kate Killick | Functional genomics and systems biology of mycobacteria-macrophage interactions in cattle | David MacHugh, Karsten Hokamp (TCD) |
| Alessandro Lusci | Prediction of properties of small molecules by machine learning models towards the in silico identification of novel neuritogenic compounds | Gianluca Pollastri, Keith Murphy |
| Sarah Maguire | Comparative Yeast Genomics | Geraldine Butler |
| Gian Luca Negri | Integrated data analysis for discovery of biologically important patterns in networks of protein and gene | Denis Shields, Ger Cagney |
| Kevin O'Brien | Discovery of oligopeptides modulating platelet signalling processes | Denis Shields, Niamh Moran (RCSI) |
| Eanna O'Keefe | Modelling the evolution of protein interactions and discovery of protein sequence motif/oligopeptide mediated signalling | Denis Shields, Niall Haslam |
| Alessandro Riccomenbi | Comparative Genomics Of Pathogenic Yeast | Geraldine Butler, Ken Wolfe (TCD) |
| Thomas Schwarzl | Stem Cell Commitment: transcriptional networks regulating mesenchymal stem cell (MSC) differentiation to chondrocytes | Des Higgins, Andrew Hillmann (NUIG) |
| Finbarr Tarrant | Bioinformatic and Molecular Analysis of Alternative Transcript Expression in Malignant Melanoma | Peadar O.Gaora, William Gallagher |
| Thong Nguyen | Design and Function of Transcription Factors in the Chromatin Environment | Cathal Seoighe (NUIG), Andrew Flaus (NUIG) |
The following students started their studies in the 2008/2009 academic year:
| Student | Project Title | Supervisors |
| Colm Ryan | Computational Analysis of protein interaction networks | Padraig Cunningham, Gerard Cagney |
| Nyamundanda Gift | Novel statistical methods for the analysis of metabolomic data | Lorraine Brennan, Claire Gormley |
| Surendran Praveen | The Oxidatice stress interactome: Modelling Atherosclerosis in Populations, from Whole Genome SNP Association Arrays | Alice Stanton (RCSI), Denis Shields |
| Vasanth Singan | Organelle footprinting through global analysis of Rab protein localisation | Kathleen Curran, Jeremy Simpson |
| Magdalena Golden | Advanced computational and NMR studies of GIP with extracellular domain of GPCR | Chandralal Hewage, Jens Nielsen |
| Yuan Ho | Defining regulatory networks important in endocrine resistant breast cancer | Peadar O'Gaora, Leonie Young (RCSI) |
| Marie Galligan | Statistical Methods for the Analysis of HPLC Glycan Data for Biomarker Discovery and Validation | Pauline Rudd, Brendan Murphy |
| Luca Cerone | Systems biology of hypoxia: cross talk between NFkB and HIF1 in intestinal epithelial cells | Zoltan Neufeld, Cormac Taylor, Ted Cox |
| Manuela Salvucci | Systems biology models of insulin release from pancreatic islet cells | Philip Newsholme, Zoltan Neufeld, Gavin Davey (TCD) |
| Pin Tong | Bioinformatics analysis of transcriptional and epigenetic data and its role in Bovine embryo development | Brendan Loftus |
| Weifeng Shi | Visualisation and bioinformatic analysis of alignments of large numbers of viral sequences | Des Higgins |
The following students started their studies in the 2007/2008 academic year:
| Student | Project Title | Supervisors | |
| Alessandro Guido | Computational methods to compare hypoxia transcriptional responses across yeast species | Geraldine Butler, Des Higgins | |
| Yue Fan | Multivariate analysis integrating metabolomic and proteomic patient data in prostate cancer | William Watson, Brendan Murphy | |
| Denise Lynch | Comparative genomics of Candida species to explore pathogenesis | Ken Wolfe (TCD), Geraldine Butler | |
| Jun Yin | Analysis of Zebrafish circadian rhythms: integrating gene expression and knock-out data | Breandan Kennedy, Des Higgins | |
| Ross Foley | Advanced Image Analysis of Histopathological Data | Liam Gallagher, Padraig Cunningham | |
| Mick Clarke | Proteomic and transcriptomic elucidation of the uptake of bacteria into eukaryotic cells | Brendan Loftus, Padraig Cunningham | |
| Naisha Shah | Computational analysis of chromosomal abnormalities and copy number variations in Autism. | Sean Ennis Louise Gallagher (TCD), Denis Shields | |
| Ilias Stavrapoulos | Computational and experimental evaluation of protein motifs influencing breast cancer adhesion and tumorigenesis | Finian Martin, Denis Shields | |
| Melissa Morine | .... | Helen Roche, Peadar O.Gaora | |
| Federica Lombardi | Delineating the platelet signaling network through a dose-matrix response approach | Denis Shields, Niamh Moran (RCSI) | |
| Predrag Kukic | Principal component analysis of the pH-dependent conformation states in enzymes - Electrostatic properties of protein-tyrosine phosphatases | Gianluca Pollastri, Jens Nielsen |
Further details of the bioinformatics research teams are to be found at bioinformatics.ucd.ie. Further details of the computational science research teams are to be found at www.ucd.ie/computationalscience/staff.html.