• Curating the innate immunity interactome.

      Lynn, David J; Chan, Calvin; Naseer, Misbah; Yau, Melissa; Lo, Raymond; Sribnaia, Anastasia; Ring, Giselle; Que, Jaimmie; Wee, Kathleen; Winsor, Geoffrey L; et al. (2010)
      The innate immune response is the first line of defence against invading pathogens and is regulated by complex signalling and transcriptional networks. Systems biology approaches promise to shed new light on the regulation of innate immunity through the analysis and modelling of these networks. A key initial step in this process is the contextual cataloguing of the components of this system and the molecular interactions that comprise these networks. InnateDB (http://www.innatedb.com) is a molecular interaction and pathway database developed to facilitate systems-level analyses of innate immunity.
    • High-throughput proteomics detection of novel splice isoforms in human platelets.

      Power, Karen A; McRedmond, James P; de Stefani, Andreas; Gallagher, William M; Gaora, Peadar O; UCD Conway Institute and UCD School of Biomolecular & Biomedical Sciences, UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland. (2009)
      Alternative splicing (AS) is an intrinsic regulatory mechanism of all metazoans. Recent findings suggest that 100% of multiexonic human genes give rise to splice isoforms. AS can be specific to tissue type, environment or developmentally regulated. Splice variants have also been implicated in various diseases including cancer. Detection of these variants will enhance our understanding of the complexity of the human genome and provide disease-specific and prognostic biomarkers. We adopted a proteomics approach to identify exon skip events - the most common form of AS. We constructed a database harboring the peptide sequences derived from all hypothetical exon skip junctions in the human genome. Searching tandem mass spectrometry (MS/MS) data against the database allows the detection of exon skip events, directly at the protein level. Here we describe the application of this approach to human platelets, including the mRNA-based verification of novel splice isoforms of ITGA2, NPEPPS and FH. This methodology is applicable to all new or existing MS/MS datasets.
    • Proton pump inhibitors: potential cost reductions by applying prescribing guidelines.

      Cahir, Caitriona; Fahey, Tom; Tilson, Lesley; Teljeur, Conor; Bennett, Kathleen; HRB Centre for Primary Care Research, Division of Population Health Science, Royal College of Surgeons in Ireland, 123 St Stephens Green, Dublin 2, Ireland. caitrionacahir@rcsi.ie (2012)
      There are concerns that proton pump inhibitors (PPI) are being over prescribed in both primary and secondary care. This study aims to establish potential cost savings in a community drug scheme for a one year period according to published clinical and cost-effective guidelines for PPI prescribing.