I completed my undergraduate degree in Natural Science at Trinity College Dublin (B.A. Mod., Hons), specialising in Neuroscience. During this time I completed a bioinformatics project examining the depressive and anxiogenic effects of Interferon-alpha treatment, with Prof Cliona O'Farrelly and Prof Shane O'Meara.
I began my PhD research in 2009 as part of the UCD Bioinformatics and Systems Biology PhD programme (http://bioinfo-casl.ucd.ie/PhD). My project was based both at the Animal Genomics Laboratory at UCD under the supervision of Prof. David MacHugh, and at the Smurfit Institute of Genetics at Trinity College Dublin under the supervision of Dr. Karsten Hokamp. My PhD project involved applying a range of bioinformatics and systems biology methods to functional genomic data to reconstruct the molecular mechanisms underlying the bovine host response to mycobacterial pathogens. Mycobacteria are a genus of intracellular pathogens that include Mycobacterium bovis, the causative agent of bovine tuberculosis (BTB) and M. tuberculosis, the causative agent of human TB.
I began working at Systems Biology Ireland as a post-doctoral researcher in 2013, under the supervision of Prof. Des Higgins and Prof. Walter Kolch. My postdoctoral research involves the bioinformatic and systems biology analyses of multiple next-generation sequecing datasets across various cancer projects. Particular examples of this work include the identification of regions of intergenic expression within neuroblastoma cell lines and the network reconstruction of both gene expression and proteomic datasets.
Peer Reviewed Journals
|Nalpas NC, Magee DA;Conlon KM;Browne JA;Healy C;McLoughlin KE;Rue-Albrecht K;McGettigan PA;Killick KE;Gormley E;Gordon SV;MacHugh DE (2015) 'RNA sequencing provides exquisite insight into the manipulation of the alveolar macrophage by tubercle bacilli'. Scientific Reports, 5 . [DOI] [Details]|
|Casey ME, Meade KG;Nalpas NC;Taraktsoglou M;Browne JA;Killick KE;Park SD;Gormley E;Hokamp K;Magee DA;MacHugh DE (2015) 'Analysis of the Bovine Monocyte-Derived Macrophage Response to Mycobacterium avium Subspecies Paratuberculosis Infection Using RNA-seq'. Frontiers in Immunology, 6 . [DOI] [Details]|
|Rue-Albrecht K, Magee DA;Killick KE;Nalpas NC;Gordon SV;MacHugh DE (2014) 'Comparative functional genomics and the bovine macrophage response to strains of the mycobacterium genus'. Frontiers in Immunology, 5 . [DOI] [Details]|
|Killick KE, Magee DA, Park SD, Taraktsoglou M, Browne JA, Conlon KM, Nalpas NC, Gormley E, Gordon SV, MacHugh DE, Hokamp K (2014) 'Key Hub and Bottleneck Genes Differentiate the Macrophage Response to Virulent and Attenuated Mycobacterium bovis'. Frontiers in immunology, 5 . [DOI] [Details]|
|McLoughlin KE, Nalpas NC, Rue-Albrecht K, Browne JA, Magee DA, Killick KE, Park SD, Hokamp K, Meade KG, O'Farrelly C, Gormley E, Gordon SV, MacHugh DE (2014) 'RNA-seq Transcriptional Profiling of Peripheral Blood Leukocytes from Cattle Infected with Mycobacterium bovis'. Frontiers in immunology, 5 . [DOI] [Details]|
|Nalpas N.C., Park S.D., Magee D.A., Taraktsoglou M., Browne J.A., Conlo (2013) 'Whole-transcriptome, high-throughput RNA sequence analysis of the bovine macrophage response to Mycobacterium bovis challenge in vitro'. BMC Genomics, 14 (1). [Details]|
|Killick K.E., Ni Cheallaigh C., O'Farrelly C., Hokamp K., MacHugh D.E., & Harris J. (2013) 'Receptor-mediated recognition of mycobacterial pathogens'. Cellular Microbiology, 15 (9). [DOI] [Details]|
|MacHugh D.E., Taraktsoglou M., Killick K.E., Nalpas N.C., Browne J.A., Park S.D., Hokamp K., Gormley E. & Magee D.A. (2012) 'Pan-genomic analysis of bovine monocyte-derived macrophage gene expression in response to in vitro infection with Mycobacterium avium subspecies paratuberculosis'. Veterinary Research, . [Details]|
|Magee D.A., Taraktsoglou M., Killick K.E., Nalpas N.C., Browne J.A., Park S.D.E., Conlon K.M., Lynn D.J., Hokamp K., Gordon S.V., Gormley E. & MacHugh D.E. (2012) 'Global gene expression and systems biology analysis of bovine monocyte-derived macrophages in response to in vitro challenge with Mycobacterium bovis'. PLoS ONE, . [DOI] [Details]|
|Killick KE, Browne JA, Park SD, Magee DA, Martin I, Meade KG, Gordon SV, Gormley E, O'Farrelly C, Hokamp K, MacHugh DE (2011) 'Genome-wide transcriptional profiling of peripheral blood leukocytes from cattle infected with Mycobacterium bovis reveals suppression of host immune genes'. BMC Genomics, 12 . [DOI] [Details]|