Postdoctoral Researcher in Computational Genomics
I studied Biological Engineering at the Polytech Nice-Sophia Antipolis engineering school. During this 3-year course, I acquired field experience from summer placements in the U725 INSERM 'Biology of Human Dendritic Cells' (France), the UCD Complex and Adaptive Systems Laboratory (Ireland), and the MEDIT chemoinformatics software development company (France).
In 2011 I joined the Wellcome Trust's 4-year PhD programme 'Computational Infection Biology' at University College Dublin (Republic of Ireland). For the first year, I conduced three rotation projects: 1) in silico structure-based prediction of Mycobacterium bovis epitopes in cattle, 2) expression and purification of a Hepatitis B protein construct for experimental screening of interacting drug fragments, and 3) prediction and evaluation of a gene candidate underlying Staphylococcus aureus antibiotic resistance. Under the co-supervision of Prof. Stephen Gordon and Prof. David MacHugh, I then continued applying and developing functional genomics methods to comparatively study the bovine innate immune response to virulent and attenuated mycobacterial infections. In particular, I developed the Bioconductor package GOexpress that facilitates the identification and visualisation of gene ontology categories most relevant to the classification of biological samples.
Since 2015, my early postdoctoral work has included the computational analysis and integration of genetic variation, proteomic and metabolomics data with associated deep phenotype data in the group of Prof. Martin Wilkins (Imperial College London, UK), and the management, quality control, and coordination of data sets for integrative analyses of DNA targeted resequencing, ChIP-seq, and RNA-seq in the context of oxygen sensing and renal cancer, under the supervision of Prof. David Mole in the Ratcliffe group (University of Oxford).
Having developed ongoing collaborations and a keen interest for single-cell genomics, I have now joined the Computational Genomics group at the Kennedy Institute led by Dr. Stephen Sansom. In addition to a continuing interest in the innate immune response to infection, I collaborate closely with the groups of Prof. Fiona Powrie and Prof. Georg Holländer, to explore and develop single-cell approaches for understanding inflammatory disorders and the mechanics of promiscuous gene expression (PGE) in thymic epithelial cells (TECs) as part of their role in central tolerance.
Plasma Metabolomics Implicates Modified Transfer RNAs and Altered Bioenergetics in the Outcomes of Pulmonary Arterial Hypertension.
Rhodes CJ. et al, (2017), Circulation, 135, 460 - 475
Integrated computational prediction and experimental validation identifies promiscuous T cell epitopes in the proteome of Mycobacterium bovis.
Farrell D. et al, (2016), Microb Genom, 2
GOexpress: an R/Bioconductor package for the identification and visualisation of robust gene ontology signatures through supervised learning of gene expression data.
Rue-Albrecht K. et al, (2016), BMC Bioinformatics, 17
High-throughput transcriptomics reveals common and strain-specific responses of human macrophages to infection with Mycobacterium abscessus Smooth and Rough variants.
Aulicino A. et al, (2015), BMC Genomics, 16
Genome sequencing of the extinct Eurasian wild aurochs, Bos primigenius, illuminates the phylogeography and evolution of cattle.
Park SDE. et al, (2015), Genome Biol, 16