Ingénieur diplômé, PhD
Postdoctoral Researcher in Computational Genomics
- Conduct original research projects, guided by relevant literature, own experience, and discussion with supervisors and scientists
- Work closely with wet-lab researchers to design, analyse and interpret single-cell genomics experiments
Developing methods for 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.
Orchestrating Single-Cell Analysis with Bioconductor
Amezquita R. et al, (2019)
The Short Chain Fatty Acid Butyrate Imprints an Antimicrobial Program in Macrophages.
Schulthess J. et al, (2019), Immunity, 50, 432 - 445.e7
The bovine alveolar macrophage DNA methylome is resilient to infection with Mycobacterium bovis.
O'Doherty AM. et al, (2019), Sci rep, 9
Invasive Salmonella exploits divergent immune evasion strategies in infected and bystander dendritic cell subsets.
Aulicino A. et al, (2018), Nat commun, 9
Publisher Correction: Telomerecat: A ploidy-agnostic method for estimating telomere length from whole genome sequencing data.
Farmery JHR. et al, (2018), Sci rep, 8