Ph.D., Dipl. Ing.
Computational Biologist and biomedical data science trainer
- Trainer for the OBDS training programme
- Postdoctoral Computational Biologist
- Software development for single-cell biology
- Bioconductor package maintainer
I train participants to the Oxford Biomedical Data Science training programme and I develop software for research with a focus on single-cell biology.
I obtained the degree of Ingénieur Diplômé in the field of Biological Engineering at the Polytech Nice-Sophia Antipolis engineering school (France). During this 3-year curriculum, I acquired broad knowledge and 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 across wet-lab and computational biology. 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); 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); and the analysis of single-cell genomics data in collaboration with the group of Alison Simmons (University of Oxford).
Having developed ongoing collaborations and a keen interest for single-cell genomics, I joined the Computational Genomics and Single Cell Genomics group led by Dr. Stephen Sansom at the Kennedy Institute Of Rheumatology in 2017, and collaborated 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.
I have now joined the Sims Group of Computational Genomics at the MRC WIMM Centre for Computational Biology to continue my academic work as Computational Biologist and Bioinformatics software developer, and to train cohorts of new computational biologists as part of the Oxford Biomedical Data Science Training Programme.
Author Correction: Capture-C: a modular and flexible approach for high-resolution chromosome conformation capture.
Downes DJ. et al, (2023), Nat Protoc
Capture-C: a modular and flexible approach for high-resolution chromosome conformation capture.
Downes DJ. et al, (2022), Nat Protoc
IL-1-driven stromal-neutrophil interactions define a subset of patients with inflammatory bowel disease that does not respond to therapies.
Friedrich M. et al, (2021), Nat Med, 27, 1970 - 1981
RNA-Seq Transcriptome Analysis of Peripheral Blood From Cattle Infected With Mycobacterium bovis Across an Experimental Time Course.
McLoughlin KE. et al, (2021), Front Vet Sci, 8
Whole-genome sequencing of a sporadic primary immunodeficiency cohort.
Thaventhiran JED. et al, (2020), Nature, 583, 90 - 95