Current role
Postdoctoral Research Associate. Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, and Cambridge Centre for AI in Medicine
Areas of expertise
- Object-oriented programming and package development (Python, R).
- Version control and CI/CD (Git, GitHub Actions).
- Containerisation systems (Docker, Singularity) and package/environment management systems (Conda, venv).
- API deployment and web app development: back-end (Flask, FastAPI, gunicorn, uvicorn) and front-end (React, Shiny).
- Database handling and migration (PostgreSQL, SQLite, MySQL).
- Deployment to high-performance computing (HPC) clusters and on cloud-based platforms (AWS).
- Integrative analysis of genome-scale omics data sets (genomics, transcriptomics, proteomics, epigenomics, CRISPR).
- Bioinformatics pipeline development using modern workflow management systems (Nextflow, Snakemake, bash).
Research interests
Functional genomics, comparative genomics, population-level genotype-phenotype analyses.
Research experience and education
2020 - Present
MRC Laboratory of Molecular Biology and Department of Medicine, University of Cambridge, UK
- Analysis, integration, and interpretation of high-dimensional “omics” data sets and clinical data sets
- Driving research objectives; developing data analysis pipelines and packages; writing and editing manuscripts for publication
- Close collaboration with clinicians, statisticians, molecular biologists, and industry partners
2016 - 2019
Department of Pathology, University of Cambridge, UK
- Analysis and interpretation of high-throughput biological sequence data sets
- Training and supervising PhD students, undergraduates, and summer students
2012 - 2016
School of Medicine, University College Dublin, Ireland
- Wellcome Trust Computational Infection Biology PhD programme
- Formal training in statistical analyses using Python, R, linux
Conference presentations
2022
Genome Informatics conference, Sanger Institute, UK
2022
EMBO BactNet conference, San Feliu de Guixols, Spain
2019
Microbiology Society - Annual Conference, Belfast, UK
2016
EMBO Bioinformatics and Genome Analyses workshop, Turkey
2015
Microbiology Society, Irish Division Meeting, Galway, Ireland
2014
International Symposium on the Biology of the Actinomycetes, Izmir, Turkey
Other experience
2016-2019
Postdoctoral Demonstrator, Mathematical Biology, University of Cambridge.
2016
Completed EMBO practical course on Bioinformatics and Genome Analyses.
2012-2016
Postgraduate Demonstrator, Bioinformatics, University of Cambridge.
Organising committee member
Computational Biology Symposium, University College Dublin.