CV

Work experience and Education

• 2020-Present: Research Associate in Data Science, Department of Medicine, University of Cambridge, UK

  • Analysis, integration, and interpretation of high-dimensional genomics 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: Bioinformatician, 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: PhD in Computational Infection Biology, University College Dublin, Ireland

  • Wellcome Trust Computational Infection Biology PhD programme
  • Formal training in statistical methods for genome-scale research

Skills and expertise

• Containerisation systems (Docker, Singularity) and package/environment management systems (Conda, venv).
• Integrative analysis of genome-scale omics data sets
  • Genomics, transcriptomics, proteomics, epigenomics, CRISPR.
• CI/CD and version control
• Bioinformatics pipeline development using modern workflow management systems (Nextflow, Snakemake, bash).
• Database handling and migration (PostgreSQL, SQLite, MySQL).
• API deployment and web app development: back-end (Flask, FastAPI, gunicorn, uvicorn) and front-end (React, Shiny).
• Deployment to high-performance computing (HPC) clusters and on cloud-based platforms (AWS).

Publications

Evolution and host-specific adaptation of Pseudomonas aeruginosa

Weimann A., Dinan A.M., Ruis C., Bernut A., Pont S., Brown K., …, Parkhill J., Floto R.A. (2024). "Evolution and host-specific adaptation of Pseudomonas aeruginosa" Science. 385 (6704), eadi0908.

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