Curriculum Vitae
📄 See my publications
Bioinformatician, developer, and academic leader with 15+ years' experience in microbial genomics, open-source software, and collaborative science.
30
H-Index
11,117
Citations
15
Years Experience
94,150
Software Downloads
7,130
Coffees Drunk
Education
PhD in Microbiology
University of Queensland, Australia
2010–2015
Thesis: Escherichia coli virulence: a genomic approach
Supervisor: Scott Beatson
BSc (Hons, 1st Class) in Microbiology
University of Queensland
2009
Thesis: Comparative genome analysis of Escherichia coli VR50
BSc in Biochemistry & Bachelor of Information Technology
University of Queensland
2004–2008
Employment
2024 – Present
Senior Bioinformatician
The Centre for Genomic Pathogen Surveillance (CGPS), University of Oxford, UK
Developing and integrating pathogen genomics solutions for public health.
2018 – 2023
Bioinformatics Scientific Programmer – Interim Head of Informatics
Quadram Institute Bioscience, Norwich, UK
2016 – 2018
Senior Research Fellow in Pathogen Bioinformatics
University of Warwick, UK
Integrated ancient metagenomes into EnteroBase and sequenced/analyzed 10,000 modern S. enterica genomes.
2014 – 2016
Research Fellow in Genomics of Bacterial Pathogens
University of Warwick, UK
Co-developed EnteroBase (enterobase.warwick.ac.uk) for big-data genomic analysis of enteric pathogens and adapted robotic genotyping for high-throughput sequencing library preparation.
Mar 2009 – Nov 2009
Research Associate
School of Chemistry and Molecular Biosciences, University of Queensland, Australia
System administration and technical support for Linux/MacOSX workstations. Developed automated bioinformatics pipelines for the Beatson Microbial Genomics group.
Nov 2008 – Jan 2009
Research Associate
School of Chemistry and Molecular Biosciences, University of Queensland, Australia
Programmed software pipelines for bioinformatics, especially parallelization on high-performance computer clusters. Server administration for sharing bacterial genomics data.
Skills
Bioinformatics & Analysis
De novo Assembly
Read Mapping
Population Genomics
Comparative Genome Analysis
Phylogenetics
IQTree
RAxML
Statistics (Python/R)
Linux & CLI
Programming & Development
Python
JavaScript
Java
Bash
Perl
Flask
SQL
HTML/CSS
PHP
Full-Stack Development
Infrastructure & Workflows
HPC
Nextflow
Docker
Cloud Computing
Database Design
Linux Server Administration
Workflow Parallelization