I am a bioinformatics scientist working in the bacterial genomics field.
Bacterial species identification using ribosomal multilocus sequence typing (rMLST)
I curate the ribosomal multilocus sequence typing (rMLST) scheme and associated databases. The goal of rMLST is the accurate taxonomic classification of all bacterial isolates using the DNA sequences found within the ribosomal protein-encoding genes (pubmlst.org/species-id).
My research involves applying rMLST in three ways:
- Performing phylogenetic analysis for taxonomic investigations
- Defining ribosomal sequence types for the rapid species identification of bacterial isolates
- Developing and maintaining a 'one-click' species identification server
Large-scale bacterial genomics projects
I am responsible for assembling high-throughput DNA sequencing data for the large-scale genomic projects with the Maiden Group (with a focus on Campylobacter, Neisseria and Streptococcus). As a result, I manage the exchange of large amounts of data between sequencing centres, different labs and the ENA Sequence Read Archive (SRA).
Assembled genomes are accessible on the PubMLST website (pubmlst.org) for bacterial population studies, pathogen surveillance and gene-by-gene analysis.
My research interests include:
- Pathogen strain identification
- Bacterial genome annotation and protein structure/function prediction
- Knowledge-based structural genomics target selection