Biography

I am a molecular biologist and bioinformatician working at the interface of biology, computation and applied diagnostics. I am passionate about teaching and about making bioinformatics accessible to biologists, which I achieve by designing and delivering micro-credentials built around real-world problems from diagnostic and research laboratories so that learners develop practical, immediately applicable analytical skills. I am also the developer of widely used bioinformatics platforms, including sangerFlow and blastdbbuilder, and I work collaboratively across The University of Western Australia and Murdoch University on data-driven projects in precision diagnostics, microbiome research, viral evolution and antimicrobial resistance.

I lead a virtual bioinformatics core that provides shared analytical infrastructure, reusable workflows and study design support to enable high-quality, reproducible and translational bioinformatics across plant, animal and environmental research and diagnostics.

• Shared, containerised and HPC-ready bioinformatics pipelines
• Reference database management and reproducible workflow infrastructure
• Support for pathogen diagnostics, genomic surveillance and microbiome analysis
• Training and micro-credentials for biologists and laboratory scientists

View Bioinformatics Core resources on GitHub

Publications list available on Google Scholar and on ORCID.

I am passionate about promoting bioinformatics education and its applied skills. I develop intuitive teaching resources to help facilitate bioinformatics learning and applications. Some examples are:

• Bacterial Phylogenetic Tree Reconstruction Using UBCG Pipeline: This is a widely used tool for identify pathogenic bacteria using a core set of bacterial genes.

• How to run Kraken2 on HPC using Singularity container and Nextflow?: Kraken2 is a popular metagenomics tool. It identifies organisms present in an environmental DNA (eDNA) or any other samples that contain more than one genome.

• GPU-accelerated guppy-basecalling: Guppy is a base caller used for converting the Oxford Nanopore sequencing raw data (electric signals) into strings of nucleotide bases called sequencing reads. This tutorial demonstrates how to carry out Guppy base calling.

• Why graduate students should learn R?: An introduction to R.