I am a medical Doctor in Sydney, Australia with commercial and research backgrounds in data analysis, IT administration, software development, and client-centric business administration. Amongst other things my experience includes university teaching, and organisational strategy and leadership. In early 2014 I qualified as the inaugural Certified Health Informatician Australasia (CHIA).
I intend for this website to serve as a hybrid between an informal résumé and a place to showcase my creations—thus, please excuse the hubris.
Non-synonymous single-nucleotide polymorphisms (nsSNPs) involve the substitution of a single DNA base-pair with a consequent change in protein function, often within a gene already known to be associated with disease. Novel nsSNPs in such genes require classification as disease-causing or neutral, a task partly achieved through statistical analyses.
We demonstrated that data compression algorithms can be utilised to quantify genetic diversity amongst species and utilised these values to model known nsSNPs and appropriately classify novel ones with Bayesian updating of probabilities of disease-causation.
NextGen sequencing data outputs snippets (known as reads) of genetic material. Measured in tens to hundreds of base-pairs as against the 3 billion or so in a full human genome, reads require alignment to a reference sequence, allowing for variation between the individual in question and the reference.
BarraCUDA utilises the parallel processing of GPUs to increase the speed of the alignment process. My contribution, post original publication, was to generalise the breadth-vs-depth-first search approaches to allow for hybrid searching as well as streamlining memory transfers between CPU and GPU; this resulted in a 40% throughput increase without a reduction in accuracy.
A credentialing program created by the Health Informatics Society of Australia, the Australasian College of Health Informatics, and the Health Information Management Association of Australia which focuses on 6 core competency areas. I was the first person to successfully attain the qualification.
IT Director; Sydney University Medical Society 2011-12