Genomics Aotearoa postdoctoral fellowships website blurb

Date: 13/9/2021

Blurb

I’m university trained in Ecology, completing a BSc and MSc in Ecology and Biodiversity. My MSc thesis involved studying the population genetic structure and genetic diversity of one of New Zealand’s culturally and commercially important fisheries species, Araara/Trevally, providing useful insights for sustainably fishing this species.

During my MSc, I spent a fair amount of my time taking courses in statistics, taking up the quality free training from organizations such as software carpentry and data carpentry and undertaking self directed learning in how to analyse and visualise data - I didn’t realise at the time, but I was naturally moving into the wonderful world of bioinformatics!

After university I was lucky enough to be snapped up by the amazing Human Genomics Group at ESR, here I’ve had a crash course in full on bioinformatics as I immersed myself in the Genomics Aotearoa bioinformatics capability and clinical genomics projects.

I developed pipelines that analyse the genomes of patients with rare genetic disorders that haven’t been able to be diagnosed with the type of genetic testing currently available to New Zealanders. Although these pipelines were developed with this purpose in mind, they can analyse genetic data from different species, with different reference genomes and databases

We placed a heavy focus on reproducibility, portability, scalability. This means the pipelines are publicly available (open source software), we actively encourage collaborative coding and New Zealand wide standardisation in the analysis of genetic data, and we employed tools and coding best practices to ensure the pipelines can be deployed on different compute infrastructures (a laptop, a server, a high performance cluster). If you’re lucky enough to have access to NVIDIA parabricks and graphics processing units (GPU’s) (hint. keep an eye on NeSi) you can use these same pipelines to analyse your data with insane speed…like insane! It’s akin to this: https://www.youtube.com/watch?v=-P28LKWTzrI

Use and contribute to the pipelines here: human genomics pipeline and vcf annotation pipeline

More recently, I’ve been analysing small RNA-Seq and RNA-Seq datasets in research looking into diseases such as type 2 diabetes and having a great time exploring data communication and data visualisation in this space.

Bioinformatics and coding is literally for anyone! I every much relate to Alana Alexander who eloquently describes how entering the bioinformatics field can happen through a non conventional route and how some coding experience can open up a world of opportunities in research analyses and beyond, even if you don’t want to go full bore into bioinformatics. As Alana mentions, stubbornness can become your most useful personality trait!

I recon the next generation will all be coders to some degree, hooray!

Leah’s areas of expertise: