Statistical bioinformatician: CSIRO, Sydney, Australia, 2009-2015
I worked in the division of Mathematics, Informatics and Statistics on two project areas funded by the Preventative Health Flagship. My main focus was the analysis of large “-omics” datasets to identify gut health biomarkers, particularly those useful for early detection of colorectal cancer. I also worked on the molecular characterisation of stroke. In addition, I provided general bioinformatics expertise to colleagues across CSIRO.
I also spent some time with the eHealth program, developing software tools for personalised genomics.
Research Officer: The University of Queensland, Brisbane, Australia, 2006-2009
From 2006-2009, I worked in the School of Molecular & Microbial Sciences at UQ, in the lab of Bostjan Kobe. My main project was the computational analysis of protein interaction and function, particularly protein kinases and their substrates. I also played the role of “bioinformatics guy” in the group and contributed to several projects with researchers in the Institute for Molecular Bioscience.
Postdoctoral Fellow: The University of New South Wales, Sydney, Australia, 2005-2006
ARC Postdoctoral Fellow: The University of New South Wales, Sydney, Australia, 2002-2005
Vice-Chancellor’s Research Fellow: The University of New South Wales, Sydney, Australia, 2000-2002
For 6 years prior to Brisbane, I was involved with the Cavicchioli group in the School of Biotechnology & Biomolecular Sciences at UNSW. The lab is interested in the broad area of extremophilic bacteria and archaea, with particular emphasis on marine ultramicrobacteria and psychrophilic, methanogenic Archaea from Antarctica. I worked on the following projects:
- Whole genome analysis of Methanogenium frigidum
M. frigidum is a psychrophilic (cold-loving), methanogenic (methane-producing) archaeon, isolated from Ace Lake in the Australian Antarctic Territory. Genome sequencing was performed in collaboration with the AGRF, Brisbane and Molecular Dynamics, CA. The genome sequence of this organism has allowed us to elucidate some of the mechanisms involved in low-temperature adaptation, to identify proteins with potential for biotechnology and to carry out comparative analyses with other methanogens, archaea and bacteria.
My role in this project was the construction of gene libraries and the computational analysis of the genome data. Further work on this genome is planned in collaboration with the JCVI and Moore Foundation.
- Functional genomics and proteomics of Methanococcoides burtonii
M. burtonii is a psychrotolerant methanogen, also isolated from Ace Lake. It is more experimentally amenable than M. frigidum and has become the focus for an ambitious project encompassing genomics, proteomics and transcriptomics, aimed at the identification and characterisation of proteins that are involved with low-temperature adaptation. Specialist techniques include culturing and manipulation in a chilled anaerobic chamber and 2D-PAGE analysis. My role here is largely advisory, as most of the experimental work is done by our students, most notably the supremely talented and vivacious Amber Goodchild, now of J & J.
- Comparative microbial genomics and bioinformatics
In the course of my research on the psychrophilic Archaea, I have developed a general interest in comparative genomics, bioinformatics and computational biology. This has allowed our group to address a number of interesting biological problems (see recent publications). My main interest is in using data mining techniques to ask interesting biological questions using microbial genomes and sequence/structure databases. I use a wide variety of tools, including software built using the Bioperl modules. I am particularly interested in data integration and management and in the use of parallelised software on Linux clusters.
Marie Curie Research Fellowship: Vrije Universiteit, Amsterdam, 1998-2000
Still with P. denitrificans, my first postdoc turned to the genetic regulation of denitrification. During this time, we showed that a family of small proteins from denitrifying bacteria named NosX were involved in the biosynthesis of the enzyme nitrous oxide reductase, most likely playing a role in copper insertion. We also analysed the transcription of the nos operon, determined the membrane topology of the regulatory NosR protein and elucidated the role of nitric oxide in the transcriptional regulation of denitrification.
Ph.D: University of Oxford, 1993-1997
Armed with a taste for both P. denitrificans and long project titles, my D.Phil. thesis became “Cloning, sequence analysis and studies on the expression of the nirS gene, encoding cytochrome cd1 nitrite reductase, from Thiosphaera pantotropha“. Nitrite reductase (NirS) is a key enzyme in the global nitrogen cycle, reducing nitrite to nitric oxide. We sequenced the nirS gene and obtained a number of high-resolution crystal structures for NirS in both the oxidised and reduced forms. These indicated that despite a high degree of sequence conservation, different active site residues occur in NirS from different sources. We also investigated a number of heterologous and homologous expression systems, generated a NirS site-directed mutant and analysed the transcription of the nir operon.
Honours: University of Edinburgh, 1989-1993
My career in scientific research began with an undergraduate project entitled “Spectroscopic and kinetic comparisons of cytochrome c peroxidases from Paracoccus denitrificans, Rhodobacter capsulatus and Pseudomonas stutzeri “. CCP is a dihaem cytochrome c found in the periplasm of many Gram-negative bacteria. It converts toxic hydrogen peroxide to water. During this project we showed using spectroscopy and kinetics that the activation of CCP by calcium observed in CCP from P. denitrificans was common to other CCPs and identified a putative calcium binding site on the enzyme.