My research interests stem from a fascination with the molecular basis of evolutionary change and how we can harness genetic sequence patterns to make useful predictions about biological systems. I started my academic career as a geneticist, modelling how transposable elements may be selectively retained and spread through a clonal population of bacteria. After my PhD, I moved into full-time bioinformatics, with a focus on protein...view more
About Me
My research interests stem from a fascination with the molecular basis of evolutionary change and how we can harness genetic sequence patterns to make useful predictions about biological systems. I started my academic career as a geneticist, modelling how transposable elements may be selectively retained and spread through a clonal population of bacteria. After my PhD, I moved into full-time bioinformatics, with a focus on protein sequence analysis. As a postdoc in Dublin, I developed a bioinformatics (sequence analysis) method for the rational design of biologically active short peptides. The biological activity of these short peptides got me interested in short protein-protein interaction motifs, which have been the subsequent focus of my research. During my second postdoc, I coined the term "Short Linear Motif" (SLiM) for a specific type of protein interaction motif and was instrumental in developing SLiMDisc and SLiMFinder, two of the first algorithms for successfully predicting SLiMs from protein sequences. These and other algorithms are now available in the SLiMSuite bioinformatics package and online webservers.
Since starting my own research group in 2007, I have expanded my collaborative activities, developing and applying sequence analysis pipelines for a number of different projects under the broad general umbrella of adaptation and response to climate change. In 2013, I moved to UNSW, where I have built a close working relationship with the Ramaciotti Centre for Genomics and established genomics as a core research activity. I am now involved in multiple de novo whole genome sequencing and assembly projects, using short read (Illumina), long read (PacBio & Nanopore) and linked read (10x Chromium) sequencing. These include the cane toad, venomous Australian snakes through the BABS Genome Project, and Aussie marsupials as part of the Oz Mammals Genomics initiative. I am also leading assembly of the Waratah genome as part of the pilot phase for the new Genomics of Australian Plants initiative.
Education
2010: Post-graduate Certificate in Academic Practice. University of Southampton, UK.
2002: PhD (Genetics). University of Nottingham, UK.
1998: BSc (Hons) Genetics. University of Nottingham, UK.
Employment History
Nov 2013-present: Senior Lecturer in Genomics and Bioinformatics, School of BABS, UNSW, Australia.
2014-2016: Adjunct Associate Professor. Centre for Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK.
2013-2014: Senior Lecturer. Centre for Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK.
2011-2013: Lecturer (Bioinformatics and Molecular Evolution), Centre for Biological Sciences, University of Southampton, UK.
2007-2011: Senior Research Fellow (Bioinformatics), Centre for Biological Sciences, University of Southampton, UK.
2005-2007: Postdoctoral Research Fellow in Bioinformatics, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Ireland.
2001–2005: Postdoctoral Research Fellow in Bioinformatics, Royal College of Surgeons in Ireland, Dublin, Ireland.
My Research Activities
One of the most important, interesting and challenging questions in biology is how new traits evolve at the molecular level. My lab employs sequence analysis techniques to interrogate protein and DNA sequences for the signals left behind by evolution. We are a bioinformatics lab but like to incorporate bench data through collaboration wherever possible. The core research in the lab is broadly divided into two main themes: (1) evolutionary genomics; (2) intrinsically disordered protein-protein interactions and short linear motifs (SLiMs).
Current active research projects have a focus on eukaryotic evolutionary genomics. We are using the latest generation of sequencing, assembly and scaffolding technologies (10x Chromium “linked reads”, PacBio, Oxford Nanopore, HiC) to assemble multiple species including venomous snakes, the cane toad, marsupials, dog breeds, and Australian flora. Multiple genomics-related projects are available through as range of species through various collaborations and consortia, including Oz Mammals Genomics, Genomics of Australian Plants, and Australian Amphibian and Reptile Genomics. Projects include annotating genomes and/or specific gene families, developing bioinformatics tools/workflows for assessing and tidying genome assemblies, and identifying/characterising ultraconserved elements.
<p>SLiMSuite is an open access set of bioinformatics tools for predicting and analysing short linear motifs in protein sequences. A number of other sequence analysis tools are provided in the package, with particular focus on protein family analysis and proteomics of non-model org...
https://orcid.org/0000-0002-3645-5539
