My research interests stem from a fascination with the molecular basis of evolutionary change and how we can harness the genetic sequence patterns left behind to make useful predictions about contemporary biological systems. I started my academic career as a geneticist, modelling how transposable elements may be selectively retained and spread through a clonal populations of bacteria. After my PhD, I moved into full-time...view more
My research interests stem from a fascination with the molecular basis of evolutionary change and how we can harness the genetic sequence patterns left behind to make useful predictions about contemporary biological systems. I started my academic career as a geneticist, modelling how transposable elements may be selectively retained and spread through a clonal populations 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 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 them from protein sequences.
Since starting my own research group in 2007, I have continued to work on the development and application of SLiM discovery tools. I have also developed sequence analysis pipelines for a number of different collaborative projects. I moved to UNSW in late 2013.
- 1995: 4 A-Levels (A); 1 AS-Level (A); 11 GCSEs (A). Bognor Regis Community College, UK.
- 1998: BSc (Hons) Genetics. University of Nottingham, UK.
- 2002: PhD (Genetics). University of Nottingham, UK.
- Nov 2013-present: Senior Lecturer in Bioinformatics, School of BABS, UNSW, Australia.
- Mar 2013-present: Senior Lecturer (Bioinformatics and Molecular Evolution), Centre for Biological Sciences, University of Southampton, 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 Goals
- Applying evolutionary theory to real-world problems.
- Identifying the molecular basis of protein-protein interactions.
- Understanding how genetic variation impacts disease susceptibility.
My Research in Detail
The core research in my lab is the study of Short Linear Motifs (SLiMs), which are short regions of proteins that mediate interactions with other proteins. This project originated with my postdoctoral research, during which I developed a bioinformatics (sequence analysis) method for rational design of biologically active short peptides. I subsequently developed SLiMDisc, one of the first algorithms for successfully predicting novel SLiMs from sequence data - and coined the term “SLiM” into the bargain - before developing the first SLiM prediction algorithm able to estimate the statistical significance of motif predictions (SLiMFinder), which greatly increased the reliability of predictions. SLiMFinder has since spawned a number of motif discovery tools and webservers and is still the most successful SLiM prediction tool on benchmarking data.
My current research is looking to develop these SLiM prediction tools further and apply them to important biological questions. Of particular interest is the molecular mimicry employed by viruses to interact with host proteins and the role of SLiMs in other diseases, such as cancer. Other work is concerned with the evolutionary dynamics of SLiMs within protein interaction networks.
Another area of research concerns the post-transcriptional regulation of protein expression. In collaboration with Dr Mark Coldwell (University of Southampton), we are asking the question: How does the ribosome choose where to start translating a protein? By combining bioinformatics screens with laboratory reporter assays, we are identifying proteins that are translated from non-canonical and/or multiple initiation codons. Possible roles of N-terminal variability in protein interactions and subcellular localisation are now under investigation.
I am also involved in a number of interdisciplinary collaborative projects applying bioinformatics tools and molecular evolution theory to experimental biology, often using large genomic, transcriptomic and/or proteomic datasets. These projects often involve the development of bespoke bioinformatics pipelines and a number of open source bioinformatics tools have been generated as a result.
Current Research Projects (Postdocs)
Dr Nicolas Palopoli - Integrated _in silico_ prediction of protein interaction motifs using interactome networks and high-resolution 3-dimensional structures. Dr Ranjeeta Menon - Molecular mimicry of human SLiMs by viruses in host-pathogen protein-protein interactions.
Current Student Projects (PhD and Honours)
Alex Watson-Lazowski - Using Next Generation Sequencing to understand acclimation and adaption of Plantago lanceolata to a changing environment.
Joe Jenkins - The effect of biochar on soil microbial communities.
Andreas Johansson - Tag based transcriptome analysis of gene expression in a promising green algae.
Helen Patrick - The role of alternative translation initiation codons in generating diversity in the proteome.
Enquiries are welcome to email@example.com for potential Honours/PhD supervision in any of the active research areas in the lab. Please see the BABS Honours Booklet for some specific projects. Most projects are 100% computational but collaborative interdisciplinary projects are also available.
TEACHING & OUTREACH
Courses I teach
BIOC2181: Fundamentals of Biochemistry.
BABS2202: Molecular Cell Biology.
BABS3121: Molecular Biology of Nucleic Acids.
BABS3281: Molecular Genomics.
BABS3291: Genes, Genomes and Evolution.
Professional affiliations and service positions
Member of the Society of Biology (MSB).
Member of the Genetics Society.
AWARDS & ACHIEVEMENTS
2007-2011: University of Southampton Senior Research Fellowship
2010: Fellow of the Higher Education Academy (FHEA).