Dr Richard Edwards

Position: 
Senior Lecturer
Room: 
263B, Biological Sciences
Telephone: 
(+61 2) 9385 0490
Fax: 
(+61 2) 9385 1485


Professional Experience

  • Nov 2013-current: Senior Lecturer in Bioinformatics, School of BABS
  • Mar 2013-current: Senior Lecturer (Bioinformatics and Molecular Evolution), Centre for Biological Sciences, University of Southampton
  • 2011-2013: Lecturer (Bioinformatics and Molecular Evolution), Centre for Biological Sciences, University of Southampton
  • 2007-2011: Senior Research Fellow (Bioinformatics), Centre for Biological Sciences, University of Southampton
  • 2005-2007: Postdoctoral Research Fellow in Bioinformatics, Conway Institute of Biomolecular and Biomedical Research, University College Dublin
  • 2001–2005: Postdoctoral Research Fellow in Bioinformatics, Royal College of Surgeons in Ireland, Dublin
  • 2003-2005: SFI Investigator Award (D Shields)
  • 2002-2005: HRB Programme Grant, Platelet Biology
  • 2001-2003: PRTLI HEA Cycle 2
  • 1998-2002: PhD, Institute of Genetics, University of Nottingham

Research Contribution

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.

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 web servers 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.

More details of the lab can be found at: http://edwardslab.blogspot.com.au/

Active Research Projects

Selected Bioinformatics Software 

  • Edwards RJ (2012), SLiMMaker: Short Linear Motif Maker
  • Davey NE & Edwards RJ (2012), SLiMPrints: Short Linear Motif Fingerprints
  • Edwards RJ (2009), FIESTA: Fasta Input EST Analysis
  • Edwards RJ (2009), QSLiMFinder: Query SLiMFinder
  • Edwards RJ (2008), BUDAPEST: Bioinformatics Utility for Data Analysis of Proteomics on ESTs
  • Edwards RJ (2007), SLiMSearch: Short Linear Motif Search tool
  • Edwards RJ, Davey NE & Shields DC (2007), SLiMFinder: Short Linear Motif Finder
  • Edwards RJ (2006), CompariMotif: Motif-Motif Comparison Tool
  • Davey NE, Shields DC & Edwards RJ (2006), SLiMDisc: Short Linear Motif Discovery
  • Edwards RJ & Davey NE (2006), GABLAM: Global Analysis of BLAST Local AlignMents
  • Edwards RJ (2006), GOPHER: Generation of Orthologous Proteins from High-throughput Estimation of Relationships
  • Edwards RJ (2005), HAQESAC: Homologue Alignment Quality, Establishment of Subfamilies and Ancestor Construction
  • Edwards RJ (2005), BADASP: Burst After Duplication with Ancestral Sequence Prediction
  • Edwards RJ (2004), GASP: Gapped Ancestral Sequence Prediction

Publications

Click here for Dr Edwards's publications list