Edwards, Richard - University of New South Wales - School of Biotechnology and Biomolecular Science

个人简介

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

研究领域

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.

近期论文

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Lin P; Nicholls L; Assareh H; Fang Z; Amos TG; Edwards RJ; Assareh AA; Voineagu I, 2016, 'Transcriptome analysis of human brain tissue identifies reduced expression of complement complex C1Q Genes in Rett syndrome.', BMC Genomics, vol. 17, pp. 427, http://dx.doi.org/10.1186/s12864-016-2746-7 Churton NW; Misra RV; Howlin RP; Allan RN; Jefferies J; Faust SN; Gharbia SE; Edwards RJ; Clarke SC; Webb JS, 2016, 'Parallel Evolution in Streptococcus pneumoniae Biofilms.', Genome Biology and Evolution, vol. 8, no. 5, pp. 1316 - 1326, http://dx.doi.org/10.1093/gbe/evw072 Skipp PJS; Hughes C; McKenna T; Edwards R; Langridge J; Thomson NR; Clarke IN, 2016, 'Quantitative proteomics of the infectious and replicative forms of Chlamydia trachomatis', PLoS One, vol. 11, no. 2, http://dx.doi.org/10.1371/journal.pone.0149011 Olorin E; O'Brien KT; Palopoli N; Pérez-Bercoff Å; Shields DC; Edwards RJ, 2015, 'SLiMScape 3.x: a Cytoscape 3 app for discovery of Short Linear Motifs in protein interaction networks.', F1000 Research, vol. 4, pp. 477, http://dx.doi.org/10.12688/f1000research.6773.1 Edwards RJ; Palopoli N, 2015, 'Computational prediction of Short Linear Motifs from protein sequences', Methods in Molecular Biology, vol. 1268, pp. 89 - 141, http://dx.doi.org/10.1007/978-1-4939-2285-7_6 Dillon J; Franks CJ; Murray C; Edwards RJ; Calahorro F; Ishihara T; Katsura I; Holden-Dye L; O'Connor V, 2015, 'Metabotropic glutamate receptors: Modulators of context-dependent feeding behaviour in C. elegans', Journal of Biological Chemistry, vol. 290, no. 24, pp. 15052 - 15065, http://dx.doi.org/10.1074/jbc.M114.606608 Palopoli N; Lythgow KT; Edwards RJ, 2015, 'QSLiMFinder: improved short linear motif prediction using specific query protein data.', Bioinformatics, vol. 31, no. 14, pp. 2284 - 2293, http://dx.doi.org/10.1093/bioinformatics/btv155 Gittins JR; D'Angelo C; Oswald F; Edwards RJ; Wiedenmann J, 2015, 'Fluorescent protein-mediated colour polymorphism in reef corals: Multicopy genes extend the adaptation/acclimatization potential to variable light environments', Molecular Ecology, vol. 24, no. 2, pp. 453 - 465, http://dx.doi.org/10.1111/mec.13041 Jones BM; Iglesias-Rodriguez MD; Skipp PJ; Edwards RJ; Greaves MJ; Young JR; Elderfield H; O'Connor CD, 2013, 'Responses of the Emiliania huxleyi Proteome to Ocean Acidification', PLoS One, vol. 8, no. 4, http://dx.doi.org/10.1371/journal.pone.0061868 Ient B; Edwards R; Mould R; Hannah M; Holden-Dye L; O'Connor V, 2012, 'HSP-4 endoplasmic reticulum (ER) stress pathway is not activated in a C. elegans model of ethanol intoxication and withdrawal', Invertebrate Neuroscience, vol. 12, no. 2, pp. 93 - 102, http://dx.doi.org/10.1007/s10158-012-0136-7 Edwards RJ; Davey NE; Brien KO; Shields DC, 2012, 'Interactome-wide prediction of short, disordered protein interaction motifs in humans', Molecular Biosystems, vol. 8, no. 1, pp. 282 - 295, http://dx.doi.org/10.1039/c1mb05212h Dinkel H; Michael S; Weatheritt RJ; Davey NE; Van Roey K; Altenberg B; Toedt G; Uyar B; Seiler M; Budd A; Jödicke L; Dammert MA; Schroeter C; Hammer M; Schmidt T; Jehl P; McGuigan C; Dymecka M; Chica C; Luck K; Via A; Chatr-Aryamontri A; Haslam N; Grebnev G; Edwards RJ; Steinmetz MO; Meiselbach H; Diella F; Gibson TJ, 2012, 'ELM - The database of eukaryotic linear motifs', Nucleic Acids Research, vol. 40, no. D1, http://dx.doi.org/10.1093/nar/gkr1064 Davey NE; Cowan JL; Shields DC; Gibson TJ; Coldwell MJ; Edwards RJ, 2012, 'SLiMPrints: Conservation-based discovery of functional motif fingerprints in intrinsically disordered protein regions', Nucleic Acids Research, vol. 40, no. 21, pp. 10628 - 10641, http://dx.doi.org/10.1093/nar/gks854 Jones BM; Edwards RJ; Skipp PJ; O'Connor CD; Iglesias-Rodriguez MD, 2011, 'Shotgun Proteomic Analysis of Emiliania huxleyi, a Marine Phytoplankton Species of Major Biogeochemical Importance', Marine Biotechnology, vol. 13, no. 3, pp. 496 - 504, http://dx.doi.org/10.1007/s10126-010-9320-0 Crisford A; Murray C; O'Connor V; Edwards RJ; Kruger N; Welz C; Von Samson-Himmelstjerna G; Harder A; Walker RJ; Holden-Dye L, 2011, 'Selective toxicity of the anthelmintic emodepside revealed by heterologous expression of human KCNMA1 in Caenorhabditis elegans', Molecular Pharmacology, vol. 79, no. 6, pp. 1031 - 1043, http://dx.doi.org/10.1124/mol.111.071043 Davey NE; Haslam NJ; Shields DC; Edwards RJ, 2011, 'SLiMSearch 2.0: Biological context for short linear motifs in proteins', Nucleic Acids Research, vol. 39, no. SUPPL. 2, http://dx.doi.org/10.1093/nar/gkr402 Davey NE; Edwards RJ; Shields DC, 2010, 'Estimation and efficient computation of the true probability of recurrence of short linear protein sequence motifs in unrelated proteins', BMC Bioinformatics, vol. 11, http://dx.doi.org/10.1186/1471-2105-11-14 Davey NE; Haslam NJ; Shields DC; Edwards RJ, 2010, 'SLiMFinder: A web server to find novel, significantly over-represented, short protein motifs', Nucleic Acids Research, vol. 38, no. SUPPL. 2, http://dx.doi.org/10.1093/nar/gkq440 Davey NE; Edwards RJ; Shields DC, 2010, 'Computational identification and analysis of protein short linear motifs', Frontiers in Bioscience, vol. 15, no. 3, pp. 801 - 825, http://dx.doi.org/10.2741/3647 Raab M; Daxecker H; Edwards RJ; Treumann A; Murphy D; Moran N, 2010, 'Protein interactions with the platelet integrin aIIb regulatory motif', Proteomics, vol. 10, no. 15, pp. 2790 - 2800, http://dx.doi.org/10.1002/pmic.200900621