Dr Richard   Edwards
Senior Lecturer

Dr Richard Edwards

Science
Biotech & Biomolecular Science

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.

 

 

Phone
02 9385-0490
Location
Room 2110, E26 Bioscience South

Publications

  • Book Chapters | 2018
    Dr Richard Edwards
    Edwards RJ, 2018, 'Phylogenetic tree rooting', in Encyclopedia of Bioinformatics and Computational Biology: ABC of Bioinformatics, Elsevier, pp. 727 - 735, http://dx.doi.org/10.1016/B978-0-12-809633-8.20258-6
    Book Chapters | 2015
    Dr Richard Edwards
    Edwards RJ; Palopoli N, 2015, 'Computational prediction of short linear motifs from protein sequences', in Computational Peptidology, Springer Link, pp. 89 - 141, http://dx.doi.org/10.1007/978-1-4939-2285-7_6
    Book Chapters | 2008
    Dr Richard Edwards
    Shields DC; Johnston CR; Wallace IM; Edwards RJ, 2008, 'Evolution of specificity and diversity', in Ancestral Sequence Reconstruction, Oxford University Press, http://dx.doi.org/10.1093/acprof:oso/9780199299188.003.0019
  • Journal articles | 2021
    Dr Richard Edwards
    Edwards RJ; Field MA; Ferguson JM; Dudchenko O; Keilwagen J; Rosen BD; Johnson GS; Rice ES; Hillier LD; Hammond JM; Towarnicki SG; Omer A; Khan R; Skvortsova K; Bogdanovic O; Zammit RA; Aiden EL; Warren WC; Ballard JWO, 2021, 'Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome', BMC Genomics, vol. 22, http://dx.doi.org/10.1186/s12864-021-07493-6
    Journal articles | 2021
    Dr Richard Edwards
    Sarma RR; Crossland MR; Eyck HJF; Devore JL; Edwards RJ; Cocomazzo M; Zhou J; Brown GP; Shine R; Rollins LA, 2021, 'Intergenerational effects of manipulating DNA methylation in the early life of an iconic invader', Philosophical Transactions of the Royal Society B: Biological Sciences, vol. 376, http://dx.doi.org/10.1098/rstb.2020.0125
    Journal articles | 2021
    Dr Richard Edwards
    Stuart K; Edwards R; Cheng Y; Warren W; Burt D; Sherwin W; Hofmeister N; Werner S; Ball G; Bateson M; Brandley M; Buchanan K; Cassey P; Clayton D; De Meyer T; Meddle S; Rollins L, 2021, 'Transcript- and annotation-guided genome assembly of the European starling', , http://dx.doi.org/10.1101/2021.04.07.438753
    Journal articles | 2021
    Dr Richard Edwards
    Chen S; Rossetto M; van der Merwe M; Lu-Irving P; Yap J-Y; Sauquet H; Bourke G; Bragg J; Edwards R, 2021, 'Chromosome-level de novo genome assembly of Telopea speciosissima (New South Wales waratah) using long-reads, linked-reads and Hi-C', , http://dx.doi.org/10.1101/2021.06.02.444084
    Journal articles | 2021
    Dr Richard Edwards
    Galbraith J; Ludington A; Edwards R; Sanders K; Suh A; Adelson D, 2021, 'Horizontal transfer and southern migration: the tale of Hydrophiinae’s marine journey', , http://dx.doi.org/10.1101/2021.06.22.449521
    Journal articles | 2021
    Dr Richard Edwards
    Edwards R; Field M; Ferguson J; Dudchenko O; Keilwagen J; Rosen B; Johnson G; Rice E; Hillier L; Hammond J; Towarnicki S; Omer A; Khan R; Skvortsova K; Bogdanovic O; Zammit R; Aiden EL; Warren W; Ballard W, 2021, 'Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome', BMC Genomics, http://dx.doi.org/10.1186/s12864-021-07493-6
    Journal articles | 2020
    Dr Richard Edwards
    Field MA; Rosen BD; Dudchenko O; Chan EKF; Minoche AE; Edwards RJ; Barton K; Lyons RJ; Tuipulotu DE; Hayes VM; Omer AD; Colaric Z; Keilwagen J; Skvortsova K; Bogdanovic O; Smith MA; Aiden EL; Smith TPL; Zammit RA; Ballard JWO, 2020, 'Canfam-GSD: De novo chromosome-length genome assembly of the German Shepherd Dog (Canis lupus familiaris) using a combination of long reads, optical mapping, and Hi-C', GigaScience, vol. 9, http://dx.doi.org/10.1093/gigascience/giaa027
    Journal articles | 2020
    Dr Richard Edwards
    Benaud N; Edwards RJ; Amos TG; D'Agostino PM; Gutiérrez-Chávez C; Montgomery K; Nicetic I; Ferrari BC, 2020, 'Antarctic desert soil bacteria exhibit high novel natural product potential, evaluated through long-read genome sequencing and comparative genomics', Environmental Microbiology, http://dx.doi.org/10.1111/1462-2920.15300
    Journal articles | 2020
    Dr Richard Edwards
    Sarma RR; Edwards RJ; Crino OL; Eyck HJF; Waters PD; Crossland MR; Shine R; Rollins LA, 2020, 'Do epigenetic changes drive corticosterone responses to alarm cues in larvae of an invasive Amphibian?', Integrative and Comparative Biology, vol. 60, pp. 1481 - 1494, http://dx.doi.org/10.1093/icb/icaa082
    Journal articles | 2020
    Dr Richard Edwards
    Edwards RJ; Paulsen K; Aguilar Gomez CM; Pérez-Bercoff Å, 2020, 'Computational prediction of disordered protein motifs using SLiMSuite', Methods in molecular biology (Clifton, N.J.), vol. 2141, pp. 37 - 72, http://dx.doi.org/10.1007/978-1-0716-0524-0_3
    Journal articles | 2020
    Dr Richard Edwards
    Edwards RJ; Field M; Ferguson J; Dudchenko O; Keilwagen J; Rosen B; Johnston G; Rice E; Hillier L; Hammond J; Towarnicki S; Omer A; Skvortsova K; Bogdanovic O; Zammit R; Aiden E; Warren W; Ballard B, 2020, 'Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome', bioRxiv, http://dx.doi.org/10.1101/2020.11.11.379073
    Journal articles | 2020
    Dr Richard Edwards
    Johansson SA; Stephenson PG; Edwards RJ; Yoshida K; Moore CM; Terauchi R; Zubkov MV; Terry MJ; Bibby TS, 2020, 'Isolation and molecular characterisation of Dunaliella tertiolecta with truncated light-harvesting antenna for enhanced photosynthetic efficiency', Algal Research, vol. 48, http://dx.doi.org/10.1016/j.algal.2020.101917
    Journal articles | 2019
    Dr Richard Edwards
    Holland SI; Edwards RJ; Ertan H; Wong YK; Russell TL; Deshpande NP; Manefield MJ; Lee M, 2019, 'Whole genome sequencing of a novel, dichloromethane-fermenting Peptococcaceae from an enrichment culture', PeerJ, vol. 2019, http://dx.doi.org/10.7717/peerj.7775
    Journal articles | 2019
    Dr Richard Edwards
    Davey NE; Babu MM; Blackledge M; Bridge A; Capella-Gutierrez S; Dosztanyi Z; Drysdale R; Edwards RJ; Elofsson A; Felli IC; Gibson TJ; Gutmanas A; Hancock JM; Harrow J; Higgins D; Jeffries CM; Le Mercier P; Meszaros B; Necci M; Notredame C; Orchard S; Ouzounis CA; Pancsa R; Papaleo E; Pierattelli R; Piovesan D; Promponas VJ; Ruch P; Rustici G; Romero P; Sarntivijai S; Saunders G; Schuler B; Sharan M; Shields DC; Sussman JL; Tedds JA; Tompa P; Turewicz M; Vondrasek J; Vranken WF; Wallace BA; Wichapong K; Tosatto SCE, 2019, 'An intrinsically disordered proteins community for elixir [version 1; peer review: 2 approved]', F1000Research, vol. 8, http://dx.doi.org/10.12688/f1000research.20136.1
    Journal articles | 2019
    Dr Richard Edwards
    Song W; Thomas T; Edwards RJ, 2019, 'Complete genome sequences of pooled genomic DNA from 10 marine bacteria using PacBio long-read sequencing', Marine Genomics, vol. 48, http://dx.doi.org/10.1016/j.margen.2019.05.002
    Journal articles | 2018
    Dr Richard Edwards
    Edwards RJ; Tuipulotu DE; Amos TG; O'Meally D; Richardson MF; Russell TL; Vallinoto M; Carneiro M; Ferrand N; Wilkins MR; Sequeira F; Rollins LA; Holmes EC; Shine R; White PA, 2018, 'Draft genome assembly of the invasive cane toad, Rhinella marina', GigaScience, vol. 7, http://dx.doi.org/10.1093/gigascience/giy095
    Journal articles | 2018
    Dr Richard Edwards
    Idrees S; Perez-Bercoff A; Edwards RJ, 2018, 'SLiM-Enrich: computational assessment of protein-protein interaction data as a source of domain-motif interactions', PEERJ, vol. 6, http://dx.doi.org/10.7717/peerj.5858
    Journal articles | 2018
    Dr Richard Edwards
    Idrees S; Pérez-Bercoff Å; Edwards RJ, 2018, 'Correction: SLiMEnrich: computational assessment of protein-protein interaction data as a source of domain-motif interactions.', PeerJ, vol. 6, http://dx.doi.org/10.7717/peerj.5858/correction-1
    Journal articles | 2017
    Dr Richard Edwards
    Jenkins JR; Viger M; Arnold EC; Harris ZM; Ventura M; Miglietta F; Girardin C; Edwards RJ; Rumpel C; Fornasier F; Zavalloni C; Tonon G; Alberti G; Taylor G, 2017, 'Biochar alters the soil microbiome and soil function: results of next-generation amplicon sequencing across Europe', GCB Bioenergy, vol. 9, pp. 591 - 612, http://dx.doi.org/10.1111/gcbb.12371
    Journal articles | 2017
    Dr Richard Edwards
    Glenn WK; Ngan CC; Amos TG; Edwards RJ; Swift J; Lutze-Mann L; Shang F; Whitaker NJ; Lawson JS, 2017, 'High risk human papilloma viruses (HPVs) are present in benign prostate tissues before development of HPV associated prostate cancer', INFECTIOUS AGENTS AND CANCER, vol. 12, http://dx.doi.org/10.1186/s13027-017-0157-2
    Journal articles | 2016
    Dr Richard Edwards
    Watson-Lazowski A; Lin Y; Miglietta F; Edwards RJ; Chapman MA; Taylor G, 2016, 'Plant adaptation or acclimation to rising CO2? Insight from first multigenerational RNA-Seq transcriptome', Global Change Biology, vol. 22, pp. 3760 - 3773, http://dx.doi.org/10.1111/gcb.13322
    Journal articles | 2016
    Dr Richard Edwards
    Churton NWV; 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, pp. 1316 - 1326, http://dx.doi.org/10.1093/gbe/evw072
    Journal articles | 2016
    Dr Richard Edwards
    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, http://dx.doi.org/10.1371/journal.pone.0149011
    Journal articles | 2016
    Dr Richard Edwards
    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. 1 - 11, http://dx.doi.org/10.1186/s12864-016-2746-7
    Journal articles | 2015
    Dr Richard Edwards
    Palopoli N; Lythgow KT; Edwards RJ, 2015, 'QSLiM Finder: Improved short linear motif prediction using specific query protein data', Bioinformatics, vol. 31, pp. 2284 - 2293, http://dx.doi.org/10.1093/bioinformatics/btv155
    Journal articles | 2015
    Dr Richard Edwards
    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
    Journal articles | 2015
    Dr Richard Edwards
    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, pp. 15052 - 15065, http://dx.doi.org/10.1074/jbc.M114.606608
    Journal articles | 2015
    Dr Richard Edwards
    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, pp. 453 - 465, http://dx.doi.org/10.1111/mec.13041
    Journal articles | 2015
    Dr Richard Edwards
    Atwood TK; Bongcam-Rudloff E; Brazas ME; Corpas M; Gaudet P; Lewitter F; Mulder N; Palagi PM; Schneider MV; van Gelder CWG; Attwood TK; Banag C; Blackford S; Blatter MC; Brazas MD; Brooksbank C; Budd A; Charleston M; Christoffels A; Conesa A; Crowe M; Davies A; de Crecy-Lagard V; De Las Rivas J; Doyle M; Edwards R; Facchiano A; Fernandes P; Gaeta B; Heger A; Herringa J; Hughes D; Jimenez RC; Kille P; Korpelainen E; Kumuthini J; MacLean D; Martinez SAR; McGrath A; Michalopoulos I; Mulder N; Ouellette BF; Palagi PM; Pearson WR; Qi W; Romano P; Rother K; Sansone SA; Schneider MV; Schönbach C; Tastan-Bishop O; Trelles O; Twells R; Via A; Vriend G; Warnow T; Watson M; Westervelt N; Zanzoni A, 2015, 'GOBLET: The Global Organisation for Bioinformatics Learning, Education and Training', PLoS Computational Biology, vol. 11, http://dx.doi.org/10.1371/journal.pcbi.1004143
    Journal articles | 2015
    Dr Richard Edwards
    Olorin E; O Brien KT; Palopoli N; Perez-Bercoff A; Shields DC; Edwards RJ, 2015, 'SLiMScape 3.x: a Cytoscape 3 app for discovery of Short Linear Motifs in protein interaction networks', F1000Research, vol. 4, pp. 477, http://dx.doi.org/10.12688/f1000research.6773.1
    Journal articles | 2015
    Dr Richard Edwards
    Attwood TK; Bongcam-Rudloff E; Brazas ME; Corpas M; Gaudet P; Lewitter F; Mulder N; Palagi PM; Schneider MV; van Gelder CWG; GOBLET Consortium , 2015, 'Correction: GOBLET: The Global Organisation for Bioinformatics Learning, Education and Training.', PLoS Comput Biol, vol. 11, pp. e1004281, http://dx.doi.org/10.1371/journal.pcbi.1004281
    Journal articles | 2013
    Dr Richard Edwards
    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, http://dx.doi.org/10.1371/journal.pone.0061868
    Journal articles | 2012
    Dr Richard Edwards
    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, http://dx.doi.org/10.1093/nar/gkr1064
    Journal articles | 2012
    Dr Richard Edwards
    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, pp. 10628 - 10641, http://dx.doi.org/10.1093/nar/gks854
    Journal articles | 2012
    Dr Richard Edwards
    Edwards RJ; Davey NE; Brien KO; Shields DC, 2012, 'Interactome-wide prediction of short, disordered protein interaction motifs in humans', Molecular BioSystems, vol. 8, pp. 282 - 295, http://dx.doi.org/10.1039/c1mb05212h
    Journal articles | 2012
    Dr Richard Edwards
    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, pp. 93 - 102, http://dx.doi.org/10.1007/s10158-012-0136-7
    Journal articles | 2011
    Dr Richard Edwards
    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, pp. 1031 - 1043, http://dx.doi.org/10.1124/mol.111.071043
    Journal articles | 2011
    Dr Richard Edwards
    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, http://dx.doi.org/10.1093/nar/gkr402
    Journal articles | 2011
    Dr Richard Edwards
    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, pp. 496 - 504, http://dx.doi.org/10.1007/s10126-010-9320-0
    Journal articles | 2010
    Dr Richard Edwards
    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
    Journal articles | 2010
    Dr Richard Edwards
    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, http://dx.doi.org/10.1093/nar/gkq440
    Journal articles | 2010
    Dr Richard Edwards
    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, pp. 2790 - 2800, http://dx.doi.org/10.1002/pmic.200900621
    Journal articles | 2010
    Dr Richard Edwards
    Davey NE; Edwards RJ; Shields DC, 2010, 'Computational identification and analysis of protein short linear motifs', Frontiers in Bioscience, vol. 15, pp. 801 - 825, http://dx.doi.org/10.2741/3647
    Journal articles | 2010
    Dr Richard Edwards
    Davey NE; Haslam NJ; Shields DC; Edwards RJ, 2010, 'SLiMSearch: A webserver for finding novel occurrences of short linear motifs in proteins, incorporating sequence context', Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 6282 LNBI, pp. 50 - 61, http://dx.doi.org/10.1007/978-3-642-16001-1_5
    Journal articles | 2009
    Dr Richard Edwards
    Davey NE; Shields DC; Edwards RJ, 2009, 'Masking residues using context-specific evolutionary conservation significantly improves short linear motif discovery', Bioinformatics, vol. 25, pp. 443 - 450, http://dx.doi.org/10.1093/bioinformatics/btn664
    Journal articles | 2008
    Dr Richard Edwards
    Edwards RJ; Davey NE; Shields DC, 2008, 'CompariMotif: Quick and easy comparisons of sequence motifs', Bioinformatics, vol. 24, pp. 1307 - 1309, http://dx.doi.org/10.1093/bioinformatics/btn105
    Journal articles | 2007
    Dr Richard Edwards
    Edwards RJ; Davey NE; Shields DC, 2007, 'SLiMFinder: A probabilistic method for identifying over-represented, convergently evolved, short linear motifs in proteins', PLoS ONE, vol. 2, http://dx.doi.org/10.1371/journal.pone.0000967
    Journal articles | 2007
    Dr Richard Edwards
    Edwards RJ; Moran N; Devocelle M; Kiernan A; Meade G; Signac W; Foy M; Park SDE; Dunne E; Kenny D; Shields DC, 2007, 'Bioinformatic discovery of novel bioactive peptides', Nature Chemical Biology, vol. 3, pp. 108 - 112, http://dx.doi.org/10.1038/nchembio854
    Journal articles | 2007
    Dr Richard Edwards
    Davey NE; Edwards RJ; Shields DC, 2007, 'The SLiMDisc server: Short, linear motif discovery in proteins', Nucleic Acids Research, vol. 35, http://dx.doi.org/10.1093/nar/gkm400
    Journal articles | 2007
    Dr Richard Edwards
    Johnston CR; O'Dushlaine C; Fitzpatrick DA; Edwards RJ; Shields DC, 2007, 'Evaluation of whether accelerated protein evolution in chordates has occurred before, after, or simultaneously with gene duplication', Molecular Biology and Evolution, vol. 24, pp. 315 - 323, http://dx.doi.org/10.1093/molbev/msl162
    Journal articles | 2006
    Dr Richard Edwards
    Moran N; Kiernan A; Dunne E; Edwards RJ; Shields DC; Kenny D, 2006, 'Monitoring modulators of platelet aggregation in a microtiter plate assay', Analytical Biochemistry, vol. 357, pp. 77 - 84, http://dx.doi.org/10.1016/j.ab.2006.06.037
    Journal articles | 2006
    Dr Richard Edwards
    Parthasarathi L; Devocelle M; Søndergaard C; Baran I; O'Dushlaine CT; Davey NE; Edwards RJ; Moran N; Kenny D; Shields DC, 2006, 'Absolute net charge and the biological activity of oligopeptides', Journal of Chemical Information and Modeling, vol. 46, pp. 2183 - 2190, http://dx.doi.org/10.1021/ci0600760
    Journal articles | 2006
    Dr Richard Edwards
    Davey NE; Shields DC; Edwards RJ, 2006, 'SLiMDisc: Short, linear motif discovery, correcting for common evolutionary descent', Nucleic Acids Research, vol. 34, pp. 3546 - 3554, http://dx.doi.org/10.1093/nar/gkl486
    Journal articles | 2006
    Dr Richard Edwards
    Parthasarathi L; Devocelle M; Soendergaard C; Baran I; O'Dushlaine CT; Davey NE; Edwards RJ; Moran N; Kenny D; Shields DC, 2006, 'Absolute Net Charge and the Biological Activity of Oligopeptides.', ChemInform, vol. 37, http://dx.doi.org/10.1002/chin.200649229
    Journal articles | 2005
    Dr Richard Edwards
    Kelly P; Maguire PB; Bennett M; Fitzgerald DJ; Edwards RJ; Thiede B; Treumann A; Collins JK; O'Sullivan GC; Shanahan F; Dunne C, 2005, 'Correlation of probiotic Lactobacillus salivarius growth phase with its cell wall-associated proteome', FEMS Microbiology Letters, vol. 252, pp. 153 - 159, http://dx.doi.org/10.1016/j.femsle.2005.08.051
    Journal articles | 2005
    Dr Richard Edwards
    O'Dushlaine CT; Edwards RJ; Park SD; Shields DC, 2005, 'Tandem repeat copy-number variation in protein-coding regions of human genes.', Genome biology, vol. 6
    Journal articles | 2005
    Dr Richard Edwards
    Edwards RJ; Shields DC, 2005, 'BADASP: Predicting functional specificity in protein families using ancestral sequences', Bioinformatics, vol. 21, pp. 4190 - 4191, http://dx.doi.org/10.1093/bioinformatics/bti678
    Journal articles | 2005
    Dr Richard Edwards
    Harney DF; Butler RK; Edwards RJ, 2005, 'Tyrosine phosphorylation of myosin heavy chain during skeletal muscle differentiation: An integrated bioinformatics approach', Theoretical Biology and Medical Modelling, vol. 2, http://dx.doi.org/10.1186/1742-4682-2-12
    Journal articles | 2004
    Dr Richard Edwards
    Edwards RJ; Shields DC, 2004, 'GASP: Gapped ancestral sequence prediction for proteins', BMC Bioinformatics, vol. 5, http://dx.doi.org/10.1186/1471-2105-5-123
    Journal articles | 2003
    Dr Richard Edwards
    Edwards RJ; Brookfield JFY, 2003, 'Transiently beneficial insertions could maintain mobile DNA sequences in variable environments', Molecular Biology and Evolution, vol. 20, pp. 30 - 37, http://dx.doi.org/10.1093/molbev/msg001
    Journal articles | 2002
    Dr Richard Edwards
    Edwards RJ; Sockett RE; Brookfield JFY, 2002, 'A simple method for genome-wide screening for advantageous insertions of mobile DNAs in Escherichia coli', Current Biology, vol. 12, pp. 863 - 867, http://dx.doi.org/10.1016/S0960-9822(02)00837-0
  • Working Papers | 2020
    Dr Richard Edwards
    Yadav S; Dudchenko O; Esvaran M; Rosen B; Field M; Skvortsova K; Gopalakrishnan S; Keilwagen J; Cockran B; Manandhar B; Bucknall M; Bustamante S; Rasmussen J; Melvin R; Omer A; Colaric, Z; Chan E; Minoche A; Smith T; Gilbert T; Bogdanovic O; Zammit R; Thomas T; Aiden E; Ballard B, 2020, Desert Dingo (Canis lupus dingo) genome provides insights into their role in the Australian ecosystem, Cold Spring Harbor, http://dx.doi.org10.1101/2020.11.15.384057, https://www.biorxiv.org/content/10.1101/2020.11.15.384057v1
    Other | 2020
    Dr Richard Edwards
    Edwards RA; Ballard B, 2020, Basenji: Canus lupus familiaris female, https://www.ncbi.nlm.nih.gov/assembly/GCA_013276365.1
    Other | 2020
    Dr Richard Edwards
    Edwards R; Ballard B, 2020, Alpine Dingo: Canus lupus dingo female, https://www.ncbi.nlm.nih.gov/assembly/GCF_012295265.1
    Conference Papers | 2012
    Dr Richard Edwards
    Mooney C; O'Brien K; Haslam NJ; Edwards RJ; Davey NE; Duffy FJ; Golla K; Stavropoulos I; Khaldi N; Chubb AJ; Lombardi F; Holton T; Vijay V; Devocelle M; Moran N; Shields DC, 2012, 'Computational prediction of bioactive peptides', in JOURNAL OF PEPTIDE SCIENCE, WILEY-BLACKWELL, pp. S38 - S39, http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000308091500055&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1
    Conference Papers | 2007
    Dr Richard Edwards
    Edwards RJ; Moran N; Devocelle M; Kieman A; Dunne E; Meade G; Park SDE; Foy M; Signac W; Shields DC; Kenny D, 2007, 'Identification of novel bioactive oligopeptides from macrophages human proteins', in BIOPOLYMERS, JOHN WILEY & SONS INC, Montreal, CANADA, pp. 588 - 588, presented at 20th American-Peptide-Society Symposium, Montreal, CANADA, 26 June 2007 - 30 June 2007, http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000247425900301&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

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