Select Publications

Book Chapters

Edwards RJ, 2019, 'Phylogenetic Tree Rooting', in , Elsevier, pp. 727 - 735,

Edwards RJ; Palopoli N, 2015, 'Computational prediction of short linear motifs from protein sequences', in Computational Peptidology, Springer Link, pp. 89 - 141,

Shields DC; Johnston CR; Wallace IM; Edwards RJ, 2008, 'Evolution of specificity and diversity', in Ancestral Sequence Reconstruction, Oxford University Press,

Journal articles

Holland S; Edwards R; Ertan H; Wong YK; Russell T; Deshpande N; Manefield M; Lee M, 2019, 'Whole genome sequencing of a novel, dichloromethane-fermenting Peptococcaceae from an enrichment culture', ,

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,

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,

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,

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,

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,

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,

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,

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,

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,

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,

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,

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.', F1000Res, vol. 4, pp. 477,

Edwards RJ; Palopoli N, 2015, 'Computational prediction of Short Linear Motifs from protein sequences', Methods in Molecular Biology, vol. 1268, pp. 89 - 141,

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; Bongcam-Rudloff E; Brazas MD; Brooksbank C; Budd A; Charleston M; Christoffels A; Conesa A; Corpas M; Crowe M; Davies A; de Crecy-Lagard V; De Las Rivas J; Doyle M; Edwards R; Facchiano A; Fernandes P; Gaeta B; Gaudet P; Heger A; Herringa J; Hughes D; Jimenez RC; Kille P; Korpelainen E; Kumuthini J; Lewitter F; 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; van Gelder CWG; 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,

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,

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,

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,

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,

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,

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,

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,

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,

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,

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,

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,

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,

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,

Davey NE; Edwards RJ; Shields DC, 2010, 'Computational identification and analysis of protein short linear motifs', Frontiers in Bioscience, vol. 15, pp. 801 - 825,

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,

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,

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,

Edwards RJ; Davey NE; Shields DC, 2008, 'CompariMotif: Quick and easy comparisons of sequence motifs', Bioinformatics, vol. 24, pp. 1307 - 1309,

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,

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,

Davey NE; Edwards RJ; Shields DC, 2007, 'The SLiMDisc server: Short, linear motif discovery in proteins', Nucleic Acids Research, vol. 35,

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,

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,

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,

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,

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,

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,

Edwards RJ; Shields DC, 2005, 'BADASP: Predicting functional specificity in protein families using ancestral sequences', Bioinformatics, vol. 21, pp. 4190 - 4191,

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

Edwards RJ; Shields DC, 2004, 'GASP: Gapped ancestral sequence prediction for proteins', BMC Bioinformatics, vol. 5,

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,

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,

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