By Dr Richard Edwards

Journal articles

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, 8, 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, 12, pp. 93 - 102, http://dx.doi.org/10.1007/s10158-012-0136-7

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, 40, pp. 10628 - 10641, http://dx.doi.org/10.1093/nar/gks854

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, 40, http://dx.doi.org/10.1093/nar/gkr1064

Edwards RJ; Davey NE; Brien KO; Shields DC, 2012, 'Interactome-wide prediction of short, disordered protein interaction motifs in humans', Molecular BioSystems, 8, pp. 282 - 295, http://dx.doi.org/10.1039/c1mb05212h

Davey NE; Haslam NJ; Shields DC; Edwards RJ, 2011, 'SLiMSearch 2.0: Biological context for short linear motifs in proteins', Nucleic Acids Research, 39, http://dx.doi.org/10.1093/nar/gkr402

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, 79, pp. 1031 - 1043, http://dx.doi.org/10.1124/mol.111.071043

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, 13, pp. 496 - 504, http://dx.doi.org/10.1007/s10126-010-9320-0

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), 6282 LNBI, pp. 50 - 61, http://dx.doi.org/10.1007/978-3-642-16001-1_5

Raab M; Daxecker H; Edwards RJ; Treumann A; Murphy D; Moran N, 2010, 'Protein interactions with the platelet integrin aIIb regulatory motif', Proteomics, 10, pp. 2790 - 2800, http://dx.doi.org/10.1002/pmic.200900621

Davey NE; Edwards RJ; Shields DC, 2010, 'Computational identification and analysis of protein short linear motifs', Frontiers in Bioscience, 15, pp. 801 - 825, http://dx.doi.org/10.2741/3647

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, 38, http://dx.doi.org/10.1093/nar/gkq440

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, 11, http://dx.doi.org/10.1186/1471-2105-11-14

Davey NE; Shields DC; Edwards RJ, 2009, 'Masking residues using context-specific evolutionary conservation significantly improves short linear motif discovery', Bioinformatics, 25, pp. 443 - 450, http://dx.doi.org/10.1093/bioinformatics/btn664

Edwards RJ; Davey NE; Shields DC, 2008, 'CompariMotif: Quick and easy comparisons of sequence motifs', Bioinformatics, 24, pp. 1307 - 1309, http://dx.doi.org/10.1093/bioinformatics/btn105

Edwards RJ; Davey NE; Shields DC, 2007, 'SLiMFinder: A probabilistic method for identifying over-represented, convergently evolved, short linear motifs in proteins', PLoS ONE, 2, http://dx.doi.org/10.1371/journal.pone.0000967

Davey NE; Edwards RJ; Shields DC, 2007, 'The SLiMDisc server: Short, linear motif discovery in proteins', Nucleic Acids Research, 35, http://dx.doi.org/10.1093/nar/gkm400

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, 3, pp. 108 - 112, http://dx.doi.org/10.1038/nchembio854

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, 24, pp. 315 - 323, http://dx.doi.org/10.1093/molbev/msl162

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, 37, http://dx.doi.org/10.1002/chin.200649229

Davey NE; Shields DC; Edwards RJ, 2006, 'SLiMDisc: Short, linear motif discovery, correcting for common evolutionary descent', Nucleic Acids Research, 34, pp. 3546 - 3554, http://dx.doi.org/10.1093/nar/gkl486

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, 357, pp. 77 - 84, http://dx.doi.org/10.1016/j.ab.2006.06.037

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, 46, pp. 2183 - 2190, http://dx.doi.org/10.1021/ci0600760

Edwards RJ; Shields DC, 2005, 'BADASP: Predicting functional specificity in protein families using ancestral sequences', Bioinformatics, 21, pp. 4190 - 4191, http://dx.doi.org/10.1093/bioinformatics/bti678

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, 252, pp. 153 - 159, http://dx.doi.org/10.1016/j.femsle.2005.08.051

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, 2, http://dx.doi.org/10.1186/1742-4682-2-12

O'Dushlaine CT; Edwards RJ; Park SD; Shields DC, 2005, 'Tandem repeat copy-number variation in protein-coding regions of human genes.', Genome biology, 6

Edwards RJ; Shields DC, 2004, 'GASP: Gapped ancestral sequence prediction for proteins', BMC Bioinformatics, 5, http://dx.doi.org/10.1186/1471-2105-5-123

Edwards RJ; Brookfield JFY, 2003, 'Transiently beneficial insertions could maintain mobile DNA sequences in variable environments', Molecular Biology and Evolution, 20, pp. 30 - 37, http://dx.doi.org/10.1093/molbev/msg001

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, 12, pp. 863 - 867, http://dx.doi.org/10.1016/S0960-9822(02)00837-0

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