Select Publications

Book Chapters

Edwards RJ;Palopoli N, 2015, 'Computational prediction of short linear motifs from protein sequences', in Computational Peptidology, pp. 89 - 141, http://dx.doi.org/10.1007/978-1-4939-2285-7_6

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

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.', Infect Agent Cancer, vol. 12, pp. 46, http://dx.doi.org/10.1186/s13027-017-0157-2

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

Churton NW V;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

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, http://dx.doi.org/10.1186/s12864-016-2746-7

Watson-Lazowski A;Lin Y;Miglietta F;Edwards RJ;Chapman MA;Taylor G, 2016, 'Plant adaptation or acclimation to rising CO 2 ? Insight from first multigenerational RNA-Seq transcriptome', Global Change Biology, vol. 22, pp. 3760 - 3773, http://dx.doi.org/10.1111/gcb.13322

Skipp PJ S;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

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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, pp. 2790 - 2800, http://dx.doi.org/10.1002/pmic.200900621

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

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

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

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

Edwards RJ;Moran N;Devocelle M;Kiernan A;Meade G;Signac W;Foy M;Park SD E;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

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

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

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

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

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

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

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

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

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, http://dx.doi.org/10.1186/1471-2105-5-123

Edwards RJ;Brookfield JF Y, 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

Edwards RJ;Sockett RE;Brookfield JF Y, 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

Conference Papers

Edwards RJ;Moran N;Devocelle M;Kieman A;Dunne E;Meade G;Park SD E;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 - 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=891bb5ab6ba270e68a


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