Publications

OPEN IN: [PubMed] [Web of Science] [Blog Posts]

Year: 2002 ~ 2003 ~ 2004 ~ 2005 ~ 2006 ~ 2007 ~ 2008 ~ 2009 ~ 2010 ~ 2011 ~ 2012 ~ 2013 ~ 2015 ~ 2016 ~ 2017

Note that Web of Science tends to lag behind pubmed and recent publications may not be found via the above links. Please make sure that you or your library have the correct subscriptions before downloading PDFs from this site.

2017

2016

2015

2013

  • Jones BM, Iglesias-Rodriguez MD, Skipp PJS, Edwards RJ, Greaves MJ, Young JR, Elderfield H & O'Connor CD (2013): Responses of the Emiliania huxleyi proteome to ocean acidification. PLoS One 8(4): e61868. [PubMed] [PLoS One] [PDF] [Press Release]

2012

  • 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(21): 10628-41. [PubMed] [Nucleic Acids Res.] [PDF]

  • Ient B, Edwards RJ, Mould R, Hannah M, Holden-Dye LM & 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(2): 93-102. [PubMed] [Invert. Neurosci.] [PDF]

  • 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(D1): D242-D251. [PubMed] [Nucleic Acids Res.] [ELM]

  • Edwards RJ, Davey NE, O'Brien K & Shields DC (2012): Interactome-wide prediction of short, disordered protein interaction motifs in humans. Molecular Biosystems 8: 282-95. [Mol. BioSyst.] [PubMed] [PDF] [SI] [SLiMdb]

2011

  • Davey NE, Haslam NJ, Shields DC & Edwards RJ (2011): SLiMSearch 2.0: biological context for short linear motifs in proteins. Nucleic Acids Research 39: W56-W60. [Nucleic Acids Res.] [PubMed] [PDF] [Webserver]

  • 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 (6): 1031-43. [Mol. Pharmacol.] [PubMed] [PDF]

  • 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(3): 496-504. [Mar Biotechnol.] [PubMed] [PDF] [SI] *Joint first authors

2010

  • 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. In: Pattern Recognition in Bioinformatics Edited by Dijkstra TMH, Tsivtsivadze E, Marchiori E & Heskes T. Springer-Verlag, Berlin. Lecture Notes in Bioinformatics 6282: 50-61. [Springer] [PDF] [Webserver] [Video]

  • Davey NE, Edwards RJ & Shields DC (2010): Computational identification and analysis of protein short linear motifs. Frontiers in Bioscience 15: 801-25. [Front Biosci.] [PubMed] [PDF]

  • 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: W534-W539. [Nucleic Acids Res.] [PubMed] [PDF] [Webserver]

  • Raab M, Daxecker H, Edwards RJ, Treumann A, Murphy D & Moran N (2010): Protein interactions with the platelet integrin alpha(IIb) regulatory motif. Proteomics 10: 2790-2800. [Proteomics] [PubMed]

  • 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: 14. [BMC Bioinformatics.] [PubMed]

2009

  • Davey NE, Shields DC & Edwards RJ (2009): Masking residues using context-specific evolutionary conservation significantly improves short linear motif discovery. Bioinformatics 25(4): 443-50. [Bioinformatics.] [PubMed] [PDF]

2008

  • Edwards RJ, Davey NE & Shields DC (2008): CompariMotif: Quick and easy comparisons of sequence motifs. Bioinformatics 24(10):1307-9. [Bioinformatics] [PubMed] [PDF] [Webserver]

2007

  • 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(10): e967. [PLoS One.] [PubMed] [PDF]

  • 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 Chem. Biol. 3(2):108-112. [Nature Chem. Biol.] [NCB News & Views] [PubMed] [PDF] *Joint first authors

  • Davey NE*, Edwards RJ* & Shields DC (2007): The SLiMDisc server: short, linear motif discovery in proteins. Nucleic Acids Res. 35(Web Server issue):W455-9. [Nucleic Acids Res.] [PubMed] [Webserver] *Joint first authors

  • Shields DC, Johnston CR, Wallace IM & Edwards RJ (2007): Evolution of specificity and diversity. In: Ancestral Sequence Reconstruction Edited by DH Ardell, DA Liberles, G Matassi. Oxford University Press.

  • 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. Mol. Biol. Evol. 24:315-323. [Mol. Biol. Evol.] [PubMed] [PDF]

2006

  • Moran N, Kiernan A, Dunne E, Edwards RJ, Shields DC & Kenny D (2006): Monitoring Modulators of Platelet Aggregation in a Microtitre Plate Assay. Anal. Biochem. 357(1):77-84. [Anal. Biochem.] [PubMed] [PDF]

  • Parthasarathi L, Devocelle M, Søndergaard C, Baran I, O’Dushlaine C, Davey NE, Edwards RJ, Moran N, Kenny D & Shields DC (2006): Absolute Net Charge and the Biological Activity of Oligopeptides. J. Chem. Inf. Model. 46(5):2183-2190. [J. Chem. Inf. Model.] [PubMed] [PDF]

  • Davey NE, Shields DC & Edwards RJ (2006): SLiMDisc: short, linear motif discovery, correcting for common evolutionary descent. Nucleic Acids Res. 34(12):3546-54. [Nucleic Acids Res.] [PubMed] [PDF]

2005

  • Edwards RJ & Shields DC (2005): BADASP: predicting functional specificity in protein families using ancestral sequences. Bioinformatics 21(22):4190-1. [Bioinformatics] [PubMed] [PDF]

  • O'Dushlaine CT, Edwards RJ, Park SD & Shields DC (2005): Tandem repeat copy-number variation in protein-coding regions of human genes. Genome Biol. 6(9):R69. [Genome Biol] [PubMed] [PDF]

  • 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 Microbiol. Lett. 252(1):153-159. [PubMed] [PDF]

  • Harney DF, Butler RK & Edwards RJ (2005): Tyrosine phosphorylation of myosin heavy chain during skeletal muscle differentiation: an integrated bioinformatics approach. Theor. Biol. Med. Model. 2(1):12. [TBioMed] [PubMed] [PDF]

2004

  • Edwards RJ & Shields DC (2004): GASP: Gapped Ancestral Sequence Prediction for proteins. BMC Bioinformatics 5(1):123. [BMC] [PubMed] [PDF]

2003

  • Edwards RJ & Brookfield JFY (2003): Transiently beneficial insertions could maintain mobile DNA sequences in variable environments. Mol Biol Evol. 20(1):30-37. [MBE] [PubMed] [PDF]

2002

  • Edwards RJ, Sockett RE & Brookfield JFY (2002): A simple method for genome-wide screening for advantageous insertions of mobile DNAs in Escherichia coli. Curr Biol. 12(10):863-867. [Curr Biol] [PubMed] [PDF]

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