Select Publications

Journal articles

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', bioRix, http://dx.doi.org/10.1101/2020.11.15.384057

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

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?', Integr Comp Biol, http://dx.doi.org/10.1093/icb/icaa082

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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; 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

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, '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; 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

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; 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; 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

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

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

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

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

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

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


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