By Dr Richard Edwards

Journal articles

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, 24, pp. 453 - 465, http://dx.doi.org/10.1111/mec.13041

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, 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, 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, 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

Conference Papers

Mooney C; O'Brien K; Haslam NJ; Edwards RJ; Davey NE; Duffy FJ; Golla K; Stavropoulos I; Khaldi N; Chubb AJ; Lombardi F; Holton T; Vijay V; Devocelle M; Moran N; Shields DC, 2012, 'Computational prediction of bioactive peptides', in JOURNAL OF PEPTIDE SCIENCE, WILEY-BLACKWELL, pp. S38 - S39, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000308091500055&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Edwards RJ; Moran N; Devocelle M; Kieman A; Dunne E; Meade G; Park SDE; Foy M; Signac W; Shields DC; Kenny D, 2007, 'Identification of novel bioactive oligopeptides from macrophages human proteins', in BIOPOLYMERS, JOHN WILEY & SONS INC, CANADA, Montreal, pp. 588 - 588, presented at 20th American-Peptide-Society Symposium, CANADA, Montreal, 26 June 2007 - 30 June 2007, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000247425900301&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Working Papers

Edwards R; Field M; Ferguson J; Dudchenko O; Keilwagen J; Rosen B; Johnson G; Rice E; Hillier L; Hammond J; Towarnicki S; Omer A; Khan R; Skvortsova K; Bogdanovic O; Zammit R; Aiden EL; Warren W; Ballard W, 2021, Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome, BioMed Central, http://dx.doi.org10.1186/s12864-021-07493-6

Stuart K; Edwards R; Cheng Y; Warren W; Burt D; Sherwin W; Hofmeister N; Werner S; Ball G; Bateson M; Brandley M; Buchanan K; Cassey P; Clayton D; De Meyer T; Meddle S; Rollins L, 2021, Transcript- and annotation-guided genome assembly of the European starling, http://dx.doi.org10.1101/2021.04.07.438753

Yadav S; Dudchenko O; Esvaran M; Rosen B; Field M; Skvortsova K; Gopalakrishnan S; Keilwagen J; Cochran 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; Edwards R, 2020, Desert Dingo (Canis lupus dingo) genome provides insights into their role in the Australian ecosystem, Cold Spring Harbor, http://dx.doi.org10.1101/2020.11.15.384057, https://www.biorxiv.org/content/10.1101/2020.11.15.384057v1

Preprints

Chen SH; Yap J-YS; Viler V; Stehn C; Sandhu KS; Percival J; Pegg GS; Menzies T; Jones A; Guo K; Giblin FR; Cohen J; Edwards RJ; Rossetto M; Bragg JG, 2024, Genomics and resistance assays inform the management of two tree species being devastated by the invasive myrtle rust pathogen, http://dx.doi.org/10.1101/2024.10.30.612564

Hanrahan BJ; Alreja K; Reis ALM; Chang JK; Dissanayake DSB; Edwards RJ; Bertozzi T; Hammond JM; O’Meally D; Deveson IW; Georges A; Waters P; Patel HR, 2024, A genome assembly and annotation for the Australian alpine skinkBassiana duperreyiusing long-read technologies, http://dx.doi.org/10.1101/2024.09.05.611471

Tobias P; Downs J; Epaina P; Singh G; Park R; Edwards R; Brugman E; Zulkifli A; Muhammad J; Purwantara A; Guest D, 2024, Parental assigned chromosomes for cultivated cacao provides insights into genetic architecture underlying resistance to vascular streak dieback, http://dx.doi.org/10.1101/2024.05.26.595985

Cheung K; Rollins LA; Hammond JM; Barton K; Ferguson JM; Eyck HJF; Shine R; Edwards RJ, 2024, Repeat-rich regions cause false positive detection of NUMTs: a case study in amphibians using an improved cane toad reference genome, http://dx.doi.org/10.1101/2024.07.04.601973

Chen S; Jones A; Lu-Irving P; Yap J-Y; van der Merwe M; Bragg J; Edwards R, 2024, Small but mitey: long-read assembly of a streamlined mite genome from contaminated host plant sequencing data, http://dx.doi.org/10.1101/2024.05.17.594625

Ballard JWO; Field MA; Edwards RJ; Wilson LAB; Koungoulos LG; Rosen BD; Chernoff B; Dudchenko O; Omer A; Keilwagen J; Skvortsova K; Bogdanovic O; Chan E; Zammit R; Hayes V; Aiden EL, 2023, The Australasian dingo archetype: De novo chromosome-length genome assembly, DNA methylome, and cranial morphology., http://dx.doi.org/10.1101/2023.01.26.525801

Chen S; Martino A; Luo Z; Schwessinger B; Jones A; Tolessa T; Bragg J; Tobias P; Edwards R, 2023, A high-quality pseudo-phased genome forMelaleuca quinquenerviashows allelic diversity of NLR-type resistance genes, http://dx.doi.org/10.1101/2023.04.27.538497

Hogg C; Edwards R; Farquharson K; Silver L; Brandies P; Peel E; Escalona M; Jaya F; Sun R; Batley K; Bradford T; Chang K; Chen Z; Deshpande N; Dziminski M; Ewart K; Griffith O; Marin-Gual L; Moon K; Travouillon K; Waters P; Whittington C; Wilkins M; Helgen K; Lo N; Ho S; Ruiz-Herrera A; Paltridge R; Graves J; Renfree M; Shapiro B; Ottewell K; Rangers KC; Belov K, 2023, Extant and extinct bilby genomes combined with Indigenous knowledge improve conservation of a unique Australian marsupial, http://dx.doi.org/10.21203/rs.3.rs-3723914/v1

Eyck HJF; Edwards R; Brown G; Shine R; Rollins L, 2023, First in family Rhabdiasidae: the reference-guided genome assembly of an invasive parasite, the cane toad lungworm (Rhabdias pseudosphaerocephala), http://dx.doi.org/10.1101/2023.02.28.530339

Yagound B; Sarma R; Edwards R; Richardson M; Lopez CR; Crossland M; Brown G; DeVore J; Shine R; Rollins L, 2023, Is developmental plasticity triggered by DNA methylation changes in the invasive cane toad (Rhinella marina)?, http://dx.doi.org/10.1101/2023.10.26.564158

Cheung K; Amos TG; Shine R; DeVore JL; DeVore JL; Ducatez S; Edwards RJ; Rollins LA, 2023, Mitochondrial genome analyses uncover intriguing population structure across the invasive trajectory of an iconic invader, http://dx.doi.org/10.1101/2023.09.17.558141

Tobias P; Edwards R; Surana P; Mangelson H; Inácio V; do Céu Silva M; Várzea V; Park R; Batista D, 2022, A chromosome-level genome resource for studying virulence mechanisms and evolution of the coffee rust pathogen Hemileia vastatrix, http://dx.doi.org/10.1101/2022.07.29.502101

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