Select Publications

Journal articles

de Jong E; Parata L; Bayer PE; Corrigan S; Edwards RJ, 2024, 'Toward genome assemblies for all marine vertebrates: current landscape and challenges', GigaScience, 13,

Stuart KC; Edwards RJ; Sherwin WB; Rollins LA, 2023, 'Contrasting Patterns of Single Nucleotide Polymorphisms and Structural Variation Across Multiple Invasions', Molecular Biology and Evolution, 40,

Stuart KC; Sherwin WB; Edwards RJ; Rollins LA, 2023, 'Evolutionary genomics: Insights from the invasive European starlings', Frontiers in Genetics, 13,

Chen SH; Martino AM; Luo Z; Schwessinger B; Jones A; Tolessa T; Bragg JG; Tobias PA; Edwards RJ, 2023, 'A high-quality pseudo-phased genome for Melaleuca quinquenervia shows allelic diversity of NLR-type resistance genes', GigaScience, 12,

Ballard JOW; 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', GigaScience, 12,

Holland SI; Vázquez-Campos X; Ertan H; Edwards RJ; Manefield MJ; Lee M, 2022, 'Metaproteomics reveals methyltransferases implicated in dichloromethane and glycine betaine fermentation by ‘Candidatus Formimonas warabiya’ strain DCMF', Frontiers in Microbiology, 13,

Stuart KC; Edwards RJ; Cheng Y; Warren WC; Burt DW; Sherwin WB; Hofmeister NR; Werner SJ; Ball GF; Bateson M; Brandley MC; Buchanan KL; Cassey P; Clayton DF; De Meyer T; Meddle SL; Rollins LA, 2022, 'Transcript- and annotation-guided genome assembly of the European starling', Molecular Ecology Resources, 22, pp. 3141 - 3160,

Chen SH; Rossetto M; van der Merwe M; Lu-Irving P; Yap JYS; Sauquet H; Bourke G; Amos TG; Bragg JG; Edwards RJ, 2022, 'Chromosome-level de novo genome assembly of Telopea speciosissima (New South Wales waratah) using long-reads, linked-reads and Hi-C', Molecular Ecology Resources, 22, pp. 1836 - 1854,

Field MA; Yadav S; Dudchenko O; Esvaran M; Rosen BD; Skvortsova K; Edwards RJ; Keilwagen J; Cochran BJ; Manandhar B; Bustamante S; Rasmussen JA; Melvin RG; Chernoff B; Omer A; Colaric Z; Chan EKF; Minoche AE; Smith TPL; Gilbert MTP; Bogdanovic O; Zammit RA; Thomas T; Aiden EL; Ballard JWO, 2022, 'The Australian dingo is an early offshoot of modern breed dogs', Science Advances, 8,

Galbraith JD; Ludington AJ; Sanders KL; Amos TG; Thomson VA; Tuipulotu DE; Dunstan N; Edwards RJ; Suh A; Adelson DL, 2022, 'Horizontal Transposon Transfer and Its Implications for the Ancestral Ecology of Hydrophiine Snakes', Genes, 13,

Potter S; Bragg JG; Turakulov R; Eldridge MDB; Deakin J; Kirkpatrick M; Edwards RJ; Moritz C, 2022, 'Limited Introgression between Rock-Wallabies with Extensive Chromosomal Rearrangements', Molecular Biology and Evolution, 39,

Edwards RJ; Field MA; Ferguson JM; Dudchenko O; Keilwagen J; Rosen BD; Johnson GS; Rice ES; Hillier LD; Hammond JM; Towarnicki SG; Omer A; Khan R; Skvortsova K; Bogdanovic O; Zammit RA; Aiden EL; Warren WC; Ballard JWO, 2021, 'Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome', BMC Genomics, 22,

Benaud N; Edwards RJ; Amos TG; D'Agostino PM; Gutiérrez-Chávez C; Montgomery K; Nicetic I; Ferrari BC, 2021, 'Antarctic desert soil bacteria exhibit high novel natural product potential, evaluated through long-read genome sequencing and comparative genomics', Environmental Microbiology, 23, pp. 3646 - 3664,

Sarma RR; Crossland MR; Eyck HJF; Devore JL; Edwards RJ; Cocomazzo M; Zhou J; Brown GP; Shine R; Rollins LA, 2021, 'Intergenerational effects of manipulating DNA methylation in the early life of an iconic invader', Philosophical Transactions of the Royal Society B: Biological Sciences, 376,

Chen S; Rossetto M; van der Merwe M; Lu-Irving P; Yap J-Y; Sauquet H; Bourke G; Amos T; Bragg J; Edwards R, 2021, 'Chromosome-levelde novogenome assembly ofTelopea speciosissima(New South Wales waratah) using long-reads, linked-reads and Hi-C', ,

Galbraith J; Ludington A; Sanders K; Amos T; Thomson V; Tuipulotu DE; Dunstan N; Edwards R; Suh A; Adelson D, 2021, 'Horizontal transposon transfer and its implications for the ancestral ecology of hydrophiine snakes', ,

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?', Integrative and Comparative Biology, 60, pp. 1481 - 1494,

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,

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, 48,

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, 9,

Edwards RJ; Paulsen K; Aguilar Gomez CM; Pérez-Bercoff Å, 2020, 'Computational prediction of disordered protein motifs using SLiMSuite', , 2141, pp. 37 - 72,

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, 48,

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, 8,

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, 2019,

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, 6,

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, 7,

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, 6,

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, 12,

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, 9, pp. 591 - 612,

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, 22, pp. 3760 - 3773,

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, 8, pp. 1316 - 1326,

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, 11,

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, 17, pp. 1 - 11,

Palopoli N; Lythgow KT; Edwards RJ, 2015, 'QSLiM Finder: Improved short linear motif prediction using specific query protein data', Bioinformatics, 31, pp. 2284 - 2293,

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, 290, pp. 15052 - 15065,

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, 11,

Edwards RJ; Palopoli N, 2015, 'Computational prediction of short linear motifs from protein sequences', , pp. 89 - 141,

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,

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,

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,

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,

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,

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,

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,

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,

Davey NE; Haslam NJ; Shields DC; Edwards RJ, 2011, 'SLiMSearch 2.0: Biological context for short linear motifs in proteins', Nucleic Acids Research, 39,

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,

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,

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,

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,

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