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 ~ 2018 ~ 2019 ~ 2020 ~ 2021 ~ 2022

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.

Preprints

• Eyck HJF, Edwards RJ Brown GP, Shine R & Rollins LA (preprint): First in family Rhabdiasidae: the reference-guided genome assembly of an invasive parasite, the cane toad lungworm (Rhabdias pseudosphaerocephala). bioRxiv 2023.02.28.530339 [bioRxiv]
• Tobias PA, Edwards RJ, Surana P, Mangelson H, Inácio V, do Céu Silva M, Várzea V, Park RF & Batista D (preprint): A chromosome-level genome resource for studying virulence mechanisms and evolution of the coffee rust pathogen Hemileia vastatrix. bioRxiv2022.07.29.502101; [bioRxiv]
• Edwards RJ, Dong C, Park RF & Tobias PA (preprint):A phased chromosome-level genome and full mitochondrial sequence for the dikaryotic myrtle rust pathogen, Austropuccinia psidii. bioRxiv 2022.04.22.489119v1; doi: [10.1101/2022.04.22.489119v1] [bioRxiv]

2023

• 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 (accepted): The Australasian dingo archetype: De novo chromosome-length genome assembly, DNA methylome, and cranial morphology. Gigascience. [bioRxiv]
• Stuart KC, Edwards RJ, Sherwin WB & Rollins LA (accepted): Contrasting patterns of single nucleotide polymorphisms and structural variations across multiple invasions. Mol. Biol. Evol. msad046. [Mol. Biol. Evol.] [PubMed] [bioRxiv]
• Stuart KC, Sherwin WB, Edwards RJ & Rollins LA (2023): Evolutionary genomics: Insights from the invasive European starlings. Frontier in Genetics 13:1010456. [Front Genet] [PubMed]

2022

• 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. Front Microbiol. 13:1035247. doi: 10.3389/fmicb.2022.1035247 [Front Microbiol.] [PubMed]

• 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 22(8):3141-3160. doi: 10.1111/1755-0998.13679. [*Joint first authors] [Mol Ecol Res] [PubMed] [bioRxiv]

• 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, Chernoffl 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(16):abm5944; DOI: 10.1126/sciadv.abm5944. [Sci Adv] [PubMed] [PDF]

• Galbraith JD, Ludington AJ, Sanders KL, Amos TG, Thomson VA, Enosi Tuipulotu D, Dunstan N, Edwards RJ, Suh A, Adelson DL (2022): Horizontal transposon transfer and its implications for the ancestral ecology of hydrophiine snakes. Genes 13(2):217. [Genes] [PubMed] [PDF] [bioRxiv]

• Chen SH, Rossetto M, van der Merwe M, Lu-Irving P, Yap JS, 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 22:1836–1854. [Mol Ecol Res] [PubMed] [bioRxiv]

• Potter P, 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(1):msab333; doi: 10.1093/molbev/msab333 [Mol Biol Evol] [PubMed] [PDF]

2021

• Sarma RR, Crossland MR, Eyck HJF, Edwards RJ, DeVore JL, 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 376:20200125. [Phil Trans Roy Soc B] [PubMed]

• Edwards RJ, Field MA, Ferguson JM, Dudchenko O, Keilwagen K, Rosen BD, Johnson GS, Rice ES, Hillier L, 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 22:188 [BMC Genomics] [PubMed] [bioRxiv]

2020

• Benaud N, Edwards RJ, Amos TG, D’Agostino PM, Gutiérrez-Cháveza 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. 23:3646-3664. [Env. Micro.] [PubMed]

• 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(6):1481-1494. [Integrative and Comparative Biology] [PubMed]

• Edwards RJ, Paulsen K, Aguilar Gomez CM & Pérez-Bercoff Å (2020): Computational Prediction of Disordered Protein Motifs using SLiMSuite. Methods Mol Biol. 2141:37-72. [MiMB] [PubMed]

• Johansson SA, Stephenson P, Edwards RJ, Yoshida K, Moore M, 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 48:101917. [Algal Research]

• Field MA, Rosen BD, Dudchenko O, Chan EKF, Minoche AM, Edwards RJ, Barton K, Lyons RJ, Enosi Tuipulotu D, Hayes VM, Omer AD, Colaric Z, Keilwagen J, Skvortsova K, Bogdanovic O, Smith MA, Lieberman Aiden E, 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(4):giaa027. [GigaScience] [PubMed]

2019

• 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, Mészáros 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. F1000Res. 8(ELIXIR):1753. [F1000Research] [PubMed]

• Holland SI*, Edwards RJ*, Ertan H, Wong YK, Russell TL, Deshpande NP, Manefield M & Lee MJ (2019): Whole genome sequencing of a novel, dichloromethane-fermenting Peptococcaceae from an enrichment culture. PeerJ 7:e7775. [*Joint first authors] [PeerJ] [PubMed] [PDF] [SI]

• 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 48:100687. [Marine Genomics] [PDF]

• Schneider MV, Griffin PC, Tyagi S, Flannery M, Dayalan S, Gladman S, Watson-Haigh N, Bayer PE, Charleston M, Cooke I, Cook R, Edwards RJ, Edwards D, Gorse D, McConville M, Powell D, Wilkins MR & Lonie A (2019): Establishing a distributed national research infrastructure providing bioinformatics support to life science researchers in Australia. Briefings in Bioinformatics 20(2):384-389. [Full Text] [PubMed]

• Edwards RJ (2019): Phylogenetic Tree Rooting, In Encyclopedia of Bioinformatics and Computational Biology, Elsevier Volume 2, Pages 727-735. [Science Direct]

2018

• Idrees S, Pérez-Bercoff Å & Edwards RJ (2018): SLiMEnrich: computational assessment of protein–protein interaction data as a source of domain-motif interactions. PeerJ 6:e5858 [PeerJ] [PubMed] [PDF]

• Edwards RJ, Enosi Tuipulotu D, 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(9):giy095. [GigaScience] [PubMed] [PDF]

2017

• 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 12:46. [FullText] [PubMed]

• 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(3):591–612. DOI: 10.1111/gcbb.12371 [GCB Energy] [PDF]

2016

• 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. Glob Chang Biol. 22(11):3760-3773. doi: 10.1111/gcb.13322 [Glob Chang Biol.] [PubMed]

• 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(1):427. (doi: 10.1186/s12864-016-2746-7). [BMC Genomics] [PDF] [PubMed]

• 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 (5): 1316-1326. [GBE] [PDF] [PubMed]

• Skipp PJS, Hughes C, McKenna T, Edwards RJ, Langridge J, Thomson NR & Clarke IN (2016): Quantitative Proteomics of the Infectious and Replicative Forms of Chlamydia trachomatis. PLoS ONE 11(2): e0149011. [PLoS One] [PDF] [PubMed]

2015

• Olorin E, O’Brien KT, Palopoli N, Pérez-Bercoff A, Shields DC, Edwards RJ (2015): SLiMScape 3.x: a Cytoscape 3 app for discovery of Short Linear Motifs in protein interaction networks (2015) [version 1; referees: 2 approved] F1000Research 4:477. (doi: 10.12688/f1000research.6773.1) [F1000Research] [App Store] [PubMed]

• 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. J Biol Chem. 290: 15052-15065. [PubMed] [J Biol Chem.]

• Palopoli N, Lythgow KT & Edwards RJ (2015): QSLiMFinder: improved short linear motif prediction using specific query protein data. Bioinformatics 31(14): 2284-2293. [PubMed] [Bioinformatics] [PDF]

• Attwood TK, Bongcam-Rudloff E, Brazas ME, Corpas M, Gaudet P, Lewitter F, Mulder N, Palagi PM, Schneider MV, van Gelder CW & GOBLET Consortium (2015): GOBLET: The Global Organisation for Bioinformatics Learning, Education and Training. PLoS Comput Biol. 11(4):e1004143. [PubMed] [Bioinformatics] [PDF]

• Edwards RJ & Palopoli N (2015): Computational Prediction of Short Linear Motifs from Protein Sequences. Methods Mol Biol. 1268: 89-141. [PubMed] [Methods Mol Biol.] [PDF]

• Gittins JR, D’Angelo C, Oswald F, Edwards RJ & Wiedenmann J (2015): Fluorescent protein-mediated colour polymorphism in reef corals: Multi-copy genes extend the adaptation/acclimatization potential to variable light environments. Mol Ecol 24(2): 453-465. [PubMed] [Molecular Ecology] [PDF]

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

• 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

• 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]

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]

• 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): 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]

• 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]

• 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]

• 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

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]

• 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]

• 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]

• 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]