By Dr Richard Edwards

Book Chapters

Edwards RJ, 2018, 'Phylogenetic tree rooting', in Encyclopedia of Bioinformatics and Computational Biology: ABC of Bioinformatics, pp. 727 - 735, http://dx.doi.org/10.1016/B978-0-12-809633-8.20258-6

Edwards RJ; Palopoli N, 2015, 'Computational prediction of short linear motifs from protein sequences', in Computational Peptidology, Springer Link, pp. 89 - 141, http://dx.doi.org/10.1007/978-1-4939-2285-7_6

Shields DC; Johnston CR; Wallace IM; Edwards RJ, 2008, 'Evolution of specificity and diversity', in Ancestral Sequence Reconstruction, http://dx.doi.org/10.1093/acprof:oso/9780199299188.003.0019

Journal articles

Tobias PA; Downs J; Epaina P; Singh G; Park RF; Edwards RJ; Brugman E; Zulkifli A; Muhammad J; Purwantara A; Guest DI, 2024, 'Parental assigned chromosomes for cultivated cacao provides insights into genetic architecture underlying resistance to vascular streak dieback', Plant Genome, 17, http://dx.doi.org/10.1002/tpg2.20524

Chen SH; Jones A; Lu-Irving P; Yap JYS; Van Der Merwe M; Bragg JG; Edwards RJ, 2024, 'Chromosome-Level Genome Assembly of the Australian Rainforest Tree Rhodamnia argentea (Malletwood)', Genome Biology and Evolution, 16, http://dx.doi.org/10.1093/gbe/evae238

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', Genome Biology and Evolution, 16, http://dx.doi.org/10.1093/gbe/evae246

Hogg CJ; Edwards RJ; Farquharson KA; Silver LW; Brandies P; Peel E; Escalona M; Jaya FR; Thavornkanlapachai R; Batley K; Bradford TM; Chang JK; Chen Z; Deshpande N; Dziminski M; Ewart KM; Griffith OW; Marin Gual L; Moon KL; Travouillon KJ; Waters P; Whittington CM; Wilkins MR; Helgen KM; Lo N; Ho SYW; Ruiz Herrera A; Paltridge R; Marshall Graves JA; Renfree M; Shapiro B; Ottewell K; Belov K, 2024, 'Erratum: Author Correction: Extant and extinct bilby genomes combined with Indigenous knowledge improve conservation of a unique Australian marsupial (Nature ecology & evolution (2024) 8 7 DOI: 10.1038/s41559-024-02436-2)', Nature ecology & evolution, 8, pp. 1776, http://dx.doi.org/10.1038/s41559-024-02519-0

MacDonald E; Whibley A; Waters PD; Patel H; Edwards RJ; Ganley ARD, 2024, 'Origin and maintenance of large ribosomal RNA gene repeat size in mammals', Genetics, 228, http://dx.doi.org/10.1093/genetics/iyae121

Cummins M; Watson C; Edwards RJ; Mattick JS, 2024, 'The Evolution of Ultraconserved Elements in Vertebrates.', Mol Biol Evol, 41, http://dx.doi.org/10.1093/molbev/msae146

Hogg CJ; Edwards RJ; Farquharson KA; Silver LW; Brandies P; Peel E; Escalona M; Jaya FR; Thavornkanlapachai R; Batley K; Bradford TM; Chang JK; Chen Z; Deshpande N; Dziminski M; Ewart KM; Griffith OW; Marin Gual L; Moon KL; Travouillon KJ; Waters P; Whittington CM; Wilkins MR; Helgen KM; Lo N; Ho SYW; Ruiz Herrera A; Paltridge R; Marshall Graves JA; Renfree M; Shapiro B; Ottewell K; Belov K; Gibson C; Maxwell R; Spencer Z; Napangati Y; Butler M; West J; West J; James M; Napangati N; Gibson L; West P; Gibson A; West S; West K; Japaltjari W; Blackwood E, 2024, 'Extant and extinct bilby genomes combined with Indigenous knowledge improve conservation of a unique Australian marsupial', Nature Ecology and Evolution, 8, pp. 1311 - 1326, http://dx.doi.org/10.1038/s41559-024-02436-2

Cummins M; Watson C; Edwards RJ; Mattick JS, 2024, 'The Evolution of Ultraconserved Elements in Vertebrates', Molecular Biology and Evolution, 41, pp. msae146, http://dx.doi.org/10.1093/molbev/msae146

Yagound B; Sarma RR; Edwards RJ; Richardson MF; Rodriguez Lopez CM; Crossland MR; Brown GP; DeVore JL; Shine R; Rollins LA, 2024, 'Is developmental plasticity triggered by DNA methylation changes in the invasive cane toad (Rhinella marina)?', Ecology and Evolution, 14, http://dx.doi.org/10.1002/ece3.11127

Cheung K; Amos TG; Shine R; DeVore JL; Ducatez S; Edwards RJ; Rollins LA, 2024, 'Whole-mitogenome analysis unveils previously undescribed genetic diversity in cane toads across their invasion trajectory', Ecology and Evolution, 14, http://dx.doi.org/10.1002/ece3.11115

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, http://dx.doi.org/10.1093/gigascience/giad119

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, http://dx.doi.org/10.1093/molbev/msad046

Stuart KC; Sherwin WB; Edwards RJ; Rollins LA, 2023, 'Evolutionary genomics: Insights from the invasive European starlings', Frontiers in Genetics, 13, http://dx.doi.org/10.3389/fgene.2022.1010456

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, http://dx.doi.org/10.1093/gigascience/giad102

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, http://dx.doi.org/10.1093/gigascience/giad018

Holland SI; Vázquez-Campos X; Ertan H; Edwards RJ; Manefield MJ; Lee M; Vazquez Campos X, 2022, 'Metaproteomics reveals methyltransferases implicated in dichloromethane and glycine betaine fermentation by ‘Candidatus Formimonas warabiya’ strain DCMF', Frontiers in Microbiology, 13, pp. 1035247, http://dx.doi.org/10.3389/fmicb.2022.1035247

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, http://dx.doi.org/10.1111/1755-0998.13679

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, http://dx.doi.org/10.1111/1755-0998.13574

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, http://dx.doi.org/10.1126/sciadv.abm5944

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, http://dx.doi.org/10.3390/genes13020217

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, http://dx.doi.org/10.1093/molbev/msab333

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, http://dx.doi.org/10.1186/s12864-021-07493-6

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, http://dx.doi.org/10.1111/1462-2920.15300

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, http://dx.doi.org/10.1098/rstb.2020.0125

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', , http://dx.doi.org/10.1101/2021.06.02.444084

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', , http://dx.doi.org/10.1101/2021.06.22.449521

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, http://dx.doi.org/10.1093/icb/icaa082

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, pp. 2020.11.11.379073, http://dx.doi.org/10.1101/2020.11.11.379073

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, 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, 9, http://dx.doi.org/10.1093/gigascience/giaa027

Edwards RJ; Paulsen K; Aguilar Gomez CM; Pérez-Bercoff Å, 2020, 'Computational prediction of disordered protein motifs using SLiMSuite', , 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, 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, 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, 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, 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, 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, 6, http://dx.doi.org/10.7717/peerj.5858/correction-1

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, http://dx.doi.org/10.1111/gcbb.12371

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, pp. 46, http://dx.doi.org/10.1186/s13027-017-0157-2

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, http://dx.doi.org/10.1111/gcb.13322

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, http://dx.doi.org/10.1093/gbe/evw072

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, http://dx.doi.org/10.1371/journal.pone.0149011

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, http://dx.doi.org/10.1186/s12864-016-2746-7

Palopoli N; Lythgow KT; Edwards RJ, 2015, 'QSLiM Finder: Improved short linear motif prediction using specific query protein data', Bioinformatics, 31, pp. 2284 - 2293, http://dx.doi.org/10.1093/bioinformatics/btv155

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, 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; Ouellette BF; Palagi PM; Pearson WR; Qi W; Romano P; Rother K; Sansone SA; 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, http://dx.doi.org/10.1371/journal.pcbi.1004143

Edwards RJ; Palopoli N, 2015, 'Computational prediction of short linear motifs from protein sequences', , pp. 89 - 141, http://dx.doi.org/10.1007/978-1-4939-2285-7_6

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