Select Publications

Book Chapters

Pang I, 2019, 'Protein Post-Translational Modification Prediction', in Encyclopedia of Bioinformatics and Computational Biology, pp. 15 - 27, http://dx.doi.org/10.1016/B978-0-12-809633-8.20265-3

Wong J; Pang I; Wilkins M; Tree J, 2018, 'Systems-level analysis of bacterial regulatory small RNA networks', in Systems Biology, Springer, pp. 97 - 127

Wilkins MR, 2012, 'Interpreting data from large-scale screens.', in Roberts G (ed.), Encyclopedia of Biophysics, edn. 1st Edition, Springer, 11, http://www.springerreference.com/docs/html/chapterdbid/305477.html

Wilkins MR, 2008, 'Biomarker Identification: The Role of Experimental Design, Statistics, and Data Sharing', in Clinical Proteomics, pp. 113 - 120, http://dx.doi.org/10.1002/9783527622153.ch9

Bek EJ; Wilkins MR, 2008, 'Using Yeast to Study Protein-Protein Interactions Relevant to Disease', in Witt S (ed.), Yeast as a model for Human Disease, edn. Original, Signpost Research Press, pp. 145 - 176

Wilkins MR, 2007, 'Biomarker Identification: The Role of Experimental Design, Statistics, and Data Sharing', in Clinical Proteomics, edn. Original, pp. 113 - 120

Packer N; Gooley AA; Wilkins MR, 2007, 'One gene, many proteins', in Wilkins M; Appel R; Williams K; Hochstrasser D (ed.), Proteome Research: concepts, technology and practice, edn. 2nd, Springer Publishing Company, Netherlands, pp. 95 - 121

Pang CN; Wilkins MR, 2007, 'Online resources for the molecular contextualisation of disease', in Clinical Bioinformatics, Humana Press, USA, pp. 287 - 308

Hernandez P; Binz PA; Wilkins MR, 2007, 'Protein Identification in Proteomics', in Wilkins M; Appel R; Williams K; Hochstrasser D (ed.), Proteome Research: concepts, technology and practice, edn. 2nd, Springer Publishing Company, Netherlands, pp. 41 - 67

Wilkins MR; Appel RD, 2007, 'Ten years of the proteome', in Wilkins M; Appel R; Williams K; Hochstrasser D (ed.), Proteome Research: concepts, technology and practice, edn. 2nd, Springer Publishing Company, Netherlands, pp. 1 - 13

Wilkins MR; Hunt S, 2006, 'Bioinformatics and Experimental Design for Biomarker Discovery', in Proteomics of Human Bodyfluids: Principles, Methods and Applications, Humana Press, USA, pp. 147, http://dx.doi.org/10.1007/978-1-59745-432-2_8

Binz PA; Muller M; Walther D; Bienvenut WV; Gras R; Hoogland C; Bouchet G; Gasteiger E; Fabbretti R; Gay S; Palagi P; Wilkins MR; Rouge V; Tonella L; Paesano S; Rossellat G; Karmime A; Bairoch A; Sanchez JC; Appel RD; Hochstrasser DF, 2005, 'Signal traitment and virtual images production (1/2): A molecular scanner to highly automate proteomic research and to display proteome images', in Acceleration and Improvement of Protein Identification by Mass Spectrometry, pp. 151 - 168, http://dx.doi.org/10.1007/1-4020-3319-2_4

Gasteiger E; Hoogland C; Gattiker A; Duvaud S; Wilkins MR; Appel R; Bairoch A, 2005, 'Protein Identification and Analysis Tools in the ExPASy Server', in Link AJ (ed.), 2-D Protein Gel Electrophoresis Protocols, edn. 2nd, Humana Press, Totowa, N.J., pp. 571 - 607

Cooper CA; Joshi HJ; Harrison M; Wilkins MR; Packer N, 2003, 'Querying GlycosuiteDB', in Conn PM (ed.), Handbook of Proteomic Methods, edn. Original, Humana Press, Totowa, NJ, pp. 233 - 240

Journal articles

Yang L; Chen Z; Stout ES; Delerue F; Ittner LM; Wilkins MR; Quinlan KGR; Crossley M, 2020, 'Methylation of a CGATA element inhibits binding and regulation by GATA-1', Nature Communications, vol. 11, pp. 2560, http://dx.doi.org/10.1038/s41467-020-16388-1

Emery-Corbin SJ; Hamey JJ; Ansell BRE; Balan B; Tichkule S; Stroehlein AJ; Cooper C; McInerney BV; Zadeh SH; Vuong D; Crombie A; Lacey E; Davis MJ; Wilkins MR; Bahlo M; Svärd SG; Gasser RB; Jex AR, 2020, 'Eukaryote-conserved methylarginine is absent in diplomonads and functionally compensated in Giardia.', Mol Biol Evol, http://dx.doi.org/10.1093/molbev/msaa186

Anande G; Deshpande NP; Mareschal S; Batcha AMN; Hampton HR; Herold T; Lehmann S; Wilkins MR; Wong JWH; Unnikrishnan A; Pimanda JE, 2020, 'RNA Splicing Alterations Induce a Cellular Stress Response Associated with Poor Prognosis in Acute Myeloid Leukemia', Clinical cancer research : an official journal of the American Association for Cancer Research, vol. 26, pp. 3597 - 3607, http://dx.doi.org/10.1158/1078-0432.CCR-20-0184

Kim KW; Allen DW; Briese T; Couper JJ; Barry SC; Colman PG; Cotterill AM; Davis EA; Giles LC; Harrison LC; Harris M; Haynes A; Horton JL; Isaacs SR; Jain K; Lipkin WI; McGorm K; Morahan G; Morbey C; Pang ICN; Papenfuss AT; Penno MAS; Sinnott RO; Soldatos G; Thomson RL; Vuillermin P; Wentworth JM; Wilkins MR; Rawlinson WD; Craig ME, 2020, 'Higher frequency of vertebrate-infecting viruses in the gut of infants born to mothers with type 1 diabetes', Pediatric Diabetes, vol. 21, pp. 271 - 279, http://dx.doi.org/10.1111/pedi.12952

Bartolec TK; Smith DL; Pang CNI; Xu YD; Hamey JJ; Wilkins MR, 2020, 'Cross-linking Mass Spectrometry Analysis of the Yeast Nucleus Reveals Extensive Protein-Protein Interactions Not Detected by Systematic Two-Hybrid or Affinity Purification-Mass Spectrometry', Analytical Chemistry, vol. 92, pp. 1874 - 1882, http://dx.doi.org/10.1021/acs.analchem.9b03975

Smith DL; Erce MA; Lai YW; Tomasetig F; Hart-Smith G; Hamey JJ; Wilkins MR, 2020, 'Crosstalk of Phosphorylation and Arginine Methylation in Disordered SRGG Repeats of Saccharomyces cerevisiae Fibrillarin and Its Association with Nucleolar Localization', Journal of Molecular Biology, vol. 432, pp. 448 - 466, http://dx.doi.org/10.1016/j.jmb.2019.11.006

Bayat A; Deshpande NP; Wilkins MR; Parameswaran S, 2020, 'Fast Short Read De-Novo Assembly Using Overlap-Layout-Consensus Approach', IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 17, pp. 334 - 338, http://dx.doi.org/10.1109/TCBB.2018.2875479

Kim KW; Horton JL; Pang CNI; Jain K; Leung P; Isaacs SR; Bull RA; Luciani F; Wilkins MR; Catteau J; Lipkin WI; Rawlinson WD; Briese T; Craig ME, 2019, 'Higher abundance of enterovirus A species in the gut of children with islet autoimmunity', Scientific Reports, vol. 9, pp. 1749, http://dx.doi.org/10.1038/s41598-018-38368-8

Corley SM; Troy NM; Bosco A; Wilkins MR, 2019, 'QuantSeq. 3′ Sequencing combined with Salmon provides a fast, reliable approach for high throughput RNA expression analysis', Scientific Reports, vol. 9, pp. 18895, http://dx.doi.org/10.1038/s41598-019-55434-x

Lai YW; Pang CNI; Campbell LT; Chen SCA; Wilkins MR; Carter DA, 2019, 'Different Pathways Mediate Amphotericin-Lactoferrin Drug Synergy in Cryptococcus and Saccharomyces', Frontiers in Microbiology, vol. 10, pp. 2195, http://dx.doi.org/10.3389/fmicb.2019.02195

Winter DL; Mastellone J; Kabir KMM; Wilkins MR; Donald WA, 2019, 'Separation of Isobaric Mono- And Dimethylated RGG-Repeat Peptides by Differential Ion Mobility-Mass Spectrometry', Analytical Chemistry, vol. 91, pp. 11827 - 11833, http://dx.doi.org/10.1021/acs.analchem.9b02504

Tay AP; Liang A; Hamey JJ; Hart-Smith G; Wilkins MR, 2019, 'MS2-Deisotoper: A Tool for Deisotoping High-Resolution MS/MS Spectra in Normal and Heavy Isotope-Labelled Samples', Proteomics, vol. 19, http://dx.doi.org/10.1002/pmic.201800444

Vázquez-Campos X; Kinsela A; Bligh M; Payne T; Wilkins M; Waite D, 2019, 'Genomic insights into the Archaea inhabiting an Australian radioactive legacy site', , http://dx.doi.org/10.1101/728089

Bertoldo MJ; Cheung MY; Sia ZK; Agapiou D; Corley SM; Wilkins MR; Richani D; Harrison CA; Gilchrist RB, 2019, 'Non-canonical cyclic AMP SMAD1/5/8 signalling in human granulosa cells', Molecular and Cellular Endocrinology, vol. 490, pp. 37 - 46, http://dx.doi.org/10.1016/j.mce.2019.04.003

Tay AP; Liang A; Wilkins MR; Pang CNI, 2019, 'Visualizing Post-Translational Modifications in Protein Interaction Networks Using PTMOracle', Current Protocols in Bioinformatics, vol. 66, pp. e71, http://dx.doi.org/10.1002/cpbi.71

Lowe BR; Maxham LA; Hamey JJ; Wilkins MR; Partridge JF, 2019, 'Histone H3 mutations: An updated view of their role in chromatin deregulation and cancer', Cancers, vol. 11, pp. 1 - 24, http://dx.doi.org/10.3390/cancers11050660

Paramsothy S; Nielsen S; Kamm MA; Deshpande NP; Faith JJ; Clemente JC; Paramsothy R; Walsh AJ; van den Bogaerde J; Samuel D; Leong RWL; Connor S; Ng W; Lin E; Borody TJ; Wilkins MR; Colombel JF; Mitchell HM; Kaakoush NO, 2019, 'Specific Bacteria and Metabolites Associated With Response to Fecal Microbiota Transplantation in Patients With Ulcerative Colitis', Gastroenterology, vol. 156, pp. 1440 - 1454.e2, http://dx.doi.org/10.1053/j.gastro.2018.12.001

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, vol. 20, pp. 384 - 389, http://dx.doi.org/10.1093/bib/bbx071

Winter DL; Wilkins MR; Donald WA, 2019, 'Differential Ion Mobility–Mass Spectrometry for Detailed Analysis of the Proteome', Trends in Biotechnology, vol. 37, pp. 198 - 213, http://dx.doi.org/10.1016/j.tibtech.2018.07.018

Kim KW; Allen DW; Briese T; Couper JJ; Barry SC; Colman PG; Cotterill AM; Davis EA; Giles LC; Harrison LC; Harris M; Haynes A; Horton JL; Isaacs SR; Jain K; Lipkin WI; Morahan G; Morbey C; Pang ICN; Papenfuss AT; Penno MAS; Sinnott RO; Soldatos G; Thomson RL; Vuillermin PJ; Wentworth JM; Wilkins MR; Rawlinson WD; Craig ME, 2019, 'Distinct gut virome profile of pregnant women with type 1 diabetes in the ENDIA study', Open Forum Infectious Diseases, vol. 6, http://dx.doi.org/10.1093/ofid/ofz025

Uthicke S; Deshpande NP; Liddy M; Patel F; Lamare M; Wilkins MR, 2019, 'Little evidence of adaptation potential to ocean acidification in sea urchins living in “Future Ocean” conditions at a CO2 vent', Ecology and Evolution, vol. 9, pp. 10004 - 10016, http://dx.doi.org/10.1002/ece3.5563

Deshpande NP; Riordan SM; Castaño-Rodríguez N; Wilkins MR; Kaakoush NO, 2018, 'Signatures within the esophageal microbiome are associated with host genetics, age, and disease', Microbiome, vol. 6, pp. 227, http://dx.doi.org/10.1186/s40168-018-0611-4

Chia SZ; Lai YW; Yagoub D; Lev S; Hamey JJ; Ignatius Pang CN; Desmarini D; Chen Z; Djordjevic JT; Erce MA; Hart-Smith G; Wilkins MR, 2018, 'Knockout of the Hmt1p arginine methyltransferase in saccharomyces cerevisiae leads to the dysregulation of phosphate-associated genes and processes', Molecular and Cellular Proteomics, vol. 17, pp. 2462 - 2479, http://dx.doi.org/10.1074/mcp.RA117.000214

You J; Corley SM; Wen L; Hodge C; Höllhumer R; Madigan MC; Wilkins MR; Sutton G, 2018, 'RNA-Seq analysis and comparison of corneal epithelium in keratoconus and myopia patients', Scientific Reports, vol. 8, http://dx.doi.org/10.1038/s41598-017-18480-x

Alshekaili J; Chand R; Lee CE; Corley S; Kwong K; Papa I; Fulcher DA; Randall KL; Leiding JW; Ma CS; Wilkins MR; Uzel G; Goodnow CC; Vinuesa CG; Tangye SG; Cook MC, 2018, 'STAT3 regulates cytotoxicity of human CD57+ CD4+ T cells in blood and lymphoid follicles', Scientific Reports, vol. 8, http://dx.doi.org/10.1038/s41598-018-21389-8

Corley S; Mendoza-Reinoso V; Giles N; Singer ES; Common JE; Wilkins M; Beverdam A, 2018, 'Plau and Tgfbr3 are YAP-regulated genes that promote keratinocyte proliferation', Cell Death and Disease, vol. 9, pp. 1106, http://dx.doi.org/10.1038/s41419-018-1141-5

Hamey JJ; Separovich RJ; Wilkins MR, 2018, 'MT-MAMS: Protein Methyltransferase Motif Analysis by Mass Spectrometry', Journal of Proteome Research, vol. 17, pp. 3485 - 3491, http://dx.doi.org/10.1021/acs.jproteome.8b00396

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

Varela C; Schmidt SA; Borneman AR; Pang CNI; Krömerx JO; Khan A; Song X; Hodson MP; Solomon M; Mayr CM; Hines W; Pretorius IS; Baker MS; Roessner U; Mercurio M; Henschke PA; Wilkins MR; Chambers PJ, 2018, 'Systems-based approaches enable identification of gene targets which improve the flavour profile of low-ethanol wine yeast strains', Metabolic Engineering, vol. 49, pp. 178 - 191, http://dx.doi.org/10.1016/j.ymben.2018.08.006

Smith DL; Götze M; Bartolec TK; Hart-Smith G; Wilkins MR, 2018, 'Characterization of the Interaction between Arginine Methyltransferase Hmt1 and Its Substrate Npl3: Use of Multiple Cross-Linkers, Mass Spectrometric Approaches, and Software Platforms', Analytical Chemistry, vol. 90, pp. 9101 - 9108, http://dx.doi.org/10.1021/acs.analchem.8b01525

Johnson RN; O’Meally D; Chen Z; Etherington GJ; Ho SYW; Nash WJ; Grueber CE; Cheng Y; Whittington CM; Dennison S; Peel E; Haerty W; O’Neill RJ; Colgan D; Russell TL; Alquezar-Planas DE; Attenbrow V; Bragg JG; Brandies PA; Chong AYY; Deakin JE; Di Palma F; Duda Z; Eldridge MDB; Ewart KM; Hogg CJ; Frankham GJ; Georges A; Gillett AK; Govendir M; Greenwood AD; Hayakawa T; Helgen KM; Hobbs M; Holleley CE; Heider TN; Jones EA; King A; Madden D; Graves JAM; Morris KM; Neaves LE; Patel HR; Polkinghorne A; Renfree MB; Robin C; Salinas R; Tsangaras K; Waters PD; Waters SA; Wright B; Wilkins MR; Timms P; Belov K, 2018, 'Adaptation and conservation insights from the koala genome', Nature Genetics, vol. 50, pp. 1102 - 1111, http://dx.doi.org/10.1038/s41588-018-0153-5

Hamey JJ; Wilkins MR, 2018, 'Methylation of Elongation Factor 1A: Where, Who, and Why?', Trends in Biochemical Sciences, vol. 43, pp. 211 - 223, http://dx.doi.org/10.1016/j.tibs.2018.01.004

Pang I; Goel A; Wilkins MR, 2018, 'Investigating the network basis of negative genetic interactions in Saccharomyces cerevisiae with integrated biological networks and triplet motif analysis', Journal of Proteome Research, vol. 17, pp. 1014 - 1030, http://dx.doi.org/10.1021/acs.jproteome.7b00649

Winter DL; Hart-Smith G; Wilkins MR, 2018, 'Characterization of Protein Methyltransferases Rkm1, Rkm4, Efm4, Efm7, Set5 and Hmt1 Reveals Extensive Post-Translational Modification', Journal of Molecular Biology, vol. 430, pp. 102 - 118, http://dx.doi.org/10.1016/j.jmb.2017.11.009

Tay AP; Geoghegan V; Yagoub D; Wilkins MR; Hart-Smith G, 2018, 'MethylQuant: A Tool for Sensitive Validation of Enzyme-Mediated Protein Methylation Sites from Heavy-Methyl SILAC Data', Journal of Proteome Research, vol. 17, pp. 359 - 373, http://dx.doi.org/10.1021/acs.jproteome.7b00601

Hobbs M; King A; Salinas R; Chen Z; Tsangaras K; Greenwood AD; Johnson RN; Belov K; Wilkins MR; Timms P, 2017, 'Long-read genome sequence assembly provides insight into ongoing retroviral invasion of the koala germline', Scientific Reports, vol. 7, http://dx.doi.org/10.1038/s41598-017-16171-1


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