Select Publications

Book Chapters

Pang I, 2019, 'Protein Post-Translational Modification Prediction', in ,

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,

Wilkins MR, 2008, 'Biomarker Identification: The Role of Experimental Design, Statistics, and Data Sharing', in Clinical Proteomics: From Diagnosis to Therapy, pp. 113 - 120,

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

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

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

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

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

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,

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,

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

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,

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,

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', ,

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,

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,

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,

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,

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,

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,

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,

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,

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,

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,

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,

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,

Bayat A; Deshpande NP; Wilkins MR; Parameswaran S, 2018, 'Fast Short Read De-novo Assembly Using Overlap-Layout-Consensus Approach', IEEE/ACM Transactions on Computational Biology and Bioinformatics,

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,

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,

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,

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,

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,

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,

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,

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,

Hamey JJ; Wilkins MR, 2018, 'Methylation of Elongation Factor 1A: Where, Who, and Why?', Trends in Biochemical Sciences, vol. 43, pp. 211 - 223,

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,

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,

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,

Noorian P; Hu J; Chen Z; Kjelleberg S; Wilkins MR; Sun S; McDougald D, 2017, 'Pyomelanin produced by Vibrio cholerae confers resistance to predation by Acanthamoeba castellanii', FEMS microbiology ecology, vol. 93,

Hamey JJ; Wienert B; Quinlan KGR; Wilkins MR, 2017, 'METTL21B Is a Novel Human lysine methyltransferase of translation elongation factor 1A: Discovery by CRISPR/Cas9 Knockout', Molecular and Cellular Proteomics, vol. 16, pp. 2229 - 2242,

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,

Hart-Smith G; Reis RS; Waterhouse PM; Wilkins MR, 2017, 'Improved quantitative plant proteomics via the combination of targeted and untargeted data acquisition', Frontiers in Plant Science, vol. 8,

Unnikrishnan A; Papaemmanuil E; Beck D; Deshpande NP; Verma A; Kumari A; Woll PS; Richards LA; Knezevic K; Chandrakanthan V; Thoms JAI; Tursky ML; Huang Y; Ali Z; Olivier J; Galbraith S; Kulasekararaj AG; Tobiasson M; Karimi M; Pellagatti A; Wilson SR; Lindeman R; Young B; Ramakrishna R; Arthur C; Stark R; Crispin P; Curnow J; Warburton P; Roncolato F; Boultwood J; Lynch K; Jacobsen SEW; Mufti GJ; Hellstrom-Lindberg E; Wilkins MR; MacKenzie KL; Wong JWH; Campbell PJ; Pimanda JE, 2017, 'Integrative Genomics Identifies the Molecular Basis of Resistance to Azacitidine Therapy in Myelodysplastic Syndromes', Cell Reports, vol. 20, pp. 572 - 585,

Tay AP; Pang CNI; Winter DL; Wilkins MR, 2017, 'PTMOracle: A Cytoscape App for Covisualizing and Coanalyzing Post-Translational Modifications in Protein Interaction Networks', Journal of Proteome Research, vol. 16, pp. 1988 - 2003,

Corley S; MacKenzie K; Beverdam A; Roddam LF; Wilkins , 2017, 'Differentially expressed genes from RNA-Seq and functional enrichment results are affected by the choice of single-end versus paired-end reads and stranded versus non-stranded protocols.', BMC Genomics, vol. 18,

Soboleva TA; Parker BJ; Nekrasov M; Hart-Smith G; Tay YJ; Tng WQ; Wilkins M; Ryan D; Tremethick DJ, 2017, 'A new link between transcriptional initiation and pre-mRNA splicing: The RNA binding histone variant H2A.B', PLoS Genetics, vol. 13,

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