By Professor Marc Wilkins

Journal articles

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, 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, 9, 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, 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, 91, pp. 11827 - 11833, http://dx.doi.org/10.1021/acs.analchem.9b02504

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, 9, pp. 10004 - 10016, http://dx.doi.org/10.1002/ece3.5563

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, 19, pp. e1800444, http://dx.doi.org/10.1002/pmic.201800444

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, 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, 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, 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, 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, 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, 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, 6, http://dx.doi.org/10.1093/ofid/ofz025

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

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, 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; Pang I, 2018, 'Knockout of the Hmt1p arginine methyltransferase in saccharomyces cerevisiae leads to the dysregulation of phosphate-associated genes and processes', Molecular and Cellular Proteomics, 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, 8, pp. 389, 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, 8, pp. 3529, 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, 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, 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, 7, http://dx.doi.org/10.1093/gigascience/giy095

Twine NA; Harkness L; Adjaye J; Aldahmash A; Wilkins MR; Kassem M, 2018, 'Molecular Phenotyping of Telomerized Human Bone Marrow Skeletal Stem Cells Reveals a Genetic Program of Enhanced Proliferation and Maintenance of Differentiation Responses', JBMR Plus, 2, pp. 257 - 267, http://dx.doi.org/10.1002/jbm4.10050

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, 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, 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, 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, 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, 17, pp. 1014 - 1030, http://dx.doi.org/10.1021/acs.jproteome.7b00649

Paramsothy S; Kamm M; Nielsen S; Deshpande N; Faith J; Clemente J; Paramsothy R; Walsh A; van den Bogaerde J; Samuel D; Leong R; Connor S; Ng W; Lin E; Wilkins M; Colombel J-F; Borody T; Mitchell H; Kaakoush N, 2018, 'OP019 In faecal microbiota transplantation (FMT) for ulcerative colitis, fusobacterium is associated with lack of remission, while metabolic shifts to starch degradation and short-chain fatty acid production are associated with remission (FOCUS study)', Journal of Crohn's and Colitis, 12, pp. S013 - S014, http://dx.doi.org/10.1093/ecco-jcc/jjx180.018

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, 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, 17, pp. 359 - 373, http://dx.doi.org/10.1021/acs.jproteome.7b00601

Paramsothy S; Kamm MA; Nielsen S; Deshpande N; Faith J; Clemente JC; Paramsothy R; Walsh A; van den Bogaerde J; Samuel D; Leong RW; Connor SJ; Ng WSW; Lin E; Wilkins M; Colombel JF; Borody TJ; Mitchell HM; Kaakoush NO, 2018, '130 - In Fecal Microbiota Transplantation (FMT) for Ulcerative Colitis, Fusobacterium is Associated with Lack of Remission, while Metabolic Shifts to Starch Degradation and Short Chain Fatty Acid Production are Associated with Remission – Results from the Randomized Controlled Focus Study', Gastroenterology, 154, pp. S - 35, http://dx.doi.org/10.1016/s0016-5085(18)30588-2

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, 7, pp. 15838, http://dx.doi.org/10.1038/s41598-017-16171-1

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, 16, pp. 2229 - 2242, http://dx.doi.org/10.1074/mcp.M116.066308

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, 93, http://dx.doi.org/10.1093/femsec/fix147

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, 8, pp. 1669, http://dx.doi.org/10.3389/fpls.2017.01669

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, 20, pp. 572 - 585, http://dx.doi.org/10.1016/j.celrep.2017.06.067

Mendoza-Reinoso V; Corley S; Wilkins M; Beverdam A, 2017, 'Yap regulates wnt16 expression to activate the canonical wnt pathway in keratinocyte proliferation', Cells and Development, 145, pp. s50, http://dx.doi.org/10.1016/j.mod.2017.04.092

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, 18, pp. 399, http://dx.doi.org/10.1186/s12864-017-3797-0

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, 16, pp. 1988 - 2003, http://dx.doi.org/10.1021/acs.jproteome.6b01052

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, 13, pp. e1006633, http://dx.doi.org/10.1371/journal.pgen.1006633

Waters SA; McAteer SP; Kudla G; Pang I; Deshpande NP; Amos TG; Leong KW; Wilkins MR; Strugnell R; Gally DL; Tollervey D; Tree JJ, 2017, 'Small RNA interactome of pathogenic E. coli revealed through crosslinking of RNase E', EMBO Journal, 36, pp. 374 - 387, http://dx.doi.org/10.15252/embj.201694639

Pang CNI; Lai YW; Campbell LT; Chen SC; Carter DA; Wilkins MR, 2017, 'Transcriptome and network analyses in Saccharomyces cerevisiae reveal that amphotericin B and lactoferrin synergy disrupt metal homeostasis and stress response.', Scientific Reports, 7, pp. 40232 - 40232, http://dx.doi.org/10.1038/srep40232

Hamey JJ; Hart-Smith G; Erce MA; Wilkins MR, 2016, 'The activity of a yeast Family 16 methyltransferase, Efm2, is affected by a conserved tryptophan and its N-terminal region', FEBS Open Bio, 6, pp. 1320 - 1330, http://dx.doi.org/10.1002/2211-5463.12153

Corley SM; Tsai SY; Wilkins MR; Weickert CS, 2016, 'Transcriptomic analysis shows decreased cortical expression of nr4a1, nr4a2 and rxrb in schizophrenia and provides evidence for nuclear receptor dysregulation', PLoS ONE, 11, pp. e0166944, http://dx.doi.org/10.1371/journal.pone.0166944

Twine NA; Harkness L; Kassem M; Wilkins MR, 2016, 'Transcription factor ZNF25 is associated with osteoblast differentiation of human skeletal stem cells', BMC Genomics, 17, pp. 872, http://dx.doi.org/10.1186/s12864-016-3214-0

Tan MK; Raman H; Chambers G; Sharma I; Chen Z; Deshpande N; Wilkins MR, 2016, 'Characterization of SNP and structural variations in the mitochondrial genomes of Tilletia indica and its closely related species formed basis for a simple diagnostic assay', PLoS ONE, 11, pp. e0166086, http://dx.doi.org/10.1371/journal.pone.0166086

Kasumovic MM; Chen Z; Wilkins MR, 2016, 'Australian black field crickets show changes in neural gene expression associated with socially-induced morphological, life-history, and behavioral plasticity', BMC Genomics, 17, pp. 827, http://dx.doi.org/10.1186/s12864-016-3119-y

Lai YW; Campbell LT; Wilkins MR; Pang CNI; Chen S; Carter DA, 2016, 'Synergy and antagonism between iron chelators and antifungal drugs in Cryptococcus', International Journal of Antimicrobial Agents, 48, pp. 388 - 394, http://dx.doi.org/10.1016/j.ijantimicag.2016.06.012

Deshpande NP; Wilkins MR; Castaño-Rodríguez N; Bainbridge E; Sodhi N; Riordan SM; Mitchell HM; Kaakoush NO, 2016, 'Campylobacter concisus pathotypes induce distinct global responses in intestinal epithelial cells', Scientific Reports, 6, pp. 34288, http://dx.doi.org/10.1038/srep34288

Taha ; Siddiqui KS; Campanaro S; Najnin T; Deshpande N; Williams TJ; Aldrich-Wright J; Wilkins M; Curmi PMG; Cavicchioli R, 2016, 'Single TRAM domain RNA-binding proteins in Archaea: functional insight from Ctr3 from the Antarctic methanogen Methanococcoides burtonii', Environmental microbiology, 18, pp. 2810 - 2824, http://dx.doi.org/10.1111/1462-2920.13229

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