By Professor Marc Wilkins

Journal articles

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

Corley SM; Canales CP; Carmona-Mora P; Mendoza-Reinosa V; Beverdam A; Hardeman EC; Wilkins MR; Palmer SJ; Carmona Mora P; Mendoza Reinoso V, 2016, 'RNA-Seq analysis of Gtf2ird1 knockout epidermal tissue provides potential insights into molecular mechanisms underpinning Williams-Beuren syndrome', BMC Genomics, 17, pp. 450, http://dx.doi.org/10.1186/s12864-016-2801-4

Hart-Smith G; Yagoub D; Tay AP; Pickford R; Wilkins MR, 2016, 'Large scale mass spectrometry-based identifications of enzyme-mediated protein methylation are subject to high false discovery rates', Molecular and Cellular Proteomics, 15, pp. 989 - 1006, http://dx.doi.org/10.1074/mcp.M115.055384

Low JKK; Im H; Erce MA; Hart-Smith G; Snyder MP; Wilkins MR, 2016, 'Protein substrates of the arginine methyltransferase Hmt1 identified by proteome arrays', Proteomics, 16, pp. 465 - 476, http://dx.doi.org/10.1002/pmic.201400564

Hamey JJ; Winter DL; Yagoub D; Overall CM; Hart-Smith G; Wilkins MR, 2016, 'Novel N-terminal and lysine methyltransferases that target translation elongation factor 1A in yeast and human', Molecular and Cellular Proteomics, 15, pp. 164 - 176, http://dx.doi.org/10.1074/mcp.M115.052449

McGill M; Shum A; Mahendradatta T; Bentley N; Chan E; Chen Z; Wilkins M; Tan T; Polly P, 2016, 'Expression Patterns of APLN and OSMR, Potential Novel Modulators of Cancer-induced Cardiac Cachexia, are Altered due to Elevated Inflammatory Cytokines', Heart, Lung and Circulation, 25, pp. S108 - S109, http://dx.doi.org/10.1016/j.hlc.2016.06.257

McGill M; Shum A; Mahendradatta T; Bentley N; Chan E; Chen Z; Wilkins M; Tan T; Polly P, 2016, 'Expression Patterns of APLN and OSMR, Potential Novel Regulators of Cancer-Induced Cardiac Cachexia, are Altered due to Elevated Inflammatory Cytokines', Heart, Lung and Circulation, 25, pp. S109 - S109, http://dx.doi.org/10.1016/j.hlc.2016.06.258

Yagoub D; Tay AP; Chen Z; Hamey JJ; Cai C; Chia SZ; Hart-Smith G; Wilkins MR, 2015, 'Proteogenomic Discovery of a Small, Novel Protein in Yeast Reveals a Strategy for the Detection of Unannotated Short Open Reading Frames', Journal of Proteome Research, 14, pp. 5038 - 5047, http://dx.doi.org/10.1021/acs.jproteome.5b00734

Shum AMY; Fung DCY; Corley SM; McGill MC; Bentley NL; Tan TC; Wilkins MR; Polly P, 2015, 'Cardiac and skeletal muscles show molecularly distinct responses to cancer cachexia', Physiological Genomics, 47, pp. 588 - 599, http://dx.doi.org/10.1152/physiolgenomics.00128.2014

Harkness L; Twine NA; Abu Dawud R; Jafari A; Aldahmash A; Wilkins MR; Adjaye J; Kassem M, 2015, 'Molecular characterisation of stromal populations derived from human embryonic stem cells: Similarities to immortalised bone marrow derived stromal stem cells', Bone Reports, 3, pp. 32 - 39, http://dx.doi.org/10.1016/j.bonr.2015.07.002

Reis RS; Hart-Smith G; Eamens AL; Wilkins MR; Waterhouse PM, 2015, 'MicroRNA regulatory mechanisms play different roles in arabidopsis', Journal of Proteome Research, 14, pp. 4743 - 4751, http://dx.doi.org/10.1021/acs.jproteome.5b00616

Deshpande NP; Wilkins MR; Mitchell HM; Kaakoush NO, 2015, 'Novel genetic markers define a subgroup of pathogenic Escherichia coli strains belonging to the B2 phylogenetic group', FEMS Microbiology Letters, 362, http://dx.doi.org/10.1093/femsle/fnv193

Nahidi L; Corley SM; Wilkins MR; Wei J; Alhagamhmad M; Day AS; Lemberg DA; Leach ST, 2015, 'The major pathway by which polymeric formula reduces inflammation in intestinal epithelial cells: a microarray-based analysis', Genes and Nutrition, 10, http://dx.doi.org/10.1007/s12263-015-0479-x

Tay AP; Pang CNI; Twine NA; Hart-Smith G; Harkness L; Kassem M; Wilkins MR, 2015, 'Proteomic validation of transcript isoforms, including those assembled from RNA-Seq data', Journal of Proteome Research, 14, pp. 3541 - 3554, http://dx.doi.org/10.1021/pr5011394

Yagoub D; Hart-Smith G; Moecking J; Erce MA; Wilkins MR, 2015, 'Yeast proteins Gar1p, Nop1p, Npl3p, Nsr1p, and Rps2p are natively methylated and are substrates of the arginine methyltransferase Hmt1p', Proteomics, 15, pp. 3209 - 3218, http://dx.doi.org/10.1002/pmic.201500075

Winter DL; Abeygunawardena D; Hart-Smith G; Erce MA; Wilkins MR, 2015, 'Lysine methylation modulates the protein-protein interactions of yeast cytochrome C Cyc1p', Proteomics, 15, pp. 2166 - 2176, http://dx.doi.org/10.1002/pmic.201400521

Yap JYS; Rohner T; Greenfield A; Van Der Merwe M; McPherson H; Glenn W; Kornfeld G; Marendy E; Pan AYH; Wilton A; Wilkins MR; Rossetto M; Delaney SK; Yap J-Y, 2015, 'Complete chloroplast genome of the Wollemi pine (Wollemia nobilis): Structure and evolution', PLoS ONE, 10, pp. e0128126, http://dx.doi.org/10.1371/journal.pone.0128126

Reis RS; Hart-Smith G; Eamens AL; Wilkins MR; Waterhouse PM, 2015, 'Gene regulation by translational inhibition is determined by Dicer partnering proteins', Nature Plants, 1, pp. 14027 - 14027, http://dx.doi.org/10.1038/nplants.2014.27

Kaakoush NO; Deshpande NP; Man SM; Burgos-Portugal JA; Khattak FA; Raftery MJ; Wilkins MR; Mitchell HM, 2015, 'Transcriptomic and proteomic analyses reveal key innate immune signatures in the host response to the gastrointestinal pathogen Campylobacter concisus', Infection and Immunity, 83, pp. 832 - 845, http://dx.doi.org/10.1128/IAI.03012-14

Gilchrist AS; Shearman DCA; Frommer M; Raphael KA; Deshpande NP; Wilkins MR; Sherwin WB; Sved JA, 2014, 'The draft genome of the pest tephritid fruit fly Bactrocera tryoni: Resources for the genomic analysis of hybridising species', BMC Genomics, 15, pp. 1 - 17, http://dx.doi.org/10.1186/1471-2164-15-1153

Gilchrist AS; Shearman DCA; Frommer M; Raphael KA; Deshpande NP; Wilkins MR; Sherwin WB; Sved JA, 2014, 'The draft genome of the pest tephritid fruit fly Bactrocera tryoni: Resources for the genomic analysis of hybridising species', BMC Genomics, 15, http://dx.doi.org/10.1186/1471-2164-15-1153

Winter DL; Erce MA; Wilkins MR, 2014, 'A web of possibilities: Network-based discovery of protein interaction codes', Journal of Proteome Research, 13, pp. 5333 - 5338, http://dx.doi.org/10.1021/pr500585p

Hobbs M; Pavasovic A; King AG; Prentis PJ; Eldridge MDB; Chen Z; Colgan DJ; Polkinghorne A; Wilkins MR; Flanagan C; Gillett A; Hanger J; Johnson RN; Timms P, 2014, 'A transcriptome resource for the koala (Phascolarctos cinereus): Insights into koala retrovirus transcription and sequence diversity', BMC Genomics, 15, http://dx.doi.org/10.1186/1471-2164-15-786

Zhang L; Hamey JJ; Hart-Smith G; Erce MA; Wilkins MR, 2014, 'Elongation factor methyltransferase 3 - A novel eukaryotic lysine methyltransferase', Biochemical and Biophysical Research Communications, 451, pp. 229 - 234, http://dx.doi.org/10.1016/j.bbrc.2014.07.110

Tan M; Collins D; Chen Z; Englezou A; Wilkins MR, 2014, 'A brief overview of the size and composition of the myrtle rust genome and its taxonomic status', Mycology: an International Journal on Fungal Biology, 5, pp. 52 - 63, http://dx.doi.org/10.1080/21501203.2014.919967

Johnson RN; Hobbs M; Eldridge MDB; King AG; Colgan DJ; Wilkins MR; Chen Z; Prentis PJ; Pavasovic A; Polkinghorne A; Timms P, 2014, 'The Koala Genome Consortium', Technical Reports of the Australian Museum, Online, 24, pp. 91 - 92, http://dx.doi.org/10.3853/j.1835-4211.24.2014.1624

Nadkarni MA; Chen Z; Wilkins MR; Hunter N, 2014, 'Comparative genome analysis of Lactobacillus rhamnosus clinical isolates from initial stages of dental pulp infection: Identification of a new exopolysaccharide cluster', PLoS ONE, 9, http://dx.doi.org/10.1371/journal.pone.0090643

Hart-Smith G; Chia SZ; Low JKK; McKay MJ; Molloy MP; Wilkins MR, 2014, 'Stoichiometry of Saccharomyces cerevisiae lysine methylation: Insights into non-histone protein lysine methyltransferase activity', Journal of Proteome Research, 13, pp. 1744 - 1756, http://dx.doi.org/10.1021/pr401251k

Low JKK; Hart-Smith G; Erce MA; Wilkins MR, 2014, 'The Saccharomyces cerevisiae poly(A)-binding protein is subject to multiple post-translational modifications, including the methylation of glutamic acid', Biochemical and Biophysical Research Communications, 443, pp. 543 - 548, http://dx.doi.org/10.1016/j.bbrc.2013.12.009

Pang CNI; Tay AP; Aya C; Twine NA; Harkness L; Hart-Smith G; Chia SZ; Chen Z; Deshpande NP; Kaakoush NO; Mitchell HM; Kassem M; Wilkins MR, 2014, 'Tools to covisualize and coanalyze proteomic data with genomes and transcriptomes: Validation of genes and Alternative mRNA splicing', Journal of Proteome Research, 13, pp. 84 - 98, http://dx.doi.org/10.1021/pr400820p

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