Select Publications

Journal articles

Unnikrishnan A;Papaemmanuil E;Beck D;Deshpande NP;Verma A;Kumari A;Woll PS;Richards LA;Knezevic K;Chandrakanthan V;Thoms JA I;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 SE W;Mufti GJ;Hellstrom-Lindberg E;Wilkins MR;MacKenzie KL;Wong JW H;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, http://dx.doi.org/10.1016/j.celrep.2017.06.067

Tay AP;Pang CN I;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, http://dx.doi.org/10.1021/acs.jproteome.6b01052

Hamey JJ;Wienert B;Quinlan KG R;Wilkins MR, 2017, 'METTL21B is a novel human lysine methyltransferase of translation elongation factor 1A: discovery by CRISPR/Cas9 knock out.', Mol Cell Proteomics, http://dx.doi.org/10.1074/mcp.M116.066308

Corley SM;MacKenzie KL;Beverdam A;Roddam LF;Wilkins MR, 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, http://dx.doi.org/10.1186/s12864-017-3797-0

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

Pang CN I;Lai YW;Campbell LT;Chen SC A;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, vol. 7, http://dx.doi.org/10.1038/srep40232

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, vol. 36, pp. 374 - 387, http://dx.doi.org/10.15252/embj.201694639

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, vol. 11, http://dx.doi.org/10.1371/journal.pone.0166944

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, vol. 6, pp. 1320 - 1330, http://dx.doi.org/10.1002/2211-5463.12153

Twine NA;Harkness L;Kassem M;Wilkins MR, 2016, 'Transcription factor ZNF25 is associated with osteoblast differentiation of human skeletal stem cells', BMC Genomics, vol. 17, 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, vol. 11, 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, vol. 17, http://dx.doi.org/10.1186/s12864-016-3119-y

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, vol. 6, http://dx.doi.org/10.1038/srep34288

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

Taha ;Siddiqui KS;Campanaro S;Najnin T;Deshpande N;Williams TJ;Aldrich-Wright J;Wilkins M;Curmi PM G;Cavicchioli R, 2016, 'Single TRAM domain RNA-binding proteins in Archaea: functional insight from Ctr3 from the Antarctic methanogen Methanococcoides burtonii', Environmental Microbiology, vol. 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, 2016, 'RNA-Seq analysis of Gtf2ird1 knockout epidermal tissue provides potential insights into molecular mechanisms underpinning Williams-Beuren syndrome', BMC Genomics, vol. 17, 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, vol. 15, pp. 989 - 1006, http://dx.doi.org/10.1074/mcp.M115.055384

Low JK K;Im H;Erce MA;Hart-Smith G;Snyder MP;Wilkins MR, 2016, 'Protein substrates of the arginine methyltransferase Hmt1 identified by proteome arrays', Proteomics, vol. 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, vol. 15, pp. 164 - 176, http://dx.doi.org/10.1074/mcp.M115.052449

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, vol. 1, http://dx.doi.org/10.1038/nplants.2014.27

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

Shum AM Y;Fung DC Y;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, vol. 47, pp. 588 - 599, http://dx.doi.org/10.1152/physiolgenomics.00128.2014

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, vol. 362, http://dx.doi.org/10.1093/femsle/fnv193

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, vol. 14, pp. 5038 - 5047, http://dx.doi.org/10.1021/acs.jproteome.5b00734

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, vol. 15, pp. 3209 - 3218, http://dx.doi.org/10.1002/pmic.201500075

Tay AP;Pang CN I;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, vol. 14, pp. 3541 - 3554, http://dx.doi.org/10.1021/pr5011394

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, vol. 3, pp. 32 - 39, http://dx.doi.org/10.1016/j.bonr.2015.07.002

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, vol. 10, http://dx.doi.org/10.1007/s12263-015-0479-x

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

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, http://dx.doi.org/10.1002/pmic.201400521

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, vol. 83, pp. 832 - 845, http://dx.doi.org/10.1128/IAI.03012-14

Gilchrist AS;Shearman DC A;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, vol. 15, http://dx.doi.org/10.1186/1471-2164-15-1153

Gilchrist AS;Shearman DC A;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, pp. 1 - 17, http://dx.doi.org/10.1186/1471-2164-15-1153

Hook SE;Osborn HL;Gissi F;Moncuquet P;Twine NA;Wilkins MR;Adams MS, 2014, 'RNA-Seq analysis of the toxicant-induced transcriptome of the marine diatom, Ceratoneis closterium', Marine Genomics, vol. 16, pp. 45 - 53, http://dx.doi.org/10.1016/j.margen.2013.12.004

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

Yagoub D;Wilkins MR;Lay AJ;Kaczorowski DC;Hatoum D;Bajan S;Hutvagner G;Lai JH;Wu W;Martiniello-Wilks R;Xia P;McGowan EM, 2014, 'Sphingosine kinase 1 Isoform-Specific interactions in breast cancer', Molecular Endocrinology, vol. 28, pp. 1899 - 1915, http://dx.doi.org/10.1210/me.2013-1423

Hobbs M;Pavasovic A;King AG;Prentis PJ;Eldridge MD B;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, vol. 15, http://dx.doi.org/10.1186/1471-2164-15-786

Hook SE;Simpson SL;Spadaro DA;Twine NA;Wilkins MR;Moncuquet P, 2014, '454 pyrosequencing-based analysis of gene expression profiles in the amphipod Melita plumulosa: Transcriptome assembly and toxicant induced changes', Aquatic Toxicology, vol. 153, pp. 73 - 88, http://dx.doi.org/10.1016/j.aquatox.2013.11.022

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, vol. 451, pp. 229 - 234, http://dx.doi.org/10.1016/j.bbrc.2014.07.110

Twine NA;Chen L;Pang CN;Wilkins MR;Kassem M, 2014, 'Identification of differentiation-stage specific markers that define the ex vivo osteoblastic phenotype', Bone, vol. 67, pp. 23 - 32, http://dx.doi.org/10.1016/j.bone.2014.06.027

Tan MK;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, vol. 5, pp. 52 - 63, http://dx.doi.org/10.1080/21501203.2014.919967

Williams KL;Gooley AA;Wilkins MR;Packer NH, 2014, 'A Sydney proteome story', Journal of Proteomics, vol. 107, pp. 13 - 23, http://dx.doi.org/10.1016/j.jprot.2014.04.006

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, vol. 9, http://dx.doi.org/10.1371/journal.pone.0090643

Hart-Smith G;Chia SZ;Low JK K;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, vol. 13, pp. 1744 - 1756, http://dx.doi.org/10.1021/pr401251k

Hook SE;Osborn HL;Gissi F;Moncuquet P;Twine NA;Wilkins MR;Adams MS, 2014, 'RNA-Seq analysis of the toxicant-induced transcriptome of the marine diatom, Ceratoneis closterium', Marine Genomics, http://dx.doi.org/10.1016/j.margen.2013.12.004

Hook SE;Simpson SL;Spadaro DA;Twine NA;Wilkins MR;Moncuquet P, 2014, '454 pyrosequencing-based analysis of gene expression profiles in the amphipod Melita plumulosa: Transcriptome assembly and toxicant induced changes', Aquatic Toxicology, http://dx.doi.org/10.1016/j.aquatox.2013.11.022

Pang CN I;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, vol. 13, pp. 84 - 98, http://dx.doi.org/10.1021/pr400820p

Deshpande NP;Wong YK;Manefield M;Wilkins MR;Lee M, 2013, 'Genome sequence of Dehalobacter UNSWDHB, a chloroform-dechlorinating bacterium', Genome Announcements, vol. 1, http://dx.doi.org/10.1128/genomeA.e00720-13

Chen Z;Wilkins MR;Hunter N;Nadkarni MA, 2013, 'Draft genome sequences of two clinical isolates of Lactobacillus rhamnosus from initial stages of dental pulp infection', Genome Announcements, vol. 1, http://dx.doi.org/10.1128/genomeA.00073-12

Tay AP;Kaakoush NO;Deshpande NP;Chen Z;Mitchell H;Wilkins MR, 2013, 'Genome sequence of Campylobacter showae UNSWCD, isolated from a patient with Crohn's disease', Genome Announcements, vol. 1, http://dx.doi.org/10.1128/genomeA.00193-12


Back to profile page