By Professor Marc Wilkins

Journal articles

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

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, 67, pp. 23 - 32, http://dx.doi.org/10.1016/j.bone.2014.06.027

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, 16, pp. 45 - 53, http://dx.doi.org/10.1016/j.margen.2013.12.004

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, 28, pp. 1899 - 1915, http://dx.doi.org/10.1210/me.2013-1423

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

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, 153, pp. 73 - 88, http://dx.doi.org/10.1016/j.aquatox.2013.11.022

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

Schramm SJ; Jayaswal V; Goel A; Li SS; Yang YH; Mann GJ; Wilkins MR, 2013, 'Molecular interaction networks for the analysis of human disease: Utility, limitations, and considerations', Proteomics, 13, pp. 3393 - 3405, http://dx.doi.org/10.1002/pmic.201200570

Jayaswal V; Schramm SJ; Mann GJ; Wilkins MR; Yang YH, 2013, 'VAN: An R package for identifying biologically perturbed networks via differential variability analysis', BMC Research Notes, 6, http://dx.doi.org/10.1186/1756-0500-6-430

Low JKK; Hart-Smith G; Erce MA; Wilkins MR, 2013, 'Analysis of the proteome of Saccharomyces cerevisiae for methylarginine', Journal of Proteome Research, 12, pp. 3884 - 3899, http://dx.doi.org/10.1021/pr400556c

Deshpande NP; Wong YK; Manefield M; Wilkins MR; Lee M, 2013, 'Genome Sequence of Dehalobacter UNSWDHB, a Chloroform-Dechlorinating Bacterium', GENOME ANNOUNCEMENTS, 1, http://dx.doi.org/10.1128/genomeA.00720-13

Deshpande NP; Kaakoush NO; Wilkins MR; Mitchell HM, 2013, 'Comparative genomics of Campylobacter concisus isolates reveals genetic diversity and provides insights into disease association', BMC Genomics, 14, http://dx.doi.org/10.1186/1471-2164-14-585

Erce MA; Abeygunawardena D; Low JKK; Hart-Smith G; Wilkins MR, 2013, 'Interactions affected by arginine methylation in the yeast protein-protein interaction network', Molecular & Cellular Proteomics, http://dx.doi.org/10.1074/mcp.M113.031500

Funnell APW; Mak KS; Twine NA; Pelka GJ; Norton LJ; Radziewic T; Power M; Wilkins MR; Bell-Anderson KS; Fraser ST; Perkins AC; Tam PP; Pearson RCM; Crossley M, 2013, 'Generation of Mice Deficient in both KLF3/BKLF and KLF8 Reveals a Genetic Interaction and a Role for These Factors in Embryonic Globin Gene Silencing', Molecular and Cellular Biology, 33, pp. 2976 - 2987, http://dx.doi.org/10.1128/MCB.00074-13

Chen Z; Wilkins MR; Hunter N; Nadkarni M, 2013, 'Draft Genome Sequences of Two Clinical Isolates of Lactobacillus rhamnosus from Initial Stages of Dental Pulp Infection', Genome Announcements, 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, 1, http://dx.doi.org/10.1128/genomeA.00193-12

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

Erce MA; Low JKK; Hart-Smith GO; Wilkins MR, 2013, 'A conditional two-hybrid (C2H) system for the detection of protein-protein interactions that are mediated by post-translational modification', Proteomics, 13, pp. 1059 - 1064, http://dx.doi.org/10.1002/pmic.201200477

Schramm S-J; Li SS; Jayaswal V; Fung D; Campain AE; Pang CNI; Scolyer RA; Yang YH; Mann GJ; Wilkins MR, 2013, 'Disturbed protein-protein interaction networks in metastatic melanoma are associated with worse prognosis and increased functional mutation burden', Pigment Cell & Melanoma Research, 26, pp. 708 - 722, http://onlinelibrary.wiley.com/doi/10.1111/pcmr.12126/abstract

Twine NA; Janitz C; Wilkins MR; Janitz M, 2013, 'Sequencing of hippocampal and cerebellar transcriptomes provides new insights into the complexity of gene regulation in the human brain.', Neuroscience Letters, 541, pp. 263 - 268, http://dx.doi.org/10.1016/j.neulet.2013.02.034

Pang CNI; Goel A; Li SS; Wilkins MR, 2012, 'A multidimensional matrix for systems biology research and its application to interaction networks.', Journal of Proteome Research, 11, pp. 5204 - 5220, http://dx.doi.org/10.1021/pr300405y

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