By Professor Marc Wilkins

Journal articles

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

Yeung WCG; Pang CNI; Wilkins MR; Catteau J; Howard N; Rawlinson WD; Craig ME; Al-Shabeeb A, 2012, 'Children with islet autoimmunity and enterovirus infection demonstrate a distinct cytokine profile', Diabetes, 61, pp. 1500 - 1508, http://dx.doi.org/10.2337/db11-0264

Scott GM; Chow SS; Craig ME; Pang CN; Hall B; Wilkins MR; Jones C; Lloyd AR; Rawlinson WD; hall B, 2012, 'Cytomegalovirus infection during pregnancy with maternofetal transmission induces a proinflammatory cytokine bias in placenta and amniotic fluid', Journal of Infectious Diseases, 205, pp. 1305 - 1310, http://dx.doi.org/10.1093/infdis/jis186

Goel A; Wilkins MR, 2012, 'Dynamic hubs show competitive and static hubs non-competitive regulation of their interaction partners.', PLoS One, 7, pp. e48209, http://dx.doi.org/10.1371/journal.pone.0048209

Hart-Smith GO; Low JKK; Erce MA; Wilkins MR, 2012, 'Enhanced methylarginine characterization by post-translational modification-specific targeted data acquisition and electron-transfer dissociation mass spectrometry', Journal of the American Society for Mass Spectrometry, 23, pp. 1376 - 1389, http://dx.doi.org/10.1007/s13361-012-0417-8

Couttas TA; Raftery MJ; Padula M; Herbert BR; Wilkins MR, 2012, 'Methylation of translation-associated proteins in Saccharomyces cerevisiae: Identification of methylated lysines and their methyltransferases', Proteomics, 12, pp. 960 - 972, http://dx.doi.org/10.1002/pmic.201100570

Low JKK; Wilkins MR, 2012, 'Protein arginine methylation in Saccharomyces cerevisiae', FEBS Journal, 279, pp. 4423 - 4443, http://dx.doi.org/10.1111/febs.12039

Funnell AP; Norton LJ; Mak KS; Burdach J; Artuz CM; Twine NA; Wilkins MR; Power C; Hung TT; Perdomo JS; Bell-Anderson K; Orkin SH; Pearson RC; Crossley M, 2012, 'The CACCC-binding protein KLF3/BKLF represses a subset of KLF1/EKLF target genes and is required for proper erythroid maturation in vivo', Molecular and Cellular Biology, 32, pp. 3281 - 3292, http://dx.doi.org/10.1128/MCB.00173-12

Erce MA; Pang CN; Hart-Smith GO; Wilkins MR, 2012, 'The methylproteome and the intracellular methylation network.', Proteomics, 12, pp. 564 - 586, http://dx.doi.org/10.1002/pmic.201100397

Webster R; Blaber SP; Herbert BR; Wilkins MR; Vesey G, 2012, 'The role of mesenchymal stem cells in veterinary therapeutics - A Review', New Zealand Veterinary Journal, 60, pp. 265 - 272, http://dx.doi.org/10.1080/00480169.2012.683377

Chong HS; Campbell LT; Padula MP; Hill CJ; Harry EJ; Li SS; Wilkins MR; Herbert BR; Carter DA, 2012, 'Time-course proteome analysis reveals the dynamic response of cryptococcus gattii cells to fluconazole', PLoS One, 7, pp. August - Article numbere42835, http://dx.doi.org/10.1371/journal.pone.0042835

Fung DCY; Li SS; Goel A; Hong S-H; Wilkins MR, 2012, 'Visualization of the interactome: what are we looking at?', Proteomics, 12, pp. 1669 - 1686, http://dx.doi.org/10.1002/pmic.201100454

Kaakoush NO; Deshpande N; Wilkins MR; Raftery MJ; Janitz K; Mitchell HM, 2011, 'Comparative analyses of Campylobacter concisusstrains reveal the genome of the reference strain BAA-1457 is not representative of the species.', Gut Pathogens, 3, pp. 15, http://dx.doi.org/10.1186/1757-4749-3-15

Goel A; Li SS; Wilkins MR, 2011, 'Four-dimensional visualisation and analysis of protein-protein interaction networks', Proteomics, 11, pp. 2672 - 2682

Couttas TA; Raftery MJ; Erce MA; Wilkins MR, 2011, 'Monitoring cytoplasmic protein complexes with blue native gel electrophoresis and stable isotope labelling with amino acids in cell culture: analysis of changes in the 20S proteasome', Electrophoresis, 32, pp. 1819 - 1823, http://dx.doi.org/10.1002/elps.201100122

Deshpande NP; Kaakoush NO; Mitchell HM; Janitz K; Raftery MJ; Li SS; Wilkins MR, 2011, 'Sequencing and validation of the genome of a Campylobacter concisus reveals intra-species diversity', PLoS ONE, 6, pp. e22170, http://dx.doi.org/10.1371/journal.pone/0022170

Kaakoush NO; Deshpande NP; Wilkins MR; Tan C; Burgos-Portugal J; Raftery MJ; Day AS; Lemberg DA; Mitchell HM, 2011, 'The pathogenic potential of campylobacter concisus strains associated with chronic intestinal diseases', PLoS One, 6, pp. e29045, http://dx.doi.org/10.1371

Campbell M; Hayes C; Struwe WB; Wilkins MR; Aoki-kinoshita K; Harvey D; Rudd P; Kolarich D; Karlsson N; Packer N, 2011, 'UniCarbKB: putting the pieces together for glycomics research.', Proteomics, 11, pp. 4117 - 4121, http://dx.doi.org/10.1002

Li SS; Xu K; Wilkins MR, 2011, 'Visualization and analysis of the complexome network of Saccharomyces cerevisiae', Journal of Proteome Research, 10, pp. 4744 - 4756, http://dx.doi.org/10.1021/pr200548c

Twine NA; Janitz K; Wilkins MR; Janitz M, 2011, 'Whole transcriptome sequencing reveals gene expression and splicing differences in brain regions affected by Alzheimer's disease', PLoS One, 6, pp. e16266, http://dx.doi.org/10.1371/journal.pone.0016266

Erce MA; Low J; Wilkins MR, 2010, 'Analysis of the RNA degradosome complex in Vibrio angustum S14', FEBS Journal, 277, pp. 5161 - 5173, http://dx.doi.org/10.1111/j.1742-4658.2010.07934.x

Wilkins MR, 2010, 'GlycoViewer: a tool for visual summary and comparative analysis of the glycome.', Nucleic Acids Research, 38, pp. 667 - 670

Wilkins MR; Pang I, 2010, 'Identification of arginine- and lysine-methylation in the proteome of Saccharomyces cerevisiae and its functional implications', BMC Genomics, 11, pp. 92, http://dx.doi.org/10.1186/1471-2164-11-92

Wilkins MR, 2010, 'Proteins deleterious on overexpression are associated with high intrinsic disorder, specific interaction domains, and low abundance.', Journal of Proteome Research, 9, pp. 1218 - 1225

Okoli AS; Wilkins MR; Raftery MJ; Mendz GL, 2010, 'Response of Helicobacter hepaticus to bovine bile', Journal of Proteome Research, 9, pp. 1374 - 1384

Kaakoush NO; Man SM; Lamb S; Raftery MJ; Wilkins MR; Kovach Z; Mitchell HM, 2010, 'The secretome of Campylobacter concisus.', FEBS Journal, 277, pp. 1606 - 1617

Fung DCY; Wilkins MR; Hart D; Hong S-H, 2010, 'Using the clustered circular layout as an informative method for visualizing protein-protein interaction networks.', Proteomics, 10, pp. 2327 - 2723, http://dx.doi.org/10.1002/pmic.201000046

Wilkins M, 2009, 'A celebration of protein-protein interactions', Proteomics, 9, pp. 5207 - 5208, http://dx.doi.org/10.1002/pmic.200990092

Wilkins MR, 2009, 'Hares and tortoises: The high- versus low-throughput proteomic race', Electrophoresis, 30, pp. S150 - S155, http://dx.doi.org/10.1002/elps.200900175

Erce MA; Low J; March P; Wilkins MR; Takayama KM, 2009, 'Identification and functional analysis of RNase E of Vibrio angustum S14 and two-hybrid analysis of its interaction partners', Biochimica et Biophysica ACTA - Proteins and Proteomics, 1794, pp. 1107 - 1114

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