Select Publications

Books

Wilkins MR;Appel RD;Williams KK;Hochstrasser DF, (eds.), 2007, Proteome Research: Concepts, Technology and Application, 2, Springer Publishing Company, Heidelberg

Book Chapters

Wilkins MR, 2012, 'Interpreting data from large-scale screens.', in Roberts G (ed.), Encyclopedia of Biophysics, edn. 1st Edition, Springer, 11, http://www.springerreference.com/docs/html/chapterdbid/305477.html

Wilkins MR, 2008, 'Biomarker Identification: The Role of Experimental Design, Statistics, and Data Sharing', in Clinical Proteomics: From Diagnosis to Therapy, pp. 113 - 120, http://dx.doi.org/10.1002/9783527622153.ch9

Pang CN I;Wilkins MR, 2008, 'Online resources for the molecular contextualization of disease.', in Methods in molecular medicine, pp. 287 - 308

Bek EJ;Wilkins MR, 2008, 'Using Yeast to Study Protein-Protein Interactions Relevant to Disease', in Witt S (ed.), Yeast as a model for Human Disease, edn. Original, Signpost Research Press, pp. 145 - 176

Wilkins MR;Hunt SM N, 2007, 'Bioinformatics and experimental design for biomarker discovery', in Proteomics of Human Body Fluids: Principles, Methods, and Applications, pp. 147 - 174, http://dx.doi.org/10.1007/978-1-59745-432-2_8

Wilkins MR, 2007, 'Biomarker Identification: The Role of Experimental Design, Statistics, and Data Sharing', in Clinical Proteomics, edn. Original, pp. 113 - 120

Hernandez P;Binz PA;Wilkins MR, 2007, 'Protein Identification in Proteomics', in Wilkins M;Appel R;Williams K;Hochstrasser D (ed.), Proteome Research: concepts, technology and practice, edn. 2nd, Springer Publishing Company, Netherlands, pp. 41 - 67

Packer N;Gooley AA;Wilkins MR, 2007, 'One gene, many proteins', in Wilkins M;Appel R;Williams K;Hochstrasser D (ed.), Proteome Research: concepts, technology and practice, edn. 2nd, Springer Publishing Company, Netherlands, pp. 95 - 121

Wilkins MR;Appel RD, 2007, 'Ten years of the proteome', in Wilkins M;Appel R;Williams K;Hochstrasser D (ed.), Proteome Research: concepts, technology and practice, edn. 2nd, Springer Publishing Company, Netherlands, pp. 1 - 13

Binz PA;Muller M;Walther D;Bienvenut WV;Gras R;Hoogland C;Bouchet G;Gasteiger E;Fabbretti R;Gay S;Palagi P;Wilkins MR;Rouge V;Tonella L;Paesano S;Rossellat G;Karmime A;Bairoch A;Sanchez JC;Appel RD;Hochstrasser DF, 2005, 'Signal traitment and virtual images production (1/2): A molecular scanner to highly automate proteomic research and to display proteome images', in Acceleration and Improvement of Protein Identification by Mass Spectrometry, pp. 151 - 168, http://dx.doi.org/10.1007/1-4020-3319-2_4

Gasteiger E;Hoogland C;Gattiker A;Duvaud S;Wilkins MR;Appel R;Bairoch A, 2005, 'Protein Identification and Analysis Tools in the ExPASy Server', in Link AJ (ed.), 2-D Protein Gel Electrophoresis Protocols, edn. 2nd, Humana Press, Totowa, N.J., pp. 571 - 607

Cooper CA;Joshi HJ;Harrison M;Wilkins MR;Packer N, 2003, 'Querying GlycosuiteDB', in Conn PM (ed.), Handbook of Proteomic Methods, edn. Original, Humana Press, Totowa, NJ, pp. 233 - 240

Journal articles

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, vol. 8, 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 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


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