Marc Wilkins

Director, Ramaciotti Centre for Genomics and Director, Systems Biology Initiative
Professor

Biography

About Me

In 1994, Marc Wilkins developed the concept of the proteome and coined the term. In 1997 he co-wrote and co-edited the first book on proteomics (4,000+ copies sold). This, and a series of other seminal works, substantially contributed to the establishment of the proteome and of proteome research. Proteomics is now widely adopted, is included in biochemistry textbooks and is part of the undergraduate curriculum.

Marc has published >200 peer-reviewed research papers, review papers and book chapters and has edited 2 books.  Marc's research has tackled many of the key issues in proteomics. A particular strength has been the capacity to combine large-scale analytical techniques with complex bioinformatics to open new avenues for biological investigation. Current research interests are (i) the role of protein methylation in the proteome (ii) the dynamics of protein interaction networks, studied with crosslinking mass spectrometry. Marc is also an active researcher in genomics and transcriptomics, where his extended team has technical expertise in next-generation sequencing and the bioinformatic analysis of resulting data. Recent highlights include the koala genome project. You can find all Marc's publications and citations here.

Marc directs two centres at UNSW: the NSW Systems Biology Initiative and the Ramaciotti Centre for Genomics. These centres are or have been funded by NCRIS, EIF Super Science, ARC LIEF and the NSW State Government SLF and RAAP schemes. 

Marc co-founded Proteome Systems Pty Ltd in 1999. Recently renamed to Tyrian Diagnostics, this proteomic diagnostics company was listed on the Australian Securities Exchange (ASX) and has developed technology for rapid point-of-care diagnostic testing . Marc is also a co-founder of Regeneus Pty Ltd, a regenerative medicine company which uses autologous adult stem cells to treat a range of musculoskeletal disorders. This company was listed on the ASX in 2013. 

Professional Experience

  • 2016 - Executive Management, Genomics, Bioplatforms Australia 
  • 2011 - Director, Ramaciotti Centre for Genomics
  • 2008 - Director, NSW Systems Biology Initiative
  • 2005 - Professor of Systems Biology, UNSW
  • 1999 - 2005 Vice President Bioinformatics then Head of Proteomics, Proteome Systems Limited

Honours and Awards

  • Awarded a Doctor of Science (D. Sc.) in October 2017 for outstanding contributions to research in proteomics, post-translational modifications and protein interaction networks.
  • ASBMB Beckman Coulter Discovery Science Award 2012 for distinguished contributions to the field of biochemistry and molecular biology.
  • Elected as Council Member of the Human Proteome Organisation (HUPO) 2009-2011, 2011-2014, 2015-2018, 2019-2021.
  • Senior Editor of Proteomics (2004-2013).
  • Member of the Scientific Advisory Boards of the Integrated Materials Design Centre (IMDC, 2015-2017), EMBL Australia Bioinformatics Advisory Committee (2011-2015), Victorian Life Science Computational Initiative (VLSCI) (2009-2015), the Macquarie University Biomolecular Frontiers Centre of Research
    Excellence (2009-), the NHMRC Australian Proteomics Computational Facility (APCF) (2007-2011) and the ARC Centre of Excellence in Bioinformatics (2006-2011). 
  • Contributions to policy in NSW State Government on the NSW Health Genomics Strategy (2018, 2019), the Australian National Genomics Policy framework (2017), New Zealand Government genomics research strategy (2017) and member of the Australian Government's Expert Task Force for Bioinformatics (2003-2005).

Research

My research questions are centred around proteomics.

1. What is the regulatory network of histone methylation?

Histone methylation is a crucial process that affects the compaction and relaxation of chromatin, and thus gene expression in the cell. The sites of histone methylation are understood and the enzymes responsible are known, at least in the model system of yeast. However we know little about how the four 'writer' enzymes and the four 'eraser' enzymes are actually regulated and how they work as a single integrated system. We are exploring:

  • Are the histone methyltransferases and demethylases phosphorylated?
  • If phosphorylation on these enzymes affect their activity and if so, how?
  • What kinases are responsible for this phosphorylation?
  • Do the modification of writer and eraser enzyme control where they act, on chromatin in the genome?

We aim to connect the cell's signalling system with its histone-based system of gene regulation in this project.

The project is supported by ARC Discovery Project grant 2020: The Regulatory Network of Histone Methylating and Demethylating Enzymes.

Recent papers on protein methylation:

  • Characterization of Protein Methyltransferases Rkm1, Rkm4, Efm4, Efm7, Set5 and Hmt1 Reveals Extensive Post-Translational Modification. Winter DL, Hart-Smith G, Wilkins MR. J Mol Biol. 2018 430(1):102-118.
  • Methylation of Elongation Factor 1A: Where, Who, and Why? Hamey JJ, Wilkins MR. Trends Biochem Sci. 2018 43(3):211-223.
  • METTL21B Is a Novel Human Lysine Methyltransferase of Translation Elongation Factor 1A: Discovery by CRISPR/Cas9 Knockout. Hamey JJ, Wienert B, Quinlan KGR, Wilkins MR. Mol Cell Proteomics. 2017 Dec;16(12):2229-2242.

2. How do cells make decisions via protein interaction networks?

Cells use protein post-translational modifications as an 'information management' and 'status management' system. Yet how this information is integrated, to make actual decisions inside networks, is poorly understood. We are exploring:

  • How often are two post-translational modifications found next to each other in the proteome? Especially methylation, phosphorylation and acetylation?
  • For modifications that are nearby, what is their 'logic' - do they block each other? Is one required before the other?
  • Do nearby modifications form small 'decision making modules' in interaction networks?
  • Do nearby modifications change the interaction choice of a protein? Or change its localisation in the cell?

The project is supported by ARC Discovery Project grant 2017: The discovery of decision-making modules in protein interaction networks.

Recent papers on crosstalk of post-translational modifications:

  • Crosstalk of Phosphorylation and Arginine Methylation in Disordered SRGG Repeats of Saccharomyces cerevisiae Fibrillarin and Its Association with Nucleolar Localization. Smith DL, Erce MA, Lai YW, Tomasetig F, Hart-Smith G, Hamey JJ, Wilkins MR. J Mol Biol. 2020 432(2):448-466.
  • Knockout of the Hmt1p Arginine Methyltransferase in Saccharomyces cerevisiae Leads to the Dysregulation of Phosphate-associated Genes and Processes. Chia SZ, Lai YW, Yagoub D, Lev S, Hamey JJ, Pang CNI, Desmarini D, Chen Z, Djordjevic JT, Erce MA, Hart-Smith G, Wilkins MR. Mol Cell Proteomics. 2018 17(12): 2462-2479.

3. How is the protein interactome regulated?

Recent, breakthroughs in crosslinking mass spectrometry (XL-MS) have made it possible to measure thousands of protein-protein interactions in a single sample. These generate a 'protein interactome' which reflects the biological state of a system, at a point in time. Use of heavy isotope-based techniques with XL-MS allows 'protein interactomes' to then be compared. We are exploring: 

  • The optimisation of techniques for XL-MS.
  • The roles of gene expression and protein post-translational modifications in the regulation of the protein interactome.
  • The role of alternate splicing of mRNA and resulting isoforms in regulating the protein interactome.

Recent papers on crosslinking mass spectrometry:

  • Cross-linking Mass Spectrometry Analysis of the Yeast Nucleus Reveals Extensive Protein-Protein Interactions Not Detected by Systematic Two-Hybrid or Affinity Purification-Mass Spectrometry. Bartolec TK, Smith DL, Pang CNI, Xu YD, Hamey JJ, Wilkins MR. Anal Chem. 2020 92(2):1874-1882.
  • Characterization of the Interaction between Arginine Methyltransferase Hmt1 and Its Substrate Npl3: Use of Multiple Cross-Linkers, Mass Spectrometric Approaches, and Software Platforms. Smith DL, Götze M, Bartolec TK, Hart-Smith G, Wilkins MR. Anal Chem. 2018 90(15):9101-9108.

Supervision

I am always interested to have enthusiastic students join the lab!

Previous lab members include 25 honours students (including 5 who won the UNSW University Medal), 12 PhD students and 5 Masters by Research students 

Students in my lab can obtain experience in the following areas:

  • Wet lab - proteomics of protein methylation, regulation of histone and non-histone protein methyltransferases, proteome-scale crosslinking mass spectrometry for network generation, large-scale monitoring of changes in protein-protein interactions via crosslinking mass spectrometry
  • Dry lab - bioinformatics tool development for proteomics, bioinformatics of next-generation sequencing (genome assembly, transcriptomics)

Teaching

I am the Coordinator of BIOC3111 Molecular Biology of Proteins. I teach into 7 other undergraduate courses.

Journal articles
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Smith DL; Erce MA; Lai YW; Tomasetig F; Hart-Smith G; Hamey JJ; Wilkins MR, 2020, 'Crosstalk of Phosphorylation and Arginine Methylation in Disordered SRGG Repeats of Saccharomyces cerevisiae Fibrillarin and Its Association with Nucleolar Localization', Journal of Molecular Biology, vol. 432, pp. 448 - 466, http://dx.doi.org/10.1016/j.jmb.2019.11.006
2020
Kim KW; Allen DW; Briese T; Couper JJ; Barry SC; Colman PG; Cotterill AM; Davis EA; Giles LC; Harrison LC; Harris M; Haynes A; Horton JL; Isaacs SR; Jain K; Lipkin WI; McGorm K; Morahan G; Morbey C; Pang ICN; Papenfuss AT; Penno MAS; Sinnott RO; Soldatos G; Thomson RL; Vuillermin P; Wentworth JM; Wilkins MR; Rawlinson WD; Craig ME, 2020, 'Higher frequency of vertebrate-infecting viruses in the gut of infants born to mothers with type 1 diabetes', Pediatric Diabetes, vol. 21, pp. 271 - 279, http://dx.doi.org/10.1111/pedi.12952
2020
Yang L; Chen Z; Stout ES; Delerue F; Ittner LM; Wilkins MR; Quinlan KGR; Crossley M, 2020, 'Methylation of a CGATA element inhibits binding and regulation by GATA-1', Nature Communications, vol. 11, pp. 2560, http://dx.doi.org/10.1038/s41467-020-16388-1
2020
Bayat A; Deshpande NP; Wilkins MR; Parameswaran S, 2020, 'Fast Short Read De-Novo Assembly Using Overlap-Layout-Consensus Approach', IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 17, pp. 334 - 338, http://dx.doi.org/10.1109/TCBB.2018.2875479
2020
Emery-Corbin SJ; Hamey JJ; Ansell BRE; Balan B; Tichkule S; Stroehlein AJ; Cooper C; McInerney BV; Zadeh SH; Vuong D; Crombie A; Lacey E; Davis MJ; Wilkins MR; Bahlo M; Svärd SG; Gasser RB; Jex AR, 2020, 'Eukaryote-conserved methylarginine is absent in diplomonads and functionally compensated in Giardia.', Mol Biol Evol, http://dx.doi.org/10.1093/molbev/msaa186
2020
Pang CNI; Ballouz S; Weissberger D; Thibaut LM; Hamey JJ; Gillis J; Wilkins MR; Hart-Smith G, 2020, 'Analytical guidelines for co-fractionation mass spectrometry obtained through global profiling of gold standard Saccharomyces cerevisiae protein complexes.', Mol Cell Proteomics, pp. mcp.RA120.002154 - mcp.RA120.002154, http://dx.doi.org/10.1074/mcp.RA120.002154
2020
Separovich RJ; Pang CNI; Wilkins MR, 2020, 'Controlling the Controllers: Regulation of Histone Methylation by Phosphosignalling', Trends in Biochemical Sciences, http://dx.doi.org/10.1016/j.tibs.2020.08.004
2020
Nadkarni MA; Deshpande NP; Wilkins MR; Hunter N, 2020, 'Intra-species variation within Lactobacillus rhamnosus correlates to beneficial or harmful outcomes: lessons from the oral cavity', BMC genomics, vol. 21, pp. 661, http://dx.doi.org/10.1186/s12864-020-07062-3
2020
Adhikari S; Nice EC; Deutsch EW; Lane L; Omenn GS; Pennington SR; Paik Y-K; Overall CM; Corrales FJ; Cristea IM; Van Eyk JE; Uhlén M; Lindskog C; Chan DW; Bairoch A; Waddington JC; Justice JL; LaBaer J; Rodriguez H; He F; Kostrzewa M; Ping P; Gundry RL; Stewart P; Srivastava S; Srivastava S; Nogueira FCS; Domont GB; Vandenbrouck Y; Lam MPY; Wennersten S; Vizcaino JA; Wilkins M; Schwenk JM; Lundberg E; Bandeira N; Marko-Varga G; Weintraub ST; Pineau C; Kusebauch U; Moritz RL; Ahn SB; Palmblad M; Snyder MP; Aebersold R; Baker MS, 2020, 'A high-stringency blueprint of the human proteome.', Nat Commun, vol. 11, pp. 5301, http://dx.doi.org/10.1038/s41467-020-19045-9
2020
Leitner A; Bonvin AMJJ; Borchers CH; Chalkley RJ; Chamot-Rooke J; Combe CW; Cox J; Dong M-Q; Fischer L; Götze M; Gozzo FC; Heck AJR; Hoopmann MR; Huang L; Ishihama Y; Jones AR; Kalisman N; Kohlbacher O; Mechtler K; Moritz RL; Netz E; Novak P; Petrotchenko E; Sali A; Scheltema RA; Schmidt C; Schriemer D; Sinz A; Sobott F; Stengel F; Thalassinos K; Urlaub H; Viner R; Vizcaíno JA; Wilkins MR; Rappsilber J, 2020, 'Toward Increased Reliability, Transparency, and Accessibility in Cross-linking Mass Spectrometry.', Structure, http://dx.doi.org/10.1016/j.str.2020.09.011
2020
Bartolec TK; Smith DL; Pang CNI; Xu YD; Hamey JJ; Wilkins MR, 2020, 'Cross-linking Mass Spectrometry Analysis of the Yeast Nucleus Reveals Extensive Protein-Protein Interactions Not Detected by Systematic Two-Hybrid or Affinity Purification-Mass Spectrometry', Analytical Chemistry, vol. 92, pp. 1874 - 1882, http://dx.doi.org/10.1021/acs.analchem.9b03975
2020
Anande G; Deshpande NP; Mareschal S; Batcha AMN; Hampton HR; Herold T; Lehmann S; Wilkins MR; Wong JWH; Unnikrishnan A; Pimanda JE, 2020, 'RNA Splicing Alterations Induce a Cellular Stress Response Associated with Poor Prognosis in Acute Myeloid Leukemia', Clinical cancer research : an official journal of the American Association for Cancer Research, vol. 26, pp. 3597 - 3607, http://dx.doi.org/10.1158/1078-0432.CCR-20-0184
2020
Vázquez-Campos X; Kinsela A; Bligh M; Payne T; Wilkins M; Waite D, 2019, 'Genomic insights into the Archaea inhabiting an Australian radioactive legacy site', , http://dx.doi.org/10.1101/728089
2019
Corley SM; Troy NM; Bosco A; Wilkins MR, 2019, 'QuantSeq. 3′ Sequencing combined with Salmon provides a fast, reliable approach for high throughput RNA expression analysis', Scientific Reports, vol. 9, pp. 18895, http://dx.doi.org/10.1038/s41598-019-55434-x
2019
Tay AP; Liang A; Hamey JJ; Hart-Smith G; Wilkins MR, 2019, 'MS2-Deisotoper: A Tool for Deisotoping High-Resolution MS/MS Spectra in Normal and Heavy Isotope-Labelled Samples', Proteomics, vol. 19, http://dx.doi.org/10.1002/pmic.201800444
2019
Kim KW; Allen DW; Briese T; Couper JJ; Barry SC; Colman PG; Cotterill AM; Davis EA; Giles LC; Harrison LC; Harris M; Haynes A; Horton JL; Isaacs SR; Jain K; Lipkin WI; Morahan G; Morbey C; Pang ICN; Papenfuss AT; Penno MAS; Sinnott RO; Soldatos G; Thomson RL; Vuillermin PJ; Wentworth JM; Wilkins MR; Rawlinson WD; Craig ME, 2019, 'Distinct gut virome profile of pregnant women with type 1 diabetes in the ENDIA study', Open Forum Infectious Diseases, vol. 6, http://dx.doi.org/10.1093/ofid/ofz025
2019
Paramsothy S; Nielsen S; Kamm MA; Deshpande NP; Faith JJ; Clemente JC; Paramsothy R; Walsh AJ; van den Bogaerde J; Samuel D; Leong RWL; Connor S; Ng W; Lin E; Borody TJ; Wilkins MR; Colombel JF; Mitchell HM; Kaakoush NO, 2019, 'Specific Bacteria and Metabolites Associated With Response to Fecal Microbiota Transplantation in Patients With Ulcerative Colitis', Gastroenterology, vol. 156, pp. 1440 - 1454.e2, http://dx.doi.org/10.1053/j.gastro.2018.12.001
2019
Winter DL; Mastellone J; Kabir KMM; Wilkins MR; Donald WA, 2019, 'Separation of Isobaric Mono- And Dimethylated RGG-Repeat Peptides by Differential Ion Mobility-Mass Spectrometry', Analytical Chemistry, vol. 91, pp. 11827 - 11833, http://dx.doi.org/10.1021/acs.analchem.9b02504
2019
Lai YW; Pang CNI; Campbell LT; Chen SCA; Wilkins MR; Carter DA, 2019, 'Different Pathways Mediate Amphotericin-Lactoferrin Drug Synergy in Cryptococcus and Saccharomyces', Frontiers in Microbiology, vol. 10, pp. 2195, http://dx.doi.org/10.3389/fmicb.2019.02195
2019
Tay AP; Liang A; Wilkins MR; Pang CNI, 2019, 'Visualizing Post-Translational Modifications in Protein Interaction Networks Using PTMOracle', Current Protocols in Bioinformatics, vol. 66, pp. e71, http://dx.doi.org/10.1002/cpbi.71
2019
Uthicke S; Deshpande NP; Liddy M; Patel F; Lamare M; Wilkins MR, 2019, 'Little evidence of adaptation potential to ocean acidification in sea urchins living in “Future Ocean” conditions at a CO2 vent', Ecology and Evolution, vol. 9, pp. 10004 - 10016, http://dx.doi.org/10.1002/ece3.5563
2019
Winter DL; Wilkins MR; Donald WA, 2019, 'Differential Ion Mobility–Mass Spectrometry for Detailed Analysis of the Proteome', Trends in Biotechnology, vol. 37, pp. 198 - 213, http://dx.doi.org/10.1016/j.tibtech.2018.07.018
2019
Bertoldo MJ; Cheung MY; Sia ZK; Agapiou D; Corley SM; Wilkins MR; Richani D; Harrison CA; Gilchrist RB, 2019, 'Non-canonical cyclic AMP SMAD1/5/8 signalling in human granulosa cells', Molecular and Cellular Endocrinology, vol. 490, pp. 37 - 46, http://dx.doi.org/10.1016/j.mce.2019.04.003
2019
Lowe BR; Maxham LA; Hamey JJ; Wilkins MR; Partridge JF, 2019, 'Histone H3 mutations: An updated view of their role in chromatin deregulation and cancer', Cancers, vol. 11, pp. 1 - 24, http://dx.doi.org/10.3390/cancers11050660
2019
Kim KW; Horton JL; Pang CNI; Jain K; Leung P; Isaacs SR; Bull RA; Luciani F; Wilkins MR; Catteau J; Lipkin WI; Rawlinson WD; Briese T; Craig ME, 2019, 'Higher abundance of enterovirus A species in the gut of children with islet autoimmunity', Scientific Reports, vol. 9, pp. 1749, http://dx.doi.org/10.1038/s41598-018-38368-8
2019
Johnson RN; O’Meally D; Chen Z; Etherington GJ; Ho SYW; Nash WJ; Grueber CE; Cheng Y; Whittington CM; Dennison S; Peel E; Haerty W; O’Neill RJ; Colgan D; Russell TL; Alquezar-Planas DE; Attenbrow V; Bragg JG; Brandies PA; Chong AYY; Deakin JE; Di Palma F; Duda Z; Eldridge MDB; Ewart KM; Hogg CJ; Frankham GJ; Georges A; Gillett AK; Govendir M; Greenwood AD; Hayakawa T; Helgen KM; Hobbs M; Holleley CE; Heider TN; Jones EA; King A; Madden D; Graves JAM; Morris KM; Neaves LE; Patel HR; Polkinghorne A; Renfree MB; Robin C; Salinas R; Tsangaras K; Waters PD; Waters SA; Wright B; Wilkins MR; Timms P; Belov K, 2018, 'Adaptation and conservation insights from the koala genome', Nature Genetics, vol. 50, pp. 1102 - 1111, http://dx.doi.org/10.1038/s41588-018-0153-5
2018
Alshekaili J; Chand R; Lee CE; Corley S; Kwong K; Papa I; Fulcher DA; Randall KL; Leiding JW; Ma CS; Wilkins MR; Uzel G; Goodnow CC; Vinuesa CG; Tangye SG; Cook MC, 2018, 'STAT3 regulates cytotoxicity of human CD57+ CD4+ T cells in blood and lymphoid follicles', Scientific Reports, vol. 8, http://dx.doi.org/10.1038/s41598-018-21389-8
2018
Varela C; Schmidt SA; Borneman AR; Pang CNI; Krömerx JO; Khan A; Song X; Hodson MP; Solomon M; Mayr CM; Hines W; Pretorius IS; Baker MS; Roessner U; Mercurio M; Henschke PA; Wilkins MR; Chambers PJ, 2018, 'Systems-based approaches enable identification of gene targets which improve the flavour profile of low-ethanol wine yeast strains', Metabolic Engineering, vol. 49, pp. 178 - 191, http://dx.doi.org/10.1016/j.ymben.2018.08.006
2018
Winter DL; Hart-Smith G; Wilkins MR, 2018, 'Characterization of Protein Methyltransferases Rkm1, Rkm4, Efm4, Efm7, Set5 and Hmt1 Reveals Extensive Post-Translational Modification', Journal of Molecular Biology, vol. 430, pp. 102 - 118, http://dx.doi.org/10.1016/j.jmb.2017.11.009
2018
You J; Corley SM; Wen L; Hodge C; Höllhumer R; Madigan MC; Wilkins MR; Sutton G, 2018, 'RNA-Seq analysis and comparison of corneal epithelium in keratoconus and myopia patients', Scientific Reports, vol. 8, http://dx.doi.org/10.1038/s41598-017-18480-x
2018
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, vol. 17, pp. 359 - 373, http://dx.doi.org/10.1021/acs.jproteome.7b00601
2018
Edwards RJ; Tuipulotu DE; Amos TG; O'Meally D; Richardson MF; Russell TL; Vallinoto M; Carneiro M; Ferrand N; Wilkins MR; Sequeira F; Rollins LA; Holmes EC; Shine R; White PA, 2018, 'Draft genome assembly of the invasive cane toad, Rhinella marina', GigaScience, vol. 7, http://dx.doi.org/10.1093/gigascience/giy095
2018
Chia SZ; Lai YW; Yagoub D; Lev S; Hamey JJ; Ignatius Pang CN; Desmarini D; Chen Z; Djordjevic JT; Erce MA; Hart-Smith G; Wilkins MR, 2018, 'Knockout of the Hmt1p arginine methyltransferase in saccharomyces cerevisiae leads to the dysregulation of phosphate-associated genes and processes', Molecular and Cellular Proteomics, vol. 17, pp. 2462 - 2479, http://dx.doi.org/10.1074/mcp.RA117.000214
2018
Hamey JJ; Wilkins MR, 2018, 'Methylation of Elongation Factor 1A: Where, Who, and Why?', Trends in Biochemical Sciences, vol. 43, pp. 211 - 223, http://dx.doi.org/10.1016/j.tibs.2018.01.004
2018
Smith DL; Götze M; Bartolec TK; Hart-Smith G; Wilkins MR, 2018, 'Characterization of the Interaction between Arginine Methyltransferase Hmt1 and Its Substrate Npl3: Use of Multiple Cross-Linkers, Mass Spectrometric Approaches, and Software Platforms', Analytical Chemistry, vol. 90, pp. 9101 - 9108, http://dx.doi.org/10.1021/acs.analchem.8b01525
2018
Hamey JJ; Separovich RJ; Wilkins MR, 2018, 'MT-MAMS: Protein Methyltransferase Motif Analysis by Mass Spectrometry', Journal of Proteome Research, vol. 17, pp. 3485 - 3491, http://dx.doi.org/10.1021/acs.jproteome.8b00396
2018
Pang I; Goel A; Wilkins MR, 2018, 'Investigating the network basis of negative genetic interactions in Saccharomyces cerevisiae with integrated biological networks and triplet motif analysis', Journal of Proteome Research, vol. 17, pp. 1014 - 1030, http://dx.doi.org/10.1021/acs.jproteome.7b00649
2018
Corley S; Mendoza-Reinoso V; Giles N; Singer ES; Common JE; Wilkins M; Beverdam A, 2018, 'Plau and Tgfbr3 are YAP-regulated genes that promote keratinocyte proliferation', Cell Death and Disease, vol. 9, pp. 1106, http://dx.doi.org/10.1038/s41419-018-1141-5
2018
Deshpande NP; Riordan SM; Castaño-Rodríguez N; Wilkins MR; Kaakoush NO, 2018, 'Signatures within the esophageal microbiome are associated with host genetics, age, and disease', Microbiome, vol. 6, pp. 227, http://dx.doi.org/10.1186/s40168-018-0611-4
2018
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
2017
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, vol. 20, pp. 572 - 585, http://dx.doi.org/10.1016/j.celrep.2017.06.067
2017
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, vol. 16, pp. 2229 - 2242, http://dx.doi.org/10.1074/mcp.M116.066308
2017
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, vol. 16, pp. 1988 - 2003, http://dx.doi.org/10.1021/acs.jproteome.6b01052
2017
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
2017
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, vol. 18, http://dx.doi.org/10.1186/s12864-017-3797-0
2017
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, vol. 7, http://dx.doi.org/10.1038/s41598-017-16171-1
2017
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, vol. 7, pp. 40232 - 40232, http://dx.doi.org/10.1038/srep40232
2017
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, vol. 93, http://dx.doi.org/10.1093/femsec/fix147
2017
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
2017
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
2016
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
2016
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
2016
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
2016
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
2016
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
2016
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, vol. 16, pp. 465 - 476, http://dx.doi.org/10.1002/pmic.201400564
2016
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, vol. 48, pp. 388 - 394, http://dx.doi.org/10.1016/j.ijantimicag.2016.06.012
2016
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
2016
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
2016
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, vol. 18, pp. 2810 - 2824, http://dx.doi.org/10.1111/1462-2920.13229
2016
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
2016
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, vol. 14, pp. 3541 - 3554, http://dx.doi.org/10.1021/pr5011394
2015
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, vol. 47, pp. 588 - 599, http://dx.doi.org/10.1152/physiolgenomics.00128.2014
2015
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
2015
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
2015
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, pp. 14027 - 14027, http://dx.doi.org/10.1038/nplants.2014.27
2015
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
2015
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
2015
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
2015
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
2015
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, 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
2015
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
2015
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, vol. 15, pp. 2166 - 2176, http://dx.doi.org/10.1002/pmic.201400521
2015
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
2014
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
2014
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, vol. 15, http://dx.doi.org/10.1186/1471-2164-15-1153
2014
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
2014
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
2014
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
2014
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, vol. 5, pp. 52 - 63, http://dx.doi.org/10.1080/21501203.2014.919967
2014
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
2014
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, vol. 13, pp. 1744 - 1756, http://dx.doi.org/10.1021/pr401251k
2014
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
2014
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
2014
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, vol. 443, pp. 543 - 548, http://dx.doi.org/10.1016/j.bbrc.2013.12.009
2014
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, vol. 13, pp. 84 - 98, http://dx.doi.org/10.1021/pr400820p
2014
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, pp. 1 - 17, http://dx.doi.org/10.1186/1471-2164-15-1153
2014
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
2014
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, vol. 15, http://dx.doi.org/10.1186/1471-2164-15-786
2014
Low JKK; Hart-Smith G; Erce MA; Wilkins MR, 2013, 'Analysis of the proteome of Saccharomyces cerevisiae for methylarginine', Journal of Proteome Research, vol. 12, pp. 3884 - 3899, http://dx.doi.org/10.1021/pr400556c
2013
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, vol. 13, pp. 1059 - 1064, http://dx.doi.org/10.1002/pmic.201200477
2013
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
2013
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, vol. 12, pp. 3184 - 3198, http://dx.doi.org/10.1074/mcp.M113.031500
2013
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, vol. 14, http://dx.doi.org/10.1186/1471-2164-14-585
2013
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, vol. 33, pp. 2976 - 2987, http://dx.doi.org/10.1128/MCB.00074-13
2013
Deshpande NP; Wong YK; Manefield M; Wilkins MR; Lee M, 2013, 'Genome Sequence of Dehalobacter UNSWDHB, a Chloroform-Dechlorinating Bacterium.', Genome Announc, vol. 1, http://dx.doi.org/10.1128/genomeA.00720-13
2013
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, vol. 6, http://dx.doi.org/10.1186/1756-0500-6-430
2013
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, vol. 13, pp. 3393 - 3405, http://dx.doi.org/10.1002/pmic.201200570
2013
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, vol. 1, http://dx.doi.org/10.1128/genomeA.00073-12
2013
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, vol. 541, pp. 263 - 268, http://dx.doi.org/10.1016/j.neulet.2013.02.034
2013
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, vol. 26, pp. 708 - 722, http://dx.doi.org/10.1111/pcmr.12126
2013
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
2013
Low JKK; Wilkins MR, 2012, 'Protein arginine methylation in Saccharomyces cerevisiae', FEBS Journal, vol. 279, pp. 4423 - 4443, http://dx.doi.org/10.1111/febs.12039
2012
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, vol. 60, pp. 265 - 272, http://dx.doi.org/10.1080/00480169.2012.683377
2012
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, vol. 12, pp. 960 - 972, http://dx.doi.org/10.1002/pmic.201100570
2012
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, vol. 23, pp. 1376 - 1389, http://dx.doi.org/10.1007/s13361-012-0417-8
2012
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, vol. 32, pp. 3281 - 3292, http://dx.doi.org/10.1128/MCB.00173-12
2012
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, vol. 7, pp. August - Article numbere42835, http://dx.doi.org/10.1371/journal.pone.0042835
2012
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, vol. 11, pp. 5204 - 5220, http://dx.doi.org/10.1021/pr300405y
2012
Fung DCY; Li SS; Goel A; Hong S-H; Wilkins MR, 2012, 'Visualization of the interactome: what are we looking at?', Proteomics, vol. 12, pp. 1669 - 1686, http://dx.doi.org/10.1002/pmic.201100454
2012
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, vol. 61, pp. 1500 - 1508, http://dx.doi.org/10.2337/db11-0264
2012
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, vol. 205, pp. 1305 - 1310, http://dx.doi.org/10.1093/infdis/jis186
2012
Goel A; Wilkins MR, 2012, 'Dynamic hubs show competitive and static hubs non-competitive regulation of their interaction partners.', PLoS One, vol. 7, pp. e48209, http://dx.doi.org/10.1371/journal.pone.0048209
2012
Erce MA; Pang CN; Hart-Smith GO; Wilkins MR, 2012, 'The methylproteome and the intracellular methylation network.', Proteomics, vol. 12, pp. 564 - 586, http://dx.doi.org/10.1002/pmic.201100397
2012
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, vol. 11, pp. 4117 - 4121, http://dx.doi.org/10.1002/pmic.201100302
2011
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, vol. 3, pp. 15, http://dx.doi.org/10.1186/1757-4749-3-15
2011
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, vol. 6, pp. e22170, http://dx.doi.org/10.1371/journal.pone/0022170
2011
Li SS; Xu K; Wilkins MR, 2011, 'Visualization and analysis of the complexome network of Saccharomyces cerevisiae', Journal of Proteome Research, vol. 10, pp. 4744 - 4756, http://dx.doi.org/10.1021/pr200548c
2011
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, vol. 6, pp. e29045, http://dx.doi.org/10.1371/journal.pone.0029045
2011
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, vol. 32, pp. 1819 - 1823, http://dx.doi.org/10.1002/elps.201100122
2011
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, vol. 6, pp. e16266, http://dx.doi.org/10.1371/journal.pone.0016266
2011
Goel A; Li SS; Wilkins MR, 2011, 'Four-dimensional visualisation and analysis of protein-protein interaction networks', Proteomics, vol. 11, pp. 2672 - 2682, http://dx.doi.org/10.1002/pmic.201000546
2011
Erce MA; Low J; Wilkins MR, 2010, 'Analysis of the RNA degradosome complex in Vibrio angustum S14', FEBS Journal, vol. 277, pp. 5161 - 5173, http://dx.doi.org/10.1111/j.1742-4658.2010.07934.x
2010
Wilkins MR, 2010, 'Identification of arginine- and lysine-methylation in the proteome of Saccharomyces cerevisiae and its functional implications', BMC Genomics, vol. 11, pp. 92, http://dx.doi.org/10.1186/1471-2164-11-92
2010
Wilkins MR, 2010, 'GlycoViewer: a tool for visual summary and comparative analysis of the glycome.', Nucleic Acids Research, vol. 38, pp. 667 - 670, http://dx.doi.org/10.1093/nar/gkq446
2010
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, vol. 10, pp. 2327 - 2723, http://dx.doi.org/10.1002/pmic.201000046
2010
Kaakoush NO; Man SM; Lamb S; Raftery MJ; Wilkins MR; Kovach Z; Mitchell HM, 2010, 'The secretome of Campylobacter concisus.', FEBS Journal, vol. 277, pp. 1606 - 1617, http://dx.doi.org/10.1111/j.1742-4658.2010.07587.x
2010
Okoli AS; Wilkins MR; Raftery MJ; Mendz GL, 2010, 'Response of Helicobacter hepaticus to bovine bile', Journal of Proteome Research, vol. 9, pp. 1374 - 1384, http://dx.doi.org/10.1021/pr900915f
2010
Wilkins MR, 2010, 'Proteins deleterious on overexpression are associated with high intrinsic disorder, specific interaction domains, and low abundance.', Journal of Proteome Research, vol. 9, pp. 1218 - 1225, http://dx.doi.org/10.1021/pr900693e
2010
Widjaja YY; Pang CN; Wilkins MR; Lambert TD; Li SS, 2009, 'The Interactorium: visualising proteins, complexes and interaction networks in a virtual 3-D cell.', Proteomics, vol. 9, pp. 5309 - 5315, http://dx.doi.org/10.1002/pmic.200900260
2009
Wilkins M, 2009, 'A celebration of protein-protein interactions', Proteomics, vol. 9, pp. 5207 - 5208, http://dx.doi.org/10.1002/pmic.200990092
2009
Wilkins MR, 2009, 'Hares and tortoises: The high- versus low-throughput proteomic race', Electrophoresis, vol. 30, pp. S150 - S155, http://dx.doi.org/10.1002/elps.200900175
2009
Wilkins MR, 2009, 'Proteomic data mining', Expert Review of Proteomics, vol. 6, pp. 599 - 603, http://dx.doi.org/10.1586/epr.09.81
2009
Huang K; Filarsky M; Padula M; Raftery MJ; Herbert B; Wilkins MR, 2009, 'Micropreparative fractionation of the complexome by blue native continuous elution electrophoresis', Proteomics, vol. 9, pp. 2494 - 2502, http://dx.doi.org/10.1002/pmic.200800525
2009
Little P; Williams RA; Wilkins MR, 2009, 'Inter-individual variation in expression: a missing link in biomarker biology?', Trends in Biotechnology, vol. 27, pp. 5 - 10, http://dx.doi.org/10.1016/j.tibtech.2008.10.002
2009
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, vol. 1794, pp. 1107 - 1114, http://dx.doi.org/10.1016/j.bbapap.2009.03.016
2009
Ho E; Webber R; Wilkins MR, 2008, 'Interactive three-dimensional visualization and contextual analysis of protein interaction networks', Journal of Proteome Research, vol. 7, pp. 104 - 112, http://dx.doi.org/10.1021/pr070274m
2008
Krycer JR; Pang CN; Wilkins MR, 2008, 'High throughput protein-protein interaction data: clues for the architecture of protein complexes', Proteome Science, vol. 6, pp. 32 - 32, http://dx.doi.org/10.1186/1477-5956-6-32
2008
Pang CN; Krycer JR; Lek A; Wilkins MR, 2008, 'Are protein complexes made of cores, modules and attachments?', Proteomics, vol. 8, pp. 425 - 434, http://dx.doi.org/10.1002/pmic.200700801
2008
Deshpande N; Wilkins MR; Packer N; Nevalainen H, 2008, 'Protein glycosylation pathways in filamentous fungi', Glycobiology, vol. 18, pp. 626 - 637, http://dx.doi.org/10.1093/glycob/cwn044
2008
Wilkins MR; Kummerfeld SK, 2008, 'Sticking together? Falling apart? Exploring the dynamics of the interactome', Trends in Biochemical Sciences, vol. 33, pp. 195 - 200, http://dx.doi.org/10.1016/j.tibs.2008.03.001
2008
Wilkins MR; Arthur J; Junius F; Harrison M; Traini M; Bizannes P; Doggett P; McDonald W, 2008, 'Information management for proteomics: a perspective', Expert Review of Proteomics, vol. 5, pp. 663 - 678, http://dx.doi.org/10.1586/14789450.5.5.663
2008
Couttas TA; Raftery MJ; Bernardini G; Wilkins MR, 2008, 'Immonium ion scanning for the discovery of post-translational modifications and its application to histones', Journal of Proteome Research, vol. 7, pp. 2632 - 2641, http://dx.doi.org/10.1021/pr700644t
2008
Okoli AS; Wilkins MR; Raftery M; Mendz GL, 2007, 'Comparative proteomics study of effects of Helicobacter bilis on Huh7, Huh7 NNeo3-5B(RG), and cured-Huh7 NNeo3-SB(RG) cell lines', Helicobacter, vol. 12, pp. 382 - 383, http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000249017800026&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a
2007
Hsu W; Pang CN; Sheetal J; Wilkins MR, 2007, 'Protein-protein interactions and disease: Use of S-cerevisiae as a model system', Biochimica et Biophysica ACTA - Proteins and Proteomics, vol. 1774, pp. 838 - 847, http://dx.doi.org/10.1016/j.bbapap.2007.04.014
2007
Pang CN; Hayen A; Wilkins MR, 2007, 'Surface accessibility of protein post-translational modifications', Journal of Proteome Research, vol. 6, pp. 1833 - 1845, http://dx.doi.org/10.1021/pr060674u
2007
Taylor C; Paton N; Lilley K; Binz P; Julian R; Jones AR; Zhu W; Apweiler R; Aebersold R; Deutsch E; Dunn MJ; Heck A; Leitner A; Macht M; Mann M; Martens L; Neubert T; Patterson S; Ping P; Seymour S; Souda P; Tsugita A; Vandekerckhove J; Vondriska T; Whitelegge J; Wilkins MR; Xenarios I; Yates J; Hermjakob H, 2007, 'The minimum information about a proteomics experiment (MIAPE)', Nature Biotechnology, vol. 25, pp. 887 - 893, http://dx.doi.org/10.1038/nbt1329
2007
Wilkins MR, 2007, 'Lower-order versus higher-order proteomics: Time to move up?', Journal of Proteome Research, vol. 6, pp. 2403, http://dx.doi.org/10.1021/pr070757q
2007
Ho E; Hayen A; Wilkins MR, 2006, 'Characterisation of organellar proteomes: A guide to subcellular proteomic fractionation and analysis', Proteomics, vol. 6, pp. 5746 - 5757, http://dx.doi.org/10.1002/pmic.200600241
2006
Wilkins MR, 2006, 'How proteomics can assist in the detection and avoidance of adverse drug reactions', Transfusion Medicine and Hemotherapy, vol. 33, pp. 97 - 105, http://dx.doi.org/10.1159/000090205
2006
Wilkins MR; Appel R; Van Eyk J; Chung M; Gorg A; Hecker M; Huber L; Langen H; Link A; Paik Y; Patterson S; Pennington S; Rabilloud T; Simpson RJ; Weiss WA; Dunn MJ, 2006, 'Guidelines for the next 10 years of proteomics', Proteomics, vol. 6, pp. 4 - 8, http://dx.doi.org/10.1002/pmic.200500856
2006
Hunt S; Thomas MR; Sebastian LT; Pedersen SK; Harcourt RL; Sloane AJ; Wilkins MR, 2005, 'Optimal replication and the importance of experimental design for gel-based quantitative proteomics', Journal of Proteome Research, vol. 4, pp. 663, http://dx.doi.org/10.1021/pr049758y
2005
Arthur J; Wilkins MR, 2004, 'Using proteomics to mine genome sequences', Journal of Proteome Research, vol. 3, pp. 393 - 402, http://dx.doi.org/10.1021/pr034056e
2004
Breen EJ; Holstein WL; Hopwood FG; Smith PE; Thomas ML; Wilkins MR, 2003, 'Automated peak harvesting of MALDI-MS spectra for high throughput proteomics', Spectroscopy-An International Journal, vol. 17, pp. 579 - 596
2003
Pedersen SK; Harry JL; Sebastian LT; Baker J; Traini M; McCarthy JT; Manoharan A; Wilkins MR; Gooley AA; Righetti PG; Packer N; Williams KL; Herbert B, 2003, 'Unseen proteome: mining below the tip of the iceberg to find low abundance and membrane proteins', Journal of Proteome Research, vol. 2, pp. 303 - 311, http://dx.doi.org/10.1021/pr025588i
2003
Cooper CA; Joshi HJ; Harrison M; Wilkins MR; Packer N, 2003, 'GlycosuiteDB : a curated relational database of glycoprotein glycan structures and their biological sources', Nucleic Acids Research, vol. 31, pp. 511 - 513, http://dx.doi.org/10.1093/nar/gkg099
2003
Van Dyk DD; Misztal DD; Wilkins MR; Poljak A; Mackintosh JA; Varnai JC; Teber E; Walsh B; Gray PP, 2003, 'Identification of cellular changes associated with increased production of human growth hormone in a recombinant Chinese hamster ovary cell line.', Proteomics, vol. 3, pp. 147 - 156, http://dx.doi.org/10.1002/pmic.200390023
2003
Cooper CA; Harrison MJ; Webster JM; Wilkins MR; Packer NH, 2002, 'Data standardisation in GlycoSuiteDB.', Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, pp. 297 - 309
2002
Lisacek FC; Traini MD; Sexton D; Harry JL; Wilkins MR, 2001, 'Strategy for protein isoform identification from expressed sequence tags and its application to peptide mass fingerprinting', Proteomics, vol. 1, pp. 186 - 193, http://dx.doi.org/10.1002/1615-9861(200102)1:2<186::AID-PROT186>3.0.CO;2-G
2001
Cooper CA; Harrison MJ; Wilkins MR; Packer NH, 2001, 'GlycoSuiteDB: A new curated relational database of glycoprotein glycan structures and their biological sources', Nucleic Acids Research, vol. 29, pp. 332 - 335, http://dx.doi.org/10.1093/nar/29.1.332
2001
Wilkins M, 2000, 'Proteomic paradigms for perceiving purpose', Trends in Biotechnology, vol. 18, pp. 91 - 92, http://dx.doi.org/10.1016/S0167-7799(99)01403-1
2000
Kojima T; Andersen E; Sanchez JC; Wilkins MR; Hochstrasser DF; Pralong WF; Cimasoni G, 2000, 'Human gingival crevicular fluid contains mrp8 (s100a8) and mrp 14 (s100a9), two calcium-binding proteins of the s100 family', Journal of Dental Research, vol. 79, pp. 740 - 747, http://dx.doi.org/10.1177/00220345000790020701
2000
Emslie KR; Molloy MP; Barardi CRM; Jardine D; Wilkins MR; Bellamy AR; Williams KL, 2000, 'Serotype classification and characterisation of the rotavirus SA11 VP6 protein using mass spectrometry and two-dimensional gel electrophoresis', Functional and Integrative Genomics, vol. 1, pp. 12 - 24, http://dx.doi.org/10.1007/s101420000002
2000
Breen EJ; Hopwood FG; Williams KL; Wilkins MR, 2000, 'Automatic Poisson peak harvesting for high throughput protein identification', Electrophoresis, vol. 21, pp. 2243 - 2251, http://dx.doi.org/10.1002/1522-2683(20000601)21:11<2243::AID-ELPS2243>3.0.CO;2-K
2000
Harry JL; Wilkins MR; Herbert BR; Packer NH; Gooley AA; Williams KL, 2000, 'Proteomics: Capacity versus utility', Electrophoresis, vol. 21, pp. 1071 - 1081, http://dx.doi.org/10.1002/(SICI)1522-2683(20000401)21:6<1071::AID-ELPS1071>3.0.CO;2-M
2000
Wilkins MR; Gasteiger E; Gooley AA; Herbert BR; Molloy MP; Binz PA; Ou K; Sanchez JC; Bairoch A; Williams KL; Hochstrasser DF, 1999, 'High-throughput mass spectrometric discovery of protein post-translational modifications', Journal of Molecular Biology, vol. 289, pp. 645 - 657, http://dx.doi.org/10.1006/jmbi.1999.2794
1999
Wilkins MR; Yan JX; Gooley AA, 1999, '2-DE spot amino acid analysis with 9-fluorenylmethyl chloroformate.', Methods in molecular biology (Clifton, N.J.), vol. 112, pp. 445 - 460
1999
Cooper CA; Wilkins MR; Williams KL; Packer NH, 1999, 'BOLD - A biological O-linked glycan database', Electrophoresis, vol. 20, pp. 3589 - 3598, http://dx.doi.org/10.1002/(SICI)1522-2683(19991201)20:18<3589::AID-ELPS3589>3.0.CO;2-M
1999
Ou K; Wilkins MR; Gooley AA; Tonella L; Sanchez JC; Tyler M; Walsh BJ; Pasquali C; Hochstrasser DF; Williams KL, 1999, 'Rapid identification and quantitation of Escherichia coli proteins separated by 2-D electrophoresis', American Biotechnology Laboratory, vol. 17, pp. 16 - 20
1999
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, 1999, 'A molecular scanner to automate proteomic research and to display proteome images', Analytical Chemistry, vol. 71, pp. 4981 - 4988, http://dx.doi.org/10.1021/ac990449e
1999
Wilkins MR; Gasteiger E; Bairoch A; Sanchez JC; Williams KL; Appel RD; Hochstrasser DF, 1999, 'Protein identification and analysis tools in the ExPASy server.', Methods in molecular biology (Clifton, N.J.), vol. 112, pp. 531 - 552
1999
Wilkins MR; Gasteiger E; Sanchez JC; Bairoch A; Hochstrasser DF, 1998, 'Two-dimensional gel electrophoresis for proteome projects: The effects of protein hydrophobicity and copy number', Electrophoresis, vol. 19, pp. 1501 - 1505, http://dx.doi.org/10.1002/elps.1150190847
1998
Tonella L; Walsh BJ; Sanchez JC; Ou K; Wilkins MR; Tyler M; Frutiger S; Gooley AA; Pescaru I; Appel RD; Yan JX; Bairoch A; Hoogland C; Morch FS; Hughes GJ; Williams KL; Hochstrasser DF, 1998, ''98 Escherichia coli SWISS-2DPAGE database update', Electrophoresis, vol. 19, pp. 1960 - 1971, http://dx.doi.org/10.1002/elps.1150191114
1998
Traini M; Gooley AA; Ou K; Wilkins MR; Tonella L; Sanchez JC; Hochstrasser DF; Williams KL, 1998, 'Towards an automated approach for protein identification in proteome projects', Electrophoresis, vol. 19, pp. 1941 - 1949, http://dx.doi.org/10.1002/elps.1150191112
1998
Wilkins MR; Gasteiger E; Wheeler CH; Lindskog I; Sanchez JC; Bairoch A; Appel RD; Dunn MJ; Hochstrasser DF, 1998, 'Multiple parameter cross-species protein identification using MultiIdent - A world-wide web accessible tool', Electrophoresis, vol. 19, pp. 3199 - 3206, http://dx.doi.org/10.1002/elps.1150191824
1998
Wilkins MR; Gasteiger E; Tonella L; Ou K; Tyler M; Sanchez JC; Gooley AA; Walsh BJ; Bairoch A; Appel RD; Williams KL; Hochstrasser DF, 1998, 'Protein identification with N and C-terminal sequence tags in proteome projects', Journal of Molecular Biology, vol. 278, pp. 599 - 608, http://dx.doi.org/10.1006/jmbi.1998.1726
1998
Sarto C; Marocchi A; Sanchez JC; Giannone D; Frutiger S; Golaz O; Wilkins MR; Doro G; Cappellano F; Hughes G; Hochstrasser DF; Mocarelli P, 1997, 'Renal cell carcinoma and normal kidney protein expression', Electrophoresis, vol. 18, pp. 599 - 604, http://dx.doi.org/10.1002/elps.1150180343
1997
Yan JX; Tonella L; Sanchez JC; Wilkins MR; Packer NH; Gooley AA; Hochstrasser DF; Williams KL, 1997, 'The Dictyostelium discoideum proteome - The SWISS-2DPAGE database of the multicellular aggregate (slug)', Electrophoresis, vol. 18, pp. 491 - 497, http://dx.doi.org/10.1002/elps.1150180325
1997
Sanchez JC; Schaller D; Ravier F; Golaz O; Jaccoud S; Belet M; Wilkins MR; James R; Deshusses J; Hochstrasser D, 1997, 'Translationally condrolled tumor protein: A protein identified in several nontumoral cells including erythrocytes', Electrophoresis, vol. 18, pp. 150 - 155, http://dx.doi.org/10.1002/elps.1150180127
1997
Sanchez JC; Wirth P; Jaccoud S; Appel RD; Sarto C; Wilkins MR; Hochstrasser DF, 1997, 'Simultaneous analysis of cyclin and oncogene expression using multiple monoclonal antibody immunoblots', Electrophoresis, vol. 18, pp. 638 - 641, http://dx.doi.org/10.1002/elps.1150180349
1997
Hochstrasser DF; Frutiger S; Wilkins MR; Hughes G; Sanchez JC, 1997, 'Elevation of apolipoprotein E in the CSF of cattle affected by BSE', FEBS Letters, vol. 416, pp. 161 - 163, http://dx.doi.org/10.1016/S0014-5793(97)01191-5
1997
Sanchez JC; Rouge V; Pisteur M; Ravier F; Tonella L; Moosmayer M; Wilkins MR; Hochstrasser DF, 1997, 'Improved and simplified in-gel sample application using reswelling of dry immobilized pH gradients', Electrophoresis, vol. 18, pp. 324 - 327, http://dx.doi.org/10.1002/elps.1150180305
1997
Yan JX; Packer NH; Tonella L; Ou K; Wilkins MR; Sanchez JC; Gooley AA; Hochstrasser DF; Williams KL, 1997, 'High sample throughput phosphoamino acid analysis of proteins separated by one- and two-dimensional gel electrophoresis', Journal of Chromatography A, vol. 764, pp. 201 - 210, http://dx.doi.org/10.1016/S0021-9673(96)00931-4
1997
Pennington SR; Wilkins MR; Hochstrasser DF; Dunn MJ, 1997, 'Proteome analysis: From protein characterization to biological function', Trends in Cell Biology, vol. 7, pp. 168 - 173, http://dx.doi.org/10.1016/S0962-8924(97)01033-7
1997
Wilkins MR; Williams KL, 1997, 'Cross-species protein identification using amino acid composition, peptide mass fingerprinting, isoelectric point and molecular mass: A theoretical evaluation', Journal of Theoretical Biology, vol. 186, pp. 7 - 15, http://dx.doi.org/10.1006/jtbi.1996.0346
1997
Liberatori S; Bini L; De Felice C; Magi B; Marzocchi B; Raggiaschi R; Frutiger S; Sanchez JC; Wilkins MR; Hughes G; Hochstrasser DF; Bracci R; Pallini V, 1997, 'A two-dimensional protein map of human amniotic fluid at 17 weeks' gestation', Electrophoresis, vol. 18, pp. 2816 - 2822, http://dx.doi.org/10.1002/elps.1150181517
1997
Gooley AA; Ou K; Russell J; Wilkins MR; Sanchez JC; Hochstrasser DF; Williams KL, 1997, 'A role for Edman degradation in proteome studies', Electrophoresis, vol. 18, pp. 1068 - 1072, http://dx.doi.org/10.1002/elps.1150180707
1997
Peitsch MC; Wilkins MR; Tonella L; Sanchez JC; Appel RD; Hochstrasser DF, 1997, 'Large-scale protein modelling and integration with the SWISS-PROT and SWISS-2DPAGE databases: The example of Escherichia coli', Electrophoresis, vol. 18, pp. 498 - 501, http://dx.doi.org/10.1002/elps.1150180326
1997
Wilkins MR; Lindskog I; Gasteiger E; Bairoch A; Sanchez JC; Hochstrasser DF; Appel RD, 1997, 'Detailed peptide characterization using PEPTIDEMASS - A World-Wide-Web-accessible tool', Electrophoresis, vol. 18, pp. 403 - 408, http://dx.doi.org/10.1002/elps.1150180314
1997
Wilkins MR; Sanchez JC; Williams KL; Hochstrasser DF, 1996, 'Current challenges and future applications for protein maps and post-translational vector maps in proteome projects', Electrophoresis, vol. 17, pp. 830 - 838, http://dx.doi.org/10.1002/elps.1150170504
1996
Wilkins MR; Gasteiger E; Sanchez JC; Appel RD; Hochstrasser DF, 1996, 'Protein identification with sequence tags', Current Biology, vol. 6, pp. 1543 - 1544, http://dx.doi.org/10.1016/S0960-9822(02)70764-1
1996
Yan JX; Wilkins MR; Ou K; Gooley AA; Williams KL; Sanchez JC; Golaz O; Pasquali C; Hochstrasser DF, 1996, 'Large-scale amino-acid analysis for proteome studies', Journal of Chromatography A, vol. 736, pp. 291 - 302, http://dx.doi.org/10.1016/0021-9673(95)01285-0
1996
Packer NH; Wilkins MR; Golaz O; Lawson MA; Gooley AA; Hochstrasser DF; Redmond JW; Williams KL, 1996, 'Characterization of human plasma glycoproteins separated by two-dimensional gel electrophoresis', Bio/Technology, vol. 14, pp. 66 - 70, http://dx.doi.org/10.1038/nbt0196-66
1996
Wheeler CH; Berry SL; Wilkins MR; Corbett JM; Ou K; Gooley AA; Humphery-Smith I; Williams KL; Dunn MJ, 1996, 'Characterisation of proteins from two-dimensional electrophoresis gels by matrix-assisted laser desorption mass spectrometry and amino acid compositional analysis', Electrophoresis, vol. 17, pp. 580 - 587, http://dx.doi.org/10.1002/elps.1150170329
1996
Pasquali C; Frutiger S; Wilkins MR; Hughes GJ; Appel RD; Bairoch A; Schaller D; Sanchez JC; Hochstrasser DF, 1996, 'Two-dimensional gel electrophoresis of Escherichia coli homogenates: The Escherichia coli SWISS-2DPAGE database', Electrophoresis, vol. 17, pp. 547 - 555, http://dx.doi.org/10.1002/elps.1150170325
1996
Wilkins MR; Sanchez JC; Gooley AA; Appel RD; Humphery-Smith I; Hochstrasser DF; Williams KL, 1996, 'Progress with proteome projects: Why all proteins expressed by a genome should be identified and how to do it', Biotechnology and Genetic Engineering Reviews, vol. 13, pp. 19 - 50, http://dx.doi.org/10.1080/02648725.1996.10647923
1996
Wilkins MR; Pasquali C; Appel RD; Ou K; Golaz O; Sanchez JC; Yan JX; Gooley AA; Hughes G; Humphery-Smith I; Williams KL; Hochstrasser DF, 1996, 'From proteins to proteomes: Large scale protein identification by two-dimensional electrophoresis and amino acid analysis', Bio/Technology, vol. 14, pp. 61 - 65, http://dx.doi.org/10.1038/nbt0196-61
1996
Wilkins MR; Hochstrasser DF; Sanchez JC; Bairoch A; Appel RD, 1996, 'Integrating two-dimensional gel databases using the Melanie II software', Trends in Biochemical Sciences, vol. 21, pp. 496 - 497, http://dx.doi.org/10.1016/S0968-0004(96)30043-1
1996
Ou K; Wilkins MR; Yan JX; Gooley AA; Fung Y; Sheumack D; Williams KL, 1996, 'Improved high-performance liquid chromatography of amino acids derivatised with 9-fluorenylmethyl chloroformate', Journal of Chromatography A, vol. 723, pp. 219 - 225, http://dx.doi.org/10.1016/0021-9673(95)00879-9
1996
Golaz O; Wilkins MR; Sanchez JC; Appel RD; Hochstrasser DF; Williams KL, 1996, 'Identification of proteins by their amino acid composition: An evaluation of the method', Electrophoresis, vol. 17, pp. 573 - 579, http://dx.doi.org/10.1002/elps.1150170328
1996
Wilkins MR; Ou K; Appel RD; Sanchez JC; Yan JX; Golaz O; Farnsworth V; Cartier P; Hochstrasser DF; Williams KL; Gooley AA, 1996, 'Rapid protein identification using N-terminal "Sequence tag" and amino acid analysis', Biochemical and Biophysical Research Communications, vol. 221, pp. 609 - 613, http://dx.doi.org/10.1006/bbrc.1996.0643
1996
Zhou-Chou T; Wilkins MR; Vabdy PH; Gooley AA; Williams KL, 1995, 'Glycoprotein complexes interacting with cellulose in the "cell print" zones of the Dictyostelium discoideum extracellular matrix', Developmental Biology, vol. 168, pp. 332 - 341, http://dx.doi.org/10.1006/dbio.1995.1084
1995
Cordwell SJ; Wilkins MR; Poljak A; Gooley AA; Duncan MW; Williams KM; Humphery-Smith I, 1995, 'Cross-species identification of proteins separated by two-dimensional gel electrophoresis using MALDI-TOF mass spectrometry and amino acid composition', Electrophoresis, vol. 16, pp. 438 - 443, http://dx.doi.org/10.1002/elps.1150160171
1995
Wasinger VC; Cordwell SJ; Poljak A; Yan JX; Gooley AA; Wilkins MR; Duncan MW; Harris RI; Williams KM; Humphery-Smith I, 1995, 'Progress with gene-product mapping of the mollicutes: mycroplasma genitalium', Electrophoresis, vol. 16, pp. 1090 - 1094, http://dx.doi.org/10.1002/elps.11501601185
1995
Wilkins MR; Williams KL, 1995, 'The extracellular matrix of the Dictyostelium discoideum slug', Experientia, vol. 51, pp. 1189 - 1196, http://dx.doi.org/10.1007/BF01944736
1995
Hunt SMN; Wilkins MR; Stokes HW; Daggard GE; Frankham R, 1992, 'Induced expression of a Drosophila hsp70 promoter-fusion transgene is reduced after repeated heat shocks', Genetical Research, vol. 59, pp. 183 - 188, http://dx.doi.org/10.1017/S0016672300030469
1992
Anande G; Deshpande NP; Mareschal S; Batcha AMN; Hampton HR; Herold T; Lehmann S; Wilkins MR; Wong JWH; Unnikrishnan A; Pimanda JE, 'RNA splicing alterations induce a cellular stress response associated with poor prognosis in AML', , http://dx.doi.org/10.1101/2020.01.10.895714
Book Chapters
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Pang I, 2019, 'Protein Post-Translational Modification Prediction', in Encyclopedia of Bioinformatics and Computational Biology, pp. 15 - 27, http://dx.doi.org/10.1016/B978-0-12-809633-8.20265-3
2019
Wong J; Pang I; Wilkins M; Tree J, 2018, 'Systems-level analysis of bacterial regulatory small RNA networks', in Systems Biology, Springer, pp. 97 - 127
2018
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
2012
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
2008
Wilkins MR, 2008, 'Biomarker Identification: The Role of Experimental Design, Statistics, and Data Sharing', in Clinical Proteomics, pp. 113 - 120, http://dx.doi.org/10.1002/9783527622153.ch9
2008
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
2007
Pang CN; Wilkins MR, 2007, 'Online resources for the molecular contextualisation of disease', in Clinical Bioinformatics, Humana Press, USA, pp. 287 - 308
2007
Wilkins MR, 2007, 'Biomarker Identification: The Role of Experimental Design, Statistics, and Data Sharing', in Clinical Proteomics, edn. Original, pp. 113 - 120
2007
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
2007
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
2007
Wilkins MR; Hunt S, 2006, 'Bioinformatics and Experimental Design for Biomarker Discovery', in Proteomics of Human Bodyfluids: Principles, Methods and Applications, Humana Press, USA, pp. 147, http://dx.doi.org/10.1007/978-1-59745-432-2_8
2006
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
2005
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
2005
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
2003
Conference Posters
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Vazquez Campos X; Kinsela AS; Wilkins MR; Payne TE; Waite D, 2017, 'Phylogenomics of a radioactive legacy site reveals new Archaea phyla of unknown function', Sydney, Australia, presented at Sydney Bioinformatics Research Symposium 2017, Sydney, Australia, 13 June 2017 - 13 June 2017
2017
Dong C; Vazquez Campos X; Deshpande NANDAN; Zhang P; Wilkins M; Park RF, 2017, 'Understanding oat stem rust pathogen genome by PacBio sequencing', Sydney, Australia, presented at Sydney Bioinformatics Research Symposium 2017, Sydney, Australia, 13 June 2017 - 13 June 2017
2017
CORLEY SM; Wilkins MR, 2016, 'RNA-Seq: Is paired-end sequencing always better for gene expression analysis', Sydney, presented at SBRS 2016, Sydney, 22 July 2016 - 22 July 2016
2016
Deshpande N; Wilkins M; Mitchell H; Kaakoush N, 2016, 'Deciphering the role of Campylobacter concisus in host pathogenesis using multi-omics techniques', Charles Perkins Centre, University of Sydney, presented at SBRS 2016, Charles Perkins Centre, University of Sydney, 22 July 2016 - 22 July 2016
2016
Deshpande N; Wilkins M; Mitchell H; Kaakoush NO, 2016, 'SBRS 2016', Charles Perkins Centre, University of Sydney, presented at SBRS 2016, Charles Perkins Centre, University of Sydney, 22 July 2016 - 22 July 2016, http://www.abacbs.org/sbrs_2016/
2016
Kaakoush NO; Mitchell H; Wilkins M; Deshpande N, 2013, 'Comparative genomics of eight Campylobacter concisus isolates provides insights into pathogenesis', presented at Lorne Genome Conference 2013, 17 February 2013 - 19 February 2013
2013
Conference Papers
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Horton JL; Kim KW; Pang CN; Jain K; Leung P; Isaacs SR; Bull RA; Luciani F; Wilkins MR; Lipkin WI; Rawlinson WD; Briese T; Craig ME, 2017, 'Virome-Capture Sequencing of the Gut and Plasma Virome in Children with Islet Autoimmunity', in DIABETES, AMER DIABETES ASSOC, pp. LB51 - LB52, http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000463087200190&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1
2017
Kim KW; Allen DW; Briese T; Pang CN; Jain K; Horton JL; Isaacs SR; Wilkins MR; Couper J; Penno MAS; Harrison LC; Morahan G; Harris M; Cotterill AM; Morbey C; Barry SC; Haynes A; Davis E; Colman P; Giles L; Dodd J; Wentworth J; Sinnott R; Papenfuss TA; Vuillermin P; Lipkin WI; Rawlinson WD; Craig ME, 2017, 'Gut Virome Dynamics during Pregnancy in Mothers with Type 1 Diabetes', in DIABETES, AMER DIABETES ASSOC, pp. LB51 - LB51, http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000463087200189&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1
2017
Al-Shabeeb A; ALSHABEEB AKIL AS; FINLAY A; HARDIKAR A; PANG C; WILKINS MR; RAWLINSON WD; Craig ME, 2013, 'MicroRNA Expression Profiling Reveals Disease-Associated Signatures in Type 1 Diabetes Cellular Models', AMERICAN DIABETES ASSOCIATION, Chicago, USA, pp. A556 - A587, presented at American Diabetes Association 37th Scientific meeting, Chicago, USA, 21 June 2013 - 25 June 2013, http://dx.doi.org/10.2337/db13-2161-2296
2013
Chia S; Wilkins M, 2013, 'Post-translational arginine methylation during yeast quiescence', in YEAST, WILEY-BLACKWELL, Frankfurt Main, GERMANY, pp. 187 - 187, presented at 26th International Conference on Yeast Genetics and Molecular Biology, Frankfurt Main, GERMANY, 29 August 2013 - 03 September 2013, http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000327927400396&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1
2013
Twine N; Pang C; Chen L; Wilkins M; Kassem M, 2013, 'Identification of differentiation-stage specific molecular markers for the osteoblastic phenotype', in JOURNAL OF BONE AND MINERAL RESEARCH, WILEY-BLACKWELL, Baltimore, MD, presented at Annual Meeting of the American-Society-for-Bone-and-Mineral-Research, Baltimore, MD, 04 October 2013 - 07 October 2013, http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000332035801271&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1
2013
Conference Presentations
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Carter A; Lai YW; Pang CNI; Campbell LT; Truong M; Chen S; Wilkins M, 2014, 'Understanding synergy between iron chelators and antifungals using gene co-expression networks', Vol. 57, pp. 107 - 107, http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=000335090600227&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1
2014
Software / Code
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Van Dyk DD; Misztal D; Wilkins MR; Mackintosh JA; Walsh BR; Gray PP, 1999, Chinese hamster ovary two dimensional polyacrylamide gel electrophonesis database, Video, Published: 1999, Software / Code
1999

Proteomics (the global analysis of proteins in biological systems) and its application in biomedical research with particular interests in protein methylation and protein-protein interaction networks. 

Genomics, including emerging technology, and use in biomedical research. 

Molecular systems biology using the bioinformatics of proteomics, transcriptomics and networks.