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Research

Professor Marc Wilkins
Having defined the proteome in 1994 and coined the term, my research has continued to ask large-scale questions about protein function.

We are currently examining the role of protein-protein interactions in the proteome, which can be called interactome research, and are exploring the following:

  • What does the interactome look like? How can it best be visualised?
  • What protein complexes exist? How can they be separated?
  • Are protein complexes made of core, attachment and module proteins?
  • What is the role of post-translational modifications in the interactome?
  • How, when and why do proteins interact with each other? What are the dynamics of this process?
  • How common is a loss or gain of protein-protein interaction in association with human disease?

We are exploring these questions using a combination of proteomic and bioinformatic techniques, analysing samples from numerous biological systems. We have access to FT-ICR, Q-star, Q-TOF and MALDI-TOF mass spectrometry at the on-site Bioanalytical Mass Spectrometry Facility.

Dr David Fung
David moved from molecular genetics to bioinformatics in 2000 and after finishing his PhD in 2010, he shifted to systems biology. David believes that the underpinning of systems biology is complex systems theory. Since all complex systems can be modeled as a network, he specialises in modelling expression data as a network. Between 2005-2008, he constructed a network model of hepatocellular carcinoma (HCC) which integrated gene co-expression, protein-protein interaction, microRNA-gene interaction, gene-disease relationships, gene-Gene Ontology (GO) relationships, as well as gene-cell quiescent condition datasets. The model is novel in two ways. The first is the integration of both gene-GO and gene-disease relationships, which gives the model a richer context. The second is the integration of gene-cell quiescent condition relationships. His rationale was to use the gene expression profile of quiescent human fibroblasts as a reference cell state. The first paper from this work was published in Cancer Informatics [abstract]. Currently, he is trying to understand the systems biology of myocardial infarction in collaboration with Dr Ruby Lin.

His current research interests include:
  • How do different network constructs derived from expression, interaction, and ontology data assist hypothesis deduction? Which network models are good fits for different biological problems?
  • How many molecular interaction types and ontology types can we integrate into a network before it loses inference power?
  • What is the biological meaning of network topology (including network statistics and topology measures) in normal and disease cells?

Dr Sarah Kummerfeld
I am interested in the molecular basis of aging. Genome-scale studies of normal healthy people have identified genes that change expression level with age.

My recent research has focused on developing computational methods to determine what these groups of genes do and how they relate to known age-related conditions, for example: DNA- damage, oxidative stress, telomere shortening and inflammation. In addition to improving our understanding of human aging, my goal is to create tools for comparing diverse expression datasets for application to other biological domains.

Publications

Books

Wilkins MR, Appel RD, Williams KL, Hochstrasser DF eds. (2007). Proteome Research: concepts, technology and application. Springer. [info]

Research Papers

Goel A, Li SS, Wilkins MR (2010). Four-dimensional visualisation and analysis of protein-protein interaction networks. Molecular and Cellular Proteomics, submitted. [download software]

Joshi HJ, von der Leith CW, Packer NH, Wilkins MR (2010). GlycoViewer: a tool for visual summary and comparative analysis of the glycome. Nucleic Acids Research, published online. [read article] [access software]

Fung DC, Hong SH, Wilkins MR, Hart D (2010). Using the clustered circular layout as an informative method for visualizing protein-protein interaction networks. Proteomics, published online. [abstract]

Pang CN, Gasteiger E, Wilkins MR (2010). Identification of arginine- and lysine-methylation in the proteome of Saccharomyces cerevisiae and its functional implications. BMC Genomics, 11: 92. [abstract]

Okoli AS, Wilkins MR, Raftery MJ, Mendz GL (2010). Response of Helicobacter hepaticus to bovine bile. Journal of Proteome Research, 9: 1374-84. [abstract]

Ma L, Pang CN, Li SS, Wilkins MR (2010). Proteins deleterious on overexpression are associated with high intrinsic disorder, specific interaction domains, and low abundance. Journal of Proteome Research, 9: 1218-25. [abstract]

Widjaja YY, Pang CN, Li SS, Wilkins MR, Lambert TD (2009). The Interactorium: visualising proteins, complexes and interaction networks in a virtual 3D cell. Proteomics, 9: 5309-315. [abstract] [download software]

Featured on the cover of Proteomics [see cover].

Wilkins MR (2009). Proteomics data mining. Expert Review of Proteomics, 6: 599-603. [abstract]

Wilkins MR (2009). Hares and tortoises: the high versus low throughput proteomic race. Electrophoresis, 30: S150-155. [abstract]

Erce MA, Low JKK, March PE, Wilkins MR, Takayama KM (2009). Identification and functional analysis of RNase E of Vibrio angustum S14 and two-hybrid analysis of its interaction partners. BBA Proteins and Proteomics, 1794: 1107-1114. [abstract]

Huang K-Y, Filarsky M, Padula MP, Raftery MJ, Herbert BR, Wilkins MR (2009). Micropreparative fractionation of the complexome by blue native continuous elution electrophoresis. Proteomics, 9: 2494-2502. [abstract]

Little PFR, Williams RB, Wilkins MR (2009). Inter-individual variation in expression: a missing link in biomarker biology? Trends in Biotechnology, 27: 5-10. [abstract]

Fung DCY (2008). Modeling and Analyzing Gene Co-Expression in Hepatocellular Carcinoma Using Actor-Semiotic Networks and Centrality Signatures. Cancer Informatics, 6: 463-474. [abstract]

Krycer JR, Pang CN, Wilkins MR (2008). High throughput protein-protein interaction data: clues for the architecture of protein complexes. Proteome Science, 6: 32. [abstract]

Deshpande N, Wilkins MR, Packer NH, Nevalainen H (2008). Protein glycosylation pathways in filamentous fungi. Glycobiology, 18: 626-637. [abstract]

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, 7: 2632-2641. [abstract]

Wilkins MR, Kummerfeld SK (2008). Sticking together? Falling Apart? Exploring the dynamics of the interactome. Trends in Biochemical Sciences, 33: 195-200. [abstract]

Pang CN, Krycer JR, Lek A, Wilkins MR (2008). Are protein complexes composed of core, module and attachment proteins? Proteomics, 3: 425-434. [abstract]

Featured in Proteomics Editorial [download], also interviewed for Proteomics Podcast [download].

Ho E, Webber R, Wilkins MR (2008). Interactive three-dimensional visualization and contextual analysis of protein interaction networks. Journal of Proteome Research, 7: 104-112. [abstract] [download software]

Taylor CF, Paton NW, Lilley KS, Binz PA, Julian RK Jr, Jones AR, Zhu W, Apweiler R, Aebersold R, Deutsch EW, Dunn MJ, Heck AJ, Leitner A, Macht M, Mann M, Martens L, Neubert TA, Patterson SD, Ping P, Seymour SL, Souda P, Tsugita A, Vandekerckhove J, Vondriska TM, Whitelegge JP, Wilkins MR, Xenarios I, Yates JR 3rd, Hermjakob H (2007). The Minimum Information About a Proteomics Experiment (MIAPE). Nature Biotechnology, 25: 887-893. [abstract]

Hsu W-T, Pang CN, Sheetal J, Wilkins MR (2007). Protein-protein interactions and disease: use of S. cerevisiae as a model system. BBA Proteins and Proteomics, 1774: 838-847. [abstract]

Pang CN, Hayen A, Wilkins MR (2007). Surface accessibility of post-translational modifications. Journal of Proteome Research, 6: 1833-1845. [abstract]

Ho E, Hayen A, Wilkins MR (2006). Characterisation of organellar proteomes: a guide to subcellular proteomic fractionation and analysis. Journal of Proteome Research, 6: 5746-5757. [abstract]

Featured in Journal of Proteome Research "Currents" article [download].

Wilkins MR, Appel RD, Van Eyk JE, Chung MCM, Görg A, Hecker MA, Huber LA, Langen H, Link AJ, Paik YK, Patterson SD, Pennington SR, Rabilloud T, Simpson RJ, Weiss W, Dunn MJ (2006). Guidelines for the next 10 years of proteomics. Proteomics, 6: 4-8. [abstract]

Featured in Proteomics Editorial [download], also interviewed for Proteomics Podcast [download].

Hunt SMN, 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, 4: 809-819. [abstract]

Featured in Journal of Proteome Research "Research Profile" article [download].

Arthur JW and Wilkins MR (2004). Using proteomics to mine genome sequences. Journal of Proteome Research, 3:393-402. [abstract]

Recent Book Chapters

Bek E and Wilkins MR (2008). Using Yeast to Study Protein-Protein Interactions Relevant to Disease. In: S. Witt (Ed), Yeast as a model for Human Disease. Signpost Research Press. In Press.

Pang CN and Wilkins MR (2008). Online resources for the molecular contextualization of disease. In: Methods in Molecular Medicine, 141: 287-308. [abstract]

Wilkins MR (2007). Biomarker identification: the role of experimental design, statistics and data sharing. In: J. Van Eyk and M. Dunn (Eds.), Clinical Proteomics: from Diagnosis to Therapy, pp 113-120. Wiley-VCH. [info]

Wilkins MR and Appel RD (2007). Ten years of the proteome. In: M.R. Wilkins, R.D. Appel, K.L. Williams and D.F. Hochstrasser (Eds.), Proteome Research: concepts, technology and application, pp 1-14. Springer. [info]

Packer N, Gooley AA and Wilkins MR (2007). One gene, many proteins. In: M.R. Wilkins, R.D. Appel, K.L. Williams and D.F. Hochstrasser (Eds.), Proteome Research: concepts, technology and application, pp 95-122. Springer. [info]

Hernandez P, Binz P.-A. and Wilkins MR (2007). Protein Identification in Proteomics. In: M.R. Wilkins, R.D. Appel, K.L. Williams and D.F. Hochstrasser (Eds.), Proteome Research: concepts, technology and application, pp 41-68. Springer. [info]

Wilkins MR and Hunt SM (2006). Bioinformatics and experimental design for biomarker discovery. In: V. Thongboonkerd (Ed.), Proteomics of Human Body Fluids: Principles, Methods, and Applications, pp 147-174. Humana Press. [info]

Gasteiger E, Hoogland C, Gattiker A, Duvaud S, Wilkins MR, Appel RD and Bairoch A (2005). Protein Identification and Analysis Tools on the ExPASy Server. In: J.M. Walker (Ed.), The Proteomics Protocols Handbook, 2nd Edition, pp 571-607. Humana Press. [info]

Herbert BR, Pedersen S, Harry JL, Sebastian L, Grinyer J, Traini M, McCarthy J, Wilkins MR, Gooley AA, Righetti PG, Packer NH and Williams KL (2003). Mastering proteome complexity using two-dimensional gel electrophoresis. PharmaGenomics September 2003, pp 22-36.

Cooper CA, Joshi HJ, Harrison MJ, Wilkins MR and Packer NP (2003). Querying GlycosuiteDB. In: P.M. Conn (Ed.), Handbook of Proteomic Methods, pp 233-240. Humana Press. [info]

Presentations

Recent Conferences

Invited Presentations

  • UNSW Analytical Centre Research Meeting, University of New South Wales (March 2010)
  • Adelaide Protein Group Half-Day Conference, Adelaide (December 2009)
  • Australasian Yeast Group Products and Discovery Conference (YPD09), Adelaide (December 2009)
  • Australian Wine Research Institute & Bioplatforms Australia Wine Yeast Systems Biology Workshop, Adelaide (May and November 2009)
  • 8th HUPO World Congress [Plenary Speech, International Proteomics Forum], Toronto, Canada (September 2009)
  • Geneva University and the Swiss Institute of Bioinformatics, Switzerland (September 2009)
  • 18th International Mass Spectrometry Conference [Invited Keynote], Bremen, Germany (August 2009)
  • 57th Annual Meeting of The Cardiac Society of Australia and New Zealand, Sydney (August 2009)
  • Faculty of Medicine, University of Western Sydney (June 2009)
  • Ramaciotti Centre Next Generation Sequencing Launch, University of New South Wales (June 2009)
  • 2009 ANDS-ARCS Supporting the Data Lifecycle Symposium, University of Sydney (February 2009)
  • 2008 NSW Bioinformatics Research Symposium, University of Sydney (December 2008)
  • The Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney
  • The John Curtin Medical School, Australian National University, Canberra
  • The Diabetes Transplant Unit, Prince of Wales Hospital, Randwick