Biosciences Platform

Staff

Contact	Position	Work Area
Dr Ben Cocks	Research Director	Biosciences Platform
Prof Mike Goddard	Principal Scientist	Computational Biology
Dr Ben Hayes	Statewide Leader	Computational Biology
Dr Dadna Hartman	Section Leader	Molecular Biology
Dr Matthew McDonagh	Section Leader	Proteomics

Staff Profiles

Dr Ben Cocks BSc (Hons), PhD Research Director, Biosciences Platform Email: ben.cocks@dpi.vic.gov.au Dr Cocks has extensive expertise in the development and effective application of genomics and new technologies relevant to biological discovery. Prior to his appointment at DPI, he established a group at Incyte Corporation in California that combined expertise in genomics, high-throughput sequencing, microarrays, applied bioinformatics, genetics, and proteomics to unravel disease mechanisms and to identify and validate new drug targets.

Prior to working at Incyte, Dr Cocks participated in the discovery of new pathways in lymphocyte biology central to parasitic responses and inflammatory diseases in positions at DNAX Research Institute, Palo Alto, California, USA and in the Department of Medicine at the University of Melbourne. These included the discovery of IL-13 (McKenzie et al. 1993 Proc. Natl. Acad. Sci. USA 90, 3735-3739) and its activity as a switch factor for IgE production in human B cells (Cocks et al. 1993 Int. Immunol. 5, 657-663; Punnonen et al. 1993 Proc. Natl. Acad. Sci. 90, 3730-3734), as well as the identification of SLAM as a key signaling receptor important for T and B cell interaction and activation (Cocks et. al.1995 Nature 376, 260-263). He also contributed to the knowledge of transcription regulation and cell-cycling (Cocks et al. 1992 J.Biol.Chem. 267, 12307-12310) in models of immune cell function (Hamilton et al. 1991 Blood 77, 616-627). Dr Cocks was trained in biochemistry at the University of Melbourne where he made contributions to the discovery of new metabolic pathways and the analysis of genomic structure in infectious bacteria. At DPI, Dr Cocks directs research in the effective application of genetics genomics, and new technologies relevant to animal production, animal health, and the identification of bioactive proteins.

Selected Publications

• Cocks BG and Theriault TP (2004) Developments in effective application of small inhibitory RNA (siRNA) technology in mammalian cells. Drug Discovery: Targets 4: 165-171
  
  
• Zingoni A, Sornasse T, Cocks BG, Tanaka Y, Santoni A and Lanier LL (2004) Cross-talk between human NK cells and CD4+ T cells via OX40 - OX40 ligand interactions. J. Immunol 173: 3716-24
  
  
• Bandman O, Coleman RT, Loring JF, Seilhamer JJ and Cocks BG (2002) Complexity of inflammatory responses in endothelial cells and vascular smooth muscle cells determined by microarray analysis. Ann N Y Acad Sci 975: p. 77-90.
  
  
• Cocks BG, Chang CC, Carballido JM, Yssel H, de Vries JE, and Aversa G (1995) A novel receptor involved in T-cell activation. Nature 376: 260-3.
  
  
• Cocks BG, de Waal Malefyt R, Galizzi JP, de Vries JE, and Aversa G (1993) IL-13 induces proliferation and differentiation of human B cells activated by the CD40 ligand. Int Immunol 5(6): p. 657-63.
  
  
• Punnonen J, Aversa G, Cocks BG, McKenzie AN, Menon S, Zurawski G, de Waal Malefyt R, and de Vries JE (1993) Interleukin 13 induces interleukin 4-independent IgG4 and IgE synthesis and CD23 expression by human B cells. Proc Natl Acad Sci U S A 90(8): p. 3730-4.
  
  
• Cocks BG, Vairo G, Bodrug SE, and Hamilton JA (1992) Suppression of growth factor-induced CYL1 cyclin gene expression by antiproliferative agents. J Biol Chem 267(17): p. 12307-10.
  
  
• Cocks BG, Pyle LE, and Finch LR (1989) A physical map of the genome of Ureaplasma urealyticum 960T with ribosomal RNA loci. Nucleic Acids Res 17(16): p. 6713-9.
  
  
• Cocks BG, Brake FA, Mitchell A and Finch LR (985) Enzymes of intermediary carbohydrate metabolism in Ureaplasma urealyticum and Mycoplasma mycoides subsp. mycoides. J Gen Microbiol 131 ( Pt 9): p. 2129-35.

• Meuwissen THE and Goddard ME (2004) Mapping multiple QTL using linkage disequilibrium and linkage analysis information and multi-trait data. Genet. Sel. Evol. 36: 261-279.
  
  
• Meuwissen THE and Goddard ME (2004) Bootstrapping of gene-expression data improves and controls the false discovery rate. Genet. Sel. Evol. 36: 191-205.
  
  
• Visscher PM and Goddard ME (2004) Prediction of the Confidence Interval of QTL Location. Behaviour Genetics 34: 477-482.
  
  
• Hayes BJ and Goddard ME (2004) Break even cost of genotyping genetic mutations affecting economic traits in commercial pig enterprises. Livest. Prod. Sci. 89: 235-242.
  
  
• Haile-Mariam M, Bowman PJ and Goddard ME (2004) Genetic parameters of fertility traits and their genetic correlation with production, type, workability, live weight, survival index and somatic cell count Aust. J. Agric. Res 55: 77-87.
  
  
• Hayes BJ and Goddard ME (2003) Evaluation of Marker Assisted Selection in Commercial Pig Enterprises. Livest. Prod. Sci. 81: 197-211.
  
  
• Hayes B, Carrick M, Bowman P and Goddard ME (2003) Genotype x Environment Interaction for Milk Production of Daughters of Australian Dairy Sires from Test-Day Records. J. Dairy Sci. 86: 3736-3744.
  
  
• Reverter A, Johnston DJ, Burrow HM, Oddy VH, Perry D, Ferguson DM, Thompson JM, Goddard ME and Bindon BM (2003) Genetic and phenotypic characterisation of live animal, carcass and meat quality traits from temperate and tropically adapted beef breeds. IV. Correlations among live animal, abattoir carcass and meat quality traits. Australian Journal of Agricultural Research 54:149-158.
  
  
• Hayes BJ, Visscher PE, McPartlan H and Goddard ME (2003) A novel multi-locus measure of linkage disequilibrium and it use to estimate past effective population size. Genome Research 13: 635-643.