Research and discovery in plant, mammalian, and microbial systems.- Development of improved genomic selection approaches in animals and plants.- The discovery of bioactive compounds in milk - a peptide, made in the early stages of wallaby lactation, that kills multidrug-resistant clinical isolates (Wang J. et al 2011 PLOS1). - Successful molecular “Jurassic Park” like experiment and synthetically recreated genes for antimicrobials that existed on earth in an ancient marsupial about 60 million years ago. Djarthia the world’s oldest known and most plesiomorphic australidelphian marsupial found at Tingamara fossils @ 55 MYA is a likely candidate in the same time frame to have had the ancestral gene. The super active resurrected marsupial gene has broad spectrum and an IC50 = 70 nM for mastitis pathogen Streptococcus uberis.https://www.newscientist.com/article/mg21128314-800-resurrected-ancient-protein-is-a-potent-antibiotic/- Identified enzymes associated with oligosaccharide synthesis in bovine and wallaby mammary gland, and more recently identified through whole genome sequencing and fine mapping the genes regulating prebiotic complex sugar levels in milk. - Found the ABO blood type gene has a key role in regulating oligosaccharide prebiotic complex sugar content in milk.- Identified RNase5 as a biologically active component of milk whey, and in addition an important factor at a cellular level for muscle cell growth.- Discovered the first example of horizontal gene transfer in angiosperms from fungi, estimated to have occurred ~10 million years ago in grasses, occurring through symbiont association Shinozuka H. et al 2017 Scientific Reports.- Collaboration with Craig Venter in metagenomic analysis and mining of rumen and Australian soil microbes- Developed predictive metagenomic methods applied to gut bacteria with computational approach that enabled prediction of traits and diseases in animals and humans Ross L. et al 2013 PLOS1.

Developing better diagnosis of immune dysregulation

Co-Director for AgriBio a joint initiative of the Victorian Government and La Trobe University, accommodating up to 400 staff and students. AgriBio is Australia’s first integrated agricultural systems biology research centre and one of Australia’s premier state-of-the-art facilities, with a key emphasis on advanced research to improve productivity, fight disease and reduce environmental impact.

Research Director, Genomics and Cellular Sciences in the Department, and Professor in the School of Applied Systems Biology at La Trobe University, leading more than 100 biosciences staff and students working with industry in innovation and the practical application of biotechnology and computational biology. Team are leaders in genomic prediction, quantitative genetics, genome sequencing and imputation with sequencing capacity 10 trillion bases of DNA a week. Advanced capability in complex phenotypes and molecular phenomics utilising state of the art systems biology infrastructure working closely with industry and the private sector. Training the future innovation workforce currently 30 PhD students in the team. Many exciting new PhD project opportunities available.https://www.researchgate.net/profile/Ben_Cocks

Role of co-Director for key dairy industry programs DairyBio and DairyFeedbase. These initiatives are delivering benefit to the Australian Dairy industry, which include total investments by all parties of >$100 million over 5 years. The program teams use genetics and new technologies for the improvement of plants and animals, and are very focussed on research to improve profit on farm. The research working closely with the private sector delivers improved pasture seed and animal semen, in addition to improved management solutions. The new and more powerful breeding tools in plants and animals are delivering step change improvements. Exciting projects and PhD fellowships available in the education program.

Research Director leading 300 biosciences staff in DPI/DEPI converting discoveries into solutions for plant and animal industries. Implemented cross-disciplinary structures and the use of advanced approaches animal diseases and diagnostics, plant diseases and diagnostics, microbiome research, in advanced genetics in plants and animals, and genome modification in plants- Consolidation of managed capabilities into state of the art new facilities at AgriBio, the group now international leaders in DNA and genomic testing- Discovered and sequenced with colleagues abalone virus AbHV-1 linked to a fatal ganglioneuritis that devastated a valuable wild abalone fishery in Australia- The finding allowed the discovery of 2 viruses of the 3 members of the Aurivirus family of herpesviruses one associated with the amphioxus genome https://en.wikipedia.org/wiki/Aurivirus- Kangaroo genome and bovine genome contributions and biological implications- Applications of genomic selection and the use of epigenetic and functional information to inform imputation and identify functional mutations- Established microbiome capability and discovery

Genomics and systems biology approaches for understanding disease and providing tools and knowledge as a basis for new small molecule and therapeutic protein treatments, enabling significant investment and partnerships with leading pharmaceutical and biotechnology companies.Discovery and validation of secreted molecules, kinases (including successful target JAK2), and phosphodiesterases used as new targets and/or counter-screens.Large scale application of transcriptomics for drug discovery and diagnostic discovery in immune disease and cancer. Early systematic application of genomics, genetics, transcriptomics, bioinformatics, proteomics, and RNA interference in drug discovery.

DNAX Research Institute for Molecular and Cellular Biology, Schering Plough (now Merck)The discovery and naming of SLAM as a key signalling receptor important for T- and B-cell function (Cocks et. al., 1995, Nature, 376;260–263) enabling its subsequent identification as the measles virus receptor and key pathway mutated in immune disorders. SLAM/SLAMF1 is the prototype receptor for the SLAM family of receptors important in immune function and as targets for immunotherapy. The identification of human IL-13 (McKenzie et al., 1993, Proc. Natl. Acad. Sci. USA, 90;3735–3739) and discovery of its activity as a fundamental 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). The IL-13 pathway is a now key target for advanced effective asthma drugs. Played a key role in identification and characterisation of the human CD40 ligand and function, SelD in humans key selenium pathway enzyme conserved across all life’s kingdoms, and human lymphotactin.

Department of Medicine, University of Melbourne, Royal Melbourne HospitalIn the team of Prof John Hamilton new knowledge in activation and repression of inflammation relevant to rheumatoid arthritis. Transcriptional regulation of urokinase gene by NFkB and negative regulation by glucocorticoid receptor. The role of cytokines and cyclins in macrophage differentiation and responses.