Prof Sean O'Donoghue

Professor Sean O'Donoghue is a Lab Head and Senior Faculty Member at the Garvan Institute of Medical Research in Sydney. He is also conjointly a Chief Research Scientist in Australia's Commonwealth Scientific and Industrial Research Organisation (CSIRO), and a Professor in the School of Biotechnolog
Lab Head - Biodata Visualisation

Laboratory Head

Conjoint/Adjunct Role(s)

Chief Research Scientist, Commonwealth Scientific and Industrial Research Organisation (CSIRO) Data61
Conjoint Professor, School of Biotechnology and Biomolecular Sciences (BABS), University of New South Wales
Honorary Associate, School of Molecular Biosciences, University of Sydney

Professor Sean O'Donoghue is a Lab Head and Senior Faculty Member at the Garvan Institute of Medical Research in Sydney. He is also conjointly a Chief Research Scientist in Australia's Commonwealth Scientific and Industrial Research Organisation (CSIRO), and a Professor in the School of Biotechnology and Biomolecular Sciences at UNSW.

Sean received his BSc (Hons) and PhD in biophysics from the University of Sydney, Australia. He has been actively engaged in bioinformatics research since 1988. Sean’s contributions in life sciences have been recognised with a C.J. Martin Fellowship from the NHMRC, an Achievement Award from Lion Bioscience AG, and by election as a Fellow of the Royal Society of Chemistry. He has led several projects that have created award-winning bioinformatics resources, such as Reflect (first prize, 2009 Elsevier Grand Challenge), Minardo (finalist, 2015 Eureka Prize), and Aquaria (first prize, 2015 NSW iAward for Research and Development).

Sean also chairs VIZBI, which is an international conference series aimed at improving data visualisation methods in the life sciences. His related project, VizbiPlus, aims to improve how life science is communicated by creating exemplary scientifically-accurate animations designed to inspire and educate the public about cutting-edge biomedical research. The VIZBI website resources are accessed by tens of thousands of scientists worldwide each year. Sean recently published a review on Biomedical Data Visualisation.

Research Interests

Bioinformatics
Systems Biology
Structural Biology
Literature Mining
Data Visualisation

Awards and Honours

2016 - Winner, ISMB 2016 Art and Science Award (Orlando, USA)
2016 - Winner, Nature Methods Poster Award, VIZBI 2016 (Heidelberg, Germany)
2015 - Finalist, Eureka Prize for Excellence in Interdisciplinary Scientific Research
2015 - Finalist, the NSW Emerging Creative Talent Award
2015 - First prize, NSW iAward for Research and Development
2015 - Best Paper Award, 5th International Symposium on Biological Data Visualization (Dublin, Ireland)
2015 - Faculty of 1000 Speaker Prize, Winter School in Mathematical and Computational Biology (University of Queensland)
2014 - Fellow of the Royal Society of Chemistry
2009 - First prize, Elsevier Grand Challenge
2003 - Lion Bioscience Achievement Award for GUI of Lion Target Engine
1994 - C. J. Martin Fellowship, National Health & Medical Research Council
1993 - Eleanor Sophia Wood Travelling Fellowship, University of Sydney
1984 - Scholarship for Philosophy, Sydney University

Education

1992 - PhD, University of Sydney, Australia
1987 - BSc (Hons), University of Sydney, Australia

Patents

O'Donoghue, S., Fries, K., Meyer, J. and Schafferhans, A., Lion Bioscience AG, 2004. Method for organizing and depicting biological elements. U.S. Patent Application 10/250,571.

Hollenberg, L. and O'Donoghue, S., Lion Bioscience AG, 2002. Method of interrogating a database using a quantum computer. U.S. Patent Application 09/790,722.

Selected Publications

Gehlenborg, N., O'donoghue, S.I., Baliga, N.S., Goesmann, A., Hibbs, M.A., Kitano, H., Kohlbacher, O., Neuweger, H., Schneider, R., Tenenbaum, D. and Gavin, A.C., 2010. Visualization of omics data for systems biology. Nature methods, 7(3s), p.S56. Cited by 493

O'Donoghue, S.I., Gavin, A.C., Gehlenborg, N., Goodsell, D.S., Hériché, J.K., Nielsen, C.B., North, C., Olson, A.J., Procter, J.B., Shattuck, D.W. and Walter, T., 2010. Visualizing biological data—now and in the future. Nature methods, 7(3), p.S2. Cited by 121

O'Donoghue, S.I., Goodsell, D.S., Frangakis, A.S., Jossinet, F., Laskowski, R.A., Nilges, M., Saibil, H.R., Schafferhans, A., Wade, R.C., Westhof, E. and Olson, A.J., 2010. Visualization of macromolecular structures. Nature methods, 7(3s), p.S42. Cited by 114

Binder, J.X., Pletscher-Frankild, S., Tsafou, K., Stolte, C., O’Donoghue, S.I., Schneider, R. and Jensen, L.J., 2014. COMPARTMENTS: unification and visualization of protein subcellular localization evidence. Database, 2014, p.bau012. Cited by 113

Altman, R.B., Bergman, C.M., Blake, J., Blaschke, C., Cohen, A., Gannon, F., Grivell, L., Hahn, U., Hersh, W., Hirschman, L. and Jensen, L.J., 2008. Text mining for biology-the way forward: opinions from leading scientists. Genome biology, 9(2), p.S7. Cited by 109

Pavlopoulos, G.A., O'Donoghue, S.I., Satagopam, V.P., Soldatos, T.G., Pafilis, E. and Schneider, R., 2008. Arena3D: visualization of biological networks in 3D. BMC systems biology, 2(1), p.104. Cited by 90

Ballinger, M.L., Goode, D.L., Ray-Coquard, I., James, P.A., Mitchell, G., Niedermayr, E., Puri, A., Schiffman, J.D., Dite, G.S., Cipponi, A. and Maki, R.G., 2016. Monogenic and polygenic determinants of sarcoma risk: an international genetic studyThe Lancet Oncology17(9), pp.1261-1271. Cited by 57

Taberlay, P.C., Achinger-Kawecka, J., Lun, A.T., Buske, F.A., Sabir, K., Gould, C.M., Zotenko, E., Bert, S.A., Giles, K.A., Bauer, D.C. and Smyth, G.K., 2016. Three-dimensional disorganization of the cancer genome occurs coincident with long-range genetic and epigenetic alterationsGenome research26(6), pp.719-731. http://rondo.ws. Cited by 53

Sabir, K., Stolte, C., Tabor, B. and O'Donoghue, S.I., 2013. The Molecular Control Toolkit: Controlling 3D molecular graphics via gesture and voice. In Biological Data Visualization (BioVis), 2013 IEEE Symposium on (pp. 49-56). IEEE. Cited by 37

Santos, A., Tsafou, K., Stolte, C., Pletscher-Frankild, S., O’Donoghue, S.I. and Jensen, L.J., 2015. Comprehensive comparison of large-scale tissue expression datasets. PeerJ, 3, p.e1054. Cited by 35

Perdigão, N., Heinrich, J., Stolte, C., Sabir, K.S., Buckley, M.J., Tabor, B., Signal, B., Gloss, B.S., Hammang, C.J., Rost, B. and Schafferhans, A., 2015. Unexpected features of the dark proteomeProceedings of the National Academy of Sciences112(52), pp.15898-15903. Cited by 34

O'Donoghue, S.I., Sabir, K.S., Kalemanov, M., Stolte, C., Wellmann, B., Ho, V., Roos, M., Perdigao, N., Buske, F.A., Heinrich, J. and Rost, B., 2015. Aquaria: simplifying discovery and insight from protein structures. Nature methods, 12(2), p.98. Cited by 22

Person portrait

Prof Sean O'Donoghue

Research group