Dr Sean O'Donoghue

Group Leader - Biodata Visualisation

Senior Research Fellow

Conjoint/Adjunct Role(s)

OCE Science Leader, CSIRO Computational Informatics
Honorary Associate, School of Molecular Biosciences, University of Sydney

Seán O’Donoghue is a group leader at the Garvan Institute of Medical Research in Sydney, and also jointly an OCE Science Leader in Australia's Commonwealth Scientific and Industrial Research Organisation (CSIRO), working in the division of Computational Informatics, Sydney. Previously, he worked in the Structural and Computational Biology programme at the European Molecular Biology Laboratory (EMBL), and at Lion Bioscience AG, both in Heidelberg, Germany.

He received his BSc (Hons) and PhD in biophysics from the University of Sydney, Australia. He has been actively engaged in bioinformatics research since 1988, mostly at EMBL. His most significant contribution to date has been contributing to the development of ARIA, a method widely used for calculating 3D structures from NMR data.

Since then, he has initiated and is leading several projects, including VIZBI; the SRS 3D service that integrates 3D structure, sequence, and sequence features; the Martini service for comparing gene lists; and the Reflect service for annotating biochemical terms in web pages. The Reflect service has received international recognition, and since it was published in mid-2009 in Nature Biotechnology, the user-base of the service has grown rapidly, and it is currently used by life scientists to process thousands of documents per day.

Research Interests

Bioinformatics
Systems Biology
Structural Biology
Literature Mining
Data Visualisation

Awards and Honours

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, The University of Sydney, Australia
1987 - BSc, (Hons) The University of Sydney, Australia

Selected Publications

DKG Ma, C Stolte, S Kaur, M Bain, and SI O'Donoghue. Visual analytics of the insulin signalling pathway using phosphorylation time profiles. In Proceedings of the 2013 International Symposium on Computational Models for Life Sciences (CMLS-13), Sydney, Australia. AIP Conference Proceedings 1559, 185-96.

K Sabir, C Stolte, B Tabor, SI O'Donoghue. The Molecular Control Toolkit: controlling 3D molecular graphics via gesture and voice.  In Proceedings of the 2013 IEEE Symposium on Biological Data Visualization (BioVis), Atlanta, GA, USA.

T Soldatos, SI O'Donoghue, VP Satagopam, NP Brown, LJ Jensen, & R Schneider. Martini: using literature keywords to compare gene sets. Nucleic Acid Res. 2010; 38:26-38.

SI O'Donoghue, DS Goodsell, AS Frangakis, F Jossinet, R Laskowski, M Nilges, HR Saibil, A Schafferhans, R Wade, E Westhof, & AJ Olson. Visualization of macromolecular structures. Nature Methods 2010; 7:S42-S55.

SI O'Donoghue, A-C Gavin, N Gehlenborg, DS Goodsell, J-K Hériché, CB Nielsen, C North, AJ Olson, JB Procter, DW Shattuck, T Walter, & B Wong. Visualizing biological data - now and in the future. Nature Methods 2010; 7:S2-S4.

J Marji, SI O'Donoghue, D McClintock, VP Satagopam, R Schneider, D Ratner, HJ Worman, LB Gordon, & K Djabali. Defective lamin A-Rb signaling in Hutchinson-Gilford Progeria Syndrome and reversal by farnesyltransferase inhibition. PLoS One 2010; 5:e11132.

N Gehlenborg, SI O'Donoghue, NS Baliga, A Goesmann, MA Hibbs, H Kitano, O Kohlbacher, H Neuweger, R Schneider, D Tenenbaum, & A-C Gavin. Visualization of omics data for systems biology.  Nature Methods 2010; 7:S56-S68.

E Pafilis, SI O'Donoghue, LJ Jensen, M Kuhn, NP Brown, & R Schneider. Reflect: augmented browsing for the life scientist. Nature Biotechnology 2009; 27:308-310.

JP Linge, SI O'Donoghue, & M Nilges. Automated assignment of ambiguous nuclear overhauser effects with ARIA. In Methods in Enzymology (ed. TL James, V Doetsch, & U Schmitz), 71-90, Academic Press, San Diego (2001).

MA Andrade, C Petosa, SI O'Donoghue, CW Müller, & P Bork. Comparison of ARM and HEAT repeat proteins. J. Mol. Biol. 2001; 309:1-18.

M Nilges & SI O'Donoghue. Ambiguous NOEs and automated NOE assignment. Progress in NMR Spectroscopy 1998; 32:107-139.

MA Andrade, SI O'Donoghue, & B Rost. Adaptation of protein surfaces to subcellular location. J. Mol. Biol. 1998; 276:517-525.

M Nilges, M Macias, SI O'Donoghue, & H Oschkinat. Automated NOESY interpretation with ambiguous distance restraints: the refined NMR solution structure of the pleckstrin homology domain from b-spectrin. J. Mol. Biol. 1997; 269:408-422.

JI Fletcher, R Smith, SI O'Donoghue, M Nilges, M Connor, MEH Howden, MJ Christie, & GF King. The structure of a novel insecticidal neurotoxin, omega-atracotoxin-HV1, from the venom of an Australian funnel web spider. Nature Structural Biology 1997; 4:559-566.

FK Junius, SI O'Donoghue, M Nilges, AS Weiss, & GF King. High resolution NMR solution structure of the leucine zipper domain of the c-Jun homodimer. J. Biol. Chem. 1996; 271:13663-13667.

Dr Sean O'Donoghue



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