As modern biological experimental methods deliver data of increasing volume and complexity, researchers are becoming overwhelmed and increasingly unable to fully benefit from potential insights and advances in understanding that may be buried within data.

The Biodata Visualisation team focuses on developing methods and tools that help life scientists exploit these large datasets to gain insight into underlying biological and biomedical processes. We also use data visualisation to communicate complex science to the general public via biomedical animations.


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.

C Görg, L Hunter, J Kennedy, SI O'Donoghue, & JJ Van Wijk. Biological Data Visualization (Dagstuhl Seminar 12372). Dagstuhl Reports 2013; 2(9):131-164.

TG Soldatos, SI O'Donoghue, VP Satagopam, A Barbosa-Silva, GA Pavlopoulos, AC Wanderley-Nogueira, NM Soares-Cavalcanti, R Schneider. Caipirini: using gene sets to rank literature.  BioData Mining 2012; 5(1)

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, H Horn, M Kuhn, E Pafilis, LJ Jensen, & R Schneider.
Reflect: a practical approach to web semantics. J. Web Semantics 2010; 8:182-189.

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.

GA Pavlopoulos, SI O'Donoghue, VP Satagopam, T Soldatos, E Pafilis, & R Schneider.
Arena 3D: visualization of biological networks in 3D. BMC Systems Biology 2008; 2:104.

R Altman, CM Bergman, J Blake, C Blaschke, A Cohen, F Gannon, L Grivell, U Hahn, W Hersh, L Hirschman, LJ Jensen, M Krallinger, B Mons, SI O'Donoghue, M Peitsch, D Rebholz-Schuhmann, H Shatkay, & A Valencia.
Text mining for biology - the way forward: opinions from leading scientists. Genome Biology 2008; 9:S7.

SI O'Donoghue, JEW Meyer, A Schafferhans, & K Fries. The SRS 3D module: integrating structures, sequences, and features. Bioinformatics 2004; 20:2476-2478.

A Schafferhans, JEW Meyer, & SI O'Donoghue. The PSSH database of alignments between protein sequences and tertiary structures. Nucleic Acids Res. 2003; 31:494-498.

SI O'Donoghue.
Role of Mnemonics and virtual reality in visualizing genomics and proteomics data. In Bioinformatics and Genomics: Current Perspectives (ed. MA Andrade), 185-196, Horizon Scientific Press, Wymondham, UK (2003).

K Fries & SI O'Donoghue. Navigating around the building blocks of life. Advanced Imaging 2002; 17:18-19,39.

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.

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

More Garvan Publications

Staff in the Group

Division Overview

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