See Google Scholar Citations.

  1. Visual analytics of signalling pathways using time profiles.
    DKG Ma, C Stolte, S Kaur, M Bain, and SI O'Donoghue. In Sun C, T Bednarz, TD Pham, P Vallotton, D Wang, eds. Signal and Image Analysis for Biomedical and Life Sciences. Switzerland: Springer, 2014;3-22.
  2. Animating life: bringing science to the YouTube generation..
    SI O'Donoghue. The Conversation, 2014.
  3. COMPARTMENTS: unification and visualization of protein subcellular localization evidence..
    JX Binder, S Pletscher-Frankild, K Tsafou, C Stolte, SI O'Donoghue, R Schneider, LJ Jensen. Database, 2014, doi: 10.1093/database/bau012.
  4. Visualising Intrinsic Disorder and Conformational Variation in Protein Ensembles.
    J Heinrich, M Krone, SI O'Donoghue, D Weiskopf. Faraday Discussions, 2014, doi: 10.1039/C3FD00138E.
  5. Visualising Biological Data: Current Perspectives.
    SI O'Donoghue. In Proceedings of the 2013 International Symposium on Computational Models for Life Sciences (CMLS-13), Sydney, Australia. AIP Conference Proceedings 1559, 12-13.
  6. Visual analytics of the insulin signalling pathway using phosphorylation time profiles.
    DKG Ma, C Stolte, S Kaur, M Bain, and SI O'Donoghue. In Proceedings of the 2013 International Symposium on Computational Models for Life Sciences (CMLS-13), Sydney, Australia. AIP Conference Proceedings 1559, 185-96.
  7. The Molecular Control Toolkit: controlling 3D molecular graphics via gesture and voice
    K Sabir, C Stolte, B Tabor, SI O'Donoghue. In Proceedings of the 2013 IEEE Symposium on Biological Data Visualization (BioVis), Atlanta, GA, USA. In press.
  8. Biological Data Visualization (Dagstuhl Seminar 12372)
    C Görg, L Hunter, J Kennedy, SI O'Donoghue, & JJ Van Wijk. Dagstuhl Reports 2 (9), 131-164 (2013)
  9. Caipirini: using gene sets to rank literature
    TG Soldatos, SI O'Donoghue, VP Satagopam, A Barbosa-Silva, GA Pavlopoulos, AC Wanderley-Nogueira, NM Soares-Cavalcanti, R Schneider. BioData Mining 5(1) (2012)
  10. Martini: using literature keywords to compare gene sets
    T Soldatos, SI O'Donoghue, VP Satagopam, NP Brown, LJ Jensen, & R Schneider.
    Nucleic Acid Res. 38, 26-38 (2010).
  11. Reflect: a practical approach to web semantics
    SI O'Donoghue, H Horn, M Kuhn, E Pafilis, LJ Jensen, & R Schneider.
    J. Web Semantics 8, 182-189 (2010).
  12. Visualization of macromolecular structures
    SI O'Donoghue, DS Goodsell, AS Frangakis, F Jossinet, R Laskowski, M Nilges, HR Saibil, A Schafferhans, R Wade, E Westhof, & AJ Olson.
    Nature Methods 7, S42-S55 (2010).
  13. Visualizing biological data - now and in the future
    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.
    Nature Methods 7, S2-S4 (2010).
  14. Defective lamin A-Rb signaling in Hutchinson-Gilford Progeria Syndrome and reversal by farnesyltransferase inhibition
    J Marji, SI O'Donoghue, D McClintock, VP Satagopam, R Schneider, D Ratner, HJ Worman, LB Gordon, & K Djabali.
    PLoS One 5, e11132 (2010).
  15. Visualization of omics data for systems biology
    N Gehlenborg, SI O'Donoghue, NS Baliga, A Goesmann, MA Hibbs, H Kitano, O Kohlbacher, H Neuweger, R Schneider, D Tenenbaum, & A-C Gavin.
    Nature Methods 7, S56-S68 (2010).
  16. Reflect: augmented browsing for the life scientist
    E Pafilis, SI O'Donoghue, LJ Jensen, M Kuhn, NP Brown, & R Schneider.
    Nature Biotechnology 27, 308-310 (2009).
  17. Arena 3D: visualization of biological networks in 3D
    GA Pavlopoulos, SI O'Donoghue, VP Satagopam, T Soldatos, E Pafilis, & R Schneider.
    BMC Systems Biology 2, 104 (2008).
  18. Text mining for biology - the way forward: opinions from leading scientists
    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.
    Genome Biology 9, S7 (2008).
  19. Three-dimensional structures in target discovery and validation
    SI O'Donoghue, RB Russell, & A Schafferhans.
    In In Silico Technologies in Drug Target Identification and Validation (ed. D León & S Markel), 285-305, CRC, San Diego, USA (2006).
  20. Error distribution derived NOE distance restraints
    M Nilges, M Habeck, SI O'Donoghue, & W Rieping.
    Proteins 64, 652-664 (2006).
  21. The SRS 3D module: integrating structures, sequences, and features
    SI O'Donoghue, JEW Meyer, A Schafferhans, & K Fries.
    Bioinformatics 20, 2476-2478 (2004).
  22. The PSSH database of alignments between protein sequences and tertiary structures
    A Schafferhans, JEW Meyer, & SI O'Donoghue.
    Nucleic Acids Res. 31, 494-498 (2003).
  23. Role of Mnemonics and virtual reality in visualizing genomics and proteomics data
    SI O'Donoghue.
    In Bioinformatics and Genomics: Current Perspectives (ed. MA Andrade), 185-196, Horizon Scientific Press, Wymondham, UK (2003).
  24. Solution structure of the coiled-coil trimerization domain from lung surfactant protein D
    H Kovacs, SI O'Donoghue, HJ Hoppe, D Comfort, KB Reid, D Campbell, & M Nilges.
    J. Biomol. NMR 24, 89-102. (2002).
  25. Navigating around the building blocks of life
    K Fries & SI O'Donoghue.
    Advanced Imaging 17, 18-19,39 (2002).
  26. NMR studies of the aggregation of glucagon-like peptide-1: formation of a symmetric helical dimer
    X Chang, D Keller, SI O'Donoghue, & JJ Led.
    FEBS Letters 515, 165-170 (2002).
  27. Method for organizing and depicting biological elements
    SI O'Donoghue, K Fries, J Meyer, & A Schafferhans. European Patent Application (2001).
    [WO 02/054326 A2]
  28. Automated assignment of ambiguous nuclear overhauser effects with ARIA
    JP Linge, SI O'Donoghue, & M Nilges.
    In Methods in Enzymology (ed. TL James, V Doetsch, & U Schmitz), 71-90, Academic Press, San Diego (2001).
  29. Method of interrogating a database using a quantum computer
    L Hollenberg & SI O'Donoghue. U.S. Patent Application (2001).
  30. Comparison of ARM and HEAT repeat proteins
    MA Andrade, C Petosa, SI O'Donoghue, CW Müller, & P Bork.
    J. Mol. Biol. 309, 1-18 (2001).
  31. Unravelling the symmetry ambiguities in a symmetric hexamer: calculation of the R6 human insulin structure
    SI O'Donoghue, X Chang, R Abseher, M Nilges, & JJ Led.
    J. Biomol. NMR 16, 93-108 (2000).
  32. Calculation of symmetric oligomer structures from NMR data
    SI O'Donoghue & M Nilges.
    In Biological Magnetic Resonance 17: Structure Computation and Dynamics in Protein NMR (ed. NR Krishna & LJ Berliner), 131-161, Plenum, New York (1999).
  33. Molecular dynamics and accuracy of NMR structures: effects of error bounds and data removal
    F-R Chalaoux, SI O'Donoghue, & M Nilges.
    Proteins 34, 453-463 (1999).
  34. Ambiguous NOEs and automated NOE assignment
    M Nilges & SI O'Donoghue.
    Progress in NMR Spectroscopy 32, 107-139 (1998).
  35. Adaptation of protein surfaces to subcellular location
    MA Andrade, SI O'Donoghue, & B Rost.
    J. Mol. Biol. 276, 517-525 (1998).
  36. Sisyphus and prediction of protein structure
    B Rost & SI O'Donoghue.
    Bioinformatics 13, 345-356 (1997).
    Cited by 3
  37. Tertiary structure prediction using mean-force potentials and internal energy functions: successful prediction for coiled-coil geometries
    SI O'Donoghue & M Nilges.
    Folding & Design 2, S47-S52 (1997).
  38. Automated NOESY interpretation with ambiguous distance restraints: the refined NMR solution structure of the pleckstrin homology domain from b-spectrin
    M Nilges, M Macias, SI O'Donoghue, & H Oschkinat.
    J. Mol. Biol. 269, 408-422 (1997).
  39. The structure of a novel insecticidal neurotoxin, omega-atracotoxin-HV1, from the venom of an Australian funnel web spider
    JI Fletcher, R Smith, SI O'Donoghue, M Nilges, M Connor, MEH Howden, MJ Christie, & GF King.
    Nature Structural Biology 4, 559-566 (1997).
  40. Calculation of symmetric multimer structures from NMR data using a priori knowledge of the monomer structure, co-monomer restraints, and interface mapping: the case of leucine zippers
    SI O'Donoghue, GF King, & M Nilges.
    J. Biomol. NMR 8, 196-203 (1996).
  41. High resolution NMR solution structure of the leucine zipper domain of the c-Jun homodimer
    FK Junius, SI O'Donoghue, M Nilges, AS Weiss, & GF King.
    J. Biol. Chem. 271, 13663-13667 (1996).
  42. Homology and mutagenesis studies of hamster dihydroorotate
    NK Williams, SI O'Donoghue, & RI Christopherson.
    In Purine and Pyrimidine Metabolism in Man VIII (ed. A Sahota & WM Taylor), Plenum Press, New York (1995).
  43. Catalysis by hamster dihydroorotate: zinc binding, site-directed mutagenesis, and interaction with inhibitors
    NK Williams, MK Manthey, TW Hambley, SI O'Donoghue, M Keegan, BE Chapman, & RI Christopherson.
    Biochemistry 34, 11344-11352 (1995).
  44. Stereospecificity of substrate usage by glyoxalase-1: nuclear-magnetic-resonance studies of kinetics and hemithioacetal substrate conformation
    C Rae, SI O'Donoghue, WA Bubb, & PW Kuchel.
    Biochemistry 33, 3548-3559 (1994).
  45. Determination of the structure of symmetric coiled-coil proteins from NMR data: application of the leucine zipper proteins Jun and GCN4
    SI O'Donoghue, FK Junius, & GF King.
    Protein Engng 6, 557-564 (1993).
  46. Removing the two C-terminal residues of actin affects the interaction between filaments
    SI O'Donoghue, M Miki, & CG dos Remedios.
    Arch. Biochem. Biophys. 293, 110-116 (1992).
  47. Models of the actin monomer and filament from fluorescence resonance-energy transfer measurements
    SI O'Donoghue, BD Hambly, & CG dos Remedios.
    FEBS J. 205, 591-601 (1992).
  48. The solution structure of endothelin-3 determined using NMR spectroscopy
    RG Mills, SI O'Donoghue, R Smith, & GF King.
    Biochemistry 31, 5640-5645 (1992).
  49. The structure of actin observed by fluorescence resonance-energy transfer spectroscopy
    M Miki, SI O'Donoghue, & CG dos Remedios.
    J. Musc. Res. Cell Motil. 13, 132-145 (1992).
  50. Determination of the solution structure of a platelet-adhesion peptide of von Willebrand factor
    HM Knott, MC Berndt, AV Kralicek, SI O'Donoghue, & GF King.
    Biochemistry 31, 11152-11158 (1992).
  51. Structural interpretation of fluorescence resonance-energy transfer measurements
    SI O'Donoghue.
    Bioinformatics 7, 471-477 (1991).
  52. Actin structure and function
    SI O'Donoghue.
    The University of Sydney, Sydney (1991).
  53. Urea transport and metabolism in Chara corallina
    MR Wilson, SI O'Donoghue, & NA Walker.
    In Membrane Transport in Plants and Fungi (ed. NA Walker, JR Smith, & M Bielby), 393-394, The University of Sydney, Sydney (1990).
  54. The transport and metabolism of urea in Chara australis III: Two specific transport systems
    MR Wilson, SI O'Donoghue, & NA Walker.
    J. Exp. Bot. 39, 763-774 (1988).
  55. The transport of nitrogen-containing compounds in Chara corillina
    SI O'Donoghue.
    The University of Sydney, Sydney (1986).