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Dr Sean O'Donoghue

Dr Sean O'Donoghue

Conjoint Professor
Science
School of Biotech & Biomolecular Science

Seán O’Donoghue is a Conjoint Professor at the School of Biotechnology and Biomolecular Science (BABS), University of New South Wales. He also is a Laboratory Head and Senior Faculty Member at the Garvan Institute of Medical Research in Sydney, and a Visiting Scientist at CSIRO Data61.

He received his B.Sc. (Hons) and PhD in biophysics from the University of Sydney, Australia. Much of his career was spent in Heidelberg, Germany, where he worked in the Structural and Computational Biology programme at the European Molecular Biology Laboratory (EMBL), and at Lion Bioscience AG - then the world's largest bioinformatics company - where he was Director of Scientific Visualization.

He has been actively engaged in bioinformatics research since 1988. He contributed to the development of ARIA, a method widely used for calculating 3D structures from NMR data. Since then, he has initiated and is leading the development of several computational resources that use data visualization, graphic design, and user interface principles to simplify the discovery of insight from complex biological data. These resources are focused on structural biology, systems biology, and sequence analysis. He is also co-founder and leader of two initiatives: VIZBI, an international initiative aimed at improving data visualization in bioinformatics software, and VizbiPlus, aimed at educating and inspiring the general public about cutting-edge biomedical research.
Phone
+61 2 9325 3278
E-mail
s.odonoghue@unsw.edu.au
Location
Garvan Institute of Medical Research
  • Book Chapters | 2014
    Ma DKG; Stolte C; Kaur S; Bain M; O Donoghue SI, 2014, 'Visual analytics of signalling pathways using time profiles', in Sun C; Bednarz T; Pham TD; Vallotton P; Wang D (ed.), Signal and Image Analysis for Biomedical and Life Sciences, pp. 3 - 22
    Book Chapters | 2006
    O Donoghue SI; Russell RB; Schafferhans A, 2006, 'Three-dimensional structures in target discovery and validation', in León D; Markel S (ed.), In Silico Technologies in Drug Target Identification and Validation, pp. 285 - 305
    Book Chapters | 2003
    O Donoghue SI, 2003, 'Role of mnemonics and virtual reality in visualizing genomics and proteomics data', in Andrade MA (ed.), Bioinformatics and Genomics: Current Perspectives, pp. 185 - 196
    Book Chapters | 1999
    O Donoghue SI; Nilges M, 1999, 'Calculation of symmetric oligomer structures from NMR data', in Krishna NR; Berliner LJ (ed.), Biological Magnetic Resonance 17: Structure Computation and Dynamics in Protein NMR, pp. 131 - 161
    Book Chapters | 1990
    Wilson MR; O Donoghue SI; Walker NA, 1990, 'Urea transport and metabolism in Chara corillina', in Walker NA; Smith JR; Bielby M (ed.), Membrane Transport in Plants and Fungi, pp. 393 - 394
  • Journal articles | 2022
    De Crécy-Lagard V; Amorin De Hegedus R; Arighi C; Babor J; Bateman A; Blaby I; Blaby-Haas C; Bridge AJ; Burley SK; Cleveland S; Colwell LJ; Conesa A; Dallago C; Danchin A; De Waard A; Deutschbauer A; Dias R; Ding Y; Fang G; Friedberg I; Gerlt J; Goldford J; Gorelik M; Gyori BM; Henry C; Hutinet G; Jaroch M; Karp PD; Kondratova L; Lu Z; Marchler-Bauer A; Martin MJ; McWhite C; Moghe GD; Monaghan P; Morgat A; Mungall CJ; Natale DA; Nelson WC; O'Donoghue S; Orengo C; O'Toole KH; Radivojac P; Reed C; Roberts RJ; Rodionov D; Rodionova IA; Rudolf JD; Saleh L; Sheynkman G; Thibaud-Nissen F; Thomas PD; Uetz P; Vallenet D; Carter EW; Weigele PR; Wood V; Wood-Charlson EM; Xu J, 2022, 'A roadmap for the functional annotation of protein families: A community perspective', Database, 2022, http://dx.doi.org/10.1093/database/baac062
    Journal articles | 2022
    Munoz MA; Skinner OP; Masle-Farquhar E; Jurczyluk J; Xiao Y; Fletcher EK; Kristianto E; Hodson MP; O’Donoghue SI; Kaur S; Brink R; Zahra DG; Deenick EK; Perry KA; Robertson AAB; Mehr S; Hissaria P; Mulders-Manders CM; Simon A; Rogers MJ, 2022, 'Increased core body temperature exacerbates defective protein prenylation in mouse models of mevalonate kinase deficiency', Journal of Clinical Investigation, 132, http://dx.doi.org/10.1172/JCI160929
    Journal articles | 2022
    Rittenbruch M; Vella K; Brereton M; Hogan JM; Johnson D; Heinrich J; Ordonoghue S, 2022, 'Collaborative Sense-Making in Genomic Research: The Role of Visualisation', IEEE Transactions on Visualization and Computer Graphics, 28, pp. 4477 - 4489, http://dx.doi.org/10.1109/TVCG.2021.3090746
    Journal articles | 2021
    Bernhofer M; Dallago C; Karl T; Satagopam V; Heinzinger M; Littmann M; Olenyi T; Qiu J; Schütze K; Yachdav G; Ashkenazy H; Ben-Tal N; Bromberg Y; Goldberg T; Kajan L; O'Donoghue S; Sander C; Schafferhans A; Schlessinger A; Vriend G; Mirdita M; Gawron P; Gu W; Jarosz Y; Trefois C; Steinegger M; Schneider R; Rost B, 2021, 'PredictProtein - Predicting protein structure and function for 29 years', Nucleic Acids Research, 49, pp. W535 - W540, http://dx.doi.org/10.1093/nar/gkab354
    Journal articles | 2021
    Kaur S; Sikta N; Schafferhans A; Bordin N; Cowley M; Thomas D; Ballinger M; O’Donoghue S, 2021, 'Streamlined use of protein structures in variant analysis', , http://dx.doi.org/10.1101/2021.09.10.459756
    Journal articles | 2021
    O'Donoghue SI, 2021, 'Grand Challenges in Bioinformatics Data Visualization', Frontiers in Bioinformatics, 1, http://dx.doi.org/10.3389/fbinf.2021.669186
    Journal articles | 2021
    O’Donoghue SI; Schafferhans A; Sikta N; Stolte C; Kaur S; Ho BK; Anderson S; Procter JB; Dallago C; Bordin N; Adcock M; Rost B, 2021, 'SARS-CoV-2 structural coverage map reveals viral protein assembly, mimicry, and hijacking mechanisms', Molecular Systems Biology, 17, http://dx.doi.org/10.15252/msb.202010079
    Journal articles | 2021
    Valdés-Mora F; Salomon R; Gloss BS; Law AMK; Venhuizen J; Castillo L; Murphy KJ; Magenau A; Papanicolaou M; Rodriguez de la Fuente L; Roden DL; Colino-Sanguino Y; Kikhtyak Z; Farbehi N; Conway JRW; Sikta N; Oakes SR; Cox TR; O'Donoghue SI; Timpson P; Ormandy CJ; Gallego-Ortega D, 2021, 'Single-cell transcriptomics reveals involution mimicry during the specification of the basal breast cancer subtype', Cell Reports, 35, http://dx.doi.org/10.1016/j.celrep.2021.108945
    Journal articles | 2020
    Kaur S; Peters T; Yang P; Luu LDW; Vuong J; Krycer J; O’Donoghue S, 2020, 'Temporal ordering of omics and multiomic events inferred from time series data', , http://dx.doi.org/10.1101/2020.04.14.040527
    Journal articles | 2020
    Kaur S; Peters TJ; Yang P; Luu LDW; Vuong J; Krycer JR; O’Donoghue SI, 2020, 'Temporal ordering of omics and multiomic events inferred from time-series data', npj Systems Biology and Applications, 6, http://dx.doi.org/10.1038/s41540-020-0141-0
    Journal articles | 2020
    O’Donoghue S; Schafferhans A; Sikta N; Stolte C; Kaur S; Ho B; Anderson S; Procter J; Dallago C; Bordin N; Adcock M; Rost B, 2020, 'SARS-CoV-2 structural coverage map reveals state changes that disrupt host immunity', , http://dx.doi.org/10.1101/2020.07.16.207308
    Journal articles | 2019
    Burgess A; Vuong J; Marzec KA; Nicolai de Lichtenberg U; O'Donoghue SI; Jensen LJ, 2019, 'SnapShot: S-Phase Entry and Exit', Cell, 179, pp. 802 - 802.e1, http://dx.doi.org/10.1016/j.cell.2019.09.031
    Journal articles | 2019
    Kaur S; Baldi B; Vuong J; O'Donoghue SI, 2019, 'A benchmark dataset for analyzing and visualizing the dynamic epiproteome', Data in Brief, 25, http://dx.doi.org/10.1016/j.dib.2019.104000
    Journal articles | 2019
    Kaur S; Baldi B; Vuong J; O'Donoghue SI, 2019, 'Visualization and Analysis of Epiproteome Dynamics', Journal of Molecular Biology, 431, pp. 1519 - 1539, http://dx.doi.org/10.1016/j.jmb.2019.01.044
    Journal articles | 2019
    Martinez X; Krone M; Alharbi N; Rose AS; Laramee RS; O'Donoghue S; Baaden M; Chavent M, 2019, 'Molecular Graphics: Bridging Structural Biologists and Computer Scientists', Structure, 27, pp. 1617 - 1623, http://dx.doi.org/10.1016/j.str.2019.09.001
    Journal articles | 2018
    O'Donoghue SI; Baldi BF; Clark SJ; Darling AE; Hogan JM; Kaur S; Maier-Hein L; McCarthy DJ; Moore WJ; Stenau E; Swedlow JR; Vuong J; Procter JB, 2018, 'Visualization of Biomedical Data', Annual Review of Biomedical Data Science, 1, pp. 1 - 30, http://dx.doi.org/10.1146/annurev-biodatasci-080917-013424
    Journal articles | 2018
    Schafferhans A; O'Donoghue SI; Heinzinger M; Rost B, 2018, 'Dark Proteins Important for Cellular Function', Proteomics, 18, pp. e1800227, http://dx.doi.org/10.1002/pmic.201800227
    Journal articles | 2018
    Vuong J; Kaur S; Heinrich J; Ho BK; Hammang CJ; Baldi BF; O'Donoghue SI, 2018, 'Versus—A tool for evaluating visualizations and image quality using a 2AFC methodology', Visual Informatics, 2, pp. 225 - 234, http://dx.doi.org/10.1016/j.visinf.2018.12.003
    Journal articles | 2017
    Burgess A; Vuong J; Rogers S; Malumbres M; O Donoghue SI, 2017, 'SnapShot: Phosphoregulation of mitosis', Cell, 169, pp. 1358–1358.e1 - 1358–1358.e1, http://dx.doi.org/10.1016/j.cell.2017.06.003
    Journal articles | 2017
    Netzel R; Vuong J; Engelke U; O'Donoghue S; Weiskopf D; Heinrich J, 2017, 'Comparative eye-tracking evaluation of scatterplots and parallel coordinates', Visual Informatics, 1, pp. 118 - 131, http://dx.doi.org/10.1016/j.visinf.2017.11.001
    Journal articles | 2017
    Perdigão N; Rosa AC; O Donoghue SI, 2017, 'The dark proteome database', BioData Mining, 10, pp. 24 - 24, http://dx.doi.org/10.1186/s13040-017-0144-6
    Journal articles | 2016
    Ballinger ML; Goode DL; Ray-Coquard I; James PA; Mitchell G; Niedermayr E; Puri A; Schiffman JD; Dite GS; Cipponi A; Maki RG; Brohl AS; Myklebost O; Stratford EW; Lorenz S; Ahn S-M; Ahn J-H; Kim JE; Shanley S; Beshay V; Randall RL; Judson I; Seddon B; Campbell IG; Young M-A; Sarin R; Blay J-Y; O Donoghue SI; Thomas DM, 2016, 'Novel monogenic and polygenic determinants of sarcoma risk: An international study of 1162 families', The Lancet Oncology, 17, pp. 1261 - 1271
    Journal articles | 2016
    Ballinger ML; Goode DL; Ray-Coquard I; James PA; Mitchell G; Niedermayr E; Puri A; Schiffman JD; Dite GS; Cipponi A; Maki RG; Brohl AS; Myklebost O; Stratford EW; Lorenz S; Ahn SM; Ahn JH; Kim JE; Shanley S; Beshay V; Randall RL; Judson I; Seddon B; Campbell IG; Young MA; Sarin R; Blay JY; O'Donoghue SI; Thomas DM, 2016, 'Monogenic and polygenic determinants of sarcoma risk: an international genetic study', The Lancet Oncology, 17, pp. 1261 - 1271, http://dx.doi.org/10.1016/S1470-2045(16)30147-4
    Journal articles | 2016
    Heinrich J; Vuong J; Hammang CJ; Wu A; Rittenbruch M; Hogan J; Brereton M; O Donoghue SI, 2016, 'Evaluating viewpoint entropy for ribbon representation of protein structure', Computer Graphics Forum, 35, pp. 181–190 - 181–190
    Journal articles | 2016
    Taberlay PC; Achinger-Kawecka J; Lun ATL; Buske FA; Sabir KS; Gould CM; Zotenko E; Bert SA; Giles KA; Bauer D; Smyth GK; Stirzaker C; O Donoghue SI; Clark SJ, 2016, 'Three-dimensional disorganisation of the cancer genome occurs coincident with long range genetic and epigenetic alterations', Genome Research, 26, pp. 719 - 731
    Journal articles | 2015
    Ma DKG; Stolte C; Krycer JR; James DE; O Donoghue SI, 2015, 'SnapShot: Insulin/IGF1 signaling', Cell, 161, pp. 948 - 948
    Journal articles | 2015
    Ma DKG; Stolte C; Krycer JR; James DE; O'Donoghue SI, 2015, 'Erratum: SnapShot: Insulin/IGF1 Signaling (Cell (2015) 161 (948))', Cell, 162, pp. 689, http://dx.doi.org/10.1016/j.cell.2015.07.025
    Journal articles | 2015
    O Donoghue SI; Sabir KS; Kalemanov M; Stolte C; Wellmann B; Ho V; Roos M; Perdigão N; Buske F; Heinrich J; Rost B; Schafferhans A, 2015, 'Aquaria: Simplifying discovery and insight from protein structures', Nature Methods, 12, pp. 98–99 - 98–99
    Journal articles | 2015
    Perdigão N; Heinrich J; Stolte C; Sabir KS; Buckley MJ; Tabor B; Signal B; Gloss BS; Hammang CJ; Rost B; Schafferhans A; O Donoghue SI, 2015, 'Unexpected features of the dark proteome', Proceedings of the National Academy of Sciences of the United States of America, 112, pp. 15898–15903 - 15898–15903
    Journal articles | 2015
    Santos A; Tsafou K; Stolte C; Pletscher-Frankild S; O Donoghue SI; Jensen LJ; O'Donoghue S, 2015, 'Comprehensive comparison of large-scale tissue expression datasets', PeerJ, 3, pp. e1054 - e1054, http://dx.doi.org/10.7717/peerj.1054
    Journal articles | 2015
    Soldatos TG; Perdigão N; Brown NP; Sabir KS; O Donoghue SI, 2015, 'How to learn about gene function: Text-mining or ontologies?', Methods, 74, pp. 3 - 15, http://dx.doi.org/10.1016/j.ymeth.2014.07.004
    Journal articles | 2015
    Stolte C; Sabir KS; Heinrich J; Hammang CJ; Schafferhans A; O Donoghue SI, 2015, 'Integrated visual analysis of protein structures, sequences, and feature data', BMC Bioinformatics, 16, pp. S7 - S7, http://dx.doi.org/10.1186/1471-2105-16-S11-S7
    Journal articles | 2014
    Binder JX; Pletscher-Frankild S; Tsafou K; Stolte C; O Donoghue SI; Schneider R; Jensen LJ; O'Donoghue S, 2014, 'COMPARTMENTS: Unification and visualization of protein subcellular localization evidence', Database, 2014, http://dx.doi.org/10.1093/database/bau012
    Journal articles | 2014
    Heinrich J; Krone M; O Donoghue SI; Weiskopf D, 2014, 'Visualising intrinsic disorder and conformational variation in protein ensembles', Faraday Discussions, 169, pp. 179 - 193, http://dx.doi.org/10.1039/c3fd00138e
    Journal articles | 2013
    Görg C; Hunter L; Kennedy J; O Donoghue SI; Van Wijk JJ, 2013, 'Biological Data Visualization', Dagstuhl Reports, 2, pp. 131 - 164
    Journal articles | 2013
    O Donoghue SI, 2013, 'Visualising biological data: Current perspectives', AIP Conference Proceeding, 1559, pp. 12 - 13, http://dx.doi.org/10.1063/1.4825252
    Journal articles | 2012
    Soldatos TG; O Donoghue SI; Satagopam VP; Barbosa-Silva A; Pavlopoulos GA; Wanderley-Nogueira AC; Soares-Cavalcanti NM; Schneider R, 2012, 'Caipirini: Using gene sets to rank literature', Biodata Mining, 5, http://dx.doi.org/10.1186/1756-0381-5-1
    Journal articles | 2010
    Gehlenborg N; O Donoghue SI; Baliga NS; Goesmann A; Hibbs MA; Kitano H; Kohlbacher O; Neuweger H; Schneider R; Tenenbaum D; Gavin A-C, 2010, 'Visualization of omics data for systems biology', Nature Methods, 7, pp. S56 - S68, http://dx.doi.org/10.1038/nmeth.1436
    Journal articles | 2010
    Marji J; Donoghue SIO; McClintock D; Satagopam VP; Schneider R; Ratner D; Worman HJ; Gordon LB; Djabali K, 2010, 'Defective lamin A-Rb signaling in Hutchinson-Gilford progeria syndrome and reversal by farnesyltransferase inhibition', PLOS ONE, 5, http://dx.doi.org/10.1371/journal.pone.0011132
    Journal articles | 2010
    O Donoghue SI; Gavin A-C; Gehlenborg N; Goodsell DS; Hériché J-K; Nielsen CB; North C; Olson AJ; Procter JB; Shattuck DW; Walter T; Wong B, 2010, 'Visualizing biological data - now and in the future', Nature Methods, 7, pp. S2 - S4
    Journal articles | 2010
    O Donoghue SI; Goodsell DS; Frangakis AS; Jossinet F; Laskowski R; Nilges M; Saibil HR; Schafferhans A; Wade R; Westhof E; Olson AJ, 2010, 'Visualization of macromolecular structures', Nature Methods, 7, pp. S42 - S55
    Journal articles | 2010
    O Donoghue SI; Horn H; Kuhn M; Pafilis E; Jensen LJ; Schneider R, 2010, 'Reflect: A practical approach to web semantics', J. Web Semantics, 8, pp. 182 - 189, http://dx.doi.org/10.1016/j.websem.2010.03.003
    Journal articles | 2010
    Soldatos T; O Donoghue SI; Satagopam VP; Brown NP; Jensen LJ; Schneider R; O'Donoghue S, 2010, 'Martini: Using literature keywords to compare gene sets', Nucleic Acids Research, 38, pp. 26 - 38, http://dx.doi.org/10.1093/nar/gkp876
    Journal articles | 2009
    Pafilis E; O'Donoghue SI; Jensen LJ; Horn H; Kuhn M; Brown NP; Schneider R, 2009, 'Reflect: Augmented browsing for the life scientist', Nature Biotechnology, 27, pp. 508 - 510, http://dx.doi.org/10.1038/nbt0609-508
    Journal articles | 2008
    Altman R; Bergman CM; Blake J; Blaschke C; Cohen A; Gannon F; Grivell L; Hahn U; Hersh W; Hirschman L; Jensen LJ; Krallinger M; Mons B; O Donoghue SI; Peitsch M; Rebholz-Schuhmann D; Shatkay H; Valencia A; O'Donoghue S, 2008, 'Text mining for biology - the way forward: Opinions from leading scientists', Genome Biology, 9, pp. S7 - S7, http://dx.doi.org/10.1186/gb-2008-9-s2-s7
    Journal articles | 2008
    Pavlopoulos GA; O Donoghue SI; Satagopam VP; Soldatos T; Pafilis E; Schneider R; O'Donoghue S, 2008, 'Arena3D: Visualization of biological networks in 3D', BMC Systems Biology, 2, pp. 104 - 104, http://dx.doi.org/10.1186/1752-0509-2-104
    Journal articles | 2006
    Nilges M; Habeck M; O Donoghue SI; Rieping W, 2006, 'Error distribution derived NOE distance restraints', Proteins: Structure, Function, and Bioinformatics, 64, pp. 652 - 664, http://dx.doi.org/10.1002/prot.20985
    Journal articles | 2004
    O'Donoghue SI; Meyer JEW; Schafferhans A; Fries K, 2004, 'The SRS 3D module: Integrating structures, sequences and features', Bioinformatics, 20, pp. 2476 - 2478, http://dx.doi.org/10.1093/bioinformatics/bth260
    Journal articles | 2003
    Schafferhans A; Meyer JEW; O Donoghue SI, 2003, 'The PSSH database of alignments between protein sequences and tertiary structures', Nucleic Acids Research, 31, pp. 494 - 498, http://dx.doi.org/10.1093/nar/gkg110
    Journal articles | 2002
    Chang X; Keller D; O Donoghue SI; Led JJ, 2002, 'NMR studies of the aggregation of glucagon-like peptide-1: Formation of a symmetric helical dimer', FEBS Letters, 515, pp. 165 - 170, http://dx.doi.org/10.1016/S0014-5793(02)02466-3
    Journal articles | 2002
    Fries K; O Donoghue SI, 2002, 'Navigating around the building blocks of life', Advanced Imaging, 17, pp. 18 - 39
    Journal articles | 2002
    Kovacs H; O Donoghue SI; Hoppe HJ; Comfort D; Reid KB; Campbell D; Nilges M, 2002, 'Solution structure of the coiled-coil trimerization domain from lung surfactant protein D', Journal of Biomolecular NMR, 24, pp. 89 - 102
    Journal articles | 2001
    Andrade MA; Petosa C; O Donoghue SI; Müller CW; Bork P, 2001, 'Comparison of ARM and HEAT protein repeats', Journal of Molecular Biology, 309, pp. 1 - 18
    Journal articles | 2001
    Linge JP; O Donoghue SI; Nilges M, 2001, 'Automated assignment of ambiguous nuclear overhauser effects with ARIA', , 339, pp. 71 - 90
    Journal articles | 2000
    O Donoghue SI; Chang X; Abseher R; Nilges M; Led JJ, 2000, 'Unravelling the symmetry ambiguities in a symmetric hexamer: Calculation of the R6 human insulin structure', Journal of Biomolecular NMR, 16, pp. 93 - 108
    Journal articles | 1999
    Chalaoux F-R; O Donoghue SI; Nilges M, 1999, 'Molecular dynamics and accuracy of NMR structures: Effects of error bounds and data removal', Proteins: Structure, Function, and Bioinformatics, 34, pp. 453 - 463, https://www.ncbi.nlm.nih.gov/pubmed/10081958
    Journal articles | 1999
    Chalaoux FR; O'Donoghue SI; Nilges M, 1999, 'Molecular dynamics and accuracy of nmr structures: Effects of error bounds and data removal', Proteins: Structure, Function and Genetics, 34, pp. 453 - 463, http://dx.doi.org/10.1002/(SICI)1097-0134(19990301)34:4<453::AID-PROT5>3.0.CO;2-7
    Journal articles | 1998
    Andrade MA; O'Donoghue SI; Rost B, 1998, 'Adaptation of protein surfaces to subcellular location', Journal of Molecular Biology, 276, pp. 517 - 525, http://dx.doi.org/10.1006/jmbi.1997.1498
    Journal articles | 1998
    Nilges M; O Donoghue SI, 1998, 'Ambiguous NOEs and automated NOE assignment', Progress in Nuclear Magnetic Resonance Spectroscopy, 32, pp. 107 - 139, http://dx.doi.org/10.1016/S0079-6565(97)00025-3
    Journal articles | 1997
    Fletcher JI; Smith R; O Donoghue SI; Nilges M; Connor M; Howden MEH; Christie MJ; King GF, 1997, 'The structure of a novel insecticidal neurotoxin, atracotoxin-HVI, from the venom of an Australian funnel web spider', Nature Structural Biology, 4, pp. 559 - 566
    Journal articles | 1997
    Nilges M; Macias M; O Donoghue SI; Oschkinat H, 1997, 'Automated NOESY interpretation with ambiguous distance restraints: The refined NMR solution structure of the pleckstrin homology domain from b-spectrin', Journal of Molecular Biology, 269, pp. 408 - 422
    Journal articles | 1997
    O Donoghue SI; Nilges M, 1997, 'Tertiary structure prediction using mean-force potentials and internal energy functions: Successful prediction for coiled-coil geometries', Folding & Design, 2, pp. S47 - S52
    Journal articles | 1997
    Rost B; O Donoghue SI, 1997, 'Sisyphus and prediction of protein structure', Bioinformatics, 13, pp. 345 - 356
    Journal articles | 1996
    Junius FK; O Donoghue SI; Nilges M; Weiss AS; King GF, 1996, 'High resolution NMR solution structure of the leucine zipper domain of the c-Jun homodimer', Journal of Biological Chemistry, 271, pp. 13663 - 13667, http://dx.doi.org/10.1074/jbc.271.23.13663
    Journal articles | 1996
    O Donoghue SI; King GF; Nilges M, 1996, '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', Journal of Biomolecular NMR, 8, pp. 193 - 206, http://dx.doi.org/10.1007/BF00211165
    Journal articles | 1995
    NILGES M; ODONOGHUE SI; ABAGIAN K, 1995, 'STRUCTURE REFINEMENT FROM NMR DATA', JOURNAL OF CELLULAR BIOCHEMISTRY, pp. 21 - 21, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:A1995QT86500051&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1
    Journal articles | 1995
    Williams NK; Manthey MK; Hambley TW; O Donoghue SI; Keegan M; Chapman BE; Christopherson RI, 1995, 'Catalysis by hamster dihydroorotase: Zinc binding, site-directed mutagenesis, and interaction with inhibitors', Biochemistry, 34, pp. 11344 - 11352, http://dx.doi.org/10.1021/bi00036a007
    Journal articles | 1994
    Rae C; O Donoghue SI; Bubb WA; Kuchel PW, 1994, 'Stereospecificity of substrate usage by glyoxalase-1: Nuclear-magnetic-resonance studies of kinetics and hemithioacetal substrate conformation', Biochemistry, 33, pp. 3548 - 3559, http://dx.doi.org/10.1021/bi00178a011
    Journal articles | 1994
    Williams NK; O Donoghue SI; Christopherson RI, 1994, 'Homology and mutagenesis studies of hamster dihydroorotase', , 370, pp. 597 - 601
    Journal articles | 1993
    JUNIUS FK; ODONOGHUE SI; WEISS AS; KING GF, 1993, 'THE SOLUTION STRUCTURE OF THE LEUCINE ZIPPER MOTIF OF THE JUN ONCOPROTEIN HOMODIMER', JOURNAL OF CELLULAR BIOCHEMISTRY, pp. 295 - 295, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:A1993KN46601019&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1
    Journal articles | 1993
    KING GF; JOSEPH KA; ODONOGHUE SI; MILLS RG, 1993, 'SYSTEMATIC REFINEMENT OF THE SOLUTION STRUCTURE OF ENDOTHELIN-3 BY RELAXATION MATRIX ANALYSIS', JOURNAL OF CELLULAR BIOCHEMISTRY, pp. 254 - 254, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:A1993KN46600858&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1
    Journal articles | 1993
    O Donoghue SI; Junius FK; King GF, 1993, 'Structure determination of symmetric coiled coils by NMR; applications to the leucine zipper proteins Jun and GCN4', Protein Engineering, Design and Selection, 6, pp. 557 - 564
    Journal articles | 1992
    Knott HM; Berndt MC; Kralicek AV; O Donoghue SI; King GF, 1992, 'Determination of the solution structure of a platelet-adhesion peptide of von Willebrand factor', Biochemistry, 31, pp. 11152 - 11158, http://dx.doi.org/10.1021/bi00160a028
    Journal articles | 1992
    Miki M; O Donoghue SI; dos Remedios CG, 1992, 'Structure of actin observed by fluorescence resonance energy-transfer spectroscopy', Journal of Muscle Research and Cell Motility, 13, pp. 132 - 145
    Journal articles | 1992
    Mills RG; O Donoghue SI; Smith R; King GF, 1992, 'The solution structure of endothelin-3 determined using NMR spectroscopy', Biochemistry, 31, pp. 5640 - 5645, http://dx.doi.org/10.1021/bi00139a030
    Journal articles | 1992
    O Donoghue SI; Hambly BD; dos Remedios CG, 1992, 'Models of the actin monomer and filament from fluorescence resonance-energy transfer measurements', FEBS Journal, 205, pp. 591 - 601, http://dx.doi.org/10.1111/j.1432-1033.1992.tb16817.x
    Journal articles | 1992
    O'Donoghue SI; Miki M; dos Remedios CG, 1992, 'Removing the two C-terminal residues of actin affects the filament structure', Archives of Biochemistry and Biophysics, 293, pp. 110 - 116, http://dx.doi.org/10.1016/0003-9861(92)90372-4
    Journal articles | 1991
    O Donoghue SI, 1991, 'Structural interpretation of fluorescence resonance-energy transfer measurements', Computer Applications in the Biosciences, 7, pp. 471 - 477, http://dx.doi.org/10.1093/bioinformatics/7.4.471
    Journal articles | 1988
    Wilson MR; O Donoghue SI; Walker NA, 1988, 'The transport and metabolism of urea in Chara australis III: Two specific transport systems', Journal of Experimental Botany, 39, pp. 763 - 774
    Journal articles |
    O Donoghue SI, 'Animating life: bringing science to the YouTube generation', The Conversation
  • Conference Papers | 2019
    Tran TS; Bliuc D; O'Donoghue S; Hansen L; Abrahamsen B; van den Bergh J; van Geel T; Geusens P; Vestergaard P; Nguyen TV; Center JR, 2019, 'Trajectories to subsequent admissions and mortality following a specific fragility fracture: A nationwide population-based follow-up study', in JOURNAL OF BONE AND MINERAL RESEARCH, WILEY, FL, Orlando, pp. 386 - 386, presented at Annual Meeting of the American-Society-for-Bone-and Mineral Research, FL, Orlando, 20 September 2019 - 23 September 2019, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000508356605054&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1
    Preprints | 2018
    O'Donoghue SI; Baldi BF; Clark SJ; Darling AE; Hogan JM; Kaur S; Maier-Hein L; McCarthy DJ; Moore WJ; Stenau E; Swedlow JR; Vuong J; Procter JB, 2018, Visualization of Biomedical Data, http://dx.doi.org/10.7287/peerj.preprints.26896
    Preprints | 2018
    O'Donoghue SI; Baldi BF; Clark SJ; Darling AE; Hogan JM; Kaur S; Maier-Hein L; McCarthy DJ; Moore WJ; Stenau E; Swedlow JR; Vuong J; Procter JB, 2018, Visualization of Biomedical Data, http://dx.doi.org/10.7287/peerj.preprints.26896v1
    Other | 2016
    Fitz-Walter Z; O Donoghue S; Baldi BF; Hogan J; Johnson D; Brereton M, 2016, Using videogames to improve molecular graphics tools, , http://dx.doi.org/10.1145/3010915.3011851
    Conference Papers | 2016
    Hutson H; Johnson D; Chua X-Y; Hogan J; Brereton M; Rittenbruch M; Baldi BF; O Donoghue SI, 2016, 'Can videogame players inform better scientific visualization', in Cox A (ed.), Proceedings of the 2016 Annual Symposium on Computer-Human Interaction in Play Companion, pp. 181 - 187, http://dx.doi.org/10.1145/2968120.2987736
    Other | 2016
    Vuong J; Stolte C; Kaur S; O Donoghue S, 2016, Developing a visual analytics tool for large-scale proteomics time-series data, , http://dx.doi.org/10.1109/BDVA.2016.7787048
    Conference Papers | 2015
    Heinrich J; Kaur S; O Donoghue SI, 2015, 'Evaluating the effectiveness of color to convey uncertainty in macromolecular structures', in Engelke U; Heinrich J; Bednarz T; Klein K; Nguyen QV (eds.), 2015 Big Data Visual Analytics, BDVA 2015, IEEE, Hobart, AUSTRALIA, pp. 1 - 18, presented at 2015 Big Data Visual Analytics (BDVA), Hobart, AUSTRALIA, 22 - 25 September 2015, http://dx.doi.org/10.1109/BDVA.2015.7314292
    Conference Papers | 2015
    Perdigão N; Soldatos TG; Sabir KS; O Donoghue SI, 2015, 'Visual analytics of gene set comparison', in IEEE Symposium on Big Data Visual Analytics, http://dx.doi.org/10.1109/BDVA.2015.7314304
    Conference Papers | 2014
    Heinrich J; Burch M; O Donoghue SI, 2014, 'On the use of 1D, 2D, and 3D visualisation for molecular graphics', in IEEE VIS International Workshop on 3DVis, pp. 55 - 60, http://dx.doi.org/10.1109/3DVis.2014.7160101
    Conference Papers | 2013
    Ma DKG; Stolte C; Kaur S; Bain M; O Donoghue SI, 2013, 'Visual analytics of phosphorylation time-series data on insulin response', in AIP Conference Proceeding, pp. 185 - 196
    Conference Papers | 2013
    Ma DKG; Stolte C; Kaur S; Bain M; O'Donoghue SI, 2013, 'Visual analytics of phosphorylation time-series data on insulin response', in AIP Conference Proceedings, pp. 185 - 196, http://dx.doi.org/10.1063/1.4825010
    Conference Papers | 2013
    Sabir K; Stolte C; Tabor B; O Donoghue SI, 2013, 'The Molecular Control Toolkit: Controlling 3D molecular graphics via gesture and voice', in IEEE Symposium on Biological Data Visualization (BioVis), pp. 49 - 56
    Theses / Dissertations | 1991
    O Donoghue SI, 1991, Actin structure and function, phdthesis
    Theses / Dissertations | 1986
    O Donoghue SI, 1986, The transport of nitrogen-containing compounds in Chara corillina, phdthesis
    Other |
    O Donoghue SI; Procter JB, Data visualisation isn’t just for communication, it’s also a research tool,
    Preprints |
    Valdes-Mora F; Salomon R; Gloss B; Law AMK; Castillo L; Murphy K; Venhuizen J; Magenau A; Papanicolau M; Rodriguez de la Fuente L; Roden DL; Colino-Sanguino Y; Kikhtyak Z; Farbehi N; Conway JRW; Oakes SR; Sikta N; O'Donoghue SI; Cox TR; Timpson P; Ormandy CJ; Gallego Ortega D, Single Cell Transcriptomics Reveals Involution Mimicry During the Specification of the Basal Breast Cancer Subtype, http://dx.doi.org/10.2139/ssrn.3634808