PUBLICATIONS

91 publications, newest first.

2023

  1. Assessing 2D visual encoding of 3D spatial connectivityBaldi BF, Vuong J, O’Donoghue SIFrontiers in Bioinformatics

2022

  1. Increased core body temperature exacerbates defective protein prenylation in mouse models of mevalonate kinase deficiencyMunoz MA, Skinner OP, Masle-Farquhar E, Jurczyluk J, Xiao Y, Fletcher EK, Kristianto E, Hodson MP, O’Donoghue SI, Kaur S, Brink R, et al.Journal of Clinical Investigation

2021

  1. Grand Challenges in Bioinformatics Data VisualizationO’Donoghue SIFrontiers in Bioinformatics
  2. SARS‐CoV‐2 structural coverage map reveals viral protein assembly, mimicry, and hijacking mechanismsO’Donoghue SI, Schafferhans A, Sikta N, Stolte C, Kaur S, Ho BK, Anderson S, Procter JB, Dallago C, Bordin N, Adcock M, Rost BMolecular Systems Biology
  3. Single-cell transcriptomics reveals involution mimicry during the specification of the basal breast cancer subtypeValdés-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, …, O’Donoghue SI, et al.Cell Reports
  4. Streamlined use of protein structures in variant analysisKaur S, Sikta N, Schafferhans A, Bordin N, Cowley MJ, Thomas DM, Ballinger ML, O’Donoghue SIbioRxiv · Other

2020

  1. SARS-CoV-2 structural coverage map reveals state changes that disrupt host immunityO’Donoghue SI, Schafferhans A, Sikta N, Stolte C, Kaur S, Ho BK, Anderson S, Procter J, Dallago C, Bordin N, Adcock M, Rost BbioRxiv · Other
  2. Temporal ordering of omics and multiomic events inferred from time series dataKaur S, Peters TJ, Yang P, Luu LDW, Vuong J, Krycer JR, O’Donoghue SIbioRxiv · Preprint
  3. Temporal ordering of omics and multiomic events inferred from time-series dataKaur S, Peters TJ, Yang P, Luu LDW, Vuong J, Krycer JR, O’Donoghue SInpj Systems Biology and Applications

2019

  1. A benchmark dataset for analyzing and visualizing the dynamic epiproteomeKaur S, Baldi B, Vuong J, O’Donoghue SIData in Brief
  2. Molecular Graphics: Bridging Structural Biologists and Computer ScientistsMartinez X, Krone M, Alharbi N, Rose AS, Laramee RS, O’Donoghue SI, Baaden M, Chavent MStructure
  3. SnapShot: S-Phase Entry and ExitBurgess A, Vuong J, Marzec KA, Nicolai de Lichtenberg U, O’Donoghue SI, Jensen LJCell
  4. Visualization and Analysis of Epiproteome DynamicsKaur S, Baldi B, Vuong J, O’Donoghue SIJournal of Molecular Biology

2018

  1. Dark Proteins Important for Cellular FunctionSchafferhans A, O’Donoghue SI, Heinzinger M, Rost BPROTEOMICS
  2. Versus—A tool for evaluating visualizations and image quality using a 2AFC methodologyVuong J, Kaur S, Heinrich J, Ho BK, Hammang CJ, Baldi BF, O’Donoghue SIVisual Informatics
  3. Visualization of Biomedical DataO’Donoghue SI, Baldi BF, Clark SJ, Darling AE, Hogan JM, Kaur S, Maier-Hein L, McCarthy DJ, Moore WJ, Stenau E, Swedlow JR, et al.Annual Review of Biomedical Data Science

2017

  1. Comparative eye-tracking evaluation of scatterplots and parallel coordinatesNetzel R, Vuong J, Engelke U, O’Donoghue SI, Weiskopf D, Heinrich JVisual Informatics
  2. Data visualisation isn’t just for communication, it’s also a research toolO’Donoghue SI, Procter JBThe Conversation · Magazine article
  3. SnapShot: Phosphoregulation of MitosisBurgess A, Vuong J, Rogers S, Malumbres M, O’Donoghue SICell
  4. The Dark Proteome DatabasePerdigão N, Rosa AC, O’Donoghue SIBioData Mining

2016

  1. Can Videogame Players Inform Better Scientific Visualization'Hutson H, Johnson D, Chua XY, Hogan J, Brereton M, Rittenbruch M, Baldi BF, O’Donoghue SIProceedings of the 2016 Annual Symposium on Computer-Human Interaction in Play Companion Extended Abstracts · Conference paper
  2. Developing a Visual Analytics Tool for Large-Scale Proteomics Time-Series DataVuong J, Stolte C, Kaur S, O’Donoghue SI2016 Big Data Visual Analytics (BDVA) · Other
  3. Evaluating Viewpoint Entropy for Ribbon Representation of Protein StructureHeinrich J, Vuong J, Hammang CJ, Wu A, Rittenbruch M, Hogan J, Brereton M, O’Donoghue SIComputer Graphics Forum
  4. Monogenic and polygenic determinants of sarcoma risk: an international genetic studyBallinger ML, Goode DL, Ray-Coquard I, James PA, Mitchell G, Niedermayr E, Puri A, Schiffman JD, Dite GS, Cipponi A, Maki RG, …, O’Donoghue SI, et al.The Lancet Oncology
  5. Three-dimensional disorganization of the cancer genome occurs coincident with long-range genetic and epigenetic alterationsTaberlay PC, Achinger-Kawecka J, Lun ATL, Buske FA, Sabir K, Gould CM, Zotenko E, Bert SA, Giles KA, Bauer DC, Smyth GK, …, O’Donoghue SI, et al.Genome Research
  6. Using videogames to improve molecular graphics toolsFitz-Walter Z, O’Donoghue SI, Baldi BF, Hogan J, Johnson D, Brereton MProceedings of the 28th Australian Conference on Computer-Human Interaction - OzCHI '16 · Other

2015

  1. Aquaria: simplifying discovery and insight from protein structuresO’Donoghue SI, Sabir KS, Kalemanov M, Stolte C, Wellmann B, Ho V, Roos M, Perdigão N, Buske FA, Heinrich J, Rost B, Schafferhans ANature Methods
  2. Comprehensive comparison of large-scale tissue expression datasetsSantos A, Tsafou K, Stolte C, Pletscher-Frankild S, O’Donoghue SI, Jensen LJPeerJ
  3. Evaluating the Effectiveness of Color to Convey Alignment Quality in Macromolecular StructuresHeinrich J, Kaur S, O’Donoghue SI2015 Big Data Visual Analytics (BDVA) · Other
  4. How to learn about gene function: text-mining or ontologies?Soldatos TG, Perdigão N, Brown NP, Sabir KS, O’Donoghue SIMethods
  5. Integrated visual analysis of protein structures, sequences, and feature dataStolte C, Sabir KS, Heinrich J, Hammang CJ, Schafferhans A, O’Donoghue SIBMC Bioinformatics
  6. SnapShot: Insulin/IGF1 SignalingMa DKG, Stolte C, Krycer JR, James DE, O’Donoghue SICell
  7. SnapShot: Insulin/IGF1 SignalingMa DKG, Stolte C, Krycer JR, James DE, O’Donoghue SICell
  8. Unexpected features of the dark proteomePerdigão N, Heinrich J, Stolte C, Sabir KS, Buckley MJ, Tabor B, Signal B, Gloss BS, Hammang CJ, Rost B, Schafferhans A, O’Donoghue SIProceedings of the National Academy of Sciences
  9. Visual Analytics of Gene Sets ComparisonPerdigao N, Soldatos TG, Sabir KS, O’Donoghue SI2015 Big Data Visual Analytics (BDVA) · Conference paper

2014

  1. Animating life: bringing science to the YouTube generationO’Donoghue SIThe Conversation · Magazine article
  2. COMPARTMENTS: unification and visualization of protein subcellular localization evidenceBinder JX, Pletscher-Frankild S, Tsafou K, Stolte C, O’Donoghue SI, Schneider R, Jensen LJDatabase
  3. On the use of 1D, 2D, and 3D visualisation for molecular graphicsHeinrich J, Burch M, O’Donoghue SI2014 IEEE VIS International Workshop on 3DVis (3DVis) · Conference paper
  4. Visual Analytics of Signalling Pathways Using Time ProfilesMa DKG, Stolte C, Kaur S, Bain M, O’Donoghue SIAdvances in Experimental Medicine and Biology · Book chapter
  5. Visualising intrinsic disorder and conformational variation in protein ensemblesHeinrich J, Krone M, O’Donoghue SI, Weiskopf DFaraday Discuss.

2013

  1. Biological Data VisualizationGörg C, Hunter L, Kennedy J, O’Donoghue SI, Van Wijk JJDagstuhl Reports
  2. The Molecular Control Toolkit: Controlling 3D molecular graphics via gesture and voiceSabir K, Stolte C, Tabor B, O’Donoghue SI2013 IEEE Symposium on Biological Data Visualization (BioVis) · Conference paper
  3. Visual analytics of phosphorylation time-series data on insulin responseMa DKG, Stolte C, Kaur S, Bain M, O’Donoghue SIAIP Conference Proceedings · Conference paper
  4. Visualising biological data: Current perspectivesO’Donoghue SIAIP Conference Proceedings

2012

  1. Caipirini: using gene sets to rank literatureSoldatos TG, O’Donoghue SI, Satagopam VP, Barbosa-Silva A, Pavlopoulos GA, Wanderley-Nogueira AC, Soares-Cavalcanti NM, Schneider RBioData Mining

2010

  1. Defective Lamin A-Rb Signaling in Hutchinson-Gilford Progeria Syndrome and Reversal by Farnesyltransferase InhibitionMarji J, O’Donoghue SI, McClintock D, Satagopam VP, Schneider R, Ratner D, Worman HJ, Gordon LB, Djabali KPLoS ONE
  2. Martini: using literature keywords to compare gene setsSoldatos TG, O’Donoghue SI, Satagopam VP, Jensen LJ, Brown NP, Barbosa-Silva A, Schneider RNucleic Acids Research
  3. Reflect: A practical approach to web semanticsO’Donoghue SI, Horn H, Pafilis E, Haag S, Kuhn M, Satagopam VP, Schneider R, Jensen LJWeb Semantics: Science, Services and Agents on the World Wide Web
  4. Visualization of macromolecular structuresO’Donoghue SI, Goodsell DS, Frangakis AS, Jossinet F, Laskowski RA, Nilges M, Saibil HR, Schafferhans A, Wade RC, Westhof E, Olson AJNature Methods
  5. Visualization of omics data for systems biologyGehlenborg N, O’Donoghue SI, Baliga NS, Goesmann A, Hibbs MA, Kitano H, Kohlbacher O, Neuweger H, Schneider R, Tenenbaum D, Gavin ACNature Methods
  6. Visualizing biological data—now and in the futureO’Donoghue SI, Gavin AC, Gehlenborg N, Goodsell DS, Hériché JK, Nielsen CB, North C, Olson AJ, Procter JB, Shattuck DW, Walter T, Wong BNature Methods

2009

  1. Reflect: augmented browsing for the life scientistPafilis E, O’Donoghue SI, Jensen LJ, Horn H, Kuhn M, Brown NP, Schneider RNature Biotechnology

2008

  1. Arena3D: visualization of biological networks in 3DPavlopoulos GA, O’Donoghue SI, Satagopam VP, Soldatos TG, Pafilis E, Schneider RBMC Systems Biology
  2. Text mining for biology - the way forward: opinions from leading scientistsAltman RB, Bergman CM, Blake J, Blaschke C, Cohen A, Gannon F, Grivell L, Hahn U, Hersh W, Hirschman L, Jensen LJ, …, O’Donoghue SI, et al.Genome Biology

2006

  1. Error distribution derived NOE distance restraintsNilges M, Habeck M, O’Donoghue SI, Rieping WProteins: Structure, Function, and Bioinformatics
  2. Three-Dimensional Structures in Target Discovery and ValidationSchafferhans A, Russell R, O’Donoghue SIDrug Discovery Series · Book chapter

2004

  1. The SRS 3D module: integrating structures, sequences and featuresO’Donoghue SI, Meyer JEW, Schafferhans A, Fries KBioinformatics

2003

  1. Role of mnemonics and virtual reality in visualizing genomics and proteomics dataO’Donoghue SIBioinformatics and Genomics: Current Perspectives · Book chapter
  2. The PSSH database of alignments between protein sequences and tertiary structuresSchafferhans A, Meyer JE, O’Donoghue SINucleic Acids Research

2002

  1. Navigating around the building blocks of lifeFries K, O’Donoghue SIAdvanced Imaging · Magazine article
  2. NMR studies of the aggregation of glucagon‐like peptide‐1: formation of a symmetric helical dimerChang X, Keller D, O’Donoghue SI, Led JJFEBS Letters
  3. Solution structure of the coiled-coil trimerization domain from lung surfactant protein DKovacs H, O’Donoghue SI, Hoppe HJ, Comfort D, Reid KBM, Campbell ID, Nilges MJournal of Biomolecular NMR

2001

  1. Automated Assignment of Ambiguous Nuclear Overhauser Effects with ARIALinge JP, O’Donoghue SI, Nilges MMethods in Enzymology · Book chapter
  2. Comparison of ARM and HEAT protein repeatsAndrade MA, Petosa C, O’Donoghue SI, Müller CW, Bork PJournal of Molecular Biology

2000

  1. Unraveling the symmetry ambiguity in a hexamer: Calculation of the R6 human insulin structureO’Donoghue SI, Chang X, Abseher R, Nilges M, Led JJJournal of Biomolecular NMR

1999

  1. Calculation of symmetric oligomer structures from NMR dataO’Donoghue SI, Nilges MBiological Magnetic Resonance 17: Structure Computation and Dynamics in Protein NMR · Book chapter
  2. Molecular dynamics and accuracy of NMR structures: Effects of error bounds and data removalChalaoux FR, O’Donoghue SI, Nilges MProteins: Structure, Function, and Bioinformatics

1998

  1. Adaptation of protein surfaces to subcellular location 1 1Edited by F. E. CohenAndrade MA, O’Donoghue SI, Rost BJournal of Molecular Biology
  2. Ambiguous NOEs and automated NOE assignmentNilges M, O’Donoghue SIProgress in Nuclear Magnetic Resonance Spectroscopy

1997

  1. Automated NOESY interpretation with ambiguous distance restraints: the refined NMR solution structure of the pleckstrin homology domain from β-spectrin 1 1Edited by P. E. WrightNilges M, Macias MJ, O’Donoghue SI, Oschkinat HJournal of Molecular Biology
  2. Sisyphus and prediction of protein structureRost B, O’Donoghue SIBioinformatics
  3. Tertiary structure prediction using mean-force potentials and internal energy functions: successful prediction for coiled-coil geometriesO’Donoghue SI, Nilges MFolding and Design
  4. Tertiary structure prediction using mean-force potentials and internal energy functions: successful prediction for coiled-coil geometries.O’Donoghue SI, Nilges MFolding & design
  5. The structure of a novel insecticidal neurotoxin, ω-atracotoxin-HV1, from the venom of an Australian funnel web spiderFletcher JI, Smith R, O’Donoghue SI, Nilges M, Connor M, Howden MEH, Christie MJ, King GFNature Structural Biology

1996

  1. 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 zippersO’Donoghue SI, King G, Nilges MJournal of Biomolecular NMR
  2. High Resolution NMR Solution Structure of the Leucine Zipper Domain of the c-Jun HomodimerJunius FK, O’Donoghue SI, Nilges M, Weiss AS, King GFJournal of Biological Chemistry

1995

  1. Catalysis by Hamster Dihydroorotase: Zinc Binding, Site-Directed Mutagenesis, and Interaction with InhibitorsWilliams NK, Manthey MK, Hambley TW, O’Donoghue SI, Keegan M, Chapman BE, Christopherson RIBiochemistry

1994

  1. Homology and Mutagenesis Studies of Hamster DihydroorotaseWilliams NK, O’Donoghue SI, Christopherson RIAdvances in Experimental Medicine and Biology · Book chapter
  2. Stereospecificity of Substrate Usage by Glyoxalase 1: Nuclear Magnetic Resonance Studies of Kinetics and Hemithioacetal Substrate ConformationRae C, O’Donoghue SI, Bubb WA, Kuchel PWBiochemistry

1993

  1. Determination of the structure of symmetric coiled-coil proteins from NMR data: application of the leucine zipper proteins Jun and GCN4O’Donoghue SI, Junius FK, King GF"Protein Engineering, Design and Selection"

1992

  1. Determination of the solution structure of a platelet-adhesion peptide of von Willebrand factorKnott HM, Berndt MC, Kralicek AV, O’Donoghue SI, King GFBiochemistry
  2. Models of the actin monomer and filament from fluorescence resonance‐energy transferO’Donoghue SI, HAMBLY BD, dos REMEDIOS CGEuropean Journal of Biochemistry
  3. Removing the two C-terminal residues of actin affects the filament structureO’Donoghue SI, Miki M, dos Remedios CGArchives of Biochemistry and Biophysics
  4. Solution structure of endothelin-3 determined using NMR spectroscopyMills RG, O’Donoghue SI, Smith R, King GFBiochemistry
  5. Structure of actin observed by fluorescence resonance energy transfer spectroscopyMiki M, O’Donoghue SI, Dos Remedios CGJournal of Muscle Research and Cell Motility

1991

  1. Actin structure and functionO’Donoghue SIPh. D. Thesis · Student publication
  2. Structural interpretation of fluorescence resonance-energy transfer measurementsO’Donoghue SIComputer applications in the biosciences : CABIOS
  3. Structural interpretation of fluorescence resonance—energy transfer measurementsO’Donoghue SIBioinformatics

1990

  1. Urea transport and metabolism in Chara corillinaWilson MR, O’Donoghue SI, Walker NAMembrane Transport in Plants and Fungi · Book chapter

1988

  1. The Transport and Metabolism of Urea in Chara australisWilson MR, O’Donoghue SI, Walker NAJournal of Experimental Botany

1986

  1. The transport of nitrogen-containing compounds in Chara corillinaO’Donoghue SIB. Sc. Honours Thesis · Student publication