By Dr Sean O'Donoghue

Journal articles

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

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

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

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

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

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

Linge JP; O Donoghue SI; Nilges M, 2001, 'Automated assignment of ambiguous nuclear overhauser effects with ARIA', , 339, pp. 71 - 90

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

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

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

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

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

Nilges M; O Donoghue SI, 1998, 'Ambiguous NOEs and automated NOE assignment', Progress in Nuclear Magnetic Resonance Spectroscopy, 32, pp. 107 - 139

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

Rost B; O Donoghue SI, 1997, 'Sisyphus and prediction of protein structure', Bioinformatics, 13, pp. 345 - 356

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

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

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

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

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

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

Williams NK; O Donoghue SI; Christopherson RI, 1994, 'Homology and mutagenesis studies of hamster dihydroorotase', , 370, pp. 597 - 601

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

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

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

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

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

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

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

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

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

O Donoghue SI, 1991, 'Structural interpretation of fluorescence resonance-energy transfer measurements', Computer Applications in the Biosciences, 7, pp. 471 - 477

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

O Donoghue SI, 'Animating life: bringing science to the YouTube generation', The Conversation

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

Conference Papers

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

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

Perdigão N; Soldatos TG; Sabir KS; O Donoghue SI, 2015, 'Visual analytics of gene set comparison', in IEEE Symposium on Big Data Visual Analytics

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

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

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

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

Heinrich J; Kaur S; O Donoghue SI, 'Evaluating the effectiveness of color to convey uncertainty in macromolecular structures', pp. 1 - 18

Theses / Dissertations

O Donoghue SI, 1991, Actin structure and function

O Donoghue SI, 1986, The transport of nitrogen-containing compounds in Chara corillina

Preprints

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

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

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

Other

O Donoghue SI; Procter JB, Data visualisation isn’t just for communication, it’s also a research tool

Vuong J; Stolte C; Kaur S; O Donoghue S, Developing a visual analytics tool for large-scale proteomics time-series data

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