By Dr Sean O'Donoghue

Journal articles

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

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

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

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

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

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

O'Donoghue SI, 2021, 'Grand Challenges in Bioinformatics Data Visualization', Frontiers in Bioinformatics, 1, http://dx.doi.org/10.3389/fbinf.2021.669186

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

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

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

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

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

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

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

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

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

Schafferhans A; O'Donoghue SI; Heinzinger M; Rost B, 2018, 'Dark Proteins Important for Cellular Function', Proteomics, 18, http://dx.doi.org/10.1002/pmic.201800227

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

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

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

Perdigão N; Rosa AC; O Donoghue SI; O'Donoghue S, 2017, 'The dark proteome database', BioData Mining, 10, pp. 24 - 24, http://dx.doi.org/10.1186/s13040-017-0144-6

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

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

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

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

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

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

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

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

Stolte C; Sabir KS; Heinrich J; Hammang CJ; Schafferhans A; O Donoghue SI; O'Donoghue S, 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

Ma DKG; Stolte C; Krycer JR; James DE; O Donoghue SI, 2015, 'SnapShot: Insulin/IGF1 signaling', Cell, 161, pp. 948 - 948

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

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

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

Görg C; Hunter L; Kennedy J; O Donoghue SI; Van Wijk JJ, 2013, 'Biological Data Visualization', Dagstuhl Reports, 2, pp. 131 - 164

O Donoghue SI, 2013, 'Visualising biological data: Current perspectives', AIP Conference Proceeding, 1559, pp. 12 - 13

Soldatos TG; O Donoghue SI; Satagopam VP; Barbosa-Silva A; Pavlopoulos GA; Wanderley-Nogueira AC; Soares-Cavalcanti NM; Schneider R; O'Donoghue S, 2012, 'Caipirini: Using gene sets to rank literature', Biodata Mining, 5, http://dx.doi.org/10.1186/1756-0381-5-1

Marji J; Donoghue SIO; McClintock D; Satagopam VP; Schneider R; Ratner D; Worman HJ; Gordon LB; Djabali K; O'Donoghue S, 2010, 'Defective lamin A-Rb signaling in Hutchinson-Gilford progeria syndrome and reversal by farnesyltransferase inhibition', PLOS ONE, 5, pp. e11132, http://dx.doi.org/10.1371/journal.pone.0011132

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

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

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

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

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

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

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

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

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