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ORCIDSeán I. O'Donoghue
Person information
- affiliation: Garvan Institute of Medical Research, Sydney, Australia
- affiliation: CSIRO, Sydney, Australia
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Journal Articles
- 2023
[j18]Benedetta Frida Baldi, Jenny Vuong, Seán I. O'Donoghue:
Assessing 2D visual encoding of 3D spatial connectivity. Frontiers Bioinform. 3 (2023)- 2022
- [j17]Valérie de Crécy-Lagard
, Rocio Amorin de Hegedus, Cecilia N. Arighi, Jill Babor, Alex Bateman, Ian Blaby, Crysten Blaby-Haas, Alan J. Bridge, Stephen K. Burley, Stacey Cleveland, Lucy J. Colwell, Ana Conesa, Christian Dallago, Antoine Danchin, Anita de Waard, Adam Deutschbauer, Raquel Dias, Yousong Ding, Gang Fang, Iddo Friedberg, John Gerlt, Joshua Goldford, Mark Gorelik, Benjamin M. Gyori, Christopher S. Henry, Geoffrey Hutinet, Marshall Jaroch, Peter D. Karp, Liudmyla Kondratova, Zhiyong Lu, Aron Marchler-Bauer, Maria Jesus Martin, Claire D. McWhite, Gaurav D. Moghe, Paul Monaghan, Anne Morgat, Christopher J. Mungall, Darren A. Natale, William C. Nelson, Seán I. O'Donoghue, Christine A. Orengo, Katherine H. O'Toole, Predrag Radivojac, Colbie Reed, Richard J. Roberts, Dmitri Rodionov, Irina A. Rodionova, Jeffrey DePons, Lana Saleh, Gloria M. Sheynkman, Françoise Thibaud-Nissen, Paul D. Thomas, Peter Uetz, David Vallenet, Erica Watson Carter, Peter Weigele, Valerie Wood, Elisha M. Wood-Charlson, Jin Xu:
A roadmap for the functional annotation of protein families: a community perspective. Database J. Biol. Databases Curation 2022(2022) (2022) - [j16]Markus Rittenbruch, Kellie Vella, Margot Brereton, James M. Hogan, Daniel Johnson, Julian Heinrich, Seán I. O'Donoghue:
Collaborative Sense-Making in Genomic Research: The Role of Visualisation. IEEE Trans. Vis. Comput. Graph. 28(12): 4477-4489 (2022) - 2021
- [j15]Seán I. O'Donoghue:
Grand Challenges in Bioinformatics Data Visualization. Frontiers Bioinform. 1 (2021) - [j14]Michael Bernhofer, Christian Dallago, Timothy Karl, Venkata P. Satagopam, Michael Heinzinger, Maria Littmann, Tobias Olenyi, Jiajun Qiu, Konstantin Schütze, Guy Yachdav, Haim Ashkenazy, Nir Ben-Tal, Yana Bromberg, Tatyana Goldberg, László Kaján, Seán I. O'Donoghue, Chris Sander, Andrea Schafferhans, Avner Schlessinger, Gerrit Vriend, Milot Mirdita, Piotr Gawron, Wei Gu, Yohan Jarosz, Christophe Trefois, Martin Steinegger, Reinhard Schneider, Burkhard Rost:
PredictProtein - Predicting Protein Structure and Function for 29 Years. Nucleic Acids Res. 49(Webserver-Issue): 535-540 (2021) - 2018
- [j13]Jenny Vuong, Sandeep Kaur, Julian Heinrich, Bosco K. Ho, Christopher J. Hammang, Benedetta Frida Baldi, Seán I. O'Donoghue:
Versus - A tool for evaluating visualizations and image quality using a 2AFC methodology. Vis. Informatics 2(4): 225-234 (2018) - 2017
- [j12]Nelson Perdigao, Agostinho C. Rosa, Seán I. O'Donoghue:
The Dark Proteome Database. BioData Min. 10(1): 24:1-24:11 (2017) - [j11]Rudolf Netzel, Jenny Vuong, Ulrich Engelke, Seán I. O'Donoghue, Daniel Weiskopf, Julian Heinrich:
Comparative eye-tracking evaluation of scatterplots and parallel coordinates. Vis. Informatics 1(2): 118-131 (2017) - 2016
- [j10]Julian Heinrich, Jenny Vuong, Christopher J. Hammang, A. Wu, Markus Rittenbruch, James M. Hogan, Margot Brereton, Seán I. O'Donoghue:
Evaluating Viewpoint Entropy for Ribbon Representation of Protein Structure. Comput. Graph. Forum 35(3): 181-190 (2016) - 2015
- [j9]Christian Stolte, Kenneth Sabir, Julian Heinrich, Christopher J. Hammang, Andrea Schafferhans, Seán I. O'Donoghue:
Integrated visual analysis of protein structures, sequences, and feature data. BMC Bioinform. 16(S11): S7 (2015) - 2014
- [j8]Janos X. Binder, Sune Pletscher-Frankild, Kalliopi Tsafou, Christian Stolte, Seán I. O'Donoghue, Reinhard Schneider, Lars Juhl Jensen:
COMPARTMENTS: unification and visualization of protein subcellular localization evidence. Database J. Biol. Databases Curation 2014 (2014) - 2012
- [j7]Theodoros G. Soldatos, Seán I. O'Donoghue, Venkata P. Satagopam, Adriano Barbosa-Silva, Georgios A. Pavlopoulos, Ana Carolina Wanderley-Nogueira, Nina da Mota Soares-Cavalcanti, Reinhard Schneider:
Caipirini: using gene sets to rank literature. BioData Min. 5: 1 (2012) - 2010
- [j6]Seán I. O'Donoghue, Heiko Horn, Evangelos Pafilis, Sven Haag, Michael Kuhn, Venkata P. Satagopam, Reinhard Schneider, Lars Juhl Jensen:
Reflect: A practical approach to web semantics. J. Web Semant. 8(2-3): 182-189 (2010) - 2008
- [j5]Georgios A. Pavlopoulos, Seán I. O'Donoghue, Venkata P. Satagopam, Theodoros G. Soldatos, Evangelos Pafilis, Reinhard Schneider:
Arena3D: visualization of biological networks in 3D. BMC Syst. Biol. 2: 104 (2008) - 2004
- [j4]Seán I. O'Donoghue, Joachim E. W. Meyer, Andrea Schafferhans, Karsten Fries:
The SRS 3D module: integrating structures, sequences and features. Bioinform. 20(15): 2476-2478 (2004) - 2003
- [j3]Andrea Schafferhans, Joachim E. W. Meyer, Seán I. O'Donoghue:
The PSSH database of alignments between protein sequences and tertiary structures. Nucleic Acids Res. 31(1): 494-498 (2003) - 1997
- [j2]Burkhard Rost, Seán I. O'Donoghue:
Sisyphus and prediction of protein structure. Comput. Appl. Biosci. 13(4): 345-356 (1997) - 1991
- [j1]Seán I. O'Donoghue:
Structural interpretation of fluorescence resonance-energy transfer measurements. Comput. Appl. Biosci. 7(4): 471-477 (1991)
Conference and Workshop Papers
- 2016
- [c7]Jenny Vuong, Christian Stolte, Sandeep Kaur, Seán I. O'Donoghue:
Developing a Visual Analytics Tool for Large-Scale Proteomics Time-Series Data. BDVA 2016: 1-2 - [c6]Holly Hutson, Daniel M. Johnson, Xin-Yi Chua, James M. Hogan, Margot Brereton, Markus Rittenbruch, Benedetta Frida Baldi, Seán I. O'Donoghue:
Can Videogame Players Inform Better Scientific Visualization'. CHI PLAY (Companion) 2016: 181-187 - [c5]Zachary Fitz-Walter, Seán I. O'Donoghue, Benedetta Frida Baldi, James M. Hogan, Daniel M. Johnson, Margot Brereton:
Using videogames to improve molecular graphics tools. OZCHI 2016: 646-648 - 2015
- [c4]Julian Heinrich, Sandeep Kaur, Seán I. O'Donoghue:
Evaluating the Effectiveness of Color to Convey Alignment Quality in Macromolecular Structures. BDVA 2015: 41-48 - [c3]Nelson Perdigao, Theodoros G. Soldatos, Kenneth Sabir, Seán I. O'Donoghue:
Visual Analytics of Gene Sets Comparison. BDVA 2015: 133-134 - 2014
- [c2]Julian Heinrich, Michael Burch, Seán I. O'Donoghue:
On the use of 1D, 2D, and 3D visualisation for molecular graphics. 3DVis@IEEE VIS 2014: 55-60 - 2013
- [c1]Kenneth Sabir, Christian Stolte, Bruce Tabor, Seán I. O'Donoghue:
The Molecular Control Toolkit: Controlling 3D molecular graphics via gesture and voice. BioVis 2013: 49-56
Informal and Other Publications
- 2018
- [i3]Seán I. O'Donoghue, Masakazu Sekijima, Marc Baaden:
Web Molecular Graphics: Emerging Technologies & Standards (NII Shonan Meeting 2018-19). NII Shonan Meet. Rep. 2018 (2018) - 2016
- [i2]Andrea Schafferhans, Seán I. O'Donoghue, Haruki Nakamura:
Web-based Molecular Graphics (NII Shonan Meeting 2016-12). NII Shonan Meet. Rep. 2016 (2016) - 2012
- [i1]Carsten Görg, Lawrence Hunter, Jessie Kennedy, Seán I. O'Donoghue, Jarke J. van Wijk:
Biological Data Visualization (Dagstuhl Seminar 12372). Dagstuhl Reports 2(9): 131-164 (2012)
Coauthor Index
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