Seán I. O'Donoghue

Publication Activity (10 Years)

Years Active: 1991-2023
Publications (10 Years): 14

Top Topics

Visual Analytics

High Image Quality

Protein Structure

Grand Challenges

Top Venues

Vis. Informatics

Database J. Biol. Databases Curation

NII Shonan Meet. Rep.

Publications

Benedetta Frida Baldi, Jenny Vuong, Seán I. O'Donoghue
Assessing 2D visual encoding of 3D spatial connectivity. Frontiers Bioinform. 3 (2023)
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) (2022)
Valérie de Crécy-Lagard, Rocio Amorin de Hegedus, Cecilia N. Arighi, Jill Babor, Alex Bateman, Ian Blaby, Crysten Blaby-Haas, Alan 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 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)
Seán I. O'Donoghue
Grand Challenges in Bioinformatics Data Visualization. Frontiers Bioinform. 1 (2021)
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) (2021)
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) (2018)
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)
Nelson Perdigao, Agostinho C. Rosa, Seán I. O'Donoghue
The Dark Proteome Database. BioData Min. 10 (1) (2017)
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) (2017)
Jenny Vuong, Christian Stolte, Sandeep Kaur, Seán I. O'Donoghue
Developing a Visual Analytics Tool for Large-Scale Proteomics Time-Series Data. BDVA (2016)
Andrea Schafferhans, Seán I. O'Donoghue, Haruki Nakamura
Web-based Molecular Graphics (NII Shonan Meeting 2016-12). NII Shonan Meet. Rep. 2016 (2016)
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)
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) (2016)
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)
Julian Heinrich, Sandeep Kaur, Seán I. O'Donoghue
Evaluating the Effectiveness of Color to Convey Alignment Quality in Macromolecular Structures. BDVA (2015)
Nelson Perdigao, Theodoros G. Soldatos, Kenneth Sabir, Seán I. O'Donoghue
Visual Analytics of Gene Sets Comparison. BDVA (2015)
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) (2015)
Julian Heinrich, Michael Burch, Seán I. O'Donoghue
On the use of 1D, 2D, and 3D visualisation for molecular graphics. 3DVis@IEEE VIS (2014)
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)
Kenneth Sabir, Christian Stolte, Bruce Tabor, Seán I. O'Donoghue
The Molecular Control Toolkit: Controlling 3D molecular graphics via gesture and voice. BioVis (2013)
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 (2012)
Carsten Görg, Lawrence Hunter, Jessie Kennedy, Seán I. O'Donoghue, Jarke J. van Wijk
Biological Data Visualization (Dagstuhl Seminar 12372). Dagstuhl Reports 2 (9) (2012)
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) (2010)
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 (2008)
Seán I. O'Donoghue, Joachim E. W. Meyer, Andrea Schafferhans, Karsten Fries
The SRS 3D module: integrating structures, sequences and features. Bioinform. 20 (15) (2004)
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) (2003)
Burkhard Rost, Seán I. O'Donoghue
Sisyphus and prediction of protein structure. Comput. Appl. Biosci. 13 (4) (1997)
Seán I. O'Donoghue
Structural interpretation of fluorescence resonance-energy transfer measurements. Comput. Appl. Biosci. 7 (4) (1991)