Structural interpretation of fluorescence resonance-energy transfer measurements. - Seán I. O'Donoghue (Comput. Appl. Biosci., 1991)

Sisyphus and prediction of protein structure. - Burkhard Rost; Seán I. O'Donoghue (Comput. Appl. Biosci., 1997)

The PSSH database of alignments between protein sequences and tertiary structures. - Andrea Schafferhans; Joachim E. W. Meyer; Seán I. O'Donoghue (Nucleic Acids Res., 2003)

The SRS 3D module: integrating structures, sequences and features. - Seán I. O'Donoghue; Joachim E. W. Meyer; Andrea Schafferhans; Karsten Fries (Bioinform., 2004)

Arena3D: visualization of biological networks in 3D. - Georgios A. Pavlopoulos; Seán I. O'Donoghue; Venkata P. Satagopam; Theodoros G. Soldatos; Evangelos Pafilis; Reinhard Schneider 002 (BMC Syst. Biol., 2008)

Reflect: A practical approach to web semantics. - Seán I. O'Donoghue; Heiko Horn; Evangelos Pafilis; Sven Haag; Michael Kuhn 004; Venkata P. Satagopam; Reinhard Schneider 002; Lars Juhl Jensen (J. Web Semant., 2010)

Caipirini: using gene sets to rank literature. - 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 002 (BioData Min., 2012)

Biological Data Visualization (Dagstuhl Seminar 12372). - Carsten Görg; Lawrence Hunter; Jessie Kennedy; Seán I. O'Donoghue; Jarke J. van Wijk (Dagstuhl Reports, 2012)

The Molecular Control Toolkit: Controlling 3D molecular graphics via gesture and voice. - Kenneth Sabir; Christian Stolte; Bruce Tabor; Seán I. O'Donoghue (BioVis, 2013)

On the use of 1D, 2D, and 3D visualisation for molecular graphics. - Julian Heinrich; Michael Burch; Seán I. O'Donoghue (3DVis@IEEE VIS, 2014)

COMPARTMENTS: unification and visualization of protein subcellular localization evidence. - Janos X. Binder; Sune Pletscher-Frankild; Kalliopi Tsafou; Christian Stolte; Seán I. O'Donoghue; Reinhard Schneider 002; Lars Juhl Jensen (Database J. Biol. Databases Curation, 2014)

Evaluating the Effectiveness of Color to Convey Alignment Quality in Macromolecular Structures. - Julian Heinrich; Sandeep Kaur; Seán I. O'Donoghue (BDVA, 2015)

Visual Analytics of Gene Sets Comparison. - Nelson Perdigao; Theodoros G. Soldatos; Kenneth Sabir; Seán I. O'Donoghue (BDVA, 2015)

Integrated visual analysis of protein structures, sequences, and feature data. - Christian Stolte; Kenneth Sabir; Julian Heinrich; Christopher J. Hammang; Andrea Schafferhans; Seán I. O'Donoghue (BMC Bioinform., 2015)

Developing a Visual Analytics Tool for Large-Scale Proteomics Time-Series Data. - Jenny Vuong; Christian Stolte; Sandeep Kaur; Seán I. O'Donoghue (BDVA, 2016)

Can Videogame Players Inform Better Scientific Visualization'. - Holly Hutson; Daniel M. Johnson 001; Xin-Yi Chua; James M. Hogan; Margot Brereton; Markus Rittenbruch; Benedetta Frida Baldi; Seán I. O'Donoghue (CHI PLAY (Companion), 2016)

Using videogames to improve molecular graphics tools. - Zachary Fitz-Walter; Seán I. O'Donoghue; Benedetta Frida Baldi; James M. Hogan; Daniel M. Johnson 001; Margot Brereton (OZCHI, 2016)

Evaluating Viewpoint Entropy for Ribbon Representation of Protein Structure. - Julian Heinrich; Jenny Vuong; Christopher J. Hammang; A. Wu; Markus Rittenbruch; James M. Hogan; Margot Brereton; Seán I. O'Donoghue (Comput. Graph. Forum, 2016)

Web-based Molecular Graphics (NII Shonan Meeting 2016-12). - Andrea Schafferhans; Seán I. O'Donoghue; Haruki Nakamura (NII Shonan Meet. Rep., 2016)

The Dark Proteome Database. - Nelson Perdigao; Agostinho C. Rosa; Seán I. O'Donoghue (BioData Min., 2017)

Comparative eye-tracking evaluation of scatterplots and parallel coordinates. - Rudolf Netzel; Jenny Vuong; Ulrich Engelke; Seán I. O'Donoghue; Daniel Weiskopf; Julian Heinrich (Vis. Informatics, 2017)

Web Molecular Graphics: Emerging Technologies & Standards (NII Shonan Meeting 2018-19). - Seán I. O'Donoghue; Masakazu Sekijima; Marc Baaden (NII Shonan Meet. Rep., 2018)

Versus - A tool for evaluating visualizations and image quality using a 2AFC methodology. - Jenny Vuong; Sandeep Kaur; Julian Heinrich; Bosco K. Ho; Christopher J. Hammang; Benedetta Frida Baldi; Seán I. O'Donoghue (Vis. Informatics, 2018)

Grand Challenges in Bioinformatics Data Visualization. - Seán I. O'Donoghue (Frontiers Bioinform., 2021)

PredictProtein - Predicting Protein Structure and Function for 29 Years. - 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; et al. (Nucleic Acids Res., 2021)

A roadmap for the functional annotation of protein families: a community perspective. - 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; et al. (Database J. Biol. Databases Curation, 2022)

Collaborative Sense-Making in Genomic Research: The Role of Visualisation. - Markus Rittenbruch; Kellie Vella; Margot Brereton; James M. Hogan; Daniel Johnson 001; Julian Heinrich; Seán I. O'Donoghue (IEEE Trans. Vis. Comput. Graph., 2022)

Assessing 2D visual encoding of 3D spatial connectivity. - Benedetta Frida Baldi; Jenny Vuong; Seán I. O'Donoghue (Frontiers Bioinform., 2023)