CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures. - Eva Chovancová; Antonín Pavelka; Petr Benes; Ondrej Strnad; Jan Brezovsky; Barbora Kozlíková; Artur Góra; Vilém Sustr; Martin Klvana; Petr Medek; Lada Biedermannová; Jiri Sochor; et al. (PLoS Comput. Biol., 2012)

Detection of Intramolecular Tunnels Connecting Sequence of Sites in Protein Structures. - Ondrej Strnad; Barbora Kozlíková; Jiri Sochor (PACBB, 2014)

Visualizing Movements of Protein Tunnels in Molecular Dynamics Simulations. - Barbora Kozlíková; Adam Jurcík; Jan Byska; Ondrej Strnad; Jiri Sochor (VCBM, 2014)

CAVER Analyst 1.0: graphic tool for interactive visualization and analysis of tunnels and channels in protein structures. - Barbora Kozlíková; Eva Sebestova; Vilém Sustr; Jan Brezovsky; Ondrej Strnad; Lukas Daniel; David Bednar; Antonín Pavelka; Martin Manak; Martin Bezdeka; Petr Benes; Matus Kotry; et al. (Bioinform., 2014)

CAVER Analyst 2.0: analysis and visualization of channels and tunnels in protein structures and molecular dynamics trajectories. - Adam Jurcík; David Bednar; Jan Byska; Sérgio M. Marques; Katarína Furmanová; Lukas Daniel; Piia Kokkonen; Jan Brezovsky; Ondrej Strnad; Jan Stourac; Antonín Pavelka; Martin Manak; et al. (Bioinform., 2018)

Molecumentary: Scalable Narrated Documentaries Using Molecular Visualization. - David Kouril; Ondrej Strnad; Peter Mindek; Sarkis Halladjian; Tobias Isenberg 001; M. Eduard Gröller; Ivan Viola (CoRR, 2020)

@What does a virus actually look like? - Peter Mindek; Ivan Viola; Ondrej Strnad; Ciril Bohak; Sai Li; Tobias Klein (SIGGRAPH Computer Animation Festival, 2021)

Modeling in the Time of COVID-19: Statistical and Rule-based Mesoscale Models. - Ngan V. T. Nguyen; Ondrej Strnad; Tobias Klein; Deng Luo; Ruwayda Alharbi; Peter Wonka; Martina Maritan; Peter Mindek; Ludovic Autin; David S. Goodsell; Ivan Viola (IEEE Trans. Vis. Comput. Graph., 2021)

SynopSet: Multiscale Visual Abstraction Set for Explanatory Analysis of DNA Nanotechnology Simulations. - Deng Luo; Alexandre Kouyoumdjian; Ondrej Strnad; Haichao Miao; Ivan Barisic; Ivan Viola (CoRR, 2022)

VOICE: Visual Oracle for Interaction, Conversation, and Explanation. - Donggang Jia; Alexandra Irger; Ondrej Strnad; Johanna Björklund; Anders Ynnerman; Ivan Viola (CoRR, 2023)

Nanotilus: Generator of Immersive Guided-Tours in Crowded 3D Environments. - Ruwayda Alharbi; Ondrej Strnad; Laura Rosalia Luidolt; Manuela Waldner; David Kouril; Ciril Bohak; Tobias Klein; Eduard Gröller; Ivan Viola (IEEE Trans. Vis. Comput. Graph., 2023)

Molecumentary: Adaptable Narrated Documentaries Using Molecular Visualization. - David Kouril; Ondrej Strnad; Peter Mindek; Sarkis Halladjian; Tobias Isenberg 001; M. Eduard Gröller; Ivan Viola (IEEE Trans. Vis. Comput. Graph., 2023)

Finding Nano-Ötzi: Cryo-Electron Tomography Visualization Guided by Learned Segmentation. - Ngan V. T. Nguyen; Ciril Bohak; Dominik Engel; Peter Mindek; Ondrej Strnad; Peter Wonka; Sai Li; Timo Ropinski; Ivan Viola (IEEE Trans. Vis. Comput. Graph., 2023)

Towards Differentiable Electron Microscopy Simulation: Methods and Applications. - Ngan V. T. Nguyen; Feng Liang; Dominik Engel; Ciril Bohak; Ondrej Strnad; Timo Ropinski; Ivan Viola (PacificVis, 2024)

Nanouniverse: Virtual Instancing of Structural Detail and Adaptive Shell Mapping. - Ruwayda Alharbi; Ondrej Strnad; Markus Hadwiger; Ivan Viola (CoRR, 2024)

Volume conductor: interactive visibility management for crowded volumes. - Ziga Lesar; Ruwayda Alharbi; Ciril Bohak; Ondrej Strnad; Christoph Heinzl; Matija Marolt; Ivan Viola (Vis. Comput., 2024)

GPU Accelerated 3D Tomographic Reconstruction and Visualization From Noisy Electron Microscopy Tilt-Series. - Julio Rey Ramirez; Peter Rautek; Ciril Bohak; Ondrej Strnad; Zheyuan Zhang; Sai Li; Ivan Viola; Wolfgang Heidrich (IEEE Trans. Vis. Comput. Graph., 2024)

DiffFit: Visually-Guided Differentiable Fitting of Molecule Structures to a Cryo-EM Map. - Deng Luo; Zainab Alsuwaykit; Dawar Khan; Ondrej Strnad; Tobias Isenberg 001; Ivan Viola (IEEE Trans. Vis. Comput. Graph., 2025)

Errata to "DiffFit: Visually-Guided Differentiable Fitting of Molecule Structures to a Cryo-EM Map". - Deng Luo; Zainab Alsuwaykit; Dawar Khan; Ondrej Strnad; Tobias Isenberg 001; Ivan Viola (IEEE Trans. Vis. Comput. Graph., 2025)

Nanomatrix: Scalable Construction of Crowded Biological Environments. - Ruwayda Alharbi; Ondrej Strnad; Tobias Klein; Ivan Viola (IEEE Trans. Vis. Comput. Graph., 2025)