Geometry-based Algorithm for Detection of Asymmetric Tunnels in Protein Molecules. - Jan Byska; Adam Jurcík; Jiri Sochor (TPCG, 2013)

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

Path-planning algorithm for transportation of molecules through protein tunnel bottlenecks. - Jan Byska; Ivana Kolingerová; Barbora Kozlíková; Jirí Sochor (SCCG, 2015)

Visibility-based approach to surface detection of tunnels in proteins. - Adam Jurcík; Jan Byska; Jirí Sochor; Barbora Kozlíková (SCCG, 2015)

MoleCollar and Tunnel Heat Map Visualizations for Conveying Spatio-Temporo-Chemical Properties Across and Along Protein Voids. - Jan Byska; Adam Jurcík; M. Eduard Gröller; Ivan Viola; Barbora Kozlíková (Comput. Graph. Forum, 2015)

Unfolding and Interactive Exploration of Protein Tunnels and their Dynamics. - Ivan Kolesár; Jan Byska; Július Parulek; Helwig Hauser; Barbora Kozlíková (VCBM/MedViz, 2016)

AnimoAminoMiner: Exploration of Protein Tunnels and their Properties in Molecular Dynamics. - Jan Byska; Mathieu Le Muzic; M. Eduard Gröller; Ivan Viola; Barbora Kozlíková (IEEE Trans. Vis. Comput. Graph., 2016)

Watergate: Visual Exploration of Water Trajectories in Protein Dynamics. - Viktor Vad; Jan Byska; Adam Jurcík; Ivan Viola; M. Eduard Gröller; Helwig Hauser; Sérgio M. Marques; Jirí Damborský; Barbora Kozlíková (VCBM, 2017)

Interactive exploration of ligand transportation through protein tunnels. - Katarína Furmanová; Miroslava Jaresová; Jan Byska; Adam Jurcík; Július Parulek; Helwig Hauser; Barbora Kozlíková (BMC Bioinform., 2017)

Comparative visualization of protein secondary structures. - Lucia Kocincová; Miroslava Jaresová; Jan Byska; Július Parulek; Helwig Hauser; Barbora Kozlíková (BMC Bioinform., 2017)

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)

COZOID: contact zone identifier for visual analysis of protein-protein interactions. - Katarína Furmanová; Jan Byska; M. Eduard Gröller; Ivan Viola; Jan J. Palecek; Barbora Kozlíková (BMC Bioinform., 2018)

Visual Analysis of Ligand Trajectories in Molecular Dynamics. - Adam Jurcík; Katarína Furmanová; Jan Byska; Vojtech Vonásek; Ondrej Vávra; Pavol Ulbrich; Helwig Hauser; Barbora Kozlíková (PacificVis, 2019)

DockVis: Visual Analysis of Molecular Docking Data. - Katarína Furmanová; Barbora Kozlíková; Vojtech Vonásek; Jan Byska (VCBM, 2019)

Analysis of Long Molecular Dynamics Simulations Using Interactive Focus+Context Visualization. - Jan Byska; Thomas Trautner; Sérgio M. Marques; Jirí Damborský; Barbora Kozlíková; Manuela Waldner (Comput. Graph. Forum, 2019)

PINGU Principles of Interactive Navigation for Geospatial Understanding. - Zoltán Orémus; Kahin Akram Hassan; Jirí Chmelík; Michaela Knazková; Jan Byska; Renata Georgia Raidou; Barbora Kozlíková (PacificVis, 2020)

Visual exploration of large normal mode spaces to study protein flexibility. - Pierre Bedoucha; Nathalie Reuter; Helwig Hauser; Jan Byska (Comput. Graph., 2020)

DockVis: Visual Analysis of Molecular Docking Trajectories. - Katarína Furmanová; Ondrej Vávra; Barbora Kozlíková; Jirí Damborský; Vojtech Vonásek; David Bednar; Jan Byska (Comput. Graph. Forum, 2020)

Multiscale Visual Drilldown for the Analysis of Large Ensembles of Multi-Body Protein Complexes. - Katarína Furmanová; Adam Jurcík; Barbora Kozlíková; Helwig Hauser; Jan Byska (IEEE Trans. Vis. Comput. Graph., 2020)

Scale-Space Splatting: Reforming Spacetime for Cross-Scale Exploration of Integral Measures in Molecular Dynamics. - Juraj Pálenik; Jan Byska; Stefan Bruckner; Helwig Hauser (IEEE Trans. Vis. Comput. Graph., 2020)

Visual Analysis of Protein-Protein Interaction Docking Models Using COZOID Tool. - Jan Byska; Adam Jurcík; Katarína Furmanová; Barbora Kozlíková; Jan J. Palecek (Protein-Protein Interaction Networks, 2020)

VRdeo: Creating engaging educational material for asynchronous student-teacher exchange using virtual reality. - Vojtech Bruza; Jan Byska; Jan Mican; Barbora Kozlíková (Comput. Graph., 2021)

Foreword to the special section on molecular graphics and visual analysis of molecular data (MolVA 2021). - Jan Byska; Michael Krone; Bjorn Sommer 001 (Comput. Graph., 2021)

ChemVA: Interactive Visual Analysis of Chemical Compound Similarity in Virtual Screening. - María Virginia Sabando; Pavol Ulbrich; Matias Nicolás Selzer; Jan Byska; Jan Mican; Ignacio Ponzoni; Axel J. Soto; Maria Luján Ganuza; Barbora Kozlíková (IEEE Trans. Vis. Comput. Graph., 2021)

ChromoSkein: Untangling Three-Dimensional Chromatin Fiber With a Web-Based Visualization Framework. - Matús Talcík; Filip Opálený; Tereza Clarence; Katarína Furmanová; Jan Byska; Barbora Kozlíková; David Kouril (CoRR, 2022)

LoopGrafter: a web tool for transplanting dynamical loops for protein engineering. - Joan Planas-Iglesias; Filip Opálený; Pavol Ulbrich; Jan Stourac; Zainab K. Sanusi; Gaspar R. P. Pinto; Andrea Schenkmayerova; Jan Byska; Jirí Damborský; Barbora Kozlíková; David Bednar (Nucleic Acids Res., 2022)

Vivern-A Virtual Environment for Multiscale Visualization and Modeling of DNA Nanostructures. - David Kuták; Matias Nicolás Selzer; Jan Byska; Maria Luján Ganuza; Ivan Barisic; Barbora Kozlíková; Haichao Miao (IEEE Trans. Vis. Comput. Graph., 2022)

sMolBoxes: Dataflow Model for Molecular Dynamics Exploration. - Pavol Ulbrich; Manuela Waldner; Katarína Furmanová; Sérgio M. Marques; David Bednár; Barbora Kozlíková; Jan Byska (IEEE Trans. Vis. Comput. Graph., 2023)

Foreword: Special section on Molecular Graphics and Visual Analysis of Molecular Data (MolVA 2023). - Jan Byska; Michael Krone; Björn Sommer 001 (Comput. Graph., 2023)

xOpat: eXplainable Open Pathology Analysis Tool. - Jirí Horák; Katarína Furmanová; Barbora Kozlíková; Tomás Brázdil; Petr Holub; M. Kacenga; Matej Gallo; R. Nenutil; Jan Byska; Vít Rusnák (Comput. Graph. Forum, 2023)

State of the Art of Molecular Visualization in Immersive Virtual Environments. - David Kuták; Pere-Pau Vázquez; Tobias Isenberg 001; Michael Krone; Marc Baaden; Jan Byska; Barbora Kozlíková; Haichao Miao (Comput. Graph. Forum, 2023)

Interactive Diagrams for Software Documentation. - Adam Stspánek; David Kuták; Barbora Kozlíková; Jan Byska (VISSOFT, 2024)

Design and evaluation of alphabetic and numeric input methods for virtual reality. - David Kuták; Danielle Langlois; Roman Rozic; Jan Byska; Haichao Miao; Simone Kriglstein; Barbora Kozlíková (Comput. Graph., 2024)

Antarstick: Extracting Snow Height From Time-Lapse Photography. - Matej Lang; Radoslav Mráz; Marek Trtík; Sergej Stoppel; Jan Byska; Barbora Kozlíková (Comput. Graph. Forum, 2024)

Interactive Diagrams for Software Documentation. - Adam J. Stepánek; David Kuták; Barbora Kozlíková; Jan Byska (CoRR, 2024)

InVADo: Interactive Visual Analysis of Molecular Docking Data. - Marco Schäfer; Nicolas Brich; Jan Byska; Sérgio M. Marques; David Bednár; Philipp Thiel; Barbora Kozlíková; Michael Krone (IEEE Trans. Vis. Comput. Graph., 2024)

Tasks and Visual Abstractions for 3D Chromatin Representation. - Adam Rychlý; Jan Byska; Barbora Kozlíková; Katarína Furmanová (Comput. Graph. Forum, 2025)

Visual Support for the Loop Grafting Workflow on Proteins. - Filip Opálený; Pavol Ulbrich; Joan Planas-Iglesias; Jan Byska; Jan Stourac; David Bednár; Katarína Furmanová; Barbora Kozlíková (IEEE Trans. Vis. Comput. Graph., 2025)

Helveg: Diagrams for Software Documentation. - Adam J. Stepánek; David Kuták; Barbora Kozlíková; Jan Byska (CoRR, 2025)