Publications

Publications

2021

Katarína Furmanová, Ludvig P. Muren, Oscar Casares-Magaz, Vitali Moiseenko, John P. Einck, Sara Pilskog, Renata G. Raidou.
PREVIS: Predictive visual analytics of anatomical variability for radiotherapy decision support.
Computers & Graphics.
doi: /10.1016/j.cag.2021.04.010.

Vojtěch Brůža, Jan Byška Jan Mičan, Barbora Kozlíková.
VRdeo: Creating Engaging Educational Material for Asynchronous Student-TeacherExchange Using Virtual Reality.
Computer and Graphcis.
doi: 10.1016/j.cag.2021.06.009.

María Virginia Sabando, Pavol Ulbrich, Matías Selzer, Jan Byška, Jan Mičan, Ignacio Ponzoni, Axel Soto J., María Luján Ganuza Barbora Kozlíková.
ChemVA: Interactive Visual Analysis of Chemical Compound Similarity in Virtual Screening.
IEEE Transactions on Visualization and Computer Graphics.
doi: 10.1109/TVCG.2020.3030438.

2020

Angèle Abboud, Pierre Bédoucha, Jan Byška, Thomas Arnesen, Nathalie Reuter.
Dynamics-function relationship in the catalytic domains of N-terminal acetyltransferases.
Computational and Structural Biology Journal.
doi: 10.1016/j.csbj.2020.02.017.

Pierre Bedoucha, Nathalie Reuter, Helwig Hauser, Jan Byška.
Visual exploration of large normal mode spaces to study protein flexibility.
Computer Graphics Forum.
doi: 10.1016/j.cag.2020.05.025.

Katarína Furmanová, Ondřej Vávra, Barbora Kozlíková, Jiří Damborský, Vojtěch Vonásek, David Bednář, and Jan Byška.
DockVis: Visual Analysis of Molecular Docking Trajectories.
Computer Graphics Forum.
doi: 10.1111/cgf.14048.

Katarína Furmanová, Adam Jurčík, Barbora Kozlíková, Helwig Hauser and Jan Byška.
Multiscale Visual Drilldown for the Analysis of Large Ensembles of Multi-Body Protein Complexes.
IEEE Transactions on Visualization and Computer Graphics.
doi: 10.1109/TVCG.2019.2934333.

Orémuš, Zoltán, Kahin Akram Hassan, Jiří Chmelík, Michaela Kňažková, Jan Byška, Renata Georgia Raidou and Barbora Kozlíková.
PINGU: Principles of Interactive Navigation for Geospatial Understanding.
IEEE PacificVis 2020.
doi: 10.1109/PacificVis48177.2020.7567.

Reina, Guido, Hank Childs, Krešimir Matković, Katja Bühler, Manuela Waldner, David Pugmire, Barbora Kozlíková, Timo Ropinski, Patric Ljung, Takayuki Itoh, Eduard Gröller and Michael Krone.
The Moving Target of Visualization Software for an Ever More Complex World.
Computers & Graphics.
doi: 10.1016/j.cag.2020.01.005.

2019

Jan Byška, Thomas Trautner, Sérgio Manuel Marques, Jiří Damborský, Barbora Kozlíková, Manuela Waldner.
Analysis of Long Molecular Dynamics Simulations Using Interactive Focus+Context Visualization.
Computer Graphics Forum.
doi: 10.1111/cgf.13701.

Katarína Furmanová, Barbora Kozlíková, Vojtěch Vonásek, Jan Byška.
DockVis: Visual Analysis of Molecular Docking Data.
Eurographics Workshop on Visual Computing for Biology and Medicine.
doi: 10.2312/vcbm.20191238.

David Kouřil, Ladislav Čmolík, Barbora Kozlíková, Hsiang-Yun Wu, Graham Johnson, David S. Goodsell, Arthur Olson, Eduard M. Groeller, and Ivan Viola.
Labels on Levels: Labeling of Multi-Scale Multi-Instance and Crowded 3D Biological Environments.
IEEE Transactions on Visualization and Computer Graphics.
Best Paper Honorable Mention, SciVis 2018
doi: http://dx.doi.org/10.1109/TVCG.2018.2864491.

Duran, David, Pedro Hermosilla, Timo Ropinski, Barbora Kozlíková, Álvar Vinacua, and Pere-Pau Vazquez.
Visualization of Large Molecular Trajectories.
IEEE Transactions on Visualization and Computer Graphics.
doi: https://doi.org/10.1109/TVCG.2018.2864851.

Miao, Haichao, Tobias Klein, David Kouřil, Peter Mindek, Karsten Schatz, Eduard M. Gröller, Barbora Kozlíková, Tobias Isenberg, and Ivan Viola.
Multiscale Molecular Visualization.
Journal of Molecular Biology.
doi: https://doi.org/10.1016/j.jmb.2018.09.004.

Vonásek, Vojtěch, Adam Jurčík, Katarína Furmanová, and Barbora Kozlíková.
Sampling-based Motion Planning for Tracking Evolution of Dynamic Tunnels in Molecular Dynamics Simulations.
Journal of Intelligent Robotic Systems.
doi: http://dx.doi.org/10.1007/s10846-018-0877-6.

2018

Best Paper Honorable Mention, SciVis 2017
Klein, Tobias, Ludovic Autin, Barbora Kozlíková, David S. Goodsell, Arthur Olson, Eduard M. Gröller, and Ivan Viola.
Instant Construction and Visualization of Crowded Biological Environments.
doi: http://dx.doi.org/10.1109/TVCG.2017.2744258.

Furmanová, Katarína, Jan Byška, Eduard M. Gröller, Ivan Viola, Jan Paleček, and Barbora Kozlíková.
COZOID: COntact ZOne IDentifier for visual analysis of protein-protein interactions.
BMC Bioinformatics.
doi: http://dx.doi.org/10.1186/s12859-018-2113-6.

Jurčík, Adam, David Bednář, Jan Byška, Sérgio Manuel Marques, Katarína Furmanová, Lukáš Daniel, Piia Pauliina Kokkonen, Jan Brezovský, Ondřej Strnad, Jan Štourač, Antonín Pavelka, Martin Maňák, Jiří Damborský, and Barbora Kozlíková.
CAVER Analyst 2.0: Analysis and Visualization of Channels and Tunnels in Protein Structures and Molecular Dynamics Trajectories.
Bioinformatics.
doi: http://dx.doi.org/10.1093/bioinformatics/bty386.

2017

Best Paper Award, BioVis 2016 Kocincová, Lucia, Miroslava Jarešová, Jan Byška, Julius Parulek, Helwig Hauser, and Barbora Kozlíková.
Comparative Visualization of Protein Secondary Structures.
BMC Bioinformatics.
doi: http://dx.doi.org/10.1186/s12859-016-1449-z.

Furmanová, Katarína, Miroslava Jarešová, Jan Byška, Adam Jurčík, Julius Parulek, Helwig Hauser, and Barbora Kozlíková.
Interactive Exploration of Ligand Transportation through Protein Tunnels.
BMC Bioinformatics.
doi: https://doi.org/10.1186/s12859-016-1448-0.

Kozlíková, Barbora, Michael Krone, Martin Falk, Norbert Lindow, Marc Baaden, Daniel Baum, Ivan Viola, Julius Parulek, and Hans-Christian Hege.
Visualization of Biomolecular Structures: State of the Art Revisited.
Computer Graphics Forum.
doi: http://dx.doi.org/10.1111/cgf.13072.

Vad, Viktor, Jan Byška, Adam Jurčík, Ivan Viola, Eduard M. Gröller, Helwig Hauser, Sérgio Manuel Marques, Jiří Damborský, and Barbora Kozlíková.
Watergate: Visual Exploration of Water Trajectories in Protein Dynamics.
In Eurographics Workshop on Visual Computing for Biology and Medicine.
doi: http://dx.doi.org/10.2312/vcbm.20171235.

Malzahn, Jan, Barbora Kozlíková, and Timo Ropinski.
Protein Tunnel Reprojection for Physico-Chemical Property Analysis.
In Eurographics Workshop on Visual Computing for Biology and Medicine.
doi: http://dx.doi.org/10.2312/vcbm.20171231.

Furmanová, Katarína, Petra Urbanová, and Barbora Kozlíková.
AnthroVis: Visual Analysis of 3D Mesh Ensembles for Forensic Anthropology.
In Proceedings of the 33rd Spring Conference on Computer Graphics.
doi: http://dx.doi.org/10.1145/3154353.3154363.

2016

Byška, Jan, Mathieu Le Muzic, Eduard Gröller, Ivan Viola, and Barbora Kozlíková.
AnimoAminoMiner: Exploration of Protein Tunnels and their Properties in Molecular Dynamics.
IEEE Transactions on Visualization and Computer Graphics.
doi: https://doi.org/10.1109/TVCG.2015.2467434.

Pavelka, Antonín, Eva Šebestová, Barbora Kozlíková, Jan Brezovský, Jiří Sochor, and Jiří Damborský.
CAVER: Algorithms for Analyzing Dynamics of Tunnels in Macromolecules.
IEEE/ACM Transactions on Computational Biology and Bioinformatics.
doi: http://dx.doi.org/10.1109/TCBB.2015.2459680.

Jurčík, Adam, Julius Parulek, Jiří Sochor, and Barbora Kozlíková.
Accelerated Visualization of Transparent Molecular Surfaces in Molecular Dynamics.
In IEEE Pacific Visualization Symposium 2016.
doi:http://dx.doi.org/10.1109/PACIFICVIS.2016.7465258.

Krone, Michael, Barbora Kozlíková, Norbert Lindow, Marc Baaden, Daniel Baum, Julius Parulek, Hans-Christian Hege, and Ivan Viola.
Visual Analysis of Biomolecular Cavities: State of the Art.
Computer Graphics Forum.
doi: http://dx.doi.org/10.1111/cgf.12928.

Vonásek, Vojtěch, and Barbora Kozlíková.
Application of Sampling-based Path Planning for Tunnel Detection in Dynamic Protein Structures.
In MMAR: 21st International Conference on Methods and Models in Automation and Robotics.
doi: http://dx.doi.org/10.1109/MMAR.2016.7575276.

Kolesár, Ivan, Jan Byška, Julius Parulek, Helwig Hauser, and Barbora Kozlíková.
Unfolding and Interactive Exploration of Protein Tunnels and their Dynamics.
In EG VCBM 2016 Eurographics Workshop on Visual Computing for Biology and Medicine.
doi: http://dx.doi.org/10.2312/vcbm.20161265.

2015

Jurčík, Adam, Jan Byška, Jiří Sochor, and Barbora Kozlíková.
Visibility-Based Approach to Surface Detection of Tunnels in Proteins.
In 31st Proceedings of Spring Conference on Computer Graphics.
doi: http://dx.doi.org/10.1145/2788539.2788548.

Byška, Jan, Ivana Kolingerová, Barbora Kozlíková, and Jiří Sochor.
Path-planning algorithm for transportation of molecules through protein tunnel bottlenecks.
In 31st Proceedings of Spring Conference on Computer Graphics.
doi: http://dx.doi.org/10.1145/2788539.2788550.

Byška, Jan, Adam Jurčík, Eduard M. Gröller, Ivan Viola, and Barbora Kozlíková.
MoleCollar and Tunnel Heat Map Visualizations for Conveying Spatio-Temporo-Chemical Properties Across and Along Protein Voids.
Computer Graphics Forum.
doi: http://dx.doi.org/10.1111/cgf.12612.

Kozlíková, Barbora, Michael Krone, Norbert Lindow, Martin Falk, Marc Baaden, Daniel Baum, Ivan Viola, Julius Parulek, and Hans-Christian Hege.
Visualization of Biomolecular Structures: State of the Art.
In Eurographics Conference on Visualization (EuroVis) – STARs.
doi: http://dx.doi.org/10.2312/eurovisstar.20151112.

2014

Kozlíková, Barbora, Eva Šebestová, Vilém Šustr, Jan Brezovský, Ondřej Strnad, Lukáš Daniel, David Bednář, Antonín Pavelka, Martin Maňák, Martin Bezděka, Petr Beneš, Matúš Kotry, Artur Wiktor Gora, Jiří Damborský, and Jiří Sochor.
CAVER Analyst 1.0: Graphic tool for interactive visualization and analysis of tunnels and channels in protein structures.
Bioinformatics.
doi: http://dx.doi.org/10.1093/bioinformatics/btu364.