Výpis publikací

ŠTĚPÁNEK, Adam; David KUŤÁK; Barbora KOZLÍKOVÁ a Jan BYŠKA. Helveg: Diagrams for Software Documentation. IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS. United States of America, 2025, roč. 31, č. 10, s. 9079-9091. ISSN 1077-2626. Dostupné z: https://doi.org/10.1109/TVCG.2025.3589748.

RYCHLÝ, Adam; Jan BYŠKA; Barbora KOZLÍKOVÁ a Katarína FURMANOVÁ. Tasks and Visual Abstractions for 3D Chromatin Representation. COMPUTER GRAPHICS FORUM. HOBOKEN: WILEY, 2025, roč. 44, č. 3, s. 1-12. ISSN 0167-7055. Dostupné z: https://doi.org/10.1111/cgf.70142.

OPÁLENÝ, Filip; Pavol ULBRICH; Joan PLANAS IGLESIAS; Jan BYŠKA; Jan ŠTOURAČ; David BEDNÁŘ; Katarína FURMANOVÁ a Barbora KOZLÍKOVÁ. Visual Support for the Loop Grafting Workflow on Proteins. IEEE Transactions on Visualization and Computer Graphics. United States: IEEE Computer Society, 2025, roč. 31, č. 1, s. 580-590. ISSN 1077-2626. Dostupné z: https://doi.org/10.1109/TVCG.2024.3456401.

LANG, Matěj; Radoslav MRÁZ; Marek TRTÍK; Sergej STOPPEL; Jan BYŠKA a Barbora KOZLÍKOVÁ. Antarstick: Extracting Snow Height From Time-Lapse Photography. COMPUTER GRAPHICS FORUM. England: Wiley, 2024, roč. 43, č. 3, s. 1-11. ISSN 0167-7055. Dostupné z: https://doi.org/10.1111/cgf.15088.

KUŤÁK, David; Danielle Kathryn LANGLOIS; Roman ROZIČ; Jan BYŠKA; Haichao MIAO; Simone KRIGLSTEIN a Barbora KOZLÍKOVÁ. Design and evaluation of alphabetic and numeric input methods for virtual reality. Computers & Graphics. PERGAMON-ELSEVIER SCIENCE LTDTHE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND, 2024, roč. 122, č. 103955, s. 1-11. ISSN 0097-8493. Dostupné z: https://doi.org/10.1016/j.cag.2024.103955.

ŠTĚPÁNEK, Adam; David KUŤÁK; Barbora KOZLÍKOVÁ a Jan BYŠKA. Interactive Diagrams for Software Documentation. Online. In Fabio Petrillo. IEEE Working Conference on Software Visualization (VISSOFT). Flagstaff, Arizona, USA: IEEE, 2024, s. 12-23. ISBN 979-8-3315-2848-5. Dostupné z: https://doi.org/10.1109/VISSOFT64034.2024.00012.

SCHÄFER, Marco; Nicolas BRICH; Jan BYŠKA; Sérgio Manuel MARQUES; David BEDNÁŘ; Philipp THIEL; Barbora KOZLÍKOVÁ a Michael KRONE. InVADo: Interactive Visual Analysis of Molecular Docking Data. IEEE Transactions on Visualization and Computer Graphics. IEEE Computer Society, 2024, roč. 30, č. 4, s. 1984-1997. ISSN 1077-2626. Dostupné z: https://doi.org/10.1109/TVCG.2023.3337642.

ULBRICH, Pavol; Manuela WALDNER; Katarína FURMANOVÁ; Sérgio Manuel MARQUES; David BEDNÁŘ; Barbora KOZLÍKOVÁ a Jan BYŠKA. sMolBoxes: Dataflow Model for Molecular Dynamics Exploration. IEEE Transactions on Visualization and Computer Graphics. United States: IEEE Computer Society, 2023, roč. 29, č. 1, s. 581-590. ISSN 1077-2626. Dostupné z: https://doi.org/10.1109/TVCG.2022.3209411.

KUŤÁK, David; Pere-Pau VÁZQUEZ; Tobias ISENBERG; Michael KRONE; Marc BAADEN; Jan BYŠKA; Barbora KOZLÍKOVÁ a Haichao MIAO. State of the Art of Molecular Visualization in Immersive Virtual Environments. Computer Graphics Forum. Wiley-Blackwell, 2023, roč. 42, č. 6, s. 1-29. ISSN 0167-7055. Dostupné z: https://doi.org/10.1111/cgf.14738.

HORÁK, Jiří; Katarína FURMANOVÁ; Barbora KOZLÍKOVÁ; Tomáš BRÁZDIL; Petr HOLUB; Martin KAČENGA; Matej GALLO; Rudolf NENUTIL; Jan BYŠKA a Vít RUSŇÁK. xOpat: eXplainable Open Pathology Analysis Tool. COMPUTER GRAPHICS FORUM. England: Wiley, 2023, roč. 42, č. 3, s. 63-73. ISSN 0167-7055. Dostupné z: https://doi.org/10.1111/cgf.14812.

PLANAS IGLESIAS, Joan; Filip OPÁLENÝ; Pavol ULBRICH; Jan ŠTOURAČ; Zainab Kemi SANUSI; José Gaspar RANGEL PAMPLONA PIZARRO PINTO; Andrea SMITH; Jan BYŠKA; Jiří DAMBORSKÝ; Barbora KOZLÍKOVÁ a David BEDNÁŘ. LoopGrafter: a web tool for transplanting dynamical loops for protein engineering. Nucleic acids research. Oxford: Oxford University Press, 2022, roč. 50, W1, s. "W465"-"W473", 9 s. ISSN 0305-1048. Dostupné z: https://doi.org/10.1093/nar/gkac249.

PLANAS IGLESIAS, Joan; Filip OPÁLENÝ; Pavol ULBRICH; Jan ŠTOURAČ; Zainab Kemi SANUSI; José Gaspar RANGEL PAMPLONA PIZARRO PINTO; A. SCHENKMAYEROVÁ; Jan BYŠKA; Jiří DAMBORSKÝ; Barbora KOZLÍKOVÁ a David BEDNÁŘ. Nástroj LoopGrafter. 2022.

KUŤÁK, David; Matias Nicolás SELZER; Jan BYŠKA; María Luján GANUZA; Ivan BARIŠIĆ; Barbora KOZLÍKOVÁ a Haichao MIAO. Vivern – A Virtual Environment for Multiscale Visualization and Modeling of DNA Nanostructures. IEEE Transactions on Visualization and Computer Graphics. 2022, roč. 28, č. 12, s. 4825-4838. ISSN 1077-2626. Dostupné z: https://doi.org/10.1109/TVCG.2021.3106328.

BYŠKA, Jan; Krone MICHAEL a Sommer BJÖRN. Computers & Graphics: Special Section on Molecular Graphics and Visual Analysis of Molecular Data. Elsevier, 2021.

SABANDO, María Virginia; Pavol ULBRICH; Matías SELZER; Jan BYŠKA; Jan MIČAN; Ignacio PONZONI; Axel J. SOTO; María Luján GANUZA a Barbora KOZLÍKOVÁ. ChemVA: Interactive Visual Analysis of Chemical Compound Similarity in Virtual Screening. IEEE Transactions on Visualization and Computer Graphics. IEEE, 2021, roč. 27, č. 2, s. 891-901. ISSN 1077-2626. Dostupné z: https://doi.org/10.1109/TVCG.2020.3030438.

BRŮŽA, Vojtěch; Jan BYŠKA; Jan MIČAN a Barbora KOZLÍKOVÁ. VRdeo: Creating engaging educational material for asynchronous student-teacher exchange using virtual reality. COMPUTERS & GRAPHICS-UK. OXFORD: PERGAMON-ELSEVIER SCIENCE LTD, 2021, roč. 98, August 2021, s. 280-292. ISSN 0097-8493. Dostupné z: https://doi.org/10.1016/j.cag.2021.06.009.

FURMANOVÁ, Katarína; Ondřej VÁVRA; Barbora KOZLÍKOVÁ; Jiří DAMBORSKÝ; Vojtěch VONÁSEK; David BEDNÁŘ a Jan BYŠKA. DockVis: Visual Analysis of Molecular Docking Trajectories. Computer Graphics Forum. Wiley-Blackwell, 2020, roč. 39, č. 6, s. 452-464. ISSN 0167-7055. Dostupné z: https://doi.org/10.1111/cgf.14048.

ABBOUD, Angèle; Pierre BÉDOUCHA; Jan BYŠKA; Thomas ARNESEN a Nathalie REUTER. Dynamics-function relationship in the catalytic domains of N-terminal acetyltransferases. Computational and Structural Biology Journal. Netherlands: Elsevier, 2020, roč. 18, č. 1, s. 532-547. ISSN 2001-0370. Dostupné z: https://doi.org/10.1016/j.csbj.2020.02.017.

FURMANOVÁ, Katarína; Adam JURČÍK; Barbora KOZLÍKOVÁ; Helwig HAUSER a Jan BYŠKA. Multiscale Visual Drilldown for the Analysis of Large Ensembles of Multi-Body Protein Complexes. IEEE Transactions on Visualization and Computer Graphics. IEEE, 2020, roč. 26, č. 1, s. 843-852. ISSN 1077-2626. Dostupné z: https://doi.org/10.1109/TVCG.2019.2934333.

ORÉMUŠ, Zoltán; Kahin AKRAM HASSAN; Jiří CHMELÍK; Michaela KŇAŽKOVÁ; Jan BYŠKA; Renata Georgia RAIDOU a Barbora KOZLÍKOVÁ. PINGU: Principles of Interactive Navigation for Geospatial Understanding. Online. In IEEE. 2020 IEEE Pacific Visualization Symposium (PacificVis). Tianjin, China: IEEE PacificVis 2020, 2020, s. 216-225. ISBN 978-1-7281-5697-2. Dostupné z: https://doi.org/10.1109/PacificVis48177.2020.7567.

PÁLENIK, Juraj; Jan BYŠKA; Stefan BRUCKNER a Helwig HAUSER. Scale-Space Splatting: Reforming Spacetime for Cross-Scale Exploration of Integral Measures in Molecular Dynamics. IEEE Transactions on Visualization and Computer Graphics. IEEE, 2020, roč. 26, č. 1, s. 643-653. ISSN 1077-2626. Dostupné z: https://doi.org/10.1109/TVCG.2019.2934258.

BYŠKA, Jan; Adam JURČÍK; Katarína FURMANOVÁ; Barbora KOZLÍKOVÁ a Jan PALEČEK. Visual Analysis of Protein–Protein Interaction Docking Models Using COZOID Tool. In Stefan Canzar, Francisca Rojas Ringeling. Protein-Protein Interaction Networks. 1. vyd. New York, NY: Humana Press Inc, 2020, s. 81-94. Methods in Molecular Biology, vol. 2074. ISBN 978-1-4939-9872-2. Dostupné z: https://doi.org/10.1007/978-1-4939-9873-9_7.

BEDOUCHA, Pierre; Reuter NATHALIE; Helwig HAUSER a Jan BYŠKA. Visual exploration of large normal mode spaces to study protein flexibility. Computers & Graphics. Netherlands: Elsevier Science Direct, 2020, roč. 90, August, s. 73-83. ISSN 0097-8493. Dostupné z: https://doi.org/10.1016/j.cag.2020.05.025.

BYŠKA, Jan; Thomas TRAUTNER; Sérgio Manuel MARQUES; Jiří DAMBORSKÝ; Barbora KOZLÍKOVÁ a Manuela WALDNER. Analysis of Long Molecular Dynamics Simulations Using Interactive Focus+Context Visualization. Computer Graphics Forum. Wiley-Blackwell, 2019, roč. 38, č. 3, s. 441-453. ISSN 0167-7055. Dostupné z: https://doi.org/10.1111/cgf.13701.

FURMANOVÁ, Katarína; Barbora KOZLÍKOVÁ; Vojtěch VONÁSEK a Jan BYŠKA. DockVis: Visual Analysis of Molecular Docking Data. In Kozlíková, Barbora and Linsen, Lars and Vázquez, Pere-Pau and Lawonn, Kai and Raidou, Renata Georgia. Eurographics Workshop on Visual Computing for Biology and Medicine. Brno: The Eurographics Association, 2019, s. 113-122. ISBN 978-3-03868-081-9. Dostupné z: https://doi.org/10.2312/vcbm.20191238.

JURČÍK, Adam; Katarína FURMANOVÁ; Jan BYŠKA; Vojtěch VONÁSEK; Ondřej VÁVRA; Pavol ULBRICH; Helwig HAUSER a Barbora KOZLÍKOVÁ. Visual Analysis of Ligand Trajectories in Molecular Dynamics. Online. In IEEE Pacific Visualization Symposium 2019. Bangkok, Thailand: IEEE, 2019, s. 212-221. ISBN 978-1-5386-9226-4. Dostupné z: https://doi.org/10.1109/PacificVis.2019.00032.

BERLAND, Siren; Trine L TOFT-BERTELSEN; Ingvild AUKRUST; Jan BYŠKA; Marc VAUDEL; Laurence BINDOFF; Nanna MACAULAY a Gunnar HOUGE. A de novo Ser111Thr variant in aquaporin-4 in a patient with intellectual disability, transient signs of brain ischemia, transient cardiac hypertrophy, and progressive gait disturbance. Molecular Case Studies. Cold Spring Harbor Laboratory Press, 2018, roč. 4, č. 1.

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 MANAK; Jiří DAMBORSKÝ a Barbora KOZLÍKOVÁ. CAVER Analyst 2.0: Analysis and Visualization of Channels and Tunnels in Protein Structures and Molecular Dynamics Trajectories. Bioinformatics. 2018, roč. 34, č. 20, s. 3586-3588. ISSN 1367-4803. Dostupné z: https://doi.org/10.1093/bioinformatics/bty386.

FURMANOVÁ, Katarína; Jan BYŠKA; Eduard M. GRÖLLER; Ivan VIOLA; Jan PALEČEK a Barbora KOZLÍKOVÁ. COZOID: COntact ZOne IDentifier for visual analysis of protein-protein interactions. BMC Bioinformatics. 2018, roč. 19, APR, s. 1-17. ISSN 1471-2105. Dostupné z: https://doi.org/10.1186/s12859-018-2113-6.

KOZLÍKOVÁ, Barbora; Jiří CHMELÍK; Radek OŠLEJŠEK a Jan BYŠKA. EuroVis 2018 - 20th EG/VGTC Conference on Visualization. 2018.

KOCINCOVÁ, Lucia; Miroslava JAREŠOVÁ; Jan BYŠKA; Julius PARULEK; Helwig HAUSER a Barbora KOZLÍKOVÁ. Comparative Visualization of Protein Secondary Structures. BMC Bioinformatics. BioMed Central, 2017, roč. 18, č. 23, s. 1-12. ISSN 1471-2105. Dostupné z: https://doi.org/10.1186/s12859-016-1449-z.

FURMANOVÁ, Katarína; Miroslava JAREŠOVÁ; Jan BYŠKA; Adam JURČÍK; Julius PARULEK; Helwig HAUSER a Barbora KOZLÍKOVÁ. Interactive Exploration of Ligand Transportation through Protein Tunnels. BMC Bioinformatics. BioMed Central, 2017, roč. 18, č. 22, s. 1-16. ISSN 1471-2105. Dostupné z: https://doi.org/10.1186/s12859-016-1448-0.

VAD, Viktor; Jan BYŠKA; Adam JURČÍK; Ivan VIOLA; Eduard M. GRÖLLER; Helwig HAUSER; Sérgio Manuel MARQUES; Jiří DAMBORSKÝ a Barbora KOZLÍKOVÁ. Watergate: Visual Exploration of Water Trajectories in Protein Dynamics. Online. In S. Bruckner, A. Hennemuth, and B. Kainz. Eurographics Workshop on Visual Computing for Biology and Medicine. Bremen, Germany: Eurographics Workshop on Visual Computing for Biology and Medicine, 2017, s. 33-42. ISBN 978-3-03868-036-9.

BYŠKA, Jan; Mathieu Le MUZIC; Eduard GRÖLLER; Ivan VIOLA a Barbora KOZLÍKOVÁ. AnimoAminoMiner: Exploration of Protein Tunnels and their Properties in Molecular Dynamics. IEEE Transactions on Visualization and Computer Graphics. IEEE, 2016, roč. 22, č. 1, s. 747-756. ISSN 1077-2626. Dostupné z: https://doi.org/10.1109/TVCG.2015.2467434.

KOLESÁR, Ivan; Jan BYŠKA; Julius PARULEK; Helwig HAUSER a Barbora KOZLÍKOVÁ. Unfolding and Interactive Exploration of Protein Tunnels and their Dynamics. Online. In Stefan Bruckner and Bernhard Preim and Anna Vilanova and Helwig Hauser and Anja Hennemuth and Arvid Lundervold. EG VCBM 2016 Eurographics Workshop on Visual Computing for Biology and Medicine. Bergen: The Eurographics Association, 2016, s. nestránkováno, 10 s. ISBN 978-3-03868-010-9. Dostupné z: https://doi.org/10.2312/vcbm.20161265.

BYŠKA, Jan; Adam JURČÍK; Eduard M. GRÖLLER; Ivan VIOLA a Barbora KOZLÍKOVÁ. MoleCollar and Tunnel Heat Map Visualizations for Conveying Spatio-Temporo-Chemical Properties Across and Along Protein Voids. Computer Graphics Forum. Wiley-Blackwell, 2015, roč. 34, č. 3, s. 1-10. ISSN 0167-7055. Dostupné z: https://doi.org/10.1111/cgf.12612.

BYŠKA, Jan; Ivana KOLINGEROVÁ; Barbora KOZLÍKOVÁ a Jiří SOCHOR. Path-planning algorithm for transportation of molecules through protein tunnel bottlenecks. In Joaquim Jorge, Luis Paulo Santos, Roman Ďurikovič. 31st Proceedings of Spring Conference on Computer Graphics. Bratislava, Slovakia: ACM, 2015, s. 81-88. ISBN 978-1-4503-3693-2. Dostupné z: https://doi.org/10.1145/2788539.2788550.

JURČÍK, Adam; Jan BYŠKA; Jiří SOCHOR a Barbora KOZLÍKOVÁ. Visibility-Based Approach to Surface Detection of Tunnels in Proteins. In Joaquim Jorge, Luis Paulo Santos, Roman Ďurikovič. 31st Proceedings of Spring Conference on Computer Graphics. Bratislava, Slovakia: ACM, 2015, s. 65-72. ISBN 978-1-4503-3693-2. Dostupné z: https://doi.org/10.1145/2788539.2788548.

KOZLÍKOVÁ, Barbora; Adam JURČÍK; Jan BYŠKA; Ondřej STRNAD a Jiří SOCHOR. Visualizing Movements of Protein Tunnels in Molecular Dynamics Simulations. Online. In Dieter W. Fellner, Werner Hansmann, Werner Purgathofer, Francois Sillion. EG VCBM 2014 Eurographics Workshop on Visual Computing for Biology and Medicine. Postfach, Germany: Eurographics Association, 2014, s. 97-106. ISBN 978-3-905674-62-0.

BYŠKA, Jan; Adam JURČÍK a Jiří SOCHOR. Geometry-based Algorithm for Detection of Asymmetric Tunnels in Protein Molecules. In Silvester Czanner and Wen Tang. TPCG 2013. Germany: Eurographics Association, 2013, s. 17-24. ISBN 978-3-905673-98-2.

BYŠKA, Jan a Jiří SOCHOR. Discovering molecules: Pass planning through a gap. Viena: Vienna University of Technology, 2012, s. 25-33, 8 s. ISBN 978-3-9502533-4-4.