Curriculum Vitae

Curriculum Vitae

Person-Related Identification Information

• RNDr. Jan Byška, Ph.D.

Department

• Department of Visual Computing, Faculty of Informatics, Masaryk University

Employment - Position

• Assistant Professor

Education and Academic Qualifications

• 2011 – 2016: Doctoral Studies – Informatics, Masaryk University, Brno, Czech Republic
• 2006 – 2011: Bachelor & Master Studies – Applied Informatics & Computer Graphics

Employment

• Nov. 2019 – now: Adjunct Associate Professor at University of Bergen, Bergen, Norway
• Jul. 2018 – now: Assistant Professor at Masaryk University, Brno, Czech Republic
• Oct. 2016 – Jun. 2019: Postdoctoral Fellowship at University of Bergen, Bergen, Norway
• Apr. 2016 – Sep. 2016: Researcher at University of Bergen, Bergen, Norway
• Nov. 2011 – Dec. 2012: Researcher at Masaryk University, Brno, Czech Republic

Teaching Activities

• Computer Graphics, Visualization, Data-oriented Visual Computing

Scientific and Research Activities

• Various challenges in the field of visualization of biomolecular and time-dependent data.

Internship

• Oct. 2016 – Jun. 2019 PostDoc at University of Bergen, Bergen, Norway
• Apr. 2016 – Sep. 2016 Researcher at University of Bergen, Bergen, Norway
• Aug. 2015 - May. 2016 Intership at University of Bergen, Bergen, Norway

Activities Outside University

• General co-chair: BioVis (2023, 2024), Workshop on Molecular Graphics and Visual Analysis of Molecular Data (2018, 2019, 2020, 2021, 2023)
• Guest editor: Computers & Graphics (2020, 2021, 2023)
• Poster co-chair: EuroVis (2020, 2021), VCBM (2019, 2022), BioVis (2021)
• Tutorial co-organizer for Course in Science Communication (2018), NORBIS Summer School on Communicating Research by Visualization, Illustration, and Storytelling (2017), and Bio+Med+Vis Spring School (2021, 2022, 2023)
• Local co-organizer: VCBM (2016, 2019), EuroVis (2018)
• IPC: PacificVis (2020-2022), VCBM (2020-2022), EuroVis (2021-2024), IEEE VIS (2020-2024), BIOKDD (2020), LEVIA (2020), ACM IUI (2021)

Awards Related to Science and Research

• Best paper awards at BioVis 2016 and VCBM 2019.

Major Publications

• KUŤÁK, David, Pere-Pau VÁZQUEZ, Tobias ISENBERG, Michael KRONE, Marc BAADEN, Jan BYŠKA, Barbora KOZLÍKOVÁ and Haichao MIAO. State of the Art of Molecular Visualization in Immersive Virtual Environments. Computer Graphics Forum. Wiley-Blackwell, 2023, vol. 42, No 6, p. "e14738", 29 pp. ISSN 0167-7055. Available from: https://dx.doi.org/10.1111/cgf.14738. URL info
• KUŤÁK, David, Matias Nicolás SELZER, Jan BYŠKA, María Luján GANUZA, Ivan BARIŠIĆ, Barbora KOZLÍKOVÁ and Haichao MIAO. Vivern – A Virtual Environment for Multiscale Visualization and Modeling of DNA Nanostructures. IEEE Transactions on Visualization and Computer Graphics. 2022, vol. 28, No 12, p. 4825-4838. ISSN 1077-2626. Available from: https://dx.doi.org/10.1109/TVCG.2021.3106328. URL info
• 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 and David BEDNÁŘ. LoopGrafter: a web tool for transplanting dynamical loops for protein engineering. Nucleic acids research. Oxford: Oxford University Press, 2022, vol. 50, W1, p. "W465"-"W473", 9 pp. ISSN 0305-1048. Available from: https://dx.doi.org/10.1093/nar/gkac249. URL info
• FURMANOVÁ, Katarína, 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. IEEE, 2020, vol. 26, No 1, p. 843-852. ISSN 1077-2626. Available from: https://dx.doi.org/10.1109/TVCG.2019.2934333. URL info
• FURMANOVÁ, Katarína, Ondřej VÁVRA, Barbora KOZLÍKOVÁ, Jiří DAMBORSKÝ, Vojtěch VONÁSEK, David BEDNÁŘ and Jan BYŠKA. DockVis: Visual Analysis of Molecular Docking Trajectories. Computer Graphics Forum. Wiley-Blackwell, 2020, vol. 39, No 6, p. 452-464. ISSN 0167-7055. Available from: https://dx.doi.org/10.1111/cgf.14048. URL info
• BEDOUCHA, Pierre, Reuter NATHALIE, Helwig HAUSER and Jan BYŠKA. Visual exploration of large normal mode spaces to study protein flexibility. Computers & Graphics. Netherlands: Elsevier Science Direct, 2020, vol. 90, August, p. 73-83. ISSN 0097-8493. Available from: https://dx.doi.org/10.1016/j.cag.2020.05.025. URL info
• BYŠKA, Jan, Thomas TRAUTNER, Sérgio Manuel MARQUES, Jiří DAMBORSKÝ, Barbora KOZLÍKOVÁ and Manuela WALDNER. Analysis of Long Molecular Dynamics Simulations Using Interactive Focus+Context Visualization. Computer Graphics Forum. Wiley-Blackwell, 2019, vol. 38, No 3, p. 441-453. ISSN 0167-7055. Available from: https://dx.doi.org/10.1111/cgf.13701. URL info
• 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 and Barbora KOZLÍKOVÁ. CAVER Analyst 2.0: Analysis and Visualization of Channels and Tunnels in Protein Structures and Molecular Dynamics Trajectories. Bioinformatics. 2018, vol. 34, No 20, p. 3586-3588. ISSN 1367-4803. Available from: https://dx.doi.org/10.1093/bioinformatics/bty386. URL info
• KOCINCOVÁ, Lucia, Miroslava JAREŠOVÁ, Jan BYŠKA, Julius PARULEK, Helwig HAUSER and Barbora KOZLÍKOVÁ. Comparative Visualization of Protein Secondary Structures. BMC Bioinformatics. BioMed Central, 2017, vol. 18, No 23, p. 1-12. ISSN 1471-2105. Available from: https://dx.doi.org/10.1186/s12859-016-1449-z. URL info
• 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. IEEE, 2016, vol. 22, No 1, p. 747-756. ISSN 1077-2626. Available from: https://dx.doi.org/10.1109/TVCG.2015.2467434. info
• 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. Wiley-Blackwell, 2015, vol. 34, No 3, p. 1-10. ISSN 0167-7055. Available from: https://dx.doi.org/10.1111/cgf.12612. info

2024/01/21