Publications

• Matej Troják, David Šafránek, Samuel Pastva, and Luboš Brim. Rule-based Modelling of Biological Systems Using Regulated Rewriting. BioSystems (225), Elsevier, 2023. [doi]
• Matej Troják, David Šafránek, Branislav Brozmann, and Luboš Brim. eBCSgen 2.0: Modelling and Analysis of Regulated Rule-Based Systems. Proceedings of the 20th International Conference on Computational Methods in Systems Biology (CMSB), p. 302-309, LNBI 13447, Springer, 2022. [doi] [presentation]
• Matej Troják, Helge Hecht, Martin Čech, and Elliott James Price. MSMetaEnhancer: A Python package for mass spectra metadata annotation. Journal of Open Source Software 7(79), 2022. [doi]
• Matej Troják, David Šafránek, Lukrécia Mertová, and Luboš Brim. eBCSgen: A Software Tool for Biochemical Space Language. Proceedings of the 18th International Conference on Computational Methods in Systems Biology (CMSB), p. 356-361, LNBI 12314, Springer, 2020. [doi] [video]
• Matej Troják, David Šafránek, Lukrécia Mertová, and Luboš Brim. Executable Biochemical Space for Specification and Analysis of Biochemical Systems. PLoS ONE 15(9), Public Library of Science, 2020. [doi]
• Matej Troják, David Šafránek, Luboš Brim, Jakub Šalagovič, and Jan Červený. Executable Biochemical Space for Specification and Analysis of Biochemical Systems. Proceedings of the 9th International Workshop on Static Analysis and Systems Biology (SASB), p. 91-116, ENTCS 350, Elsevier, 2018. [doi] [paper] [presentation]
• Matej Troják, David Šafránek, Lukrécia Mertová, and Luboš Brim. Parameter Synthesis and Robustness Analysis of Rule-Based Models. Proceedings of the 12th NASA Formal Methods (NFM), p. 41-59, LNCS 12229, Springer, 2020. [doi] [paper] [presentation] [video]
• David Šafránek, Matej Troják, Vojtěch Brůža, Tomáš Vejpustek, Jan Papoušek, Martin Demko, Samuel Pastva, Aleš Pejznoch, and Luboš Brim. Barbaric Robustness Monitoring Revisited for STL* in Parasim. Proceedings of the 17th International Conference on Computational Methods in Systems Biology (CMSB), p. 356-359, LNBI 11773, Springer, 2019.
• Nikola Beneš, Luboš Brim, Jan Červený, Samuel Pastva, David Šafránek, Jakub Šalagovič, and Matej Troják. Fully Automated Attractor Analysis of Cyanobacteria Models. Proceedings of the 22nd International Conference on System Theory, Control and Computing (ICSTCC), p. 354-359, IEEE, 2018. [doi] [paper] [presentation]
• Matej Troják, David Šafránek, Jakub Hrabec, Jakub Šalagovič, Františka Romanovská, and Jan Červený. E-Cyanobacterium.org: A Web-Based Platform for Systems Biology of Cyanobacteria. Proceedings of the 14th International Conference on Computational Methods in Systems Biology (CMSB), p. 316-322, Springer, 2016. [doi] [paper] [presentation]
• Tadeáš Děd, David Šafránek, Matej Troják, Matej Klement, Jakub Šalagovič, and Luboš Brim. Formal Biochemical Space with Semantics in Kappa and BNGL. Proceedings of the 6th International Workshop on Static Analysis and Systems Biology (SASB), p. 27-49, Elsevier, 2015. [doi] [paper]

Presentations

• Matej Troják, Helge Hecht, Martin Čech, and Elliott James Price. MSMetaEnhancer: A Python package for mass spectra metadata annotation. Galaxy Community Conference (GCC 2022), 2022. [presentation]
• Matej Troják, David Šafránek, Branislav Brozmann, and Luboš Brim. Representing Biochemical Space Language in SBML-multi standard. Computational Modeling in Biology Network meeting (COMBINE 2022). [poster]
• Matej Troják, Samuel Pastva, and Ondřej Lošták. Overview of Low-Budget Photobioreactors. The Biomania Student Scientific Meeting 2022. [poster]
• Matej Troják, David Šafránek, Lukrécia Mertová, and Luboš Brim. Executable Biochemical Space for Specification and Analysis of Biochemical Systems. Hybrid Systems & Biology (HSB 2020). [poster] [presentation] [video]
• David Šafránek, Matej Troják, Vojtěch Brůža, Tomáš Vejpustek, Jan Papoušek, Martin Demko, Samuel Pastva, Aleš Pejznoch, and Luboš Brim. Barbaric Robustness Monitoring Revisited for STL* in Parasim. Computational Methods in Systems Biology (CMSB 2019). [poster]
• Matej Troják, David Šafránek, Jan Červený, Marek Havlík, Lukrécia Mertová, Matej Hajnal, Jakub Hrabec, and Jakub Šalagovič. Comprehensive Modelling Platform. Hybrid Systems & Biology (HSB 2019). [poster]
• Matej Troják, David Šafránek, Jakub Hrabec, Jakub Šalagovič, Jan Červený, Matej Hajnal, Lukrécia Mertová, Katarína Palubová, and Marek Havlík. E-cyanobacterium.org: A Web-based Platform for Systems Biology of Cyanobacteria. Computational Methods in Systems Biology (CMSB 2018). [poster]
• Matej Troják, David Šafránek, Jakub Šalagovič, Františka Romanovská, and Matej Hajnal. Biochemical Space: A Framework for Formal Description and Annotation of Complex Biological Processes. Computational Modeling in Biology Network meeting (COMBINE 2017). [presentation] [poster]
• Matej Troják, David Šafránek, Jakub Šalagovič, Františka Romanovská, and Matej Hajnal. Biochemical Space: A Framework for Formal Description and Annotation of Complex Biological Processes. Static Analysis for Systems Biology (SASB 2017). [presentation]
• Matej Troják, David Šafránek, Jakub Hrabec, Jakub Šalagovič, Františka Romanovská, Matej Hajnal, and Jan Červený. E-cyanobacterium.org: A Web-based Platform for Systems Biology of Cyanobacteria. International Conference on Systems Biology 2017 (ICSB 2017). [poster]
• Matej Troják, David Šafránek, Jakub Hrabec, Jakub Šalagovič, Františka Romanovská, Matej Hajnal, and Jan Červený. E-cyanobacterium.org: A Web-based Platform for Systems Biology of Cyanobacteria. The Biomania Student Scientific Meeting 2017. [poster]
• Matej Troják, David Šafránek, Jakub Hrabec, Jakub Šalagovič, Františka Romanovská, Matej Hajnal, and Jan Červený. E-cyanobacterium.org: A Web-based Platform for Systems Biology of Cyanobacteria. Doctoral Workshop on Mathematical and Engineering Methods in Computer Science 2017 (MEMICS 2017). [poster]
• Matej Troják, David Šafránek, Jakub Hrabec, Jakub Šalagovič, Františka Romanovská, Matej Hajnal, and Jan Červený. E-cyanobacterium.org: A Web-based Platform for Systems Biology of Cyanobacteria. Intelligent Systems for Molecular Biology & European Conference on Computational Biology (ISMB/ECCB 2017). [poster]
• Matej Troják, Tadeáš Děd, David Šafránek, Matej Klement, Jan Červený, and Františka Romanovská. Biochemical Space: A Language for Formal Description and Annotation of Complex Biological Processes. Doctoral Workshop on Mathematical and Engineering Methods in Computer Science 2016 (MEMICS 2016). [poster]
• Matej Troják, Tadeáš Děd, David Šafránek, Matej Klement, Jan Červený, and Luboš Brim. Biochemical Space: A Language for Formal Description and Annotation of Complex Biological Processes. Computational Methods in Systems Biology (CMSB 2015).
• Matej Troják, David Šafránek, Matej Klement, Tadeáš Děd, Jan Červený, and Luboš Brim. Biochemical Space: A Language for Formal Description and Annotation of Complex Biological Processes. Doctoral Workshop on Mathematical and Engineering Methods in Computer Science (MEMICS 2015).
• Matej Klement, David Šafránek, Jan Červený, Tadeáš Děd, Matej Troják, Luboš Brim, and Stefan Mueller. E-cyanobacterium.org: A Web-based Platform for Systems Biology of Cyanobacteria. Hybrid Systems Biology (HSB 2015).

Thesis

• Rule-based Modelling of Biochemical Processes: Specification and Analysis. Doctoral thesis. Masaryk University, Faculty of Informatics. Thesis supervisor Luboš Brim. [thesis] [presentation]
• Formal Biochemical Space for Specification and Analysis of Biochemical Processes. Master’s thesis. Masaryk University, Faculty of Informatics. Thesis supervisor David Šafránek. Acquired Deans’ award for the excellent master thesis. [thesis] [presentation]
• Formal specification of phosphorylation states and related reactions. Bachelor’s thesis. Masaryk University, Faculty of Informatics. Thesis supervisor David Šafránek. In Slovak Language. [thesis]