Curriculum Vitae

Curriculum vitae

Name, first names, scientific degrees

• RNDr. Matej Troják, born 1993 in Slovak republic

Department/Faculty/University

• Systems Biology Laboratory
  Faculty of Informatics
  Botanicka 68a
  60200 Brno
  Czech Republic

Function, current position

• PhD. candidate
• researcher at Systems Biology Laboratory

Education and academic qualifications

• 2020: advanced master's degree (doctor of natural sciences) conferred in Artificial intelligence and data processing; thesis: Formal Analysis of Rule-Based Models in Systems Biology
  
• 2018: master degree conferred in Applied Informatics; thesis: Formal Biochemical Space for Specification and Analysis of Biochemical Processes (acquired Deans' award for the excellent master thesis)
  
• 2015: bachelor degree conferred in Applied Informatics; thesis: Formal specification of phosphorylation states and related reactions
  
• 2012: graduation at secondary grammar school GVPT in Martin, Slovakia

Professional experience

• 2021 - present: IT specialist at RECETOX
  
• 2018 - 2022: researcher at CzechGlobe (Global Change Research Institute of the Czech Academy of Sciences)
  
• 2014 - present: researcher at SYBILA (Systems Biology Laboratory)

Research activities

• Systems Biology, general impact of Informatics, formal methods in computer science

Other academic activities, research projects, grants

• 2021 - 2022: Computational reconstruction of mechanistic framework underlying receptor tyrosine kinase function in signal transduction
  
• 2017: Dean's Program of the Faculty of Informatics MU for support of student research and development projects (MUNI33/062017)
  
• 2015: Dean's Program of the Faculty of Informatics MU for support of student research and development projects (MUNI33/092015)
  
• 2014 - 2019: e-cyanobacterium.org (https://www.e-cyanobacterium.org/)
  
• 2015 - 2023: BCSgen (https://github.com/sybila/BCSgen)

Major publications

• TROJÁK, Matej, David ŠAFRÁNEK, Samuel PASTVA and Luboš BRIM. Rule-based Modelling of Biological Systems Using Regulated Rewriting. Biosystems. Elsevier, 2023, vol. 225, No 104843, p. 1-15. ISSN 0303-2647. Available from: https://dx.doi.org/10.1016/j.biosystems.2023.104843. URL info
• TROJÁK, Matej, Helge HECHT, Martin ČECH and Elliott James PRICE. MSMetaEnhancer: A Python package for mass spectra metadata annotation. Journal of Open Source Software. 2022, vol. 7, No 79. Available from: https://dx.doi.org/10.21105/joss.04494. URL info
• TROJÁK, Matej, David ŠAFRÁNEK, Lukrécia MERTOVÁ and Luboš BRIM. Parameter Synthesis and Robustness Analysis of Rule-Based Models. In Ritchie Lee, Susmit Jha, Anastasia Mavridou. 12th International Symposium on NASA Formal Methods, NFM 2020. LNCS 12229. Moffett Field, CA, USA: Springer, 2020, p. 41-59. ISBN 978-3-030-55753-9. Available from: https://dx.doi.org/10.1007/978-3-030-55754-6_3. URL info
• TROJÁK, Matej, David ŠAFRÁNEK, Luboš BRIM, Jakub ŠALAGOVIČ and Jan ČERVENÝ. Executable Biochemical Space for Specification and Analysis of Biochemical Systems. Online. In Ankit Gupta, Tatjana Petrov. 9th International Workshop on Static Analysis and Systems Biology (SASB). ENTCS 350. Amsterdam: Elsevier, 2020, p. 91-116. ISSN 1571-0661. Available from: https://dx.doi.org/10.1016/j.entcs.2020.06.006. URL info
• TROJÁK, Matej, David ŠAFRÁNEK, Lukrécia MERTOVÁ and Luboš BRIM. Executable Biochemical Space for Specification and Analysis of Biochemical Systems. PLOS ONE. Public Library of Science, 2020, vol. 15, No 9, p. 1-23, 24 pp. ISSN 1932-6203. Available from: https://dx.doi.org/10.1371/journal.pone.0238838. URL info
• TROJÁK, Matej, David ŠAFRÁNEK, Jan ČERVENÝ, Marek HAVLÍK, Lukrécia MERTOVÁ, Matej HAJNAL, Jakub HRABEC and Jakub ŠALAGOVIČ. Comprehensive Modelling Platform. In 6th Workshop on Hybrid Systems & Biology. 2019. URL info
• ŠAFRÁNEK, David, 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. In Bortolussi L., Sanguinetti G. Computational Methods in Systems Biology (CMSB 2019). LNBI 11773. Neuveden: Springer, 2019, p. 356-359. ISBN 978-3-030-31303-6. Available from: https://dx.doi.org/10.1007/978-3-030-31304-3_26. info
• TROJÁK, Matej, 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. In 16th International Conference on Computational Methods in Systems Biology. 2018. URL info
• TROJÁK, Matej, David ŠAFRÁNEK, Jakub ŠALAGOVIČ, Františka ROMANOVSKÁ and Matej HAJNAL. Biochemical Space: A Framework for Formal Description and Annotation of Complex Biological Processes. In The 8th International Workshop on Static Analysis for Systems Biology. 2017. info
• TROJÁK, Matej, David ŠAFRÁNEK, Jakub HRABEC, Jakub ŠALAGOVIČ, Františka ROMANOVSKÁ and Jan ČERVENÝ. E-Cyanobacterium.org: A Web-Based Platform for Systems Biology of Cyanobacteria. In Ezio Bartocci et al. Computational Methods in Systems Biology. CMSB 2016. Heidelberg: Springer, 2016, p. 316-322. ISBN 978-3-319-45176-3. Available from: https://dx.doi.org/10.1007/978-3-319-45177-0_20. URL info
• DĚD, Tadeáš, David ŠAFRÁNEK, Matej TROJÁK, Matej KLEMENT, Jakub ŠALAGOVIČ and Luboš BRIM. Formal Biochemical Space with Semantics in Kappa and BNGL. Online. In Loic Pauleve et al. The 6th International Workshop on Static Analysis and Systems Biology, SASB 2015. ENTCS 326. Neuveden: Elsevier, 2016, p. 27-49. ISSN 1571-0661. Available from: https://dx.doi.org/10.1016/j.entcs.2016.09.017. info

2023/01/27