Výpis publikací

TROJÁK, Matej; David ŠAFRÁNEK; Samuel PASTVA a Luboš BRIM. Rule-based Modelling of Biological Systems Using Regulated Rewriting. Biosystems. Elsevier, 2023, roč. 225, č. 104843, s. 1-15. ISSN 0303-2647. Dostupné z: https://doi.org/10.1016/j.biosystems.2023.104843.

TROJÁK, Matej; David ŠAFRÁNEK; Branislav BROZMANN a Luboš BRIM. eBCSgen 2.0: Modelling and Analysis of Regulated Rule-Based Systems. Online. In I. Petre, A. Păun. 20th International Conference on Computational Methods in Systems Biology. LNBI 13447. Neuveden: Springer, 2022, s. 302-309. ISBN 978-3-031-15033-3. Dostupné z: https://doi.org/10.1007/978-3-031-15034-0_17.

TROJÁK, Matej; Helge HECHT; Martin ČECH a Elliott James PRICE. MSMetaEnhancer: A Python package for mass spectra metadata annotation. Journal of Open Source Software. 2022, roč. 7, č. 79. Dostupné z: https://doi.org/10.21105/joss.04494.

TROJÁK, Matej; David ŠAFRÁNEK; Lukrécia MERTOVÁ a Luboš BRIM. eBCSgen: A Software Tool for Biochemical Space Language. Online. In Abate A., Petrov T., Wolf V. 18th International Conference on Computational Methods in Systems Biology, CMSB 2020. LNBI 12314. Neuveden: Springer, 2020, s. 356-361. ISBN 978-3-030-60326-7. Dostupné z: https://doi.org/10.1007/978-3-030-60327-4_20.

TROJÁK, Matej; David ŠAFRÁNEK; Lukrécia MERTOVÁ a Luboš BRIM. Executable Biochemical Space for Specification and Analysis of Biochemical Systems. PLOS ONE. Public Library of Science, 2020, roč. 15, č. 9, s. 1-23, 24 s. ISSN 1932-6203. Dostupné z: https://doi.org/10.1371/journal.pone.0238838.

TROJÁK, Matej; David ŠAFRÁNEK; Luboš BRIM; Jakub ŠALAGOVIČ a 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, s. 91-116. ISSN 1571-0661. Dostupné z: https://doi.org/10.1016/j.entcs.2020.06.006.

TROJÁK, Matej; David ŠAFRÁNEK; Lukrécia MERTOVÁ a Luboš BRIM. Executable Biochemical Space for Specification and Analysis of Biochemical Systems. In 7th Workshop on Hybrid Systems and Biology. 2020.

TROJÁK, Matej; David ŠAFRÁNEK; Lukrécia MERTOVÁ a 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, s. 41-59. ISBN 978-3-030-55753-9. Dostupné z: https://doi.org/10.1007/978-3-030-55754-6_3.

ŠAFRÁNEK, David; Matej TROJÁK; Vojtěch BRŮŽA; Tomáš VEJPUSTEK; Jan PAPOUŠEK; Martin DEMKO; Samuel PASTVA; Aleš PEJZNOCH a 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, s. 356-359. ISBN 978-3-030-31303-6. Dostupné z: https://doi.org/10.1007/978-3-030-31304-3_26.

TROJÁK, Matej; David ŠAFRÁNEK; Jan ČERVENÝ; Marek HAVLÍK; Lukrécia MERTOVÁ; Matej HAJNAL; Jakub HRABEC a Jakub ŠALAGOVIČ. Comprehensive Modelling Platform. In 6th Workshop on Hybrid Systems & Biology. 2019.

TROJÁK, Matej; David ŠAFRÁNEK; Jakub HRABEC; Jakub ŠALAGOVIČ; Jan ČERVENÝ; Matej HAJNAL; Lukrécia MERTOVÁ; Katarína PALUBOVÁ a 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.

BENEŠ, Nikola; Luboš BRIM; Jan ČERVENÝ; Samuel PASTVA; David ŠAFRÁNEK; Jakub ŠALAGOVIČ a Matej TROJÁK. Fully Automated Attractor Analysis of Cyanobacteria Models. In Marian Barbu, Răzvan Şolea, Adrian Filipescu. 22nd International Conference on System Theory, Control and Computing. Neuveden: IEEE, 2018, s. 354-359. ISBN 978-1-5386-4444-7. Dostupné z: https://doi.org/10.1109/ICSTCC.2018.8540762.

TROJÁK, Matej; David ŠAFRÁNEK a Jakub ŠALAGOVIČ. BCSgen: Biochemical Space language software tool. 2017.

TROJÁK, Matej; David ŠAFRÁNEK; Jakub ŠALAGOVIČ; Františka ROMANOVSKÁ a Matej HAJNAL. Biochemical Space: A framework for formal description and annotation of complex biological processes. In Computational Modeling in Biology Network meeting (COMBINE 2017). 2017.

TROJÁK, Matej; David ŠAFRÁNEK; Jakub ŠALAGOVIČ; Františka ROMANOVSKÁ a 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.

TROJÁK, Matej; David ŠAFRÁNEK; Jakub HRABEC; Jakub ŠALAGOVIČ; Františka ROMANOVSKÁ; Matej HAJNAL a Jan ČERVENÝ. E-cyanobacterium.org: A Web-based Platform for Systems Biology of Cyanobacteria. In International Conference on Systems Biology 2017. 2017.

TROJÁK, Matej; David ŠAFRÁNEK; Jakub HRABEC; Jakub ŠALAGOVIČ; Františka ROMANOVSKÁ; Matej HAJNAL a Jan ČERVENÝ. E-cyanobacterium.org: A Web-based Platform for Systems Biology of Cyanobacteria. In The Biomania Student Scientific Meeting 2017. 2017.

TROJÁK, Matej; David ŠAFRÁNEK; Jakub HRABEC; Jakub ŠALAGOVIČ; Františka ROMANOVSKÁ; Matej HAJNAL a Jan ČERVENÝ. E-cyanobacterium.org: A Web-based Platform for Systems Biology of Cyanobacteria. In Doctoral Workshop on Mathematical and Engineering Methods in Computer Science. 2017.

TROJÁK, Matej; Tadeáš DĚD; David ŠAFRÁNEK; Matej KLEMENT; Jan ČERVENÝ a Františka ROMANOVSKÁ. Biochemical Space: A Language for Formal Description and Annotation of Complex Biological Processes. In MEMICS 2016. 2016.

TROJÁK, Matej; David ŠAFRÁNEK; Jakub HRABEC; Jakub ŠALAGOVIČ; Jan ČERVENÝ a Matej HAJNAL. E-cyanobacterium.org: A Web-based Platform for Systems Biology of Cyanobacteria. 2016.

TROJÁK, Matej; David ŠAFRÁNEK; Jakub HRABEC; Jakub ŠALAGOVIČ; Františka ROMANOVSKÁ a 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, s. 316-322. ISBN 978-3-319-45176-3. Dostupné z: https://doi.org/10.1007/978-3-319-45177-0_20.

DĚD, Tadeáš; David ŠAFRÁNEK; Matej TROJÁK; Matej KLEMENT; Jakub ŠALAGOVIČ a 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, s. 27-49. ISSN 1571-0661. Dostupné z: https://doi.org/10.1016/j.entcs.2016.09.017.

TROJÁK, Matej; Tadeáš DĚD; David ŠAFRÁNEK; Matej KLEMENT; Jan ČERVENÝ a Luboš BRIM. Biochemical Space: A Language for Formal Description and Annotation of Complex Biological Processes. In 13th Conference on Computational Methods in Systems Biology. 2015.

TROJÁK, Matej; David ŠAFRÁNEK; Matej KLEMENT; Tadeáš DĚD; Jan ČERVENÝ a Luboš BRIM. Biochemical Space: A Language for Formal Description and Annotation of Complex Biological Processes. In Doctoral Workshop on Mathematical and Engineering Methods in Computer Science. 2015.

KLEMENT, Matej; David ŠAFRÁNEK; Jan ČERVENÝ; Tadeáš DĚD; Matej TROJÁK; Luboš BRIM a Stefan MUELLER. E-cyanobacterium.org: A Web-based Platform for Systems Biology of Cyanobacteria. In Fourth International Workshop on Hybrid Systems Biology. 2015.