Publication Records

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.

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.

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.

BENEŠ, Nikola, Luboš BRIM, Jan ČERVENÝ, Samuel PASTVA, David ŠAFRÁNEK, Jakub ŠALAGOVIČ and 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, p. 354-359. ISBN 978-1-5386-4444-7. Available from: https://dx.doi.org/10.1109/ICSTCC.2018.8540762.

ČERVENÝ, Jan, Jakub ŠALAGOVIČ, František MUZIKA, David ŠAFRÁNEK and Igor SCHREIBER. Influence of circadian clocks on optimal regime of central C-N metabolism of cyanobacteria. Online. In Mishra, A. K.; Tiwari, D.; Rai, A. N. Cyanobacteria: From Basic Science to Applications. 1st ed. Neuveden: Academic Press, 2018, p. 193-206. ISBN 978-0-12-814667-5. Available from: https://dx.doi.org/10.1016/B978-0-12-814667-5.00009-X.

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

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 Computational Modeling in Biology Network meeting (COMBINE 2017). 2017.

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.

TROJÁK, Matej, 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. In International Conference on Systems Biology 2017. 2017.

TROJÁK, Matej, 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. In The Biomania Student Scientific Meeting 2017. 2017.

TROJÁK, Matej, 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. In Doctoral Workshop on Mathematical and Engineering Methods in Computer Science. 2017.

TROJÁK, Matej, David ŠAFRÁNEK, Jakub HRABEC, Jakub ŠALAGOVIČ, Jan ČERVENÝ and 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 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.

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.