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PUBLICATIONS

​Biochemical Space: A framework for formal description and annotation of complex biological processes

    • TROJÁK, Matej, David ŠAFRÁNEK, Jakub ŠALAGOVIÄŒ, Františka ROMANOVSKÁ and Matej HAJNAL

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

    • Materials: [presentation] [poster]

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  • Biochemical Space: A Framework for Formal Description and Annotation of Complex Biological Processes

    • TROJÁK, Matej, David ŠAFRÁNEK, Jakub ŠALAGOVIÄŒ, Františka ROMANOVSKÁ and Matej HAJNAL

    • In The 8th International Workshop on Static Analysis for Systems Biology (SASB 2017).

    • Materials: [presentation]

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  • E-cyanobacterium.org: A Web-based Platform for Systems Biology of Cyanobacteria 

    • TROJÁK, Matej, David ŠAFRÁNEK, Jakub HRABEC, Jakub ŠALAGOVIÄŒ, Františka ROMANOVSKÁ, Matej HAJNAL and Jan ÄŒERVENÝ

    • In International Conference on Systems Biology 2017 (ICSB 2017).

    • Materials: [poster]

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  • E-cyanobacterium.org: A Web-based Platform for Systems Biology of Cyanobacteria

    • TROJÁK, Matej, David ŠAFRÁNEK, Jakub HRABEC, Jakub ŠALAGOVIÄŒ, Františka ROMANOVSKÁ, Matej HAJNAL and Jan ÄŒERVENÝ

    • In The Biomania Student Scientific Meeting 2017.

    • Materials: [poster]

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  • E-cyanobacterium.org: A Web-based Platform for Systems Biology of Cyanobacteria

    • TROJÁK, Matej, David ŠAFRÁNEK, Jakub HRABEC, Jakub ŠALAGOVIÄŒ, Františka ROMANOVSKÁ, Matej HAJNAL and Jan ÄŒERVENÝ

    • In Doctoral Workshop on Mathematical and Engineering Methods in Computer Science 2017 (MEMICS 2017).

    • Materials: [poster]

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  • E-cyanobacterium.org: A Web-based Platform for Systems Biology of Cyanobacteria

    • TROJÁK, Matej, David ŠAFRÁNEK, Jakub HRABEC, Jakub ŠALAGOVIÄŒ, Františka ROMANOVSKÁ, Matej HAJNAL and Jan ÄŒERVENÝ

    • In Intelligent Systems for Molecular Biology and European Conference on Computational Biology (ISMB/ECCB 2017).

    • Materials: [poster]

2017

  • Biochemical Space: A Language for Formal Description and Annotation of Complex Biological Processes

    • TROJÁK, Matej, Tadeáš DÄšD, David ŠAFRÁNEK, Matej KLEMENT, Jan ÄŒERVENÝ and Františka ROMANOVSKÁ

    • In Doctoral Workshop on Mathematical and Engineering Methods in Computer Science 2016 (MEMICS 2016).

    • Materials: [poster]

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  • E-Cyanobacterium.org: A Web-Based Platform for Systems Biology of Cyanobacteria

    • TROJÁK, Matej, David ŠAFRÁNEK, Jakub HRABEC, Jakub ŠALAGOVIÄŒ, Františka ROMANOVSKÁ and Jan ÄŒERVENÝ

    • Computational Methods in Systems Biology (CMSB 2016).

    • Materials: [doi] [paper] [presentation]

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  • Formal Biochemical Space with Semantics in Kappa and BNGL

    • DÄšD, Tadeáš, David ŠAFRÁNEK, Matej TROJÁK, Matej KLEMENT, Jakub ŠALAGOVIÄŒ and Luboš BRIM

    • The 6th International Workshop on Static Analysis and Systems Biology (SASB 2015).

    • Materials: [doi] [paper]

  • Biochemical Space: A Language for Formal Description and Annotation of Complex Biological Processes

    • TROJÁK, Matej, Tadeáš DÄšD, David ŠAFRÁNEK, Matej KLEMENT, Jan ÄŒERVENÝ and Luboš BRIM

    • In 13th Conference on Computational Methods in Systems Biology (CMSB 2015).

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  • Biochemical Space: A Language for Formal Description and Annotation of Complex Biological Processes

    • TROJÁK, Matej, David ŠAFRÁNEK, Matej KLEMENT, Tadeáš DÄšD, Jan ÄŒERVENÝ and Luboš BRIM

    • In Doctoral Workshop on Mathematical and Engineering Methods in Computer Science (MEMICS 2015).

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  • E-cyanobacterium.org: A Web-based Platform for Systems Biology of Cyanobacteria

    • KLEMENT, Matej, David ŠAFRÁNEK, Jan ÄŒERVENÝ, Tadeáš DÄšD, Matej TROJÁK, Luboš BRIM and Stefan MUELLER

    • In Fourth International Workshop on Hybrid Systems Biology (HSB 2015).

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  • Formal specification of phosphorylation states and related reactions

    • TROJÁK, Matej.

    • Bachelor's thesis. Masaryk University, Faculty of Informatics. Thesis supervisor David Šafránek. In Slovak Language

    • Materials: [paper]

2016

2015

2018

  • Fully Automated Attractor Analysis of Cyanobacteria Models.

    • BENEŠ, Nikola, Luboš BRIM, Jan ÄŒERVENÝ, Samuel PASTVA, David ŠAFRÁNEK, Jakub ŠALAGOVIÄŒ and Matej TROJÁK​

    • In Marian Barbu, Răzvan Åžolea, Adrian Filipescu. 22nd International Conference on System Theory, Control and Computing.

    • Materials: [doi] [paper] [presentation]

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  • Formal Biochemical Space for Specification and Analysis of Biochemical Processes

    • TROJÁK, Matej​

    • Master's thesis. Masaryk University, Faculty of Informatics. Thesis supervisor David Šafránek.

    • Acquired Deans' award for the excellent master thesis.

    • Materials: [paper]​

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