Formal Biochemical Space with Semantics in Kappa and BNGL. - T. Ded; David Safránek; Matej Troják; Matej Klement; Jakub Salagovic; Lubos Brim (SASB, 2015)

E-Cyanobacterium.org: A Web-Based Platform for Systems Biology of Cyanobacteria. - Matej Troják; David Safránek; Jakub Hrabec; Jakub Salagovic; Frantiska Romanovská; Jan Cervený (CMSB, 2016)

Barbaric Robustness Monitoring Revisited for STL* in Parasim. - David Safránek; Matej Troják; Vojtech Bruza; Tomás Vejpustek; Jan Papousek; Martin Demko; Samuel Pastva; Ales Pejznoch; Lubos Brim (CMSB, 2019)

eBCSgen: A Software Tool for Biochemical Space Language. - Matej Troják; David Safránek; Lukrécia Mertová; Lubos Brim (CMSB, 2020)

Parameter Synthesis and Robustness Analysis of Rule-Based Models. - Matej Troják; David Safránek; Lukrécia Mertová; Lubos Brim (NFM, 2020)

Executable Biochemical Space for Specification and Analysis of Biochemical Systems. - Matej Troják; David Safránek; Lubos Brim; Jakub Salagovic; Jan Cervený (SASB, 2020)

Executable Biochemical Space for Specification and Analysis of Biochemical Systems. - Matej Troják; David Safránek; Lubos Brim (CoRR, 2020)

Regulated Multiset Rewriting Systems. - Matej Troják; Samuel Pastva; David Safránek; Lubos Brim (CoRR, 2021)

eBCSgen 2.0: Modelling and Analysis of Regulated Rule-Based Systems. - Matej Troják; David Safránek; Branislav Brozmann; Lubos Brim (CMSB, 2022)

Biochemical Space Language in Relation to Multiset Rewriting Systems. - Matej Troják; David Safránek; Lubos Brim (CoRR, 2022)

MSMetaEnhancer: A Python package for mass spectra metadata annotation. - Matej Troják; Helge Hecht; Martin Cech; Elliott James Price (J. Open Source Softw., 2022)

Rule-based modelling of biological systems using regulated rewriting. - Matej Troják; David Safránek; Samuel Pastva; Lubos Brim (Biosyst., 2023)