Abstraction-based segmental simulation of reaction networks using adaptive memoization. - Helfrich, Martin; Andriushchenko, Roman; Ceska, Milan; Kretínský, Jan; Marticek, Stefan; Safránek, David (BMC Bioinform., 2024)

Symbolic Model Checking of Hybrid CTL on Coloured Kripke Structures. - Benes, Nikola; Brim, Lubos; Huvar, Ondrej; Pastva, Samuel; Safránek, David (2024)

BNClassifier: Classifying Boolean Models by Dynamic Properties. - Benes, Nikola; Brim, Lubos; Huvar, Ondrej; Pastva, Samuel; Safránek, David (2024)

Boolean network sketches: a unifying framework for logical model inference. - Benes, Nikola; Brim, Lubos; Huvar, Ondrej; Pastva, Samuel; Safránek, David (Bioinform., 2023)

Temporary and permanent control of partially specified Boolean networks. - Brim, Lubos; Pastva, Samuel; Safránek, David; Smijáková, Eva (Biosyst., 2023)

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

Phenotype Control of Partially Specified Boolean Networks. - Benes, Nikola; Brim, Lubos; Pastva, Samuel; Safránek, David; Smijáková, Eva (2023)

AEON.py: Python library for attractor analysis in asynchronous Boolean networks. - Benes, Nikola; Brim, Lubos; Huvar, Ondrej; Pastva, Samuel; Safránek, David; Smijáková, Eva (Bioinform., 2022)

Exploring attractor bifurcations in Boolean networks. - Benes, Nikola; Brim, Lubos; Kadlecaj, Jakub; Pastva, Samuel; Safránek, David (BMC Bioinform., 2022)

BDD-Based Algorithm for SCC Decomposition of Edge-Coloured Graphs. - Benes, Nikola; Brim, Lubos; Pastva, Samuel; Safránek, David (Log. Methods Comput. Sci., 2022)

Extracting individual characteristics from population data reveals a negative social effect during honeybee defence. - Petrov, Tatjana; Hajnal, Matej; Klein, Julia; Safránek, David; Nouvian, Morgane (PLoS Comput. Biol., 2022)

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

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

Robust Control of Partially Specified Boolean Networks. - Brim, Lubos; Pastva, Samuel; Safránek, David; Smijáková, Eva (CoRR, 2022)

Computing Bottom SCCs Symbolically Using Transition Guided Reduction. - Benes, Nikola; Brim, Lubos; Pastva, Samuel; Safránek, David (2021)

Aeon 2021: Bifurcation Decision Trees in Boolean Networks. - Benes, Nikola; Brim, Lubos; Pastva, Samuel; Safránek, David (2021)

DiPS: A Tool for Data-Informed Parameter Synthesis for Markov Chains from Multiple-Property Specifications. - Hajnal, Matej; Safránek, David; Petrov, Tatjana (2021)

Symbolic Coloured SCC Decomposition. - Benes, Nikola; Brim, Lubos; Pastva, Samuel; Safránek, David (2021)

BDD-Based Algorithm for SCC Decomposition of Edge-Coloured Graphs. - Benes, Nikola; Brim, Lubos; Pastva, Samuel; Safránek, David (CoRR, 2021)

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

Digital Bifurcation Analysis of Internet Congestion Control Protocols. - Benes, Nikola; Brim, Lubos; Pastva, Samuel; Safránek, David (Int. J. Bifurc. Chaos, 2020)

Parallel parameter synthesis algorithm for hybrid CTL. - Benes, Nikola; Brim, Lubos; Pastva, Samuel; Safránek, David (Sci. Comput. Program., 2020)

AEON: Attractor Bifurcation Analysis of Parametrised Boolean Networks. - Benes, Nikola; Brim, Lubos; Kadlecaj, Jakub; Pastva, Samuel; Safránek, David (2020)

Parallel Parameter Synthesis for Multi-affine Hybrid Systems from Hybrid CTL Specifications. - Smijáková, Eva; Pastva, Samuel; Safránek, David; Brim, Lubos (2020)

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

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

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

Proceedings of SASB 2018, the 7th International Workshop on Static Analysis and Systems Biology, University of Edinburgh, September 7, 2016 (Elsevier, 2020)

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

Parallel One-Step Control of Parametrised Boolean Networks. - Brim, Lubos; Pastva, Samuel; Safránek, David; Smijakova, Eva (CoRR, 2020)

The need for standardisation in life science research - an approach to excellence and trust. - Hollmann, Susanne; Kremer, Andreas; Baebler, Spela; Trefois, Christophe; Gruden, Kristina; Rudnicki, Witold R.; Tong, Weida; Gruca, Aleksandra; Bongcam-Rudloff, Erik; Evelo, Chris T. A.; Nechyporenko, Alina S.; Frohme, Marcus; et al. (F1000Research, 2020)

Preface. - Feret, Jérôme; Paulevé, Loïc; Safránek, David (Theor. Comput. Sci., 2019)

Parameter space abstraction and unfolding semantics of discrete regulatory networks. - Kolcák, Juraj; Safránek, David; Haar, Stefan; Paulevé, Loïc (Theor. Comput. Sci., 2019)

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

Data-Informed Parameter Synthesis for Population Markov Chains. - Hajnal, Matej; Nouvian, Morgane; Petrov, Tatjana; Safránek, David (2019)

Data-Informed Parameter Synthesis for Population Markov Chains. - Hajnal, Matej; Nouvian, Morgane; Safránek, David; Petrov, Tatjana (2019)

Facetal abstraction for non-linear dynamical systems based on δ-decidable SMT. - Benes, Nikola; Brim, Lubos; Drazanová, Jana; Pastva, Samuel; Safránek, David (2019)

Formal Analysis of Qualitative Long-Term Behaviour in Parametrised Boolean Networks. - Benes, Nikola; Brim, Lubos; Pastva, Samuel; Polácek, Jakub; Safránek, David (2019)

Accelerating Parameter Synthesis Using Semi-algebraic Constraints. - Benes, Nikola; Brim, Lubos; Geletka, Martin; Pastva, Samuel; Safránek, David (2019)

Digital Bifurcation Analysis of TCP Dynamics. - Benes, Nikola; Brim, Lubos; Pastva, Samuel; Safránek, David (2019)

Model Checking Approach to the Analysis of Biological Systems. - Benes, Nikola; Brim, Lubos; Pastva, Samuel; Safránek, David (2019)

Preface. - Sanguinetti, Guido; Safránek, David (2018)

Unfolding of Parametric Boolean Networks. - Kolcák, Juraj; Safránek, David; Haar, Stefan; Paulevé, Loïc (2018)

Computational Methods in Systems Biology - 16th International Conference, CMSB 2018, Brno, Czech Republic, September 12-14, 2018, Proceedings (Springer, 2018)

Parameter Space Abstraction and Unfolding Semantics of Discrete Regulatory Networks. - Kolcák, Juraj; Safránek, David; Haar, Stefan; Paulevé, Loïc (CoRR, 2018)

Pithya: A Parallel Tool for Parameter Synthesis of Piecewise Multi-affine Dynamical Systems. - Benes, Nikola; Brim, Lubos; Demko, Martin; Pastva, Samuel; Safránek, David (2017)

Detecting Attractors in Biological Models with Uncertain Parameters. - Barnat, Jiri; Benes, Nikola; Brim, Lubos; Demko, Martin; Hajnal, Matej; Pastva, Samuel; Safránek, David (2017)

Parallel SMT-Based Parameter Synthesis with Application to Piecewise Multi-affine Systems. - Benes, Nikola; Brim, Lubos; Demko, Martin; Pastva, Samuel; Safránek, David (2016)

High-Performance Symbolic Parameter Synthesis of Biological Models: A Case Study. - Demko, Martin; Benes, Nikola; Brim, Lubos; Pastva, Samuel; Safránek, David (2016)

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

A Model Checking Approach to Discrete Bifurcation Analysis. - Benes, Nikola; Brim, Lubos; Demko, Martin; Pastva, Samuel; Safránek, David (2016)

Toward Modelling and Analysis of Transient and Sustained Behaviour of Signalling Pathways. - Hajnal, Matej; Safránek, David; Demko, Martin; Pastva, Samuel; Krejcí, Pavel; Brim, Lubos (2016)

Parameter Synthesis by Parallel Coloured CTL Model Checking. - Brim, Lubos; Ceska, Milan; Demko, Martin; Pastva, Samuel; Safránek, David (2015)

High-Performance Discrete Bifurcation Analysis for Piecewise-Affine Dynamical Systems. - Brim, Lubos; Demko, Martin; Pastva, Samuel; Safránek, David (2015)

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

Hybrid Systems Biology - Fourth International Workshop, HSB 2015, Madrid, Spain, September 4-5, 2015. Revised Selected Papers (Springer, 2015)

STL⁎: Extending signal temporal logic with signal-value freezing operator. - Brim, Lubos; Dluhos, Petr; Safránek, David; Vejpustek, Tomas (Inf. Comput., 2014)

Compact Representation of Photosynthesis Dynamics by Rule-based Models. - Brim, Lubos; Niznan, Juraj; Safránek, David (2014)

Biochemical Space: A Framework for Systemic Annotation of Biological Models. - Klement, Matej; Ded, T.; Safránek, David; Cervený, Jan; Müller, Stefan; Steuer, Ralf (2014)

Compact Representation of Photosynthesis Dynamics by Rule-based Models (Full Version). - Brim, Lubos; Niznan, Juraj; Safránek, David (CoRR, 2014)

Qualitative modelling and analysis of Photosystem II. - Brim, Lubos; Ded, Vilém; Safránek, David (2013)

Exploring Parameter Space of Stochastic Biochemical Systems Using Quantitative Model Checking. - Brim, Lubos; Ceska, Milan; Drazan, Sven; Safránek, David (2013)

Model Checking of Biological Systems. - Brim, Lubos; Ceska, Milan; Safránek, David (2013)

Robustness Analysis for Value-Freezing Signal Temporal Logic. - Brim, Lubos; Vejpustek, Tomas; Safránek, David; Fabriková, Jana (2013)

A Comprehensive Web-based Platform For Domain-Specific Biological Models. - Klement, Matej; Safránek, David; Ded, T.; Pejznoch, Ales; Nedbal, Ladislav; Steuer, Ralf; Cervený, Jan; Müller, Stefan (2013)

On Robustness Analysis of Stochastic Biochemical Systems by Probabilistic Model Checking. - Brim, Lubos; Ceska, Milan; Drazan, Sven; Safránek, David (CoRR, 2013)

On Parameter Synthesis by Parallel Model Checking. - Barnat, Jiri; Brim, Lubos; Krejci, Adam; Streck, Adam; Safránek, David; Vejnar, Martin; Vejpustek, Tomas (IEEE ACM Trans. Comput. Biol. Bioinform., 2012)

On Approximative Reachability Analysis of Biochemical Dynamical Systems. - Brim, Lubos; Fabriková, Jana; Drazan, Sven; Safránek, David (Trans. Comp. Sys. Biology, 2012)

Parameter Identification and Model Ranking of Thomas Networks. - Klarner, Hannes; Streck, Adam; Safránek, David; Kolcák, Juraj; Siebert, Heike (2012)

On Expressing and Monitoring Oscillatory Dynamics - Dluhos, Petr; Brim, Lubos; Safránek, David (2012)

Timed Modelling of Gene Networks with Arbitrarily Precise Expression Discretization. - Goethem, S. Van; Jacquet, Jean-Marie; Brim, Lubos; Safránek, David (2012)

E-photosynthesis: Web-based platform for modeling of complex photosynthetic processes. - Safránek, David; Cervený, Jan; Klement, Matej; Pospísilová, Jana; Brim, Lubos; Lazar, Dusan; Nedbal, Ladislav (Biosyst., 2011)

Reachability in Biochemical Dynamical Systems by Quantitative Discrete Approximation (extended abstract) - Brim, Lubos; Fabriková, Jana; Drazan, Sven; Safránek, David (2011)

Reachability in Biochemical Dynamical Systems by Quantitative Discrete Approximation - Brim, Lubos; Fabriková, Jana; Drazan, Sven; Safránek, David (CoRR, 2011)

High-performance analysis of biological systems dynamics with the DiVinE model checker. - Barnat, Jiri; Brim, Lubos; Safránek, David (Briefings Bioinform., 2010)

On algorithmic analysis of transcriptional regulation by LTL model checking. - Barnat, Jiri; Brim, Lubos; Cerná, Ivana; Drazan, Sven; Fabriková, Jana; Safránek, David (Theor. Comput. Sci., 2009)

BioDiVinE: A Framework for Parallel Analysis of Biological Models - Barnat, Jiri; Brim, Lubos; Cerná, Ivana; Drazan, Sven; Fabriková, Jana; Láník, Jan; Safránek, David; Ma, Hongwu (2009)

Parallel Model Checking Large-Scale Genetic Regulatory Networks with DiVinE. - Barnat, Jiri; Brim, Lubos; Cerná, Ivana; Drazan, Sven; Safránek, David (2007)

Verifying VHDL Designs with Multiple Clocks in SMV. - Smrcka, Ales; Rehák, Vojtech; Vojnar, Tomás; Safránek, David; Matousek, Petr; Rehák, Z. (2006)

Architectural Interoperability Checking in Visual Coordination Networks. - Safránek, David (2006)

VCD: A Visual Formalism for Specification of Heterogeneous Software Architectures. - Safránek, David; Simsa, Jirí (2005)

Visual Specification of Systems with Heterogeneous Coordination Models. - Safránek, David (2004)

Visual Specification of Concurrent Systems. - Safránek, David (2003)

SGCCS: A Graphical Language for Real-time Coordination. - Safránek, David (2002)