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

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

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

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

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

Architectural Interoperability Checking in Visual Coordination Networks. - David Safránek (CoOrg/MTCoord@COORDINATION, 2006)

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

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

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

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

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

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

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

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

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

Timed Modelling of Gene Networks with Arbitrarily Precise Expression Discretization. - S. Van Goethem; Jean-Marie Jacquet; Lubos Brim; David Safránek (CS2Bio, 2012)

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

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

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

Exploring Parameter Space of Stochastic Biochemical Systems Using Quantitative Model Checking. - Lubos Brim; Milan Ceska 002; Sven Drazan; David Safránek (CAV, 2013)

Model Checking of Biological Systems. - Lubos Brim; Milan Ceska 002; David Safránek (SFM, 2013)

On Robustness Analysis of Stochastic Biochemical Systems by Probabilistic Model Checking. - Lubos Brim; Milan Ceska 002; Sven Drazan; David Safránek (CoRR, 2013)

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

A Comprehensive Web-based Platform For Domain-Specific Biological Models. - Matej Klement; David Safránek; T. Ded; Ales Pejznoch; Ladislav Nedbal; Ralf Steuer; Jan Cervený; Stefan Müller 009 (CS2Bio, 2013)

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

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

Biochemical Space: A Framework for Systemic Annotation of Biological Models. - Matej Klement; T. Ded; David Safránek; Jan Cervený; Stefan Müller 009; Ralf Steuer (CS2Bio, 2014)

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

Parameter Synthesis by Parallel Coloured CTL Model Checking. - Lubos Brim; Milan Ceska 002; Martin Demko; Samuel Pastva; David Safránek (CMSB, 2015)

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

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

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

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

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)

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

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

Pithya: A Parallel Tool for Parameter Synthesis of Piecewise Multi-affine Dynamical Systems. - Nikola Benes; Lubos Brim; Martin Demko; Samuel Pastva; David Safránek (CAV (1), 2017)

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

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

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

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

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)

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

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

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

Digital Bifurcation Analysis of TCP Dynamics. - Nikola Benes; Lubos Brim; Samuel Pastva; David Safránek (TACAS (2), 2019)

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

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

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

AEON: Attractor Bifurcation Analysis of Parametrised Boolean Networks. - Nikola Benes; Lubos Brim; Jakub Kadlecaj; Samuel Pastva; David Safránek (CAV (1), 2020)

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

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)

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

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

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

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

Computing Bottom SCCs Symbolically Using Transition Guided Reduction. - Nikola Benes; Lubos Brim; Samuel Pastva; David Safránek (CAV (1), 2021)

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

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

Symbolic Coloured SCC Decomposition. - Nikola Benes; Lubos Brim; Samuel Pastva; David Safránek (TACAS (2), 2021)

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)

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

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

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

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

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

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

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

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

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

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

Symbolic Model Checking of Hybrid CTL on Coloured Kripke Structures. - Nikola Benes; Lubos Brim; Ondrej Huvar; Samuel Pastva; David Safránek (ATVA (2), 2024)

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

Abstraction-based segmental simulation of reaction networks using adaptive memoization. - Martin Helfrich; Roman Andriushchenko; Milan Ceska 002; Jan Kretínský; Stefan Marticek; David Safránek (BMC Bioinform., 2024)