David Safránek

Publication Activity (10 Years)

Years Active: 2003-2023
Publications (10 Years): 47

Top Topics

Boolean Networks

Top Venues

Electron. Notes Theor. Comput. Sci.

Publications

Lubos Brim, Samuel Pastva, David Safránek, Eva Smijáková
Temporary and permanent control of partially specified Boolean networks. Biosyst. 223 (2023)
Nikola Benes, Lubos Brim, Samuel Pastva, David Safránek, Eva Smijáková
Phenotype Control of Partially Specified Boolean Networks. CMSB (2023)
Nikola Benes, Lubos Brim, Ondrej Huvar, Samuel Pastva, David Safránek
Boolean network sketches: a unifying framework for logical model inference. Bioinform. 39 (4) (2023)
Matej Troják, David Safránek, Samuel Pastva, Lubos Brim
Rule-based modelling of biological systems using regulated rewriting. Biosyst. 225 (2023)
Tatjana Petrov, Matej Hajnal, Julia Klein, David Safránek, Morgane Nouvian
Extracting individual characteristics from population data reveals a negative social effect during honeybee defence. PLoS Comput. Biol. 18 (9) (2022)
Matej Troják, David Safránek, Lubos Brim
Biochemical Space Language in Relation to Multiset Rewriting Systems. CoRR (2022)
Lubos Brim, Samuel Pastva, David Safránek, Eva Smijáková
Robust Control of Partially Specified Boolean Networks. CoRR (2022)
Nikola Benes, Lubos Brim, Ondrej Huvar, Samuel Pastva, David Safránek, Eva Smijáková
AEON.py: Python library for attractor analysis in asynchronous Boolean networks. Bioinform. 38 (21) (2022)
Nikola Benes, Lubos Brim, Jakub Kadlecaj, Samuel Pastva, David Safránek
Exploring attractor bifurcations in Boolean networks. BMC Bioinform. 23 (1) (2022)
Matej Troják, David Safránek, Branislav Brozmann, Lubos Brim
eBCSgen 2.0: Modelling and Analysis of Regulated Rule-Based Systems. CMSB (2022)
Nikola Benes, Lubos Brim, Samuel Pastva, David Safránek
BDD-Based Algorithm for SCC Decomposition of Edge-Coloured Graphs. Log. Methods Comput. Sci. 18 (1) (2022)
Nikola Benes, Lubos Brim, Samuel Pastva, David Safránek
Aeon 2021: Bifurcation Decision Trees in Boolean Networks. CMSB (2021)
Matej Troják, Samuel Pastva, David Safránek, Lubos Brim
Regulated Multiset Rewriting Systems. CoRR (2021)
Nikola Benes, Lubos Brim, Samuel Pastva, David Safránek
BDD-Based Algorithm for SCC Decomposition of Edge-Coloured Graphs. CoRR (2021)
Nikola Benes, Lubos Brim, Samuel Pastva, David Safránek
Symbolic Coloured SCC Decomposition. TACAS (2) (2021)
Nikola Benes, Lubos Brim, Samuel Pastva, David Safránek
Computing Bottom SCCs Symbolically Using Transition Guided Reduction. CAV (1) (2021)
Matej Hajnal, David Safránek, Tatjana Petrov
DiPS: A Tool for Data-Informed Parameter Synthesis for Markov Chains from Multiple-Property Specifications. EPEW (2021)
Nikola Benes, Lubos Brim, Samuel Pastva, David Safránek
Digital Bifurcation Analysis of Internet Congestion Control Protocols. Int. J. Bifurc. Chaos 30 (13) (2020)
Matej Troják, David Safránek, Lubos Brim, Jakub Salagovic, Jan Cervený
Executable Biochemical Space for Specification and Analysis of Biochemical Systems. SASB (2020)
Nikola Benes, Lubos Brim, Jakub Kadlecaj, Samuel Pastva, David Safránek
AEON: Attractor Bifurcation Analysis of Parametrised Boolean Networks. CAV (1) (2020)
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, David Safránek, Babette Regierer, Domenica D'Elia
The need for standardisation in life science research - an approach to excellence and trust. F1000Research 9 (2020)
Matej Troják, David Safránek, Lubos Brim
Executable Biochemical Space for Specification and Analysis of Biochemical Systems. CoRR (2020)
Eva Smijáková, Samuel Pastva, David Safránek, Lubos Brim
Parallel Parameter Synthesis for Multi-affine Hybrid Systems from Hybrid CTL Specifications. CMSB (2020)
Matej Troják, David Safránek, Lukrécia Mertová, Lubos Brim
Parameter Synthesis and Robustness Analysis of Rule-Based Models. NFM (2020)
Matej Troják, David Safránek, Lukrécia Mertová, Lubos Brim
eBCSgen: A Software Tool for Biochemical Space Language. CMSB (2020)
Nikola Benes, Lubos Brim, Samuel Pastva, David Safránek
Parallel parameter synthesis algorithm for hybrid CTL. Sci. Comput. Program. 185 (2020)
Lubos Brim, Samuel Pastva, David Safránek, Eva Smijakova
Parallel One-Step Control of Parametrised Boolean Networks. CoRR (2020)
Matej Hajnal, Morgane Nouvian, Tatjana Petrov, David Safránek
Data-Informed Parameter Synthesis for Population Markov Chains. CMSB (2019)
Nikola Benes, Lubos Brim, Martin Geletka, Samuel Pastva, David Safránek
Accelerating Parameter Synthesis Using Semi-algebraic Constraints. IFM (2019)
Nikola Benes, Lubos Brim, Samuel Pastva, Jakub Polácek, David Safránek
Formal Analysis of Qualitative Long-Term Behaviour in Parametrised Boolean Networks. ICFEM (2019)
Jérôme Feret, Loïc Paulevé, David Safránek
Preface. Theor. Comput. Sci. 765 (2019)
Nikola Benes, Lubos Brim, Jana Drazanová, Samuel Pastva, David Safránek
Facetal abstraction for non-linear dynamical systems based on δ-decidable SMT. HSCC (2019)
David Safránek, Matej Troják, Vojtech Bruza, Tomás Vejpustek, Jan Papousek, Martin Demko, Samuel Pastva, Ales Pejznoch, Lubos Brim
Barbaric Robustness Monitoring Revisited for STL* in Parasim. CMSB (2019)
Matej Hajnal, Morgane Nouvian, David Safránek, Tatjana Petrov
Data-Informed Parameter Synthesis for Population Markov Chains. HSB (2019)
Juraj Kolcák, David Safránek, Stefan Haar, Loïc Paulevé
Parameter space abstraction and unfolding semantics of discrete regulatory networks. Theor. Comput. Sci. 765 (2019)
Nikola Benes, Lubos Brim, Samuel Pastva, David Safránek
Digital Bifurcation Analysis of TCP Dynamics. TACAS (2) (2019)
Juraj Kolcák, David Safránek, Stefan Haar, Loïc Paulevé
Parameter Space Abstraction and Unfolding Semantics of Discrete Regulatory Networks. CoRR (2018)
Guido Sanguinetti, David Safránek
Preface. SASB 335 (2018)
Juraj Kolcák, David Safránek, Stefan Haar, Loïc Paulevé
Unfolding of Parametric Boolean Networks. SASB 335 (2018)
Nikola Benes, Lubos Brim, Martin Demko, Samuel Pastva, David Safránek
Pithya: A Parallel Tool for Parameter Synthesis of Piecewise Multi-affine Dynamical Systems. CAV (1) (2017)
Jiri Barnat, Nikola Benes, Lubos Brim, Martin Demko, Matej Hajnal, Samuel Pastva, David Safránek
Detecting Attractors in Biological Models with Uncertain Parameters. CMSB (2017)
Matej Hajnal, David Safránek, Martin Demko, Samuel Pastva, Pavel Krejcí, Lubos Brim
Toward Modelling and Analysis of Transient and Sustained Behaviour of Signalling Pathways. HSB (2016)
Nikola Benes, Lubos Brim, Martin Demko, Samuel Pastva, David Safránek
A Model Checking Approach to Discrete Bifurcation Analysis. FM (2016)
T. Ded, David Safránek, Matej Troják, Matej Klement, Jakub Salagovic, Lubos Brim
Formal Biochemical Space with Semantics in Kappa and BNGL. Electron. Notes Theor. Comput. Sci. 326 (2016)
Nikola Benes, Lubos Brim, Martin Demko, Samuel Pastva, David Safránek
Parallel SMT-Based Parameter Synthesis with Application to Piecewise Multi-affine Systems. ATVA (2016)
Matej Troják, David Safránek, Jakub Hrabec, Jakub Salagovic, Frantiska Romanovská, Jan Cervený
E-Cyanobacterium.org: A Web-Based Platform for Systems Biology of Cyanobacteria. CMSB (2016)
Martin Demko, Nikola Benes, Lubos Brim, Samuel Pastva, David Safránek
High-Performance Symbolic Parameter Synthesis of Biological Models: A Case Study. CMSB (2016)
Lubos Brim, Martin Demko, Samuel Pastva, David Safránek
High-Performance Discrete Bifurcation Analysis for Piecewise-Affine Dynamical Systems. HSB (2015)
Lubos Brim, Milan Ceska, Martin Demko, Samuel Pastva, David Safránek
Parameter Synthesis by Parallel Coloured CTL Model Checking. CMSB (2015)
Lubos Brim, J. Niznan, David Safránek
Compact Representation of Photosynthesis Dynamics by Rule-based Models. Electron. Notes Theor. Comput. Sci. 316 (2015)
Lubos Brim, J. Niznan, David Safránek
Compact Representation of Photosynthesis Dynamics by Rule-based Models (Full Version). CoRR (2014)
Lubos Brim, Petr Dluhos, David Safránek, Tomas Vejpustek
: Extending signal temporal logic with signal-value freezing operator. Inf. Comput. 236 (2014)
Matej Klement, T. Ded, David Safránek, Jan Cervený, Stefan Müller, Ralf Steuer
Biochemical Space: A Framework for Systemic Annotation of Biological Models. Electron. Notes Theor. Comput. Sci. 306 (2014)
Matej Klement, David Safránek, T. Ded, Ales Pejznoch, Ladislav Nedbal, Ralf Steuer, Jan Cervený, Stefan Müller
A Comprehensive Web-based Platform For Domain-Specific Biological Models. Electron. Notes Theor. Comput. Sci. 299 (2013)
Lubos Brim, Milan Ceska, Sven Drazan, David Safránek
On Robustness Analysis of Stochastic Biochemical Systems by Probabilistic Model Checking. CoRR (2013)
Lubos Brim, Tomas Vejpustek, David Safránek, Jana Fabriková
Robustness Analysis for Value-Freezing Signal Temporal Logic. HSB (2013)
S. Van Goethem, Jean-Marie Jacquet, Lubos Brim, David Safránek
Timed Modelling of Gene Networks with Arbitrarily Precise Expression Discretization. Electron. Notes Theor. Comput. Sci. 293 (2013)
Lubos Brim, Vilém Ded, David Safránek
Qualitative modelling and analysis of Photosystem II. BioPPN@Petri Nets (2013)
Lubos Brim, Milan Ceska, Sven Drazan, David Safránek
Exploring Parameter Space of Stochastic Biochemical Systems Using Quantitative Model Checking. CAV (2013)
Lubos Brim, Milan Ceska, David Safránek
Model Checking of Biological Systems. SFM (2013)
Lubos Brim, Jana Fabriková, Sven Drazan, David Safránek
On Approximative Reachability Analysis of Biochemical Dynamical Systems. Trans. Comp. Sys. Biology 14 (2012)
Hannes Klarner, Adam Streck, David Safránek, Juraj Kolcák, Heike Siebert
Parameter Identification and Model Ranking of Thomas Networks. CMSB (2012)
Petr Dluhos, Lubos Brim, David Safránek
On Expressing and Monitoring Oscillatory Dynamics HSB (2012)
Jiri Barnat, Lubos Brim, Adam Krejci, Adam Streck, David Safránek, Martin Vejnar, Tomas Vejpustek
On Parameter Synthesis by Parallel Model Checking. IEEE ACM Trans. Comput. Biol. Bioinform. 9 (3) (2012)
Lubos Brim, Jana Fabriková, Sven Drazan, David Safránek
Reachability in Biochemical Dynamical Systems by Quantitative Discrete Approximation CoRR (2011)
Lubos Brim, Jana Fabriková, Sven Drazan, David Safránek
Reachability in Biochemical Dynamical Systems by Quantitative Discrete Approximation (extended abstract) CompMod (2011)
David Safránek, Jan Cervený, Matej Klement, Jana Pospísilová, Lubos Brim, Dusan Lazar, Ladislav Nedbal
E-photosynthesis: Web-based platform for modeling of complex photosynthetic processes. Biosyst. 103 (2) (2011)
Jiri Barnat, Lubos Brim, David Safránek
High-performance analysis of biological systems dynamics with the DiVinE model checker. Briefings Bioinform. 11 (3) (2010)
Jiri Barnat, Lubos Brim, Ivana Cerná, Sven Drazan, Jana Fabriková, David Safránek
On algorithmic analysis of transcriptional regulation by LTL model checking. Theor. Comput. Sci. 410 (33-34) (2009)
Jiri Barnat, Lubos Brim, Ivana Cerná, Sven Drazan, Jana Fabriková, Jan Láník, David Safránek, Hongwu Ma
BioDiVinE: A Framework for Parallel Analysis of Biological Models COMPMOD (2009)
Jiri Barnat, Lubos Brim, Ivana Cerná, Sven Drazan, David Safránek
Parallel Model Checking Large-Scale Genetic Regulatory Networks with DiVinE. Electron. Notes Theor. Comput. Sci. 194 (3) (2008)
David Safránek
Visual Specification of Systems with Heterogeneous Coordination Models. Electron. Notes Theor. Comput. Sci. 180 (2) (2007)
David Safránek
Architectural Interoperability Checking in Visual Coordination Networks. Electron. Notes Theor. Comput. Sci. 181 (2007)
Ales Smrcka, Vojtech Rehák, Tomás Vojnar, David Safránek, Petr Matousek, Z. Rehák
Verifying VHDL Designs with Multiple Clocks in SMV. FMICS/PDMC (2006)
David Safránek, Jirí Simsa
VCD: A Visual Formalism for Specification of Heterogeneous Software Architectures. SOFSEM (2005)
David Safránek
SGCCS: A Graphical Language for Real-time Coordination. Electron. Notes Theor. Comput. Sci. 68 (3) (2003)
David Safránek
Visual Specification of Concurrent Systems. ASE (2003)