David Safránek

85 papers A* 2B 4C 1Journal 29Unranked 45

Year	Rank	Type	Title / Venue / Authors
2025	—	`conf`	AEON 2025: Robust Control of Partially-Specified Boolean Networks. CMSB Vojtech Veselý, Eva Smijáková, Samuel Pastva, Nikola Benes, David Safránek
2024	J	`jnl`	Abstraction-based segmental simulation of reaction networks using adaptive memoization. BMC Bioinform. Martin Helfrich, Roman Andriushchenko, Milan Ceska, Jan Kretínský, Stefan Marticek, David Safránek
2024	—	`conf`	BNClassifier: Classifying Boolean Models by Dynamic Properties. CMSB Nikola Benes, Lubos Brim, Ondrej Huvar, Samuel Pastva, David Safránek
2024	—	`conf`	Symbolic Model Checking of Hybrid CTL on Coloured Kripke Structures. ATVA (2) Nikola Benes, Lubos Brim, Ondrej Huvar, Samuel Pastva, David Safránek
2023	J	`jnl`	Boolean network sketches: a unifying framework for logical model inference. Bioinform. Nikola Benes, Lubos Brim, Ondrej Huvar, Samuel Pastva, David Safránek
2023	—	`conf`	Phenotype Control of Partially Specified Boolean Networks. CMSB Nikola Benes, Lubos Brim, Samuel Pastva, David Safránek, Eva Smijáková
2023	J	`jnl`	Rule-based modelling of biological systems using regulated rewriting. Biosyst. Matej Troják, David Safránek, Samuel Pastva, Lubos Brim
2023	J	`jnl`	Temporary and permanent control of partially specified Boolean networks. Biosyst. Lubos Brim, Samuel Pastva, David Safránek, Eva Smijáková
2022	J	`jnl`	AEON.py: Python library for attractor analysis in asynchronous Boolean networks. Bioinform. Nikola Benes, Lubos Brim, Ondrej Huvar, Samuel Pastva, David Safránek, Eva Smijáková
2022	J	`jnl`	BDD-Based Algorithm for SCC Decomposition of Edge-Coloured Graphs. Log. Methods Comput. Sci. Nikola Benes, Lubos Brim, Samuel Pastva, David Safránek
2022	J	`jnl`	Biochemical Space Language in Relation to Multiset Rewriting Systems. CoRR Matej Troják, David Safránek, Lubos Brim
2022	J	`jnl`	Exploring attractor bifurcations in Boolean networks. BMC Bioinform. Nikola Benes, Lubos Brim, Jakub Kadlecaj, Samuel Pastva, David Safránek
2022	J	`jnl`	Extracting individual characteristics from population data reveals a negative social effect during honeybee defence. PLoS Comput. Biol. Tatjana Petrov, Matej Hajnal, Julia Klein, David Safránek, Morgane Nouvian
2022	J	`jnl`	Robust Control of Partially Specified Boolean Networks. CoRR Lubos Brim, Samuel Pastva, David Safránek, Eva Smijáková
2022	—	`conf`	eBCSgen 2.0: Modelling and Analysis of Regulated Rule-Based Systems. CMSB Matej Troják, David Safránek, Branislav Brozmann, Lubos Brim
2021	—	`conf`	Aeon 2021: Bifurcation Decision Trees in Boolean Networks. CMSB Nikola Benes, Lubos Brim, Samuel Pastva, David Safránek
2021	J	`jnl`	BDD-Based Algorithm for SCC Decomposition of Edge-Coloured Graphs. CoRR Nikola Benes, Lubos Brim, Samuel Pastva, David Safránek
2021	—	`conf`	Computing Bottom SCCs Symbolically Using Transition Guided Reduction. CAV (1) Nikola Benes, Lubos Brim, Samuel Pastva, David Safránek
2021	—	`conf`	DiPS: A Tool for Data-Informed Parameter Synthesis for Markov Chains from Multiple-Property Specifications. EPEW Matej Hajnal, David Safránek, Tatjana Petrov
2021	J	`jnl`	Regulated Multiset Rewriting Systems. CoRR Matej Troják, Samuel Pastva, David Safránek, Lubos Brim
2021	—	`conf`	Symbolic Coloured SCC Decomposition. TACAS (2) Nikola Benes, Lubos Brim, Samuel Pastva, David Safránek
2020	—	`conf`	AEON: Attractor Bifurcation Analysis of Parametrised Boolean Networks. CAV (1) Nikola Benes, Lubos Brim, Jakub Kadlecaj, Samuel Pastva, David Safránek
2020	J	`jnl`	Digital Bifurcation Analysis of Internet Congestion Control Protocols. Int. J. Bifurc. Chaos Nikola Benes, Lubos Brim, Samuel Pastva, David Safránek
2020	—	`conf`	Executable Biochemical Space for Specification and Analysis of Biochemical Systems. SASB Matej Troják, David Safránek, Lubos Brim, Jakub Salagovic, Jan Cervený
2020	J	`jnl`	Executable Biochemical Space for Specification and Analysis of Biochemical Systems. CoRR Matej Troják, David Safránek, Lubos Brim
2020	J	`jnl`	Parallel One-Step Control of Parametrised Boolean Networks. CoRR Lubos Brim, Samuel Pastva, David Safránek, Eva Smijakova
2020	—	`conf`	Parallel Parameter Synthesis for Multi-affine Hybrid Systems from Hybrid CTL Specifications. CMSB Eva Smijáková, Samuel Pastva, David Safránek, Lubos Brim
2020	J	`jnl`	Parallel parameter synthesis algorithm for hybrid CTL. Sci. Comput. Program. Nikola Benes, Lubos Brim, Samuel Pastva, David Safránek
2020	—	`conf`	Parameter Synthesis and Robustness Analysis of Rule-Based Models. NFM Matej Troják, David Safránek, Lukrécia Mertová, Lubos Brim
2020	—	`ed.`	Proceedings of SASB 2018, the 7th International Workshop on Static Analysis and Systems Biology, University of Edinburgh, September 7, 2016 SASB Guido Sanguinetti, David Safránek
2020	J	`jnl`	The need for standardisation in life science research - an approach to excellence and trust. F1000Research 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
2020	—	`conf`	eBCSgen: A Software Tool for Biochemical Space Language. CMSB Matej Troják, David Safránek, Lukrécia Mertová, Lubos Brim
2019	B	`conf`	Accelerating Parameter Synthesis Using Semi-algebraic Constraints. IFM Nikola Benes, Lubos Brim, Martin Geletka, Samuel Pastva, David Safránek
2019	—	`conf`	Barbaric Robustness Monitoring Revisited for STL* in Parasim. CMSB David Safránek, Matej Troják, Vojtech Bruza, Tomás Vejpustek, Jan Papousek, Martin Demko, Samuel Pastva, Ales Pejznoch, Lubos Brim
2019	—	`conf`	Data-Informed Parameter Synthesis for Population Markov Chains. CMSB Matej Hajnal, Morgane Nouvian, Tatjana Petrov, David Safránek
2019	—	`conf`	Data-Informed Parameter Synthesis for Population Markov Chains. HSB Matej Hajnal, Morgane Nouvian, David Safránek, Tatjana Petrov
2019	—	`conf`	Digital Bifurcation Analysis of TCP Dynamics. TACAS (2) Nikola Benes, Lubos Brim, Samuel Pastva, David Safránek
2019	—	`conf`	Facetal abstraction for non-linear dynamical systems based on δ-decidable SMT. HSCC Nikola Benes, Lubos Brim, Jana Drazanová, Samuel Pastva, David Safránek
2019	C	`conf`	Formal Analysis of Qualitative Long-Term Behaviour in Parametrised Boolean Networks. ICFEM Nikola Benes, Lubos Brim, Samuel Pastva, Jakub Polácek, David Safránek
2019	—	`ch.`	Model Checking Approach to the Analysis of Biological Systems. Automated Reasoning for Systems Biology and Medicine Nikola Benes, Lubos Brim, Samuel Pastva, David Safránek
2019	J	`jnl`	Parameter space abstraction and unfolding semantics of discrete regulatory networks. Theor. Comput. Sci. Juraj Kolcák, David Safránek, Stefan Haar, Loïc Paulevé
2019	J	`jnl`	Preface. Theor. Comput. Sci. Jérôme Feret, Loïc Paulevé, David Safránek
2018	—	`ed.`	Computational Methods in Systems Biology - 16th International Conference, CMSB 2018, Brno, Czech Republic, September 12-14, 2018, Proceedings CMSB Milan Ceska, David Safránek
2018	J	`jnl`	Parameter Space Abstraction and Unfolding Semantics of Discrete Regulatory Networks. CoRR Juraj Kolcák, David Safránek, Stefan Haar, Loïc Paulevé
2018	—	`conf`	Preface. SASB Guido Sanguinetti, David Safránek
2018	—	`conf`	Unfolding of Parametric Boolean Networks. SASB Juraj Kolcák, David Safránek, Stefan Haar, Loïc Paulevé
2017	—	`conf`	Detecting Attractors in Biological Models with Uncertain Parameters. CMSB Jiri Barnat, Nikola Benes, Lubos Brim, Martin Demko, Matej Hajnal, Samuel Pastva, David Safránek
2017	—	`conf`	Pithya: A Parallel Tool for Parameter Synthesis of Piecewise Multi-affine Dynamical Systems. CAV (1) Nikola Benes, Lubos Brim, Martin Demko, Samuel Pastva, David Safránek
2016	B	`conf`	A Model Checking Approach to Discrete Bifurcation Analysis. FM Nikola Benes, Lubos Brim, Martin Demko, Samuel Pastva, David Safránek
2016	—	`conf`	E-Cyanobacterium.org: A Web-Based Platform for Systems Biology of Cyanobacteria. CMSB Matej Troják, David Safránek, Jakub Hrabec, Jakub Salagovic, Frantiska Romanovská, Jan Cervený
2016	—	`conf`	High-Performance Symbolic Parameter Synthesis of Biological Models: A Case Study. CMSB Martin Demko, Nikola Benes, Lubos Brim, Samuel Pastva, David Safránek
2016	B	`conf`	Parallel SMT-Based Parameter Synthesis with Application to Piecewise Multi-affine Systems. ATVA Nikola Benes, Lubos Brim, Martin Demko, Samuel Pastva, David Safránek
2016	—	`conf`	Toward Modelling and Analysis of Transient and Sustained Behaviour of Signalling Pathways. HSB Matej Hajnal, David Safránek, Martin Demko, Samuel Pastva, Pavel Krejcí, Lubos Brim
2015	—	`conf`	Formal Biochemical Space with Semantics in Kappa and BNGL. SASB T. Ded, David Safránek, Matej Troják, Matej Klement, Jakub Salagovic, Lubos Brim
2015	—	`conf`	High-Performance Discrete Bifurcation Analysis for Piecewise-Affine Dynamical Systems. HSB Lubos Brim, Martin Demko, Samuel Pastva, David Safránek
2015	—	`ed.`	Hybrid Systems Biology - Fourth International Workshop, HSB 2015, Madrid, Spain, September 4-5, 2015. Revised Selected Papers HSB Alessandro Abate, David Safránek
2015	—	`conf`	Parameter Synthesis by Parallel Coloured CTL Model Checking. CMSB Lubos Brim, Milan Ceska, Martin Demko, Samuel Pastva, David Safránek
2014	—	`conf`	Biochemical Space: A Framework for Systemic Annotation of Biological Models. CS2Bio Matej Klement, T. Ded, David Safránek, Jan Cervený, Stefan Müller, Ralf Steuer
2014	J	`jnl`	Compact Representation of Photosynthesis Dynamics by Rule-based Models (Full Version). CoRR Lubos Brim, Juraj Niznan, David Safránek
2014	—	`conf`	Compact Representation of Photosynthesis Dynamics by Rule-based Models. SASB Lubos Brim, Juraj Niznan, David Safránek
2014	J	`jnl`	STL Inf. Comput. Lubos Brim, Petr Dluhos, David Safránek, Tomas Vejpustek
2013	—	`conf`	A Comprehensive Web-based Platform For Domain-Specific Biological Models. CS2Bio Matej Klement, David Safránek, T. Ded, Ales Pejznoch, Ladislav Nedbal, Ralf Steuer, Jan Cervený, Stefan Müller
2013	A*	`conf`	Exploring Parameter Space of Stochastic Biochemical Systems Using Quantitative Model Checking. CAV Lubos Brim, Milan Ceska, Sven Drazan, David Safránek
2013	—	`conf`	Model Checking of Biological Systems. SFM Lubos Brim, Milan Ceska, David Safránek
2013	J	`jnl`	On Robustness Analysis of Stochastic Biochemical Systems by Probabilistic Model Checking. CoRR Lubos Brim, Milan Ceska, Sven Drazan, David Safránek
2013	—	`conf`	Qualitative modelling and analysis of Photosystem II. BioPPN@Petri Nets Lubos Brim, Vilém Ded, David Safránek
2013	—	`conf`	Robustness Analysis for Value-Freezing Signal Temporal Logic. HSB Lubos Brim, Tomas Vejpustek, David Safránek, Jana Fabriková
2012	J	`jnl`	On Approximative Reachability Analysis of Biochemical Dynamical Systems. Trans. Comp. Sys. Biology Lubos Brim, Jana Fabriková, Sven Drazan, David Safránek
2012	—	`conf`	On Expressing and Monitoring Oscillatory Dynamics HSB Petr Dluhos, Lubos Brim, David Safránek
2012	J	`jnl`	On Parameter Synthesis by Parallel Model Checking. IEEE ACM Trans. Comput. Biol. Bioinform. Jiri Barnat, Lubos Brim, Adam Krejci, Adam Streck, David Safránek, Martin Vejnar, Tomas Vejpustek
2012	—	`conf`	Parameter Identification and Model Ranking of Thomas Networks. CMSB Hannes Klarner, Adam Streck, David Safránek, Juraj Kolcák, Heike Siebert
2012	—	`conf`	Timed Modelling of Gene Networks with Arbitrarily Precise Expression Discretization. CS2Bio S. Van Goethem, Jean-Marie Jacquet, Lubos Brim, David Safránek
2011	J	`jnl`	E-photosynthesis: Web-based platform for modeling of complex photosynthetic processes. Biosyst. David Safránek, Jan Cervený, Matej Klement, Jana Pospísilová, Lubos Brim, Dusan Lazar, Ladislav Nedbal
2011	J	`jnl`	Reachability in Biochemical Dynamical Systems by Quantitative Discrete Approximation CoRR Lubos Brim, Jana Fabriková, Sven Drazan, David Safránek
2011	—	`conf`	Reachability in Biochemical Dynamical Systems by Quantitative Discrete Approximation (extended abstract) CompMod Lubos Brim, Jana Fabriková, Sven Drazan, David Safránek
2010	J	`jnl`	High-performance analysis of biological systems dynamics with the DiVinE model checker. Briefings Bioinform. Jiri Barnat, Lubos Brim, David Safránek
2009	—	`conf`	BioDiVinE: A Framework for Parallel Analysis of Biological Models COMPMOD Jiri Barnat, Lubos Brim, Ivana Cerná, Sven Drazan, Jana Fabriková, Jan Láník, David Safránek, Hongwu Ma
2009	J	`jnl`	On algorithmic analysis of transcriptional regulation by LTL model checking. Theor. Comput. Sci. Jiri Barnat, Lubos Brim, Ivana Cerná, Sven Drazan, Jana Fabriková, David Safránek
2007	—	`conf`	Parallel Model Checking Large-Scale Genetic Regulatory Networks with DiVinE. FBTC@CONCUR Jiri Barnat, Lubos Brim, Ivana Cerná, Sven Drazan, David Safránek
2006	—	`conf`	Architectural Interoperability Checking in Visual Coordination Networks. CoOrg/MTCoord@COORDINATION David Safránek
2006	—	`conf`	Verifying VHDL Designs with Multiple Clocks in SMV. FMICS/PDMC Ales Smrcka, Vojtech Rehák, Tomás Vojnar, David Safránek, Petr Matousek, Z. Rehák
2005	B	`conf`	VCD: A Visual Formalism for Specification of Heterogeneous Software Architectures. SOFSEM David Safránek, Jirí Simsa
2004	—	`conf`	Visual Specification of Systems with Heterogeneous Coordination Models. FOCLASA David Safránek
2003	A*	`conf`	Visual Specification of Concurrent Systems. ASE David Safránek
2002	—	`conf`	SGCCS: A Graphical Language for Real-time Coordination. FOCLASA David Safránek