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2020 – today
- 2024
[j18]Martin Helfrich, Roman Andriushchenko, Milan Ceska, Jan Kretínský, Stefan Marticek, David Safránek:
Abstraction-based segmental simulation of reaction networks using adaptive memoization. BMC Bioinform. 25(1): 350 (2024)- [c50]Nikola Benes, Lubos Brim, Ondrej Huvar, Samuel Pastva, David Safránek:
BNClassifier: Classifying Boolean Models by Dynamic Properties. CMSB 2024: 19-26 - 2023
- [j17]Nikola Benes
, Lubos Brim, Ondrej Huvar, Samuel Pastva, David Safránek:
Boolean network sketches: a unifying framework for logical model inference. Bioinform. 39(4) (2023) - [j16]Lubos Brim, Samuel Pastva, David Safránek, Eva Smijáková:
Temporary and permanent control of partially specified Boolean networks. Biosyst. 223: 104795 (2023) - [j15]Matej Troják, David Safránek, Samuel Pastva, Lubos Brim:
Rule-based modelling of biological systems using regulated rewriting. Biosyst. 225: 104843 (2023) - [c49]Nikola Benes, Lubos Brim, Samuel Pastva, David Safránek, Eva Smijáková:
Phenotype Control of Partially Specified Boolean Networks. CMSB 2023: 18-35 - 2022
- [j14]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): 4978-4980 (2022) - [j13]Nikola Benes, Lubos Brim, Jakub Kadlecaj, Samuel Pastva, David Safránek:
Exploring attractor bifurcations in Boolean networks. BMC Bioinform. 23(1): 173 (2022) - [j12]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) - [j11]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): 1010305 (2022) - [c48]Matej Troják, David Safránek, Branislav Brozmann, Lubos Brim:
eBCSgen 2.0: Modelling and Analysis of Regulated Rule-Based Systems. CMSB 2022: 302-309 - [i11]Matej Troják, David Safránek, Lubos Brim:
Biochemical Space Language in Relation to Multiset Rewriting Systems. CoRR abs/2201.08817 (2022) - [i10]Lubos Brim, Samuel Pastva, David Safránek, Eva Smijáková:
Robust Control of Partially Specified Boolean Networks. CoRR abs/2202.13440 (2022) - 2021
- [c47]Nikola Benes, Lubos Brim, Samuel Pastva, David Safránek:
Computing Bottom SCCs Symbolically Using Transition Guided Reduction. CAV (1) 2021: 505-528 - [c46]Nikola Benes, Lubos Brim, Samuel Pastva, David Safránek:
Aeon 2021: Bifurcation Decision Trees in Boolean Networks. CMSB 2021: 230-237 - [c45]Matej Hajnal, David Safránek, Tatjana Petrov:
DiPS: A Tool for Data-Informed Parameter Synthesis for Markov Chains from Multiple-Property Specifications. EPEW 2021: 79-95 - [c44]Nikola Benes, Lubos Brim, Samuel Pastva, David Safránek:
Symbolic Coloured SCC Decomposition. TACAS (2) 2021: 64-83 - [i9]Nikola Benes, Lubos Brim, Samuel Pastva, David Safránek:
BDD-Based Algorithm for SCC Decomposition of Edge-Coloured Graphs. CoRR abs/2108.13113 (2021) - [i8]Matej Troják, Samuel Pastva, David Safránek, Lubos Brim:
Regulated Multiset Rewriting Systems. CoRR abs/2111.13036 (2021) - 2020
- [j10]Nikola Benes, Lubos Brim, Samuel Pastva, David Safránek:
Digital Bifurcation Analysis of Internet Congestion Control Protocols. Int. J. Bifurc. Chaos 30(13): 2030038:1-2030038:18 (2020) - [j9]Nikola Benes, Lubos Brim, Samuel Pastva, David Safránek:
Parallel parameter synthesis algorithm for hybrid CTL. Sci. Comput. Program. 185 (2020) - [c43]Nikola Benes, Lubos Brim, Jakub Kadlecaj, Samuel Pastva, David Safránek:
AEON: Attractor Bifurcation Analysis of Parametrised Boolean Networks. CAV (1) 2020: 569-581 - [c42]Eva Smijáková, Samuel Pastva, David Safránek, Lubos Brim:
Parallel Parameter Synthesis for Multi-affine Hybrid Systems from Hybrid CTL Specifications. CMSB 2020: 280-297 - [c41]Matej Troják, David Safránek, Lukrécia Mertová, Lubos Brim:
eBCSgen: A Software Tool for Biochemical Space Language. CMSB 2020: 356-361 - [c40]Matej Troják, David Safránek, Lukrécia Mertová, Lubos Brim:
Parameter Synthesis and Robustness Analysis of Rule-Based Models. NFM 2020: 41-59 - [c39]Matej Troják, David Safránek, Lubos Brim, Jakub Salagovic, Jan Cervený:
Executable Biochemical Space for Specification and Analysis of Biochemical Systems. SASB 2020: 91-116 - [e3]Guido Sanguinetti, David Safránek:
Proceedings of SASB 2018, the 7th International Workshop on Static Analysis and Systems Biology, University of Edinburgh, September 7, 2016. Electronic Notes in Theoretical Computer Science 335, Elsevier 2020 [contents] - [i7]Matej Troják, David Safránek, Lubos Brim:
Executable Biochemical Space for Specification and Analysis of Biochemical Systems. CoRR abs/2002.00731 (2020) - [i6]Lubos Brim, Samuel Pastva, David Safránek, Eva Smijakova:
Parallel One-Step Control of Parametrised Boolean Networks. CoRR abs/2009.00359 (2020) - [i5]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: 1398 (2020)
2010 – 2019
- 2019
- [j8]Jérôme Feret, Loïc Paulevé, David Safránek:
Preface. Theor. Comput. Sci. 765: 1-2 (2019) - [j7]Juraj Kolcák, David Safránek, Stefan Haar, Loïc Paulevé:
Parameter space abstraction and unfolding semantics of discrete regulatory networks. Theor. Comput. Sci. 765: 120-144 (2019) - [c38]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: 356-359 - [c37]Matej Hajnal, Morgane Nouvian, Tatjana Petrov, David Safránek:
Data-Informed Parameter Synthesis for Population Markov Chains. CMSB 2019: 383-386 - [c36]Matej Hajnal, Morgane Nouvian, David Safránek, Tatjana Petrov:
Data-Informed Parameter Synthesis for Population Markov Chains. HSB 2019: 147-164 - [c35]Nikola Benes, Lubos Brim, Jana Drazanová, Samuel Pastva, David Safránek:
Facetal abstraction for non-linear dynamical systems based on δ-decidable SMT. HSCC 2019: 99-108 - [c34]Nikola Benes, Lubos Brim, Samuel Pastva, Jakub Polácek, David Safránek:
Formal Analysis of Qualitative Long-Term Behaviour in Parametrised Boolean Networks. ICFEM 2019: 353-369 - [c33]Nikola Benes, Lubos Brim, Martin Geletka, Samuel Pastva, David Safránek:
Accelerating Parameter Synthesis Using Semi-algebraic Constraints. IFM 2019: 27-45 - [c32]Nikola Benes, Lubos Brim, Samuel Pastva, David Safránek:
Digital Bifurcation Analysis of TCP Dynamics. TACAS (2) 2019: 339-356 - [p1]Nikola Benes, Lubos Brim, Samuel Pastva, David Safránek:
Model Checking Approach to the Analysis of Biological Systems. Automated Reasoning for Systems Biology and Medicine 2019: 3-35 - 2018
- [c31]Guido Sanguinetti, David Safránek:
Preface. SASB 2018: 1-2 - [c30]Juraj Kolcák, David Safránek, Stefan Haar, Loïc Paulevé:
Unfolding of Parametric Boolean Networks. SASB 2018: 67-90 - [e2]Milan Ceska, David Safránek:
Computational Methods in Systems Biology - 16th International Conference, CMSB 2018, Brno, Czech Republic, September 12-14, 2018, Proceedings. Lecture Notes in Computer Science 11095, Springer 2018, ISBN 978-3-319-99428-4 [contents] - [i4]Juraj Kolcák, David Safránek, Stefan Haar, Loïc Paulevé:
Parameter Space Abstraction and Unfolding Semantics of Discrete Regulatory Networks. CoRR abs/1803.06157 (2018) - 2017
- [c29]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: 591-598 - [c28]Jiri Barnat, Nikola Benes, Lubos Brim, Martin Demko, Matej Hajnal, Samuel Pastva, David Safránek:
Detecting Attractors in Biological Models with Uncertain Parameters. CMSB 2017: 40-56 - 2016
- [c27]Nikola Benes, Lubos Brim, Martin Demko, Samuel Pastva, David Safránek:
Parallel SMT-Based Parameter Synthesis with Application to Piecewise Multi-affine Systems. ATVA 2016: 192-208 - [c26]Martin Demko, Nikola Benes, Lubos Brim, Samuel Pastva, David Safránek:
High-Performance Symbolic Parameter Synthesis of Biological Models: A Case Study. CMSB 2016: 82-97 - [c25]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: 316-322 - [c24]Nikola Benes, Lubos Brim, Martin Demko, Samuel Pastva, David Safránek:
A Model Checking Approach to Discrete Bifurcation Analysis. FM 2016: 85-101 - [c23]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: 57-66 - 2015
- [c22]Lubos Brim, Milan Ceska, Martin Demko, Samuel Pastva, David Safránek:
Parameter Synthesis by Parallel Coloured CTL Model Checking. CMSB 2015: 251-263 - [c21]Lubos Brim, Martin Demko, Samuel Pastva, David Safránek:
High-Performance Discrete Bifurcation Analysis for Piecewise-Affine Dynamical Systems. HSB 2015: 58-74 - [c20]T. Ded, David Safránek, Matej Troják, Matej Klement, Jakub Salagovic, Lubos Brim:
Formal Biochemical Space with Semantics in Kappa and BNGL. SASB 2015: 27-49 - [e1]Alessandro Abate, David Safránek:
Hybrid Systems Biology - Fourth International Workshop, HSB 2015, Madrid, Spain, September 4-5, 2015. Revised Selected Papers. Lecture Notes in Computer Science 9271, Springer 2015, ISBN 978-3-319-26915-3 [contents] - 2014
- [j6]Lubos Brim, Petr Dluhos, David Safránek, Tomas Vejpustek:
STL⁎: Extending signal temporal logic with signal-value freezing operator. Inf. Comput. 236: 52-67 (2014) - [c19]Lubos Brim, Juraj Niznan, David Safránek:
Compact Representation of Photosynthesis Dynamics by Rule-based Models. SASB 2014: 17-27 - [c18]Matej Klement, T. Ded, David Safránek, Jan Cervený, Stefan Müller, Ralf Steuer:
Biochemical Space: A Framework for Systemic Annotation of Biological Models. CS2Bio 2014: 31-44 - [i3]Lubos Brim, Juraj Niznan, David Safránek:
Compact Representation of Photosynthesis Dynamics by Rule-based Models (Full Version). CoRR abs/1410.3632 (2014) - 2013
- [c17]Lubos Brim, Vilém Ded, David Safránek:
Qualitative modelling and analysis of Photosystem II. BioPPN@Petri Nets 2013: 17-29 - [c16]Lubos Brim, Milan Ceska, Sven Drazan, David Safránek:
Exploring Parameter Space of Stochastic Biochemical Systems Using Quantitative Model Checking. CAV 2013: 107-123 - [c15]Lubos Brim, Milan Ceska, David Safránek:
Model Checking of Biological Systems. SFM 2013: 63-112 - [c14]Lubos Brim, Tomas Vejpustek, David Safránek, Jana Fabriková:
Robustness Analysis for Value-Freezing Signal Temporal Logic. HSB 2013: 20-36 - [c13]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. CS2Bio 2013: 61-67 - [i2]Lubos Brim, Milan Ceska, Sven Drazan, David Safránek:
On Robustness Analysis of Stochastic Biochemical Systems by Probabilistic Model Checking. CoRR abs/1310.4734 (2013) - 2012
- [j5]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): 693-705 (2012) - [j4]Lubos Brim, Jana Fabriková, Sven Drazan, David Safránek:
On Approximative Reachability Analysis of Biochemical Dynamical Systems. Trans. Comp. Sys. Biology 14: 77-101 (2012) - [c12]Hannes Klarner, Adam Streck, David Safránek, Juraj Kolcák, Heike Siebert:
Parameter Identification and Model Ranking of Thomas Networks. CMSB 2012: 207-226 - [c11]Petr Dluhos, Lubos Brim, David Safránek:
On Expressing and Monitoring Oscillatory Dynamics. HSB 2012: 73-87 - [c10]S. Van Goethem, Jean-Marie Jacquet, Lubos Brim, David Safránek:
Timed Modelling of Gene Networks with Arbitrarily Precise Expression Discretization. CS2Bio 2012: 67-81 - 2011
- [j3]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): 115-124 (2011) - [c9]Lubos Brim, Jana Fabriková, Sven Drazan, David Safránek:
Reachability in Biochemical Dynamical Systems by Quantitative Discrete Approximation (extended abstract). CompMod 2011: 97-112 - [i1]Lubos Brim, Jana Fabriková, Sven Drazan, David Safránek:
Reachability in Biochemical Dynamical Systems by Quantitative Discrete Approximation. CoRR abs/1107.5924 (2011) - 2010
- [j2]Jiri Barnat, Lubos Brim, David Safránek:
High-performance analysis of biological systems dynamics with the DiVinE model checker. Briefings Bioinform. 11(3): 301-312 (2010)
2000 – 2009
- 2009
- [j1]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): 3128-3148 (2009) - [c8]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: 31-45 - 2007
- [c7]Jiri Barnat, Lubos Brim, Ivana Cerná, Sven Drazan, David Safránek:
Parallel Model Checking Large-Scale Genetic Regulatory Networks with DiVinE. FBTC@CONCUR 2007: 35-50 - 2006
- [c6]Ales Smrcka, Vojtech Rehák, Tomás Vojnar, David Safránek, Petr Matousek, Z. Rehák:
Verifying VHDL Designs with Multiple Clocks in SMV. FMICS/PDMC 2006: 148-164 - [c5]David Safránek:
Architectural Interoperability Checking in Visual Coordination Networks. CoOrg/MTCoord@COORDINATION 2006: 81-96 - 2005
- [c4]David Safránek, Jirí Simsa:
VCD: A Visual Formalism for Specification of Heterogeneous Software Architectures. SOFSEM 2005: 320-329 - 2004
- [c3]David Safránek:
Visual Specification of Systems with Heterogeneous Coordination Models. FOCLASA 2004: 107-121 - 2003
- [c2]David Safránek:
Visual Specification of Concurrent Systems. ASE 2003: 369-372 - 2002
- [c1]David Safránek:
SGCCS: A Graphical Language for Real-time Coordination. FOCLASA 2002: 389-404
Coauthor Index
[c50] [j17] [j16] [j15] [c49] [j14] [j13] [j12] [c48] [i11] [i10] [c47] [c46] [c44] [i9] [i8] [j10] [j9] [c43] [c42] [c41] [c40] [c39] [i7] [i6] [c38] [c35] [c34] [c33] [c32] [p1] [c29] [c28] [c27] [c26] [c24] [c23] [c22] [c21] [c20] [j6] [c19] [i3] [c17] [c16] [c15] [c14] [i2] [j5] [j4] [c11] [c10] [j3] [c9] [i1] [j2] [j1] [c8] [c7]
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