RNDr. David Šafránek, Ph.D.

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found: 61 records, displayed 1 - 30

 
2016

BRIM, Luboš - ŠAFRÁNEK, David - DEMKO, Martin - PASTVA, Samuel - BENEŠ, Nikola.
High-Performance Symbolic Parameter Synthesis of Biological Models: A Case Study. In Computational Methods in Systems Biology. Vyd. 9859. Neuveden : Springer International Publishing, 2016. ISBN 978-3-319-45176-3, pp. 1-15. 2016, Cambridge, England.


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BRIM, Luboš - ŠAFRÁNEK, David - DEMKO, Martin - BENEŠ, Nikola - PASTVA, Samuel.
Parallel SMT-Based Parameter Synthesis with Application to Piecewise Multi-Affine Systems. In Automated Technology for Verification and Analysis. Vyd. 9938. Neuveden : Springer International Publishing, 2016. ISBN 978-3-319-46519-7, pp. 1-17. 2016, Chiba.


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2015

TROJÁK, Matej - DĚD, Tadeáš - ŠAFRÁNEK, David - KLEMENT, Matej - ČERVENÝ, Jan - BRIM, Luboš.
Biochemical Space: A Language for Formal Description and Annotation of Complex Biological Processes. 2015.


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BRIM, Luboš - DEMKO, Martin - PASTVA, Samuel - ŠAFRÁNEK, David.
Coloured Model Checking Approach to Parameter Synthesis for Executable Models in Synthetic Biology. 2015.


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BRIM, Luboš - NIŽNAN, Juraj - ŠAFRÁNEK, David.
Compact Representation of Photosynthesis Dynamics by Rule-based Models. In 5th International Workshop on Static Analysis and Systems Biology (SASB 2014). Vyd. 316. Neuveden : Elsevier, 2015. pp. 17-27. 2014, Mnichov.


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ČERVENÝ, Jan - MUELLER, Stefan - ŠAFRÁNEK, David.
CyanoNetwork workshop - Cyanobacterium in silico 2015. 2015. CZE, Brno. 28.1.2015 - 30.1.2015, Worldwide Activity.


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ABATE, Alessandro - ŠAFRÁNEK, David.
Fourth International Workshop on Hybrid Systems Biology. 2015. CZE, Madrid. 4.9.2015 - 5.9.2015, Worldwide Activity.


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BRIM, Luboš - DEMKO, Martin - PASTVA, Samuel - ŠAFRÁNEK, David.
High-Performance Discrete Bifurcation Analysis for Piecewise-Affine Dynamical Systems. In Hybrid Systems Biology Fourth International Workshop, HSB 2015, Madrid, Spain, September 4-5, 2015. Revised Selected Papers. Vyd. LNCS 9271. Neuveden : Springer International Publishing, 2015. ISBN 978-3-319-26915-3, pp. 58-74. 2015, Madrid.


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ALESSANDRO, Abate - ŠAFRÁNEK, David (Eds.).
Hybrid Systems Biology Fourth International Workshop, HSB 2015, Madrid, Spain, September 4-5, 2015. Revised Selected Papers. Springer International Publishing, 2015. 263 pp. ISBN 978-3-319-26915-3.


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ŠAFRÁNEK, David.
Parameter Synthesis by Model Checking in Formal Biochemical Space. 2015.


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BRIM, Luboš - ČEŠKA, Milan - DEMKO, Martin - PASTVA, Samuel - ŠAFRÁNEK, David.
Parameter Synthesis by Parallel Coloured CTL Model Checking. In Computational Methods in Systems Biology. Neuveden : Springer International Publishing, 2015. ISBN 978-3-319-23400-7, pp. 251-263. 2015, Nantes.


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2014

KLEMENT, Matej - DĚD, Tadeáš - ŠAFRÁNEK, David - ČERVENÝ, Jan - MUELLER, Stefan - STEUER, Ralf.
Biochemical Space: A Framework for Systemic Annotation of Biological Models. In Proceedings of the 5th International Workshop on Interactions between Computer Science and Biology (CS2Bio’14). Amsterdam : Elsevier, 2014. pp. 31-44. 2014, Berlin.


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KLEMENT, Matej - ŠAFRÁNEK, David - ČERVENÝ, Jan - DĚD, Tadeáš - MUELLER, Stefan - STEUER, Ralf.
E-cyanobacterium.org: A Web-based Platform for Systems Biology of Cyanobacteria. 2014.


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ŠAFRÁNEK, David.
From Formal Methods to Systems Biology. 2014.


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ŠAFRÁNEK, David.
Model Checking in Systems Biology. 2014.


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ČEŠKA, Milan - ŠAFRÁNEK, David - DRAŽAN, Sven - BRIM, Luboš.
Robustness Analysis of Stochastic Biochemical Systems. Plos One, SAN FRANCISCO, PUBLIC LIBRARY SCIENCE, USA. ISSN 1932-6203, 2014, vol. 9, no. 4, pp. 1-23.


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BRIM, Luboš - DLUHOŠ, Petr - ŠAFRÁNEK, David - VEJPUSTEK, Tomáš.
STL*: Extending signal temporal logic with signal-value freezing operator. Information and computation, Academic Press. ISSN 0890-5401, 2014, vol. 236, no. January, pp. 52-67.


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ČEŠKA, Milan - SCHNEIDER, Caroline - ABATE, Alessandro - ŠAFRÁNEK, David - MAHADEVAN, Louis - KWIATKOWSKA, Marta.
Stochastic Modelling of the Interface between Regulatory Enzymes and Transcription Initiation at Inducible Genes. 2014.


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2013

KLEMENT, Matej - ŠAFRÁNEK, David - DĚD, Tadeáš - PEJZNOCH, Aleš - NEDBAL, Ladislav - STEUER, Ralf - ČERVENÝ, Jan - MUELLER, Stefan.
A Comprehensive Web-based Platform For Domain-Specific Biological Models. In Proceedings of the fourth International Workshop on Interactions between Computer Science and Biology (CS2Bio'13). Neuveden : Elsevier, 2013. pp. 61-67. 2013, Florencie.


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STRECK, Adam - KOLČÁK, Juraj - SIEBERT, Heike - ŠAFRÁNEK, David.
Esther: Introducing an Online Platform for Parameter Identification of Boolean Networks. In Computational Methods in Systems Biology 11th International Conference, CMSB 2013, Klosterneuburg, Austria, September 22-24, 2013, Proceedings. Heidelberg : Springer, 2013. ISBN 978-3-642-40707-9, pp. 257-258. 2013, Vienna.


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BRIM, Luboš - ČEŠKA, Milan - DRAŽAN, Sven - ŠAFRÁNEK, David.
Exploring Parameter Space of Stochastic Biochemical Systems Using Quantitative Model Checking. In 25th International Conference, CAV 2013, Saint Petersburg, Russia, July 13-19, 2013. Proceedings. Berlin : Springer Berlin Heidelberg, 2013. ISBN 978-3-642-39798-1, pp. 107-123. 2013, Saint Petersburg.


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BRIM, Luboš - ČEŠKA, Milan - ŠAFRÁNEK, David.
Model Checking of Biological Systems. In Formal Methods for Dynamical Systems. Neuveden : Springer, 2013. ISBN 978-3-642-38873-6, pp. 63-112. 2013, Bertinoro.


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BRIM, Luboš - DĚD, Vilém - ŠAFRÁNEK, David.
Qualitative modelling and analysis of Photosystem II. In CEUR Workshop Proceedings. Aachen : Neuveden, 2013. pp. 17-29. 2013, Milano.


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BRIM, Luboš - VEJPUSTEK, Tomáš - ŠAFRÁNEK, David - FABRIKOVÁ, Jana.
Robustness Analysis for Value-Freezing Signal Temporal Logic. In Proceedings HSB 2013. Neuveden : Neuveden, 2013. pp. 20-36. 2013, Taormina.


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BRIM, Luboš - ČEŠKA, Milan - DRAŽAN, Sven - ŠAFRÁNEK, David.
Robustness Analysis of Stochastic Systems. In Electronic Proceedings in Theoretical Computer Science, Volume 116. Turku : Open Publishing Association, 2013. pp. 33-34.


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VAN GOETHEM, Simon - JACQUET, Jean-Marie - BRIM, Luboš - ŠAFRÁNEK, David.
Timed Modelling of Gene Networks with Arbitrary Expression Level Discretization. In Proceedings of the Third International Workshop on Interactions Between Computer Science and Biology (CS2Bio'12). Neuveden : Elsevier, 2013. pp. 67-81. 2012, Florencie.


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2012

BRIM, Luboš - FABRIKOVÁ, Jana - DRAŽAN, Sven - ŠAFRÁNEK, David.
On Approximative Reachability Analysis of Biochemical Dynamical Systems. In Transactions on Computational Systems Biology XIV. Heidelberg : Springer, 2012. ISBN 978-3-642-35523-3, pp. 77-101. 2012, Aachen.


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DLUHOŠ, Petr - BRIM, Luboš - ŠAFRÁNEK, David.
On Expressing and Monitoring Oscillatory Dynamics. Electronic Proceedings in Theoretical Computer Science, Newcastle Upon Tyne, EPTCS. ISSN 2075-2180, 2012, vol. 2012, no. 92, pp. 73-87.


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BARNAT, Jiří - BRIM, Luboš - KREJČÍ, Adam - STRECK, Adam - ŠAFRÁNEK, David - VEJNÁR, Martin - VEJPUSTEK, Tomáš.
On Parameter Synthesis by Parallel Model Checking. IEEE/ACM Transactions on Computational Biology and Bioinformatics, Los Alamitos, IEEE Computer Society. ISSN 1545-5963, 2012, vol. 9, no. 3, pp. 693-705.


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KLARNER, Hannes - STRECK, Adam - ŠAFRÁNEK, David - KOLČÁK, Juraj - SIEBERT, Heike.
Parameter Identification and Model Ranking of Thomas Networks. In Computational Methods in Systems Biology: 10th International Conference, CMSB 2012, London, UK, October 3-5, 2012. Proceedings. Berlin : Springer, 2012. ISBN 978-3-642-33635-5, pp. 207-226. 2012, London.


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