doc. RNDr. David Šafránek, Ph.D.

Curriculum Vitae

Person Identification

• David Šafránek, Ph.D.
  born Sep. 28, 1977 in Brno, Czechoslovakia
  nationality: Czech
  
  Home Address
  Černopolní 8, 613 00 Brno, Czech Republic

Workplace

• Work Address
  Department of Machine Learning and Data Processing
  Faculty of Informatics
  Masaryk University
  Botanicka 68a
  602 00 Brno
  Czech Republic

Employment Position

• Associate Professor

Education and Academic Qualifications

• 2020: Associate Professor (Docent) in Computer Science, Masaryk University thesis: “Formal Methods for Analysis of Biological Systems under Parameter Uncertainty”
• 2006: Ph.D. in computer science, Faculty of Informatics, Masaryk University, Brno, Czech Republic. Theses: "Visual Coordination Networks". Supervisor: Doc. RNDr. Lubos Brim, CSc. Examiners: Prof. Dr. Jean-Marie Jacquet (FUNDP Namur, Belgium), Doc. RNDr. Ivana Černá, CSc. (FI MU Brno, Czech Republic). The thesis was evaluated as "distinguished".
• 2001: Mgr. (master's degree) in computer science, Faculty of Informatics, Masaryk University, Brno, Czech Republic. Theses: "Graphical specification of concurrent systems" (in Czech)

Employment Summary

• April 2020 – now: Associate Professor of Computer Science, Department of Machine Learning and Data Processing, Faculty of Informatics, Masaryk University (FI MUNI)
• August 2009 - March 2020: Assistant Professor, Department of Information Technologies (since 2018 renamed to Department of Machine Learning and Data Processing), Faculty of Informatics, Masaryk University.
• February 2007 - January 2010: full-time postdoc (FP6 NEST project EC-MOAN), position hosted by Department of Computer Science, Faculty of Informatics, Masaryk University.
• April 2005 - January 2007: Institute for Theoretical Computer Science, Faculty of Informatics, Masaryk University, junior researcher
• January 2007 - December 2009: CESNET, z.s.p.o., Prague (Programmable Hardware research activity); junior researcher

Pedagogical Activities

• Teaching activities
  
  
• Fall 2008 - now: development of a new study branch and teaching the subjects Introduction to Systems Biology, Modeling and Prediction in Systems Biology, Formal Methods in Systems Biology, Computational Methods in Systems Biology, Systems Biology Seminar
• July 2013, July 2014: Systems Biology Summer School (SBSS 2013, SBSS 2014), Nové Hrady (http://www.cyanoteam.org/sbss-2013/, http://www.cyanoteam.org/sbss-2014/)
• June 2013: School of Formal Methods, Bertinoro (http://www.sti.uniurb.it/events/sfm13ds/programme.html)
• 2002 - 2011: Introduction to Functional Programming (exercises)
• 2009 - 2012: Innovation of bachelor and master degree programes in the direction to systems biology (OP EU)
  
  Student supervision 2004 - now
  
  
• Number of supervised bachelor theses: 41
• Number of supervised master theses: 30
• Number of co-advised doctoral students: 5

Scientific and Research Activities

• August 2009 - now: leading member of Laboratory of Systems Biology (Sybila - http://sybila.fi.muni.cz)
• April 2016 - 2019: coordinator of Computer Science research group in The National Infrastructure for Systems Biology (C4SYS), http://c4sys.cz
• March 2016 - 2020: MC member of the COST project CHARME: Harmonising standardisation strategies to increase efficiency and competitiveness of European lifescience research (CHARME); my role is the coordinator of short-term scientific missions
• May 2012 - April 2015: coordinator of Computer Science research group in CyanoTeam (http://www.cyanoteam.org)
• June 2009 - now: coordinator of e-cyanobacterium.org development team (http://www.e-cyanobacterium.org)
• February 2007 - January 2010: PostDoc on FP6-STREP-NEST project no. 043235 "Escherichia coli modeling and analysis" (EC-MOAN - http://www.ec-moan.org)
• January 2000 - December 2009: member of Parallel and Distributed Systems Laboratory (ParaDiSe - http://www.fi.muni.cz/paradise)
• January 2002 - December 2009: coordinator of verification research group in Liberouter project (funded by CESNET, FP5-IST-2001-32603 and FP6-IST-511082; http://www.liberouter.org)
• Research Interests: Model checking, formal verification; systems and synthetic Biology; modeling and computational techniques in systems biology

Academical Stays

• January 2017 - February 2017: Visiting Researcher, MExICo team, LSV, CNRS & ENS de Cachan, France
• November 2013: Visiting Researcher, Deparment of Computer Science, University of Oxford, UK
• June 2008 and January 2009: CWI Amsterdam, The Netherlands
• September - October 2005: Faculté d'informatique, Facultés Universitaires Notre-Dame de la Paix, Namur, Belgium
• October 2004: Universidade Nova de Lisboa, Portugal

University Activities

• Fall 2017 - now: member of the academic senate of Faculty of Informatics, Masaryk University

Activities Outside University

• Int. Conference on Quantitative Evaluation of SysTems (QEST), artefact evaluation committee co-chair in 2020, publicity chair in 2022 and 2023; PC member in 2023
• Int. Conference on Computational Methods in Systems Biology (CMSB), SC member 2016-2020, PC member since 2016, PC-chair and OC-chair in 2018
• Int. Workshop on Static Analysis and Systems Biology (SASB), PC member since 2014, PC-chair in 2016
• Int. Workshop on Hybrid Systems Biology (HSB), PC member since 2013, PC-chair in 2015, SC since 2016
• Doctoral Workshop on Mathematical and Engineering Methods in Computer Science (MEMICS), PC member in 2014, 2016, PC-chair in 2017
• International Symposium on on Games, Automata, Logics, and Formal Verification (GandALF), PC member in 2014
• International Workshop on Verification of Engineered Molecular Devices and Programs (VEMDP), PC member since 2014
• International Conference on Formal Methods in Macro-Biology (FMMB), PC member since 2014
• Information Technologies - Applications and Theory (ITAT), PC member in 2013

Appreciation of Science Community

• 2019 (invited): Dagstuhl seminar on Specification Formalisms for Modern Cyber-Physical Systems
• 2018: Best Paper Award at ICSTCC 2018
• 2009: Dagstuhl seminar on Formal Methods in Molecular Biology
• 2007: awarded the dean's prize for a distinguished Ph.D. thesis, Faculty of Informatics, Masaryk University
• 2002: best paper award, Ph.D. forum, SOFSEM 2002 conference

Selected Publications

• BRIM, Luboš, Samuel PASTVA, David ŠAFRÁNEK a Eva ŠMIJÁKOVÁ. Temporary and Permanent Control of Partially Specified Boolean Networks. BIOSYSTEMS. Elsevier, roč. 223, JAN, s. 104795-104808. ISSN 0303-2647. doi:10.1016/j.biosystems.2022.104795. 2023. URL info
• TROJÁK, Matej, David ŠAFRÁNEK, Samuel PASTVA a Luboš BRIM. Rule-based Modelling of Biological Systems Using Regulated Rewriting. Biosystems. Elsevier, roč. 225, č. 104843, s. 1-15. ISSN 0303-2647. doi:10.1016/j.biosystems.2023.104843. 2023. URL info
• BENEŠ, Nikola, Luboš BRIM, Ondřej HUVAR, Samuel PASTVA a David ŠAFRÁNEK. Boolean network sketches: a unifying framework for logical model inference. Bioinformatics. roč. 39, č. 4, s. "btad158", 8 s. ISSN 1367-4803. doi:10.1093/bioinformatics/btad158. 2023. URL info
• BENEŠ, Nikola, Luboš BRIM, Samuel PASTVA a David ŠAFRÁNEK. BDD-Based Algorithm for SCC Decomposition of Edge-Coloured Graphs. Logical Methods in Computer Science. Episciences, roč. 18, č. 1, s. 1-27. ISSN 1860-5974. doi:10.46298/LMCS-18(1:38)2022. 2022. URL info
• OBRUČA, Stanislav, Pavel DVOŘÁK, Petr SEDLÁČEK, Martin KOLLER, Karel SEDLÁŘ, Iva PERNICOVÁ a David ŠAFRÁNEK. Polyhydroxyalkanoates synthesis by halophiles and thermophiles: towards sustainable production of microbial bioplastics. Biotechnology Advances. Elsevier, roč. 58, September, s. 1-28. ISSN 0734-9750. doi:10.1016/j.biotechadv.2022.107906. 2022. URL info
• BENEŠ, Nikola, Luboš BRIM, Jakub KADLECAJ, Samuel PASTVA a David ŠAFRÁNEK. Exploring attractor bifurcations in Boolean networks. BMC Bioinformatics. roč. 23, č. 173, s. 1-18. ISSN 1471-2105. doi:10.1186/s12859-022-04708-9. 2022. URL info
• TROJÁK, Matej, David ŠAFRÁNEK, Branislav BROZMANN a Luboš BRIM. eBCSgen 2.0: Modelling and Analysis of Regulated Rule-Based Systems. In I. Petre, A. Păun. 20th International Conference on Computational Methods in Systems Biology. LNBI 13447. Neuveden: Springer. s. 302-309. ISBN 978-3-031-15033-3. doi:10.1007/978-3-031-15034-0_17. 2022. URL info
• PETROV, Tatjana, Matej HAJNAL, Julia KLEIN, David ŠAFRÁNEK a Morgane NOUVIAN. Extracting individual characteristics from population data reveals a negative social effect during honeybee defence. Plos Computational Biology. roč. 18, č. 9, s. 1-20. ISSN 1553-734X. doi:10.1371/journal.pcbi.1010305. 2022. URL info
• BENEŠ, Nikola, Luboš BRIM, Ondřej HUVAR, Samuel PASTVA, David ŠAFRÁNEK a Eva ŠMIJÁKOVÁ. AEON.py: Python library for attractor analysis in asynchronous Boolean networks. BIOINFORMATICS. UK: OXFORD UNIV PRESS, roč. 38, č. 21, s. 4978-4980. ISSN 1367-4803. doi:10.1093/bioinformatics/btac624. 2022. URL info
• BENEŠ, Nikola, Luboš BRIM, Samuel PASTVA a David ŠAFRÁNEK. Symbolic Coloured SCC Decomposition. In Jan Friso Groote, Kim Larsen. Tools and Algorithms for the Construction and Analysis of Systems, 27th International Conference, TACAS 2021. Neuveden: Springer Nature. s. 64-83. ISBN 978-3-030-72012-4. doi:10.1007/978-3-030-72013-1_4. 2021. URL info
• BENEŠ, Nikola, Luboš BRIM, Samuel PASTVA a David ŠAFRÁNEK. Aeon 2021: Bifurcation Decision Trees in Boolean Networks. In Cinquemani et al. International Conference on Computational Methods in Systems Biology (CMSB 2021). Cham: Springer. s. 230-237. ISBN 978-3-030-85632-8. doi:10.1007/978-3-030-85633-5_14. 2021. info
• TROJÁK, Matej, David ŠAFRÁNEK, Lukrécia MERTOVÁ a Luboš BRIM. Parameter Synthesis and Robustness Analysis of Rule-Based Models. In Ritchie Lee, Susmit Jha, Anastasia Mavridou. 12th International Symposium on NASA Formal Methods, NFM 2020. LNCS 12229. Moffett Field, CA, USA: Springer. s. 41-59. ISBN 978-3-030-55753-9. doi:10.1007/978-3-030-55754-6_3. 2020. URL info
• TROJÁK, Matej, David ŠAFRÁNEK, Luboš BRIM, Jakub ŠALAGOVIČ a Jan ČERVENÝ. Executable Biochemical Space for Specification and Analysis of Biochemical Systems. In Ankit Gupta, Tatjana Petrov. 9th International Workshop on Static Analysis and Systems Biology (SASB). ENTCS 350. Amsterdam: Elsevier. s. 91-116. ISSN 1571-0661. doi:10.1016/j.entcs.2020.06.006. 2020. URL info
• BENEŠ, Nikola, Luboš BRIM, Jakub KADLECAJ, Samuel PASTVA a David ŠAFRÁNEK. AEON: Attractor Bifurcation Analysis of Parametrised Boolean Networks. In Shuvendu K. Lahiri and Chao Wang. Computer Aided Verification. CAV 2020. LNCS 12224. Cham: Springer, Cham. s. 569-581. ISBN 978-3-030-53287-1. doi:10.1007/978-3-030-53288-8_28. 2020. URL info
• TROJÁK, Matej, David ŠAFRÁNEK, Lukrécia MERTOVÁ a Luboš BRIM. Executable Biochemical Space for Specification and Analysis of Biochemical Systems. PLOS ONE. Public Library of Science, roč. 15, č. 9, s. 1-23, 24 s. ISSN 1932-6203. doi:10.1371/journal.pone.0238838. 2020. URL info
• BENEŠ, Nikola, Luboš BRIM, Samuel PASTVA a David ŠAFRÁNEK. Digital Bifurcation Analysis of Internet Congestion Control Protocols. International Journal of Bifurcation and Chaos. roč. 30, č. 13, s. 2030038-2030055. ISSN 0218-1274. doi:10.1142/S0218127420300384. 2020. URL info
• TROJÁK, Matej, David ŠAFRÁNEK, Lukrécia MERTOVÁ a Luboš BRIM. eBCSgen: A Software Tool for Biochemical Space Language. In Abate A., Petrov T., Wolf V. 18th International Conference on Computational Methods in Systems Biology, CMSB 2020. LNBI 12314. Neuveden: Springer. s. 356-361. ISBN 978-3-030-60326-7. doi:10.1007/978-3-030-60327-4_20. 2020. URL info
• HOLLMANN, Susanne, Andreas KREMER, Špela BAEBLER, Christophe TREFOIS, Kristina GRUDEN, Witold RUDNICKY, Weida TONG, Alexandra GRUCA, Erik BONGCAM-RUDLOFF, Chris EVELO, Alina NECHYPORENKO, Marcus FROHME, David ŠAFRÁNEK, Babette REGIERER a Domenica D'ELIA. The need for standardisation in life science research - an approach to excellence and trust. F1000Research. roč. 9, č. 1398, s. 1-9. ISSN 2046-1402. doi:10.12688/f1000research.27500.2. 2020. URL info
• BENEŠ, Nikola, Luboš BRIM, Samuel PASTVA a David ŠAFRÁNEK. Digital Bifurcation Analysis of TCP Dynamics. In Tomáš Vojnar and Lijun Zhang. Tools and Algorithms for the Construction and Analysis of Systems. TACAS 2019. LNCS, volume 11428. Cham: Springer International Publishing. s. 339-356. ISBN 978-3-030-17464-4. doi:10.1007/978-3-030-17465-1_19. 2019. URL info
• BENEŠ, Nikola, Luboš BRIM, Jana DRAŽANOVÁ, Samuel PASTVA a David ŠAFRÁNEK. Facetal Abstraction for Non-linear Dynamical Systems Based on delta-decidable SMT. In Proceedings of the 22Nd ACM International Conference on Hybrid Systems: Computation and Control. New York, NY, USA: ACM. s. 99-108. ISBN 978-1-4503-6282-5. doi:10.1145/3302504.3311793. 2019. URL info
• BENEŠ, Nikola, Luboš BRIM, Samuel PASTVA a David ŠAFRÁNEK. Model Checking Approach to the Analysis of Biological Systems. In Pietro Liò, Paolo Zuliani. Automated Reasoning for Systems Biology and Medicine. Cham: Springer, Cham. s. 3-35. Computational Biology. ISBN 978-3-030-17296-1. doi:10.1007/978-3-030-17297-8_1. 2019. info
• ŠAFRÁNEK, David, Matej TROJÁK, Vojtěch BRŮŽA, Tomáš VEJPUSTEK, Jan PAPOUŠEK, Martin DEMKO, Samuel PASTVA, Aleš PEJZNOCH a Luboš BRIM. Barbaric Robustness Monitoring Revisited for STL* in Parasim. In Bortolussi L., Sanguinetti G. Computational Methods in Systems Biology (CMSB 2019). LNBI 11773. Neuveden: Springer. s. 356-359. ISBN 978-3-030-31303-6. doi:10.1007/978-3-030-31304-3_26. 2019. info
• KOLČÁK, Juraj, David ŠAFRÁNEK, Stefan HAAR a Loïc PAULEVÉ. Parameter space abstraction and unfolding semantics of discrete regulatory networks. Theoretical Computer Science. Elsevier, roč. 765, April, s. 120-144. ISSN 0304-3975. doi:10.1016/j.tcs.2018.03.009. 2019. URL info
• BENEŠ, Nikola, Luboš BRIM, Samuel PASTVA, Jakub POLÁČEK a David ŠAFRÁNEK. Formal Analysis of Qualitative Long-Term Behaviour in Parametrised Boolean Networks. In Ait Ameur et al. Formal Methods and Software Engineering - 21st International Conference on Formal Engineering Methods, ICFEM 2019, Shenzhen, China, November 5-9, 2019, Proceedings. Heidelberg: Springer. s. 353-369. ISBN 978-3-030-32408-7. doi:10.1007/978-3-030-32409-4_22. 2019. URL info
• BENEŠ, Nikola, Luboš BRIM, Martin GELETKA, Samuel PASTVA a David ŠAFRÁNEK. Accelerating Parameter Synthesis Using Semi-algebraic Constraints. In Ahrendt, Wolfgang and Tapia Tarifa, Silvia Lizeth. Integrated Formal Methods. LNCS 11918. Cham: Springer International Publishing. s. 27-45. ISBN 978-3-030-34967-7. doi:10.1007/978-3-030-34968-4_2. 2019. URL info
• HAJNAL, Matej, Morgan NOUVIAN, David ŠAFRÁNEK a Tatjana PETROV. Data-Informed Parameter Synthesis for Population Markov Chains. In Ceska, M et al. Hybrid Systems Biology (HSB 2019). LNCS 11705. Cham: Springer International Publishing. s. 147-164. ISBN 978-3-030-28041-3. doi:10.1007/978-3-030-28042-0_10. 2019. info
• BENEŠ, Nikola, Luboš BRIM, Jan ČERVENÝ, Samuel PASTVA, David ŠAFRÁNEK, Jakub ŠALAGOVIČ a Matej TROJÁK. Fully Automated Attractor Analysis of Cyanobacteria Models. In Marian Barbu, Răzvan Şolea, Adrian Filipescu. 22nd International Conference on System Theory, Control and Computing. Neuveden: IEEE. s. 354-359. ISBN 978-1-5386-4444-7. doi:10.1109/ICSTCC.2018.8540762. 2018. URL info
• ČERVENÝ, Jan, Jakub ŠALAGOVIČ, František MUZIKA, David ŠAFRÁNEK a Igor SCHREIBER. Influence of circadian clocks on optimal regime of central C-N metabolism of cyanobacteria. In Mishra, A. K.; Tiwari, D.; Rai, A. N. Cyanobacteria: From Basic Science to Applications. 1st ed. Neuveden: Academic Press. s. 193-206. ISBN 978-0-12-814667-5. doi:10.1016/B978-0-12-814667-5.00009-X. 2018. URL info
• BENEŠ, Nikola, Luboš BRIM, Martin DEMKO, Samuel PASTVA a David ŠAFRÁNEK. Pithya: A Parallel Tool for Parameter Synthesis of Piecewise Multi-Affine Dynamical Systems. In Rupak Majumdar and Viktor Kunčak. Computer Aided Verification. CAV 2017. LNCS 10426. Cham: Springer International Publishing. s. 591-598. ISBN 978-3-319-63386-2. doi:10.1007/978-3-319-63387-9_29. 2017. URL info
• BRIM, Luboš, Jiří BARNAT, David ŠAFRÁNEK, Nikola BENEŠ, Martin DEMKO, Samuel PASTVA a Matej HAJNAL. Detecting Attractors in Biological Models with Uncertain Parameters. In Jérôme Feret and Heinz Koeppl. Computational Methods in Systems Biology. CMSB 2017. LNCS 10545. Cham: Springer International Publishing. s. 40-56. ISBN 978-3-319-67470-4. doi:10.1007/978-3-319-67471-1_3. 2017. info
• BENEŠ, Nikola, Luboš BRIM, Martin DEMKO, Samuel PASTVA a David ŠAFRÁNEK. Parallel SMT-Based Parameter Synthesis with Application to Piecewise Multi-Affine Systems. In Cyrille Artho et al. Automated Technology for Verification and Analysis. ATVA 2016. LNCS 9938. Neuveden: Springer International Publishing. s. 192-208. ISBN 978-3-319-46519-7. doi:10.1007/978-3-319-46520-3_13. 2016. info
• DEMKO, Martin, Nikola BENEŠ, Luboš BRIM, Samuel PASTVA a David ŠAFRÁNEK. High-Performance Symbolic Parameter Synthesis of Biological Models: A Case Study. In Ezio Bartocci et al. Computational Methods in Systems Biology. CMSB 2016. LNBI 9859. Neuveden: Springer International Publishing. s. 82-97. ISBN 978-3-319-45176-3. doi:10.1007/978-3-319-45177-0_6. 2016. info
• HAJNAL, Matej, David ŠAFRÁNEK, Martin DEMKO, Samuel PASTVA, Pavel KREJČÍ a Luboš BRIM. Toward Modelling and Analysis of Transient and Sustained Behaviour of Signalling Pathways. In Eugenio Cinquemani. Hybrid Systems Biology. HSB 2016. LNBI 9957. Neuveden: Springer International Publishing. s. 57-66. ISBN 978-3-319-47150-1. doi:10.1007/978-3-319-47151-8_4. 2016. info
• BENEŠ, Nikola, Luboš BRIM, Martin DEMKO, Samuel PASTVA a David ŠAFRÁNEK. A Model Checking Approach to Discrete Bifurcation Analysis. In John S. Fitzgerald et al. Formal Methods. FM 2016. LNCS 9995. Neuveden: Springer International Publishing. s. 85-101. ISBN 978-3-319-48988-9. doi:10.1007/978-3-319-48989-6_6. 2016. info
• TROJÁK, Matej, David ŠAFRÁNEK, Jakub HRABEC, Jakub ŠALAGOVIČ, Františka ROMANOVSKÁ a Jan ČERVENÝ. E-Cyanobacterium.org: A Web-Based Platform for Systems Biology of Cyanobacteria. In Ezio Bartocci et al. Computational Methods in Systems Biology. CMSB 2016. Heidelberg: Springer. s. 316-322. ISBN 978-3-319-45176-3. doi:10.1007/978-3-319-45177-0_20. 2016. URL info
• DĚD, Tadeáš, David ŠAFRÁNEK, Matej TROJÁK, Matej KLEMENT, Jakub ŠALAGOVIČ a Luboš BRIM. Formal Biochemical Space with Semantics in Kappa and BNGL. In Loic Pauleve et al. The 6th International Workshop on Static Analysis and Systems Biology, SASB 2015. ENTCS 326. Neuveden: Elsevier. s. 27-49. ISSN 1571-0661. doi:10.1016/j.entcs.2016.09.017. 2016. info
• BRIM, Luboš, Juraj NIŽNAN a David ŠAFRÁNEK. Compact Representation of Photosynthesis Dynamics by Rule-based Models. In 5th International Workshop on Static Analysis and Systems Biology (SASB 2014). 316. vyd. Neuveden: Elsevier. s. 17-27. ISSN 1571-0661. doi:10.1016/j.entcs.2015.06.008. 2015. info
• BRIM, Luboš, Milan ČEŠKA, Martin DEMKO, Samuel PASTVA a David ŠAFRÁNEK. Parameter Synthesis by Parallel Coloured CTL Model Checking. In Roux, Olivier and Bourdon, Jérémie. Computational Methods in Systems Biology. Neuveden: Springer International Publishing. s. 251-263. ISBN 978-3-319-23400-7. doi:10.1007/978-3-319-23401-4_21. 2015. info
• BRIM, Luboš, Martin DEMKO, Samuel PASTVA a David ŠAFRÁNEK. High-Performance Discrete Bifurcation Analysis for Piecewise-Affine Dynamical Systems. In Alessandro Abate, David Šafránek. Hybrid Systems Biology Fourth International Workshop, HSB 2015, Madrid, Spain, September 4-5, 2015. Revised Selected Papers. LNCS 9271. Neuveden: Springer International Publishing. s. 58-74. ISBN 978-3-319-26915-3. doi:10.1007/978-3-319-26916-0_4. 2015. elektronická verze v nakladatelství Springer info
• ALESSANDRO, Abate a David ŠAFRÁNEK. Hybrid Systems Biology Fourth International Workshop, HSB 2015, Madrid, Spain, September 4-5, 2015. Revised Selected Papers. In Lecture Notes in Bioinformatics. Springer International Publishing. 263 s. ISBN 978-3-319-26915-3. doi:10.1007/978-3-319-26916-0. 2015. elektronická verze v nakladatelství Springer info
• BRIM, Luboš, Petr DLUHOŠ, David ŠAFRÁNEK a Tomáš VEJPUSTEK. STL*: Extending signal temporal logic with signal-value freezing operator. Information and computation. Academic Press, roč. 236, January, s. 52-67. ISSN 0890-5401. doi:10.1016/j.ic.2014.01.012. 2014. info
• ČEŠKA, Milan, David ŠAFRÁNEK, Sven DRAŽAN a Luboš BRIM. Robustness Analysis of Stochastic Biochemical Systems. Plos One. SAN FRANCISCO: PUBLIC LIBRARY SCIENCE, roč. 9, č. 4, s. 1-23. ISSN 1932-6203. doi:10.1371/journal.pone.0094553. 2014. URL info
• VAN GOETHEM, Simon, Jean-Marie JACQUET, Luboš BRIM a David ŠAFRÁNEK. 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. s. 67-81. ISSN 1571-0661. doi:10.1016/j.entcs.2013.02.019. 2013. URL info
• BRIM, Luboš, Vilém DĚD a David ŠAFRÁNEK. Qualitative modelling and analysis of Photosystem II. In CEUR Workshop Proceedings. Aachen: Neuveden. s. 17-29. ISSN 1613-0073. 2013. URL info
• KLEMENT, Matej, David ŠAFRÁNEK, Tadeáš DĚD, Aleš PEJZNOCH, Ladislav NEDBAL, Ralf STEUER, Jan ČERVENÝ a Stefan MUELLER. 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. s. 61-67. ISSN 1571-0661. doi:10.1016/j.entcs.2013.11.006. 2013. URL info
• BRIM, Luboš, Milan ČEŠKA a David ŠAFRÁNEK. Model Checking of Biological Systems. In Marco Bernardo. Formal Methods for Dynamical Systems. Neuveden: Springer. s. 63-112. ISBN 978-3-642-38873-6. doi:10.1007/978-3-642-38874-3_3. 2013. info
• BRIM, Luboš, Tomáš VEJPUSTEK, David ŠAFRÁNEK a Jana FABRIKOVÁ. Robustness Analysis for Value-Freezing Signal Temporal Logic. In Proceedings HSB 2013. Neuveden: Neuveden. s. 20-36. ISSN 2075-2180. doi:10.4204/EPTCS.125. 2013. URL info
• STRECK, Adam, Juraj KOLČÁK, Heike SIEBERT a David ŠAFRÁNEK. Esther: Introducing an Online Platform for Parameter Identification of Boolean Networks. In A. Gupta. Computational Methods in Systems Biology 11th International Conference, CMSB 2013, Klosterneuburg, Austria, September 22-24, 2013, Proceedings. Heidelberg: Springer. s. 257-258. ISBN 978-3-642-40707-9. 2013. info
• ŠAFRÁNEK, David. Model Checking in Systems Biology. In Formal Methods for Dynamical Systems - 13th International School on Formal Methods for the Design of Computer, Communication, and Software Systems, SFM 2013, Bertinoro. 2013. URL info
• ŠAFRÁNEK, David. Model Checking of Biological Systems. In Oxford Talks, University of Oxford. 2013. URL info
• BARNAT, Jiří, Luboš BRIM, Adam KREJČÍ, Adam STRECK, David ŠAFRÁNEK, Martin VEJNÁR a Tomáš VEJPUSTEK. On Parameter Synthesis by Parallel Model Checking. IEEE/ACM Transactions on Computational Biology and Bioinformatics. Los Alamitos: IEEE Computer Society, roč. 9, č. 3, s. 693-705. ISSN 1545-5963. doi:10.1109/TCBB.2011.110. 2012. URL info
• DLUHOŠ, Petr, Luboš BRIM a David ŠAFRÁNEK. On Expressing and Monitoring Oscillatory Dynamics. Electronic Proceedings in Theoretical Computer Science. Newcastle Upon Tyne: EPTCS, roč. 2012, č. 92, s. 73-87. ISSN 2075-2180. doi:10.4204/EPTCS.92. 2012. URL info
• KLARNER, Hannes, Adam STRECK, David ŠAFRÁNEK, Juraj KOLČÁK a Heike SIEBERT. 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. s. 207-226. ISBN 978-3-642-33635-5. doi:10.1007/978-3-642-33636-2_13. 2012. URL info
• BRIM, Luboš, Jana FABRIKOVÁ, Sven DRAŽAN a David ŠAFRÁNEK. On Approximative Reachability Analysis of Biochemical Dynamical Systems. In Corrado Priami et al. Transactions on Computational Systems Biology XIV. Heidelberg: Springer. s. 77-101. ISBN 978-3-642-35523-3. doi:10.1007/978-3-642-35524-0_4. 2012. URL info
• ŠAFRÁNEK, David, Jan ČERVENÝ, Matej KLEMENT, Jana POSPÍŠILOVÁ, Luboš BRIM, Dušan LAZÁR a Ladislav NEDBAL. E-photosynthesis: Web-based platform for modeling of complex photosynthetic processes. BioSystems. Elsevier, roč. 103, č. 2, s. 115-124. ISSN 0303-2647. doi:10.1016/j.biosystems.2010.10.013. 2011. URL info
• COLLINS, Pieter, Luc HABETS, Jan VAN SCHUPPEN, Ivana ČERNÁ, Jana FABRIKOVÁ a David ŠAFRÁNEK. Abstraction of Biochemical Reaction Systems on Polytopes. In Proceedings of the 18th IFAC World Congress. Milano: IFAC. s. 14869-14875. ISBN 978-1-1234-7890-2. 2011. URL info
• BRIM, Luboš, Jana FABRIKOVÁ, Sven DRAŽAN a David ŠAFRÁNEK. Reachability in Biochemical Dynamical Systems by Quantitative Discrete Approximation. Electronic Proceedings in Theoretical Computer Science. Neuveden, č. 67, s. 97-112, 15 s. ISSN 2075-2180. doi:10.4204/EPTCS.67.9. 2011. URL info
• BARNAT, Jiří, Luboš BRIM a David ŠAFRÁNEK. High-performance analysis of biological systems dynamics with the DiVinE model checker. Briefings in Bioinformatics. Oxford (UK): Oxford University Press, roč. 11, č. 3, s. 301-312. ISSN 1467-5463. 2010. DOI Abstract PDF reprint info
• BARNAT, Jiří, Luboš BRIM, David ŠAFRÁNEK a Martin VEJNÁR. Parameter Scanning by Parallel Model Checking with Applications in Systems Biology. In Ninth International Workshop on Parallel and Distributed Methods in Verification, and Second International Workshop on High Performance Computational Systems Biology. Los Alamitos: IEEE Computer Society. s. 95-104. ISBN 978-0-7695-4265-2. 2010. info
• BARNAT, Jiří, Luboš BRIM, Ivana ČERNÁ, Sven DRAŽAN, Jana FABRIKOVÁ a David ŠAFRÁNEK. On Algorithmic Analysis of Transcriptional Regulation by LTL Model Checking. Theoretical Computer Science. roč. 2009, č. 410, s. 3128-3148, 20 s. ISSN 0304-3975. 2009. URL info
• BARNAT, Jiří, Luboš BRIM, Ivana ČERNÁ, Sven DRAŽAN, Jana FABRIKOVÁ, Jan LÁNÍK, David ŠAFRÁNEK a Ma HONGWU. BioDiVinE: A Framework for Parallel Analysis of Biological Models. In Proceedings of 2nd International Workshop on Computational Models for Cell Processes. Neuveden: EPTCS. s. 31-45. ISSN 2075-2180. 2009. info
• SMRČKA, Aleš, Vojtěch ŘEHÁK, Tomáš VOJNAR, David ŠAFRÁNEK, Petr MATOUŠEK a Zdeněk ŘEHÁK. Verifying VHDL Designs with Multiple Clocks in SMV. In Formal Methods Applications and Technology, 11th International Workshop on Formal Methods for Industrial Critical Systems, FMICS 2006, and 5th International Workshop on Parallel and Distributed Methods in Verification, PDMC 2006. Bonn: Springer-Verlag. s. 148-164, 16 s. ISBN 978-3-540-70951-0. 2007. info
• ŠAFRÁNEK, David. Visual Coordination Networks. Brno: Masaryk University. 218 s. PhD Thesis. 2006. info
• ŠAFRÁNEK, David a Jiří ŠIMŠA. VCD: A Visual Formalism for Specification of Heterogeneous Software Architectures. In SOFSEM 2005: Theory and Practice of Computer Science. Heidelberg: Springer. s. 320-330, 10 s. ISBN 3-540-24302-X. 2005. info

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