all_our

2017

[1] Česka, M., Dannenberg, F., Paoletti, N., Kwiatkowska, M., Brim, L.: Precise parameter synthesis for stochastic biochemical systems. Acta Inf. 54(6), 589-623 (2017) [ DOI ]
[2] Beneš, N., Brim, L., Demko, M., Pastva, S., Šafránek, D.: Pithya: A parallel tool for parameter synthesis of piecewise multi-affine dynamical systems. In: Majumdar, R., Kunčak, V. (eds.) CAV 2017. LNCS, vol. 10426, pp. 591-598. Springer (2017)
[3] Barnat, J., Beneš, N., Brim, L., Demko, M., Hajnal, M., Pastva, S., Šafránek, D.: Detecting attractors in biological models with uncertain parameters. In: Feret, J., Koeppl, H. (eds.) CMSB 2017. LNBI, vol. 10545. Springer (2017)

2016

[4] Troják, M., Šafránek, D., Hrabec, J., Šalagovič, J., Romanovská, F., Červený, J.: E-cyanobacterium.org: A web-based platform for systems biology of cyanobacteria. In: CMSB 2016. LNBI, vol. 9859, pp. 316-322. Springer (2016) [ DOI ]
[5] Děd, T., Šafránek, D., Troják, M., Klement, M., Šalagovič, J., Brim, L.: Formal biochemical space with semantics in Kappa and BNGL. Electronic Notes in Theoretical Computer Science 326, 27 - 49 (2016), the 6th International Workshop on Static Analysis and Systems Biology, SASB 2015 [ DOI ]
[6] Beneš, N., Brim, L., Demko, M., Pastva, S., Šafránek, D.: Parallel SMT-based parameter synthesis with application to piecewise multi-affine systems. In: Artho, C., Legay, A., Peled, D. (eds.) ATVA 2016. LNCS, vol. 9938, pp. 192-208. Springer (2016)
[7] Demko, M., Beneš, N., Brim, L., Pastva, S., Šafránek, D.: High-performance symbolic parameter synthesis of biological models: A case study. In: Bartocci, E., Lio, P., Paoletti, N. (eds.) CMSB 2016. LNBI, vol. 9859, pp. 82-97. Springer (2016)
[8] Češka, M., Pilař, P., Paoletti, N., Brim, L., Kwiatkowska, M.Z.: PRISM-PSY: precise gpu-accelerated parameter synthesis for stochastic systems. In: Tools and Algorithms for the Construction and Analysis of Systems - 22nd International Conference, TACAS 2016, Held as Part of the European Joint Conferences on Theory and Practice of Software, ETAPS 2016, Eindhoven, The Netherlands, April 2-8, 2016, Proceedings. vol. 9636, pp. 367-384. Springer (2016)
[9] Hajnal, M., Šafránek, D., Demko, M., Pastva, S., Krejčí, P., Brim, L.: Toward modelling and analysis of transient and sustained behaviour of signalling pathways. In: Cinquemani, E., Donzé, A. (eds.) HSB 2016. LNBI, vol. 9957, pp. 57-66. Springer (2016)
[10] Beneš, N., Brim, L., Demko, M., Pastva, S., Šafránek, D.: A model checking approach to discrete bifurcation analysis. In: Fitzgerald, J., Heitmeyer, C., Gnesi, S., Philippou, A. (eds.) FM 2016. LNCS, vol. 9995, pp. 85-101. Springer (2016)

2015

[11] Brim, L., Nižnan, J., Šafránek, D.: Compact representation of photosynthesis dynamics by rule-based models. Electronic Notes in Theoretical Computer Science 316, 17 - 27 (2015), 5th International Workshop on Static Analysis and Systems Biology (SASB 2014) [ DOI ]
[12] Brim, L., Demko, M., Pastva, S., Šafránek, D.: High-performance discrete bifurcation analysis for piecewise-affine dynamical systems. In: Abate, A., Šafránek, D. (eds.) HSB 2015. LNBI, vol. 9271, pp. 58-74. Springer (2015)
[13] Brim, L., Demko, M., Češka, M., Pastva, S., Šafránek, D.: Parameter synthesis by parallel coloured CTL model checking. In: Roux, O., Bourdon, J. (eds.) CMSB 2015. LNBI, vol. 9308, pp. 251-263. Springer (2015)

2014

[14] Klement, M., Děd, T., Šafránek, D., Červený, J., Müller, S., Steuer, R.: Biochemical space: A framework for systemic annotation of biological models. Electronic Notes in Theoretical Computer Science 306(0), 31 - 44 (2014), proceedings of the 5th International Workshop on Interactions between Computer Science and Biology (CS2Bio’14)
[15] Brim, L., Dluhoš, P., Šafránek, D., Vejpustek, T.: STL*: Extending signal temporal logic with signal-value freezing operator. Information and Computation 236, 52-67 (2014), special Issue on Hybrid Systems and Biology

2013

[16] Klement, M., Šafránek, D., Děd, T., Pejznoch, A., Nedbal, L., Steuer, R., Červený, J., Müller, S.: 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). pp. 61-67-. Elsevier (2013)
[17] Goethem, S.V., Jacquet, J., Brim, L., Šafránek, D.: Timed modelling of gene networks with arbitrarily precise expression discretization. Electr. Notes Theor. Comput. Sci. 293, 67-81 (2013)
[18] Brim, L., Češka, M., Dražan, S., Šafránek, D.: Exploring parameter space of stochastic biochemical systems using quantitative model checking. In: Sharygina, N., Veith, H. (eds.) CAV 2013. LNCS, vol. 8044, pp. 107-123. Springer (2013)
[19] Brim, L., Vejpustek, T., Šafránek, D., Fabriková, J.: Robustness analysis for value-freezing signal temporal logic. In: Dang, T., Piazza, C. (eds.) HSB 2013. EPTCS, vol. 125, pp. 20-36 (2013)
[20] Brim, L., Češka, M., Dražan, S., Šafránek, D.: On robustness analysis of stochastic biochemical systems by probabilistic model checking. CoRR abs/1310.4734 (2013)
[21] Brim, L., Češka, M., Šafránek, D.: Model checking of biological systems. In: Bernardo, M., de Vink, E., Di Pierro, A., Wiklicky, H. (eds.) FMDS 2013. LNCS, vol. 7938, pp. 63-112. Springer (2013)
[22] Brim, L., Vejpustek, T., Šafránek, D., Fabriková, J.: Robustness analysis for value-freezing signal temporal logic. In: Proceedings Second International Workshop on Hybrid Systems and Biology, HSB 2013, Taormina, Italy, 2nd September 2013. EPTCS, vol. 125, pp. 20-36 (2013)

2012

[23] Brim, L., Fabriková, J., Dražan, S., Šafránek, D.: On approximative reachability analysis of biochemical dynamical systems. Trans. Computational Systems Biology 7625, 77-101 (2012)
[24] Dluhoš, P., Brim, L., Šafránek, D.: On expressing and monitoring oscillatory dynamics. In: Bartocci, E., Bortolussi, L. (eds.) HSB 2012. EPTCS, vol. 92, pp. 73-87 (2012)
[25] Barnat, J., Brim, L., Krejčí, A., Streck, A., Šafránek, D., Vejnár, M., Vejpustek, T.: On Parameter Synthesis by Parallel Model Checking. IEEE/ACM Transactions on Computational Biology and Bioinformatics 9(3), 693-705 (2012)

2011

[26] Šafránek, D., Červený, J., Klement, M., Pospíšilová, J., Brim, L., Lazár, D., Nedbal, L.: E-photosynthesis: Web-based platform for modeling of complex photosynthetic processes. BioSystems 103(2), 115-124 (2011)
[27] Brim, L., Fabriková, J., Dražan, S., Šafránek, D.: Reachability in biochemical dynamical systems by quantitative discrete approximation (extended abstract). In: Petre, I., de Vink, E.P. (eds.) CompMod 2011. EPTCS, vol. 67, pp. 97-112 (2011)
[28] Brim, L., Fabriková, J., Dražan, S., Šafránek, D.: Reachability in biochemical dynamical systems by quantitative discrete approximation. CoRR abs/1107.5924 (2011)
[29] Collins, P.J., Habets, L.C., van Schuppen, J.H., Černá, I., Fabriková, J., Šafránek, D.: Abstraction of biochemical reaction systems on polytopes. IFAC Proceedings Volumes 44(1), 14869-14875 (2011)

2010

[30] Barnat, J., Brim, L., Šafránek, D.: High-performance analysis of biological systems dynamics with the DiVinE model checker. Briefings in Bioinformatics 11(3), 301-312 (2010)
[31] Barnat, J., Brim, L., Šafránek, D., Vejnár, M.: Parameter Scanning by Parallel Model Checking with Applications in Systems Biology. In: HiBi/PDMC 2010. pp. 95-104. IEEE Computer Society Press (2010)
[32] Barnat, J., Brim, L., Šafránek, D.: High-performance analysis of biological systems dynamics with the divine model checker. Briefings in Bioinformatics 11(3), 301-312 (2010)

2009

[33] Barnat, J., Brim, L., Černá, I., Dražan, S., Fabriková, J., Šafránek, D.: On algorithmic analysis of transcriptional regulation by LTL model checking. Theor. Comput. Sci. 410(33-34), 3128-3148 (2009)
[34] Barnat, J., Brim, L., Černá, I., Dražan, S., Fabriková, J., Šafránek, D., Láník, J., Ma, H.: BioDiVinE: A Framework for Parallel Analysis of Biological Models. In: Back, R., Petre, I., de Vink, E.P. (eds.) CompMod 2009. EPTCS, vol. 6, pp. 31-45 (2009)
[35] Barnat, J., Brim, L., Černá, I., Dražan, S., Fabriková, J., Šafránek, D.: Computational Analysis of Large-Scale Multi-Affine ODE Models. In: HiBi 2009. pp. 81-90. IEEE Computer Society Press (2009)

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