Publication Records

BENEŠ, Nikola, Luboš BRIM, Ondřej HUVAR, Samuel PASTVA and David ŠAFRÁNEK. Boolean network sketches: a unifying framework for logical model inference. Bioinformatics. 2023, vol. 39, No 4, p. "btad158", 8 pp. ISSN 1367-4803. Available from: https://dx.doi.org/10.1093/bioinformatics/btad158.

BENEŠ, Nikola, Luboš BRIM, Samuel PASTVA, David ŠAFRÁNEK and Eva ŠMIJÁKOVÁ. Phenotype Control of Partially Specified Boolean Networks. In Jun Pang, Joachim Niehren. Computational Methods in Systems Biology. Luxembourg City, Luxembourg: Springer Cham, 2023, p. 18-35. ISBN 978-3-031-42696-4. Available from: https://dx.doi.org/10.1007/978-3-031-42697-1_2.

TROJÁK, Matej, David ŠAFRÁNEK, Samuel PASTVA and Luboš BRIM. Rule-based Modelling of Biological Systems Using Regulated Rewriting. Biosystems. Elsevier, 2023, vol. 225, No 104843, p. 1-15. ISSN 0303-2647. Available from: https://dx.doi.org/10.1016/j.biosystems.2023.104843.

BRIM, Luboš, Samuel PASTVA, David ŠAFRÁNEK and Eva ŠMIJÁKOVÁ. Temporary and Permanent Control of Partially Specified Boolean Networks. BIOSYSTEMS. Elsevier, 2023, vol. 223, JAN, p. 104795-104808. ISSN 0303-2647. Available from: https://dx.doi.org/10.1016/j.biosystems.2022.104795.

BENEŠ, Nikola, Luboš BRIM, Ondřej HUVAR, Samuel PASTVA, David ŠAFRÁNEK and Eva ŠMIJÁKOVÁ. AEON.py: Python library for attractor analysis in asynchronous Boolean networks. BIOINFORMATICS. UK: OXFORD UNIV PRESS, 2022, vol. 38, No 21, p. 4978-4980. ISSN 1367-4803. Available from: https://dx.doi.org/10.1093/bioinformatics/btac624.

BENEŠ, Nikola, Luboš BRIM, Samuel PASTVA and David ŠAFRÁNEK. BDD-Based Algorithm for SCC Decomposition of Edge-Coloured Graphs. Logical Methods in Computer Science. Episciences, 2022, vol. 18, No 1, p. 1-27. ISSN 1860-5974. Available from: https://dx.doi.org/10.46298/LMCS-18(1:38)2022.

BENEŠ, Nikola, Luboš BRIM, Jakub KADLECAJ, Samuel PASTVA and David ŠAFRÁNEK. Exploring attractor bifurcations in Boolean networks. BMC Bioinformatics. 2022, vol. 23, No 173, p. 1-18. ISSN 1471-2105. Available from: https://dx.doi.org/10.1186/s12859-022-04708-9.

BENEŠ, Nikola, Luboš BRIM, Samuel PASTVA and 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, 2021, p. 230-237. ISBN 978-3-030-85632-8. Available from: https://dx.doi.org/10.1007/978-3-030-85633-5_14.

BENEŠ, Nikola, Luboš BRIM, Samuel PASTVA and David ŠAFRÁNEK. Computing Bottom SCCs Symbolically Using Transition Guided Reduction. Online. In Alexandra Silva, K. Rustan, M. Leino. Computer Aided Verification - 33rd International Conference, CAV 2021. Neuveden: Springer Nature, 2021, p. 505-528. ISBN 978-3-030-81684-1. Available from: https://dx.doi.org/10.1007/978-3-030-81685-8_24.

BENEŠ, Nikola, Luboš BRIM, Samuel PASTVA and David ŠAFRÁNEK. Symbolic Coloured SCC Decomposition. Online. In Jan Friso Groote, Kim Larsen. Tools and Algorithms for the Construction and Analysis of Systems, 27th International Conference, TACAS 2021. Neuveden: Springer Nature, 2021, p. 64-83. ISBN 978-3-030-72012-4. Available from: https://dx.doi.org/10.1007/978-3-030-72013-1_4.

BENEŠ, Nikola, Luboš BRIM, Jakub KADLECAJ, Samuel PASTVA and 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, 2020, p. 569-581. ISBN 978-3-030-53287-1. Available from: https://dx.doi.org/10.1007/978-3-030-53288-8_28.

BENEŠ, Nikola, Luboš BRIM, Samuel PASTVA and David ŠAFRÁNEK. Digital Bifurcation Analysis of Internet Congestion Control Protocols. International Journal of Bifurcation and Chaos. 2020, vol. 30, No 13, p. 2030038-2030055. ISSN 0218-1274. Available from: https://dx.doi.org/10.1142/S0218127420300384.

BENEŠ, Nikola, Luboš BRIM, Samuel PASTVA and David ŠAFRÁNEK. Parallel parameter synthesis algorithm for hybrid CTL. Science of Computer Programming. 2020, vol. 185, No 102321, p. 1-19. ISSN 0167-6423. Available from: https://dx.doi.org/10.1016/j.scico.2019.102321.

ŠMIJÁKOVÁ, Eva, Samuel PASTVA, David ŠAFRÁNEK and Luboš BRIM. Parallel Parameter Synthesis for Multi-affine Hybrid Systems from Hybrid CTL Specifications. (Parallel Parameter Synthesis for Multi-affine Hybrid Systems from Hybrid CTL Specifications). Online. In Abate A., Petrov T., Wolf V. Computational Methods in Systems Biology. CMSB 2020. Lecture Notes in Computer Science, vol 12314. Cham: Springer, Cham, 2020, p. 280-297. ISBN 978-3-030-60326-7. Available from: https://dx.doi.org/10.1007/978-3-030-60327-4_15.

HAJNAL, Matej and Samuel PASTVA. Toward Model Selection by Formal Methods. Online. In Ankit Gupta, Tatjana Petrov. Proceedings of SASB 2018, the Ninth International Workshop on Static Analysis and Systems Biology, ENTCS, vol. 350. Freiburg im Breisgau, Germany: Elsevier, 2020, p. 57-71. ISSN 1571-0661. Available from: https://dx.doi.org/10.1016/j.entcs.2020.06.004.

BENEŠ, Nikola, Luboš BRIM, Martin GELETKA, Samuel PASTVA and David ŠAFRÁNEK. Accelerating Parameter Synthesis Using Semi-algebraic Constraints. Online. In Ahrendt, Wolfgang and Tapia Tarifa, Silvia Lizeth. Integrated Formal Methods. LNCS 11918. Cham: Springer International Publishing, 2019, p. 27-45. ISBN 978-3-030-34967-7. Available from: https://dx.doi.org/10.1007/978-3-030-34968-4_2.

ŠAFRÁNEK, David, Matej TROJÁK, Vojtěch BRŮŽA, Tomáš VEJPUSTEK, Jan PAPOUŠEK, Martin DEMKO, Samuel PASTVA, Aleš PEJZNOCH and 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, 2019, p. 356-359. ISBN 978-3-030-31303-6. Available from: https://dx.doi.org/10.1007/978-3-030-31304-3_26.

BENEŠ, Nikola, Luboš BRIM, Samuel PASTVA and 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, 2019, p. 339-356. ISBN 978-3-030-17464-4. Available from: https://dx.doi.org/10.1007/978-3-030-17465-1_19.

BENEŠ, Nikola, Luboš BRIM, Jana DRAŽANOVÁ, Samuel PASTVA and 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, 2019, p. 99-108. ISBN 978-1-4503-6282-5. Available from: https://dx.doi.org/10.1145/3302504.3311793.

BENEŠ, Nikola, Luboš BRIM, Samuel PASTVA, Jakub POLÁČEK and 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, 2019, p. 353-369. ISBN 978-3-030-32408-7. Available from: https://dx.doi.org/10.1007/978-3-030-32409-4_22.

BENEŠ, Nikola, Luboš BRIM, Samuel PASTVA and David ŠAFRÁNEK. Model Checking Approach to the Analysis of Biological Systems. Online. In Pietro Liò, Paolo Zuliani. Automated Reasoning for Systems Biology and Medicine. Cham: Springer, Cham, 2019, p. 3-35. Computational Biology. ISBN 978-3-030-17296-1. Available from: https://dx.doi.org/10.1007/978-3-030-17297-8_1.

DALSGAARD, Andreas E., Søren ENEVOLDSEN, Peter FOGH, Lasse S. JENSEN, Peter G. JENSEN, Tobias S. JEPSEN, Isabella KAUFMANN, Kim G. LARSEN, Søren M. NIELSEN, Mads Chr. OLESEN, Samuel PASTVA and Jiří SRBA. A Distributed Fixed-Point Algorithm for Extended Dependency Graphs. Fundamenta Informaticae. 2018, vol. 161, No 4, p. 351-381. ISSN 0169-2968. Available from: https://dx.doi.org/10.3233/FI-2018-1707.

BENEŠ, Nikola, Luboš BRIM, Jan ČERVENÝ, Samuel PASTVA, David ŠAFRÁNEK, Jakub ŠALAGOVIČ and 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, 2018, p. 354-359. ISBN 978-1-5386-4444-7. Available from: https://dx.doi.org/10.1109/ICSTCC.2018.8540762.

DEMKO, Martin, Samuel PASTVA, David ŠAFRÁNEK, Nikola BENEŠ and Luboš BRIM. PITHYA. 2018.

BRIM, Luboš, Jiří BARNAT, David ŠAFRÁNEK, Nikola BENEŠ, Martin DEMKO, Samuel PASTVA and 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, 2017, p. 40-56. ISBN 978-3-319-67470-4. Available from: https://dx.doi.org/10.1007/978-3-319-67471-1_3.

PASTVA, Samuel. Discrete Bifurcation Analysis of Reactive Systems. In FMCAD. 2017.

BENEŠ, Nikola, Luboš BRIM, Martin DEMKO, Matej HAJNAL, Samuel PASTVA and David ŠAFRÁNEK. Discrete Bifurcation Analysis with Pithya. In Feret J. et al. 15th International Conference on Computational Methods in Systems Biology (CMSB). LNCS 10545. Cham: Springer, 2017, p. 319-320. ISBN 978-3-319-67470-4.

DALSGAARD, Andreas E., Søren ENEVOLDSEN, Peter FOGH, Lasse S. JENSEN, Tobias S. JEPSEN, Isabella KAUFMANN, Kim G. LARSEN, Søren M. NIELSEN, Mads Chr. OLESEN, Samuel PASTVA and Jiří SRBA. Extended Dependency Graphs and Efficient Distributed Fixed-Point Computation. In van der Aalst, Wil and Best, Eike. Petri Nets 2017. Holandsko: Springer International Publishing, 2017, p. 139-158. ISBN 978-3-319-57860-6. Available from: https://dx.doi.org/10.1007/978-3-319-57861-3_10.

BENEŠ, Nikola, Luboš BRIM, Martin DEMKO, David ŠAFRÁNEK, Samuel PASTVA and Matej HAJNAL. Model Checking Approach to Discrete Bifurcation Analysis. In Doctoral Workshop on Mathematical and Engineering Methods in Computer Science. 2017.

PASTVA, Samuel. Parallel Algorithm for Terminal Components Detection in Parametrised Transition Systems. In YR-CONCUR. 2017.

BRIM, Luboš, David ŠAFRÁNEK, Nikola BENEŠ, Martin DEMKO, Samuel PASTVA and Matej HAJNAL. Parameter Synthesis of Biological Models by Model Checking: A Case Study. In 4th International Synthetic & Systems Biology Summer School. SSBSS 2017. 2017.

BENEŠ, Nikola, Luboš BRIM, Martin DEMKO, Samuel PASTVA and 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, 2017, p. 591-598. ISBN 978-3-319-63386-2. Available from: https://dx.doi.org/10.1007/978-3-319-63387-9_29.

BRIM, Luboš, Nikola BENEŠ, David ŠAFRÁNEK, Martin DEMKO, Samuel PASTVA and Matej HAJNAL. PITHYA: High-Performance Parameter Synthesis for Biological Models. In Intelligent Systems for Molecular Biology and European Conference on Computational Biology. ISMB/ECCB 2017. 2017.

BENEŠ, Nikola, Luboš BRIM, Martin DEMKO, Samuel PASTVA and 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, 2016, p. 85-101. ISBN 978-3-319-48988-9. Available from: https://dx.doi.org/10.1007/978-3-319-48989-6_6.

DEMKO, Martin, Nikola BENEŠ, Luboš BRIM, Samuel PASTVA and 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, 2016, p. 82-97. ISBN 978-3-319-45176-3. Available from: https://dx.doi.org/10.1007/978-3-319-45177-0_6.

BENEŠ, Nikola, Luboš BRIM, Martin DEMKO, Samuel PASTVA and 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, 2016, p. 192-208. ISBN 978-3-319-46519-7. Available from: https://dx.doi.org/10.1007/978-3-319-46520-3_13.

HAJNAL, Matej, David ŠAFRÁNEK, Martin DEMKO, Samuel PASTVA, Pavel KREJČÍ and 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, 2016, p. 57-66. ISBN 978-3-319-47150-1. Available from: https://dx.doi.org/10.1007/978-3-319-47151-8_4.

BRIM, Luboš, Martin DEMKO, Samuel PASTVA and David ŠAFRÁNEK. Coloured Model Checking Approach to Parameter Synthesis for Executable Models in Synthetic Biology. In Verification of Engineered Molecular Devices and Programs. 2015.

BRIM, Luboš, Martin DEMKO, Samuel PASTVA and 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, 2015, p. 58-74. ISBN 978-3-319-26915-3. Available from: https://dx.doi.org/10.1007/978-3-319-26916-0_4.

BRIM, Luboš, Milan ČEŠKA, Martin DEMKO, Samuel PASTVA and 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, 2015, p. 251-263. ISBN 978-3-319-23400-7. Available from: https://dx.doi.org/10.1007/978-3-319-23401-4_21.