Výpis publikací

VESELÝ, Vojtěch; Eva ŠMIJÁKOVÁ; Samuel PASTVA; Nikola BENEŠ a David ŠAFRÁNEK. AEON 2025: Robust Control of Partially-Specified Boolean Networks. Online. In Fages, Francois and Peres, Sabine. International Conference on Computational Methods in Systems Biology, CMSB 2025. Cham: Springer Nature Switzerland, 2026, s. 61-68. ISBN 978-3-032-01435-1. Dostupné z: https://doi.org/10.1007/978-3-032-01436-8_4.

HUVAR, Ondřej; Nikola BENEŠ; Luboš BRIM; Samuel PASTVA a David ŠAFRÁNEK. Sketchbook: logical model inference from Boolean network sketches. BIOINFORMATICS ADVANCES. OXFORD: OXFORD UNIV PRESS, 2026, roč. 6, č. 1, s. 1-5. ISSN 2635-0041. Dostupné z: https://doi.org/10.1093/bioadv/vbag014.

PASTVA, Samuel; Kyu Hyong PARK; Ondrej HUVAR; Jordan C. ROZUM a Reka ALBERT. An open problem: Why are motif-avoidant attractors so rare in asynchronous Boolean networks? JOURNAL OF MATHEMATICAL BIOLOGY. HEIDELBERG: SPRINGER HEIDELBERG, 2025, roč. 91, č. 1, s. 1-36. ISSN 0303-6812. Dostupné z: https://doi.org/10.1007/s00285-025-02235-8.

TRINH, Van-Giang; Kyu Hyong PARK; Samuel PASTVA a Jordan C. ROZUM. Mapping the attractor landscape of Boolean networks with biobalm. BIOINFORMATICS. OXFORD: OXFORD UNIVERSITY PRESS, 2025, roč. 41, č. 5, s. 1-8. ISSN 1367-4803. Dostupné z: https://doi.org/10.1093/bioinformatics/btaf280.

KABIR, Mohimenul; Van-Giang TRINH; Samuel PASTVA a Kuldeep S. MEEL. Scalable Counting of Minimal Trap Spaces and Fixed Points in Boolean Networks. Online. In DeLaBanda, MG. 31ST INTERNATIONAL CONFERENCE ON PRINCIPLES AND PRACTICE OF CONSTRAINT PROGRAMMING, CP 2025. Dagstuhl, Germany: SCHLOSS DAGSTUHL, LEIBNIZ CENTER INFORMATICS, 2025, s. 1-26. ISBN 978-3-95977-380-5. Dostupné z: https://doi.org/10.4230/LIPIcs.CP.2025.17.

BENEŠ, Nikola; Luboš BRIM; Ondřej HUVAR; Samuel PASTVA a David ŠAFRÁNEK. Symbolic Model Checking of Hybrid CTL on Coloured Kripke Structures. Online. In Akshay, S. and Niemetz, Aina and Sankaranarayanan, Sriram. International Symposium on Automated Technology for Verification and Analysis, ATVA 2024. Cham: Springer Nature Switzerland, 2025, s. 212-233. ISBN 978-3-031-78749-2. Dostupné z: https://doi.org/10.1007/978-3-031-78750-8_11.

BENEŠ, Nikola; Luboš BRIM; Ondřej HUVAR; Samuel PASTVA a David ŠAFRÁNEK. BNClassifier: Classifying Boolean Models by Dynamic Properties. Online. In Gori, Roberta; Milazzo, Paolo; Tribastone, Mirco. Computational Methods in Systems Biology. Cham: Springer, 2024, s. 19-26. ISBN 978-3-031-71670-6. Dostupné z: https://doi.org/10.1007/978-3-031-71671-3_2.

TRINH, Van-Giang; Belaid BENHAMOU; Samuel PASTVA a Sylvain SOLIMAN. Scalable Enumeration of Trap Spaces in Boolean Networks via Answer Set Programming. Online. In Wooldridge, M; Dy, J; Natarajan, S. Proceedings of the AAAI Conference on Artificial Intelligence. Washington, USA: AAAI Press, 2024, s. 10714-10722. ISSN 2159-5399. Dostupné z: https://doi.org/10.1609/aaai.v38i9.28943.

PASTVA, Samuel a Thomas HENZINGER. Binary decision diagrams on modern hardware. Online. In Nadel, Alexander; Rozier, Kristin Yvonne. Proceedings of the 23rd Conference on Formal Methods in Computer-Aided Design – FMCAD 2023. Vienna: TU Wien Academic Press, 2023, s. 122-131. ISBN 978-3-85448-060-0. Dostupné z: https://doi.org/10.34727/2023/isbn.978-3-85448-060-0_20.

BENEŠ, Nikola; Luboš BRIM; Ondřej HUVAR; Samuel PASTVA a David ŠAFRÁNEK. Boolean network sketches: a unifying framework for logical model inference. Bioinformatics. 2023, roč. 39, č. 4, s. "btad158", 8 s. ISSN 1367-4803. Dostupné z: https://doi.org/10.1093/bioinformatics/btad158.

BENEŠ, Nikola; Luboš BRIM; Samuel PASTVA; David ŠAFRÁNEK a 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, s. 18-35. ISBN 978-3-031-42696-4. Dostupné z: https://doi.org/10.1007/978-3-031-42697-1_2.

TROJÁK, Matej; David ŠAFRÁNEK; Samuel PASTVA a Luboš BRIM. Rule-based Modelling of Biological Systems Using Regulated Rewriting. Biosystems. Elsevier, 2023, roč. 225, č. 104843, s. 1-15. ISSN 0303-2647. Dostupné z: https://doi.org/10.1016/j.biosystems.2023.104843.

BRIM, Luboš; Samuel PASTVA; David ŠAFRÁNEK a Eva ŠMIJÁKOVÁ. Temporary and Permanent Control of Partially Specified Boolean Networks. BIOSYSTEMS. Elsevier, 2023, roč. 223, JAN, s. 104795-104808. ISSN 0303-2647. Dostupné z: https://doi.org/10.1016/j.biosystems.2022.104795.

TRINH, Van-Giang; Belaid BENHAMOU; Thomas HENZINGER a Samuel PASTVA. Trap spaces of multi-valued networks: definition, computation, and applications. BIOINFORMATICS. ENGLAND: OXFORD UNIV PRESS, 2023, roč. 39, Supplement_1, s. 513-522. ISSN 1367-4803. Dostupné z: https://doi.org/10.1093/bioinformatics/btad262.

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, 2022, roč. 38, č. 21, s. 4978-4980. ISSN 1367-4803. Dostupné z: https://doi.org/10.1093/bioinformatics/btac624.

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, 2022, roč. 18, č. 1, s. 1-27. ISSN 1860-5974. Dostupné z: https://doi.org/10.46298/LMCS-18(1:38)2022.

BENEŠ, Nikola; Luboš BRIM; Jakub KADLECAJ; Samuel PASTVA a David ŠAFRÁNEK. Exploring attractor bifurcations in Boolean networks. BMC Bioinformatics. 2022, roč. 23, č. 173, s. 1-18. ISSN 1471-2105. Dostupné z: https://doi.org/10.1186/s12859-022-04708-9.

PASTVA, Samuel. Variable Stabilisation in Boolean Monotonic Model Pools. Online. In Ion Petre, Andrei Păun. Computational Methods in Systems Biology. Cham: Springer, 2022, s. 122-137. ISBN 978-3-031-15033-3. Dostupné z: https://doi.org/10.1007/978-3-031-15034-0_6.

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, 2021, s. 230-237. ISBN 978-3-030-85632-8. Dostupné z: https://doi.org/10.1007/978-3-030-85633-5_14.

BENEŠ, Nikola; Luboš BRIM; Samuel PASTVA a 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, s. 505-528. ISBN 978-3-030-81684-1. Dostupné z: https://doi.org/10.1007/978-3-030-81685-8_24.

BENEŠ, Nikola; Luboš BRIM; Samuel PASTVA a 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, s. 64-83. ISBN 978-3-030-72012-4. Dostupné z: https://doi.org/10.1007/978-3-030-72013-1_4.

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, 2020, s. 569-581. ISBN 978-3-030-53287-1. Dostupné z: https://doi.org/10.1007/978-3-030-53288-8_28.

BENEŠ, Nikola; Luboš BRIM; Samuel PASTVA a David ŠAFRÁNEK. Digital Bifurcation Analysis of Internet Congestion Control Protocols. International Journal of Bifurcation and Chaos. 2020, roč. 30, č. 13, s. 2030038-2030055. ISSN 0218-1274. Dostupné z: https://doi.org/10.1142/S0218127420300384.

BENEŠ, Nikola; Luboš BRIM; Samuel PASTVA a David ŠAFRÁNEK. Parallel parameter synthesis algorithm for hybrid CTL. Science of Computer Programming. 2020, roč. 185, č. 102321, s. 1-19. ISSN 0167-6423. Dostupné z: https://doi.org/10.1016/j.scico.2019.102321.

ŠMIJÁKOVÁ, Eva; Samuel PASTVA; David ŠAFRÁNEK a Luboš BRIM. 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, s. 280-297. ISBN 978-3-030-60326-7. Dostupné z: https://doi.org/10.1007/978-3-030-60327-4_15.

HAJNAL, Matej a 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, s. 57-71. ISSN 1571-0661. Dostupné z: https://doi.org/10.1016/j.entcs.2020.06.004.

BENEŠ, Nikola; Luboš BRIM; Martin GELETKA; Samuel PASTVA a 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, s. 27-45. ISBN 978-3-030-34967-7. Dostupné z: https://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 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, 2019, s. 356-359. ISBN 978-3-030-31303-6. Dostupné z: https://doi.org/10.1007/978-3-030-31304-3_26.

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, 2019, s. 339-356. ISBN 978-3-030-17464-4. Dostupné z: https://doi.org/10.1007/978-3-030-17465-1_19.

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, 2019, s. 99-108. ISBN 978-1-4503-6282-5. Dostupné z: https://doi.org/10.1145/3302504.3311793.

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, 2019, s. 353-369. ISBN 978-3-030-32408-7. Dostupné z: https://doi.org/10.1007/978-3-030-32409-4_22.

BENEŠ, Nikola; Luboš BRIM; Samuel PASTVA a 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, s. 3-35. Computational Biology. ISBN 978-3-030-17296-1. Dostupné z: https://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 a Jiří SRBA. A Distributed Fixed-Point Algorithm for Extended Dependency Graphs. Fundamenta Informaticae. 2018, roč. 161, č. 4, s. 351-381. ISSN 0169-2968. Dostupné z: https://doi.org/10.3233/FI-2018-1707.

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, 2018, s. 354-359. ISBN 978-1-5386-4444-7. Dostupné z: https://doi.org/10.1109/ICSTCC.2018.8540762.

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

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, 2017, s. 40-56. ISBN 978-3-319-67470-4. Dostupné z: https://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 a 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, s. 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 a 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, s. 139-158. ISBN 978-3-319-57860-6. Dostupné z: https://doi.org/10.1007/978-3-319-57861-3_10.

BENEŠ, Nikola; Luboš BRIM; Martin DEMKO; David ŠAFRÁNEK; Samuel PASTVA a 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 a 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 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, 2017, s. 591-598. ISBN 978-3-319-63386-2. Dostupné z: https://doi.org/10.1007/978-3-319-63387-9_29.

BRIM, Luboš; Nikola BENEŠ; David ŠAFRÁNEK; Martin DEMKO; Samuel PASTVA a 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 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, 2016, s. 85-101. ISBN 978-3-319-48988-9. Dostupné z: https://doi.org/10.1007/978-3-319-48989-6_6.

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, 2016, s. 82-97. ISBN 978-3-319-45176-3. Dostupné z: https://doi.org/10.1007/978-3-319-45177-0_6.

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, 2016, s. 192-208. ISBN 978-3-319-46519-7. Dostupné z: https://doi.org/10.1007/978-3-319-46520-3_13.

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, 2016, s. 57-66. ISBN 978-3-319-47150-1. Dostupné z: https://doi.org/10.1007/978-3-319-47151-8_4.

BRIM, Luboš; Martin DEMKO; Samuel PASTVA a 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 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, 2015, s. 58-74. ISBN 978-3-319-26915-3. Dostupné z: https://doi.org/10.1007/978-3-319-26916-0_4.

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, 2015, s. 251-263. ISBN 978-3-319-23400-7. Dostupné z: https://doi.org/10.1007/978-3-319-23401-4_21.