Tonello, Elisa; Paulevé, Loïc Attractor identification in asynchronous Boolean dynamics with network reduction. (English) Zbl 07810893 Pang, Jun (ed.) et al., Computational methods in systems biology. 21st international conference, CMSB 2023, Luxembourg City, Luxembourg, September 13–15, 2023. Proceedings. Cham: Springer. Lect. Notes Comput. Sci. 14137, 202-219 (2023). MSC: 92C42 PDFBibTeX XMLCite \textit{E. Tonello} and \textit{L. Paulevé}, Lect. Notes Comput. Sci. 14137, 202--219 (2023; Zbl 07810893) Full Text: DOI arXiv
Riva, Sara; Lagniez, Jean-Marie; Magaña López, Gustavo; Paulevé, Loïc Tackling universal properties of minimal trap spaces of Boolean networks. (English) Zbl 07810890 Pang, Jun (ed.) et al., Computational methods in systems biology. 21st international conference, CMSB 2023, Luxembourg City, Luxembourg, September 13–15, 2023. Proceedings. Cham: Springer. Lect. Notes Comput. Sci. 14137, 157-174 (2023). MSC: 92C42 PDFBibTeX XMLCite \textit{S. Riva} et al., Lect. Notes Comput. Sci. 14137, 157--174 (2023; Zbl 07810890) Full Text: DOI arXiv
Leguizamon-Robayo, Alexander; Jiménez-Pastor, Antonio; Tribastone, Micro; Tschaikowski, Max; Vandin, Andrea Approximate constrained lumping of polynomial differential equations. (English) Zbl 07810887 Pang, Jun (ed.) et al., Computational methods in systems biology. 21st international conference, CMSB 2023, Luxembourg City, Luxembourg, September 13–15, 2023. Proceedings. Cham: Springer. Lect. Notes Comput. Sci. 14137, 106-123 (2023). MSC: 92C42 34C60 PDFBibTeX XMLCite \textit{A. Leguizamon-Robayo} et al., Lect. Notes Comput. Sci. 14137, 106--123 (2023; Zbl 07810887) Full Text: DOI
Beneš, Nikola; Brim, Luboš; Pastva, Samuel; Šafránek, David; Šmijáková, Eva Phenotype control of partially specified Boolean networks. (English) Zbl 07810881 Pang, Jun (ed.) et al., Computational methods in systems biology. 21st international conference, CMSB 2023, Luxembourg City, Luxembourg, September 13–15, 2023. Proceedings. Cham: Springer. Lect. Notes Comput. Sci. 14137, 18-35 (2023). MSC: 92C42 93C29 PDFBibTeX XMLCite \textit{N. Beneš} et al., Lect. Notes Comput. Sci. 14137, 18--35 (2023; Zbl 07810881) Full Text: DOI
Troják, Matej; Šafránek, David; Brozmann, Branislav; Brim, Luboš eBCSgen 2.0: modelling and analysis of regulated rule-based systems. (English) Zbl 1505.92083 Petre, Ion (ed.) et al., Computational methods in systems biology. 20th international conference, CMSB 2022, Bucharest, Romania, September 14–16, 2022. Proceedings. Cham: Springer. Lect. Notes Comput. Sci. 13447, 302-309 (2022). MSC: 92C42 92-04 PDFBibTeX XMLCite \textit{M. Troják} et al., Lect. Notes Comput. Sci. 13447, 302--309 (2022; Zbl 1505.92083) Full Text: DOI
Pastva, Samuel Variable stabilisation in Boolean monotonic model pools. (English) Zbl 1505.92078 Petre, Ion (ed.) et al., Computational methods in systems biology. 20th international conference, CMSB 2022, Bucharest, Romania, September 14–16, 2022. Proceedings. Cham: Springer. Lect. Notes Comput. Sci. 13447, 122-137 (2022). MSC: 92C42 92C40 94C11 PDFBibTeX XMLCite \textit{S. Pastva}, Lect. Notes Comput. Sci. 13447, 122--137 (2022; Zbl 1505.92078) Full Text: DOI
Niehren, Joachim; Vaginay, Athénaïs; Versari, Cristian Abstract simulation of reaction networks via Boolean networks. (English) Zbl 1505.92077 Petre, Ion (ed.) et al., Computational methods in systems biology. 20th international conference, CMSB 2022, Bucharest, Romania, September 14–16, 2022. Proceedings. Cham: Springer. Lect. Notes Comput. Sci. 13447, 21-40 (2022). MSC: 92C42 92C40 94C11 PDFBibTeX XMLCite \textit{J. Niehren} et al., Lect. Notes Comput. Sci. 13447, 21--40 (2022; Zbl 1505.92077) Full Text: DOI
Beneš, Nikola; Brim, Luboš; Pastva, Samuel; Šafránek, David Aeon 2021: bifurcation decision trees in Boolean networks. (English) Zbl 1491.92059 Cinquemani, Eugenio (ed.) et al., Computational methods in systems biology. 19th international conference, CMSB 2021, Bordeaux, France, September 22–24, 2021. Proceedings. Cham: Springer. Lect. Notes Comput. Sci. 12881, 230-237 (2021). MSC: 92C42 92-04 PDFBibTeX XMLCite \textit{N. Beneš} et al., Lect. Notes Comput. Sci. 12881, 230--237 (2021; Zbl 1491.92059) Full Text: DOI
Perez-Verona, Isabel Cristina; Tribastone, Mirco; Vandin, Andrea A large-scale assessment of exact lumping of quantitative models in the biomodels repository. (English) Zbl 1518.92067 Theor. Comput. Sci. 893, 41-59 (2021). MSC: 92C40 92C42 60H30 PDFBibTeX XMLCite \textit{I. C. Perez-Verona} et al., Theor. Comput. Sci. 893, 41--59 (2021; Zbl 1518.92067) Full Text: DOI Link
Beneš, Nikola; Brim, Luboš; Pastva, Samuel; Šafránek, David Symbolic coloured SCC decomposition. (English) Zbl 1474.68210 Groote, Jan Friso (ed.) et al., Tools and algorithms for the construction and analysis of systems. 27th international conference, TACAS 2021, held as part of the European joint conferences on theory and practice of software, ETAPS 2021, Luxembourg City, Luxembourg, March 27 – April 1, 2021. Proceedings. Part II. Cham: Springer. Lect. Notes Comput. Sci. 12652, 64-83 (2021). MSC: 68R10 05C15 05C85 68W30 92C42 PDFBibTeX XMLCite \textit{N. Beneš} et al., Lect. Notes Comput. Sci. 12652, 64--83 (2021; Zbl 1474.68210) Full Text: DOI
Chai, Xinwei; Ribeiro, Tony; Magnin, Morgan; Roux, Olivier; Inoue, Katsumi Static analysis and stochastic search for reachability problem. (English) Zbl 1458.92032 Gupta, Ankit (ed.) et al., Proceedings of SASB 2018, the 9th international workshop on static analysis and systems biology, Freiburg, Germany, August 28, 2018. Amsterdam: Elsevier. Electron. Notes Theor. Comput. Sci. 350, 139-158 (2020). MSC: 92C42 93B03 93A15 PDFBibTeX XMLCite \textit{X. Chai} et al., Electron. Notes Theor. Comput. Sci. 350, 139--158 (2020; Zbl 1458.92032) Full Text: DOI
Troják, Matej; Šafránek, David; Brim, Luboš; Šalagovič, Jakub; Červený, Jan Executable biochemical space for specification and analysis of biochemical systems. (English) Zbl 1458.92038 Gupta, Ankit (ed.) et al., Proceedings of SASB 2018, the 9th international workshop on static analysis and systems biology, Freiburg, Germany, August 28, 2018. Amsterdam: Elsevier. Electron. Notes Theor. Comput. Sci. 350, 91-116 (2020). MSC: 92C42 92C40 PDFBibTeX XMLCite \textit{M. Troják} et al., Electron. Notes Theor. Comput. Sci. 350, 91--116 (2020; Zbl 1458.92038) Full Text: DOI arXiv
Hajnal, Matej; Pastva, Samuel Toward model selection by formal methods. (English) Zbl 1458.92035 Gupta, Ankit (ed.) et al., Proceedings of SASB 2018, the 9th international workshop on static analysis and systems biology, Freiburg, Germany, August 28, 2018. Amsterdam: Elsevier. Electron. Notes Theor. Comput. Sci. 350, 57-71 (2020). MSC: 92C42 PDFBibTeX XMLCite \textit{M. Hajnal} and \textit{S. Pastva}, Electron. Notes Theor. Comput. Sci. 350, 57--71 (2020; Zbl 1458.92035) Full Text: DOI
Islam, Md. Ariful; Cleaveland, Rance; Fenton, Flavio H.; Grosu, Radu; Jones, Paul L.; Smolka, Scott A. Probabilistic reachability for multi-parameter bifurcation analysis of cardiac alternans. (English) Zbl 1427.92054 Theor. Comput. Sci. 765, 158-169 (2019). MSC: 92C55 34C23 93B03 PDFBibTeX XMLCite \textit{Md. A. Islam} et al., Theor. Comput. Sci. 765, 158--169 (2019; Zbl 1427.92054) Full Text: DOI
Kolčák, Juraj; Šafránek, David; Haar, Stefan; Paulevé, Loïc Parameter space abstraction and unfolding semantics of discrete regulatory networks. (English) Zbl 1423.68313 Theor. Comput. Sci. 765, 120-144 (2019). MSC: 68Q85 92C42 PDFBibTeX XMLCite \textit{J. Kolčák} et al., Theor. Comput. Sci. 765, 120--144 (2019; Zbl 1423.68313) Full Text: DOI arXiv
Děd, T.; Šafránek, D.; Troják, M.; Klement, M.; Šalagovič, J.; Brim, L. Formal biochemical space with semantics in Kappa and BNGL. (English) Zbl 1401.92076 Paulevé, Loïc (ed.) et al., Post-proceedings of the 6th international workshop on static analysis and systems biology (SASB 2015), Saint-Malo, France, September 8, 2015. Amsterdam: Elsevier. Electronic Notes in Theoretical Computer Science 326, 27-49 (2016). MSC: 92C40 68Q45 68Q55 PDFBibTeX XMLCite \textit{T. Děd} et al., Electron. Notes Theor. Comput. Sci. 326, 27--49 (2016; Zbl 1401.92076) Full Text: DOI
Brim, L.; Nižnan, J.; Šafránek, D. Compact representation of photosynthesis dynamics by rule-based models. (English) Zbl 1352.92095 Pauleve, Loic (ed.) et al., Post-proceedings of the 5th international workshop on static analysis and systems biology (SASB 2014), Munich, Germany, September 10, 2014. Amsterdam: Elsevier. Electronic Notes in Theoretical Computer Science 316, 17-27 (2015). MSC: 92C80 92C42 PDFBibTeX XMLCite \textit{L. Brim} et al., Electron. Notes Theor. Comput. Sci. 316, 17--27 (2015; Zbl 1352.92095) Full Text: DOI arXiv
Mateescu, Radu; Monteiro, Pedro T.; Dumas, Estelle; de Jong, Hidde CTRL: extension of CTL with regular expressions and fairness operators to verify genetic regulatory networks. (English) Zbl 1231.68163 Theor. Comput. Sci. 412, No. 26, 2854-2883 (2011). Reviewer: Martin Lange (Kassel) MSC: 68Q60 92C42 PDFBibTeX XMLCite \textit{R. Mateescu} et al., Theor. Comput. Sci. 412, No. 26, 2854--2883 (2011; Zbl 1231.68163) Full Text: DOI Link
Barnat, J.; Brim, L.; Černá, I.; Dražan, S.; Fabriková, J.; Šafránek, D. On algorithmic analysis of transcriptional regulation by LTL model checking. (English) Zbl 1173.68037 Theor. Comput. Sci. 410, No. 33-34, 3128-3148 (2009). MSC: 68Q60 92B05 92C37 PDFBibTeX XMLCite \textit{J. Barnat} et al., Theor. Comput. Sci. 410, No. 33--34, 3128--3148 (2009; Zbl 1173.68037) Full Text: DOI
Mateescu, Radu; Monteiro, Pedro T.; Dumas, Estelle; de Jong, Hidde Computation tree regular logic for genetic regulatory networks. (English) Zbl 1183.68380 Cha, Sungdeok (Steve) (ed.) et al., Automated technology for verification and analysis. 6th international symposium, ATVA 2008, Seoul, Korea, October 20–23, 2008. Proceedings. Berlin: Springer (ISBN 978-3-540-88386-9/pbk). Lecture Notes in Computer Science 5311, 48-63 (2008). MSC: 68Q60 03B44 03B45 92C42 PDFBibTeX XMLCite \textit{R. Mateescu} et al., Lect. Notes Comput. Sci. 5311, 48--63 (2008; Zbl 1183.68380) Full Text: DOI