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
Gibart, Laetitia; Collavizza, Hélène; Comet, Jean-Paul Greening R. Thomas’ framework with environment variables: a divide and conquer approach. (English) Zbl 1491.92062 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, 36-56 (2021). MSC: 92C42 92D40 92-08 PDFBibTeX XMLCite \textit{L. Gibart} et al., Lect. Notes Comput. Sci. 12881, 36--56 (2021; Zbl 1491.92062) Full Text: DOI
Kruff, Niclas; Lüders, Christoph; Radulescu, Ovidiu; Sturm, Thomas; Walcher, Sebastian Algorithmic reduction of biological networks with multiple time scales. (English) Zbl 1484.13058 Math. Comput. Sci. 15, No. 3, 499-534 (2021). Reviewer: Hamid Rahkooy (Saarbrücken) MSC: 13P10 68W30 34E15 37D10 92C45 PDFBibTeX XMLCite \textit{N. Kruff} et al., Math. Comput. Sci. 15, No. 3, 499--534 (2021; Zbl 1484.13058) 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
Navarro-López, E. M.; O’Toole, M. D. Automated generation of hybrid automata for multi-rigid-body mechanical systems and its application to the falsification of safety properties. (English) Zbl 1485.93277 Math. Comput. Model. Dyn. Syst. 24, No. 1, 44-75 (2018). MSC: 93C30 70Q05 92-08 PDFBibTeX XMLCite \textit{E. M. Navarro-López} and \textit{M. D. O'Toole}, Math. Comput. Model. Dyn. Syst. 24, No. 1, 44--75 (2018; Zbl 1485.93277) Full Text: DOI
Arif, M. Fareed; Mencía, Carlos; Marques-Silva, Joao Efficient MUS enumeration of Horn formulae with applications to axiom pinpointing. (English) Zbl 1471.68173 Heule, Marijn (ed.) et al., Theory and applications of satisfiability testing – SAT 2015. 18th international conference, Austin, TX, USA, September 24–27, 2015. Proceedings. Cham: Springer. Lect. Notes Comput. Sci. 9340, 324-342 (2015). MSC: 68R07 68T27 68T30 92C50 PDFBibTeX XMLCite \textit{M. F. Arif} et al., Lect. Notes Comput. Sci. 9340, 324--342 (2015; Zbl 1471.68173) Full Text: DOI arXiv
Bernot, Gilles; Comet, Jean-Paul; Richard, Adrien; Chaves, Madalena; Gouzé, Jean-Luc; Dayan, Frédéric Modeling and analysis of gene regulatory networks. (English) Zbl 1400.92178 Cazals, Frédéric (ed.) et al., Modeling in computational biology and biomedicine. A multidisciplinary endeavor. Forewords by Olivier Faugeras and Joél Janin. Berlin: Springer (ISBN 978-3-642-31207-6/hbk; 978-3-642-31208-3/ebook). 47-80 (2013). MSC: 92C40 92C42 PDFBibTeX XMLCite \textit{G. Bernot} et al., in: Modeling in computational biology and biomedicine. A multidisciplinary endeavor. Forewords by Olivier Faugeras and Joél Janin. Berlin: Springer. 47--80 (2013; Zbl 1400.92178) Full Text: DOI
Bérenguier, D.; Chaouiya, C.; Monteiro, P. T.; Naldi, A.; Remy, E.; Thieffry, D.; Tichit, L. Dynamical modeling and analysis of large cellular regulatory networks. (English) Zbl 1331.37134 Chaos 23, No. 2, 025114, 9 p. (2013). MSC: 37N25 92C42 92C40 05C90 PDFBibTeX XMLCite \textit{D. Bérenguier} et al., Chaos 23, No. 2, 025114, 9 p. (2013; Zbl 1331.37134) Full Text: DOI
Brim, Luboš; Češka, Milan; Šafránek, David Model checking of biological systems. (English) Zbl 1380.92024 Bernardo, Marco (ed.) et al., Formal methods for dynamical systems. 13th international school on formal methods for the design of computer, communication, and software systems, SFM 2013, Bertinoro, Italy, June 17–22, 2013. Advanced lectures. Berlin: Springer (ISBN 978-3-642-38873-6/pbk). Lecture Notes in Computer Science 7938, 63-112 (2013). MSC: 92C42 68Q60 92-08 PDFBibTeX XMLCite \textit{L. Brim} et al., Lect. Notes Comput. Sci. 7938, 63--112 (2013; Zbl 1380.92024) Full Text: DOI
Cook, Byron; Fisher, Jasmin; Krepska, Elzbieta; Piterman, Nir Proving stabilization of biological systems. (English) Zbl 1318.92014 Jhala, Ranjit (ed.) et al., Verification, model checking, and abstract interpretation. 12th international conference, VMCAI 2011, Austin, TX, USA, January 23–25, 2011. Proceedings. Berlin: Springer (ISBN 978-3-642-18274-7/pbk). Lecture Notes in Computer Science 6538, 134-149 (2011). MSC: 92C42 68Q60 PDFBibTeX XMLCite \textit{B. Cook} et al., Lect. Notes Comput. Sci. 6538, 134--149 (2011; Zbl 1318.92014) Full Text: DOI
Fages, François; Soliman, Sylvain Model revision from temporal logic properties in computational systems biology. (English) Zbl 1137.68534 De Raedt, Luc (ed.) et al., Probabilistic inductive logic programming. Theory and applications. Berlin: Springer (ISBN 978-3-540-78651-1/pbk). Lecture Notes in Computer Science 4911. Lecture Notes in Artificial Intelligence, 287-304 (2008). MSC: 68T05 68N17 92C40 PDFBibTeX XMLCite \textit{F. Fages} and \textit{S. Soliman}, Lect. Notes Comput. Sci. 4911, 287--304 (2008; Zbl 1137.68534) Full Text: DOI
Antoniotti, M.; Piazza, C.; Policriti, A.; Simeoni, M.; Mishra, B. Taming the complexity of biochemical models through bisimulation and collapsing: theory and practice. (English) Zbl 1070.68059 Theor. Comput. Sci. 325, No. 1, 45-67 (2004). MSC: 68Q45 68Q85 92C40 37N25 PDFBibTeX XMLCite \textit{M. Antoniotti} et al., Theor. Comput. Sci. 325, No. 1, 45--67 (2004; Zbl 1070.68059) Full Text: DOI
Chabrier-Rivier, Nathalie; Chiaverini, Marc; Danos, Vincent; Fages, François; Schächter, Vincent Modeling and querying biomolecular interaction networks. (English) Zbl 1071.68098 Theor. Comput. Sci. 325, No. 1, 25-44 (2004). MSC: 68U20 68Q60 92C40 PDFBibTeX XMLCite \textit{N. Chabrier-Rivier} et al., Theor. Comput. Sci. 325, No. 1, 25--44 (2004; Zbl 1071.68098) Full Text: DOI