References

  1. Samy Abbes & Albert Benveniste (2006): Probabilistic models for true-concurrency: branching cells and distributed probabilities for event structures. Information and Computation 204(2), pp. 231–274, doi:10.1016/j.ic.2005.10.001.
  2. Laurence Calzone, Laurent Tournier, Simon Fourquet, Denis Thieffry, Boris Zhivotovsky, Emmanuel Barillot & Andrei Zinovyev (2010): Mathematical Modelling of Cell-Fate Decision in Response to Death Receptor Engagement. PLOS Computational Biology 6(3), pp. e1000702, doi:10.1371/journal.pcbi.1000702.
  3. Thomas Chatain, Stefan Haar, Loïg Jezequel, Loïc Paulevé & Stefan Schwoon (2014): Characterization of Reachable Attractors Using Petri Net Unfoldings. In: Pedro Mendes: Proceedings of the 12th Conference on Computational Methods in System Biology (CMSB'14), Lecture Notes in Bioinformatics 8859. Springer-Verlag, Manchester, UK, pp. 129–142, doi:10.1007/978-3-319-12982-2_10.
  4. Thomas Chatain, Stefan Haar, Juraj Kolcák, Loïc Paulevé & Aalok Thakkar (2020): Concurrency in Boolean networks. Nat. Comput. 19(1), pp. 91–109, doi:10.1007/s11047-019-09748-4.
  5. David P. A. Cohen, Loredana Martignetti, Sylvie Robine, Emmanuel Barillot, Andrei Zinovyev & Laurence Calzone (2015): Mathematical Modelling of Molecular Pathways Enabling Tumour Cell Invasion and Migration. PLoS Comput Biol 11(11), pp. e1004571, doi:10.1371/journal.pcbi.1004571.
  6. J. Esparza & K. Heljanko (2008): Unfoldings – A Partial-Order Approach to Model Checking. Springer. ISBN: 978-3-540-77426-6.
  7. J. Esparza, S. Römer & W. Vogler (2002): An Improvement of McMillan's Unfolding Algorithm. FMSD 20, pp. 285–310, doi:10.1023/A:1014746130920.
  8. Louis Fippo Fitime, Olivier Roux, Carito Guziolowski & Loïc Paulevé (2017): Identification of bifurcation transitions in biological regulatory networks using Answer-Set Programming. Algorithms for Molecular Biology 12(1), pp. 19, doi:10.1186/s13015-017-0110-3.
  9. Martin Gebser, Roland Kaminski, Benjamin Kaufmann & Torsten Schaub (2014): Clingo = ASP + Control: Preliminary Report. CoRR abs/1405.3694, doi:10.48550/arXiv.1405.3694.
  10. A. Giua & X. Xie (2005): Control of safe ordinary Petri nets using unfolding. Discrete Event Dynamic Systems 15(4), pp. 349–373, doi:10.1007/s10626-005-4057-z.
  11. Stefan Haar, Loïc Paulevé & Stefan Schwoon (2020): Drawing the Line: Basin Boundaries in Safe Petri Nets. In: Alessandro Abate, Tatjana Petrov & Verena Wolf: Proc.18th Conf. on Computational Methods in System Biology (CMSB'20), Lecture Notes in Bioinformatics 12314. Springer, pp. 321–336, doi:10.1007/978-3-030-60327-4_17.
  12. Stefan Haar, César Rodríguez & Stefan Schwoon (2013): Reveal Your Faults: It's Only Fair!. In: Marta Pietkiewicz-Koutny & Mihai Teodor Lazarescu: Proc. 13th Int. Conf. on Application of Concurrency to System Design (ACSD'13). IEEE Computer Society Press, Barcelona, Spain, pp. 120–129, doi:10.1109/ACSD.2013.15.
  13. Marian V. Iordache & Panos J. Antsaklis (2006): Supervisory Control of Concurrent Systems: A Petri Net Structural Approach. Birkhäuser, Boston, Basel, Berlin.
  14. H. Klarner, H. Siebert, S. Nee & F. Heinitz (2018): Basins of Attraction, Commitment Sets and Phenotypes of Boolean Networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics, doi:10.1109/TCBB.2018.2879097.
  15. K. L. McMillan (1992): Using Unfoldings to Avoid the State Explosion Problem in the Verification of Asynchronous Circuits. In: CAV, pp. 164–177, doi:10.1007/3-540-56496-9_14.
  16. Nuno D. Mendes, Rui Henriques, Elisabeth Remy, Jorge Carneiro, Pedro T. Monteiro & Claudine Chaouiya (2018): Estimating Attractor Reachability in Asynchronous Logical Models. Frontiers in Physiology 9, doi:10.3389/fphys.2018.01161.
  17. T. Murata (1989): Petri nets: Properties, analysis and applications. Proc. of the IEEE 77(4), pp. 541–580, doi:10.1109/5.24143.
  18. M. Nielsen, G. D. Plotkin & G. Winskel (1979): Petri Nets, Event Structures and Domains. In: SCC, pp. 266–284, doi:10.1016/0304-3975(81)90112-2.
  19. David A. Orlando, Charles Y. Lin, Allister Bernard, Jean Y. Wang, Joshua E. S. Socolar, Edwin S. Iversen, Alexander J. Hartemink & Steven B. Haase (2008): Global control of cell-cycle transcription by coupled CDK and network oscillators. Nature 453(7197), pp. 944–947, doi:10.1038/nature06955.
  20. Ertugrul M. Ozbudak, Mukund Thattai, Han N. Lim, Boris I. Shraiman & Alexander van Oudenaarden (2004): Multistability in the lactose utilization network of Escherichia coli. Nature 427(6976), pp. 737–740, doi:10.1038/nature02298.
  21. Loïc Paulevé: Implementation of the search for minimal doomed configurations.. Available at https://gitub.u-bordeaux.fr/lpauleve/doomed-configurations.
  22. Loïc Paulevé (2017): Pint: a static analyzer for transient dynamics of qualitative networks with IPython interface. In: CMSB 2017 - 15th conference on Computational Methods for Systems Biology, Lecture Notes in Computer Science 10545. Springer International Publishing, pp. 309–316, doi:10.1007/978-3-319-67471-1_20.
  23. Alexander N. Pisarchik & Ulrike Feudel (2014): Control of multistability. Physics Reports 540(4), pp. 167–218, doi:10.1016/j.physrep.2014.02.007.
  24. Erik Plahte, Thomas Mestl & Stig W. Omholt (1995): Feedback Loops, Stability and Multistationarity in Dynamical Systems. J. Biol. Syst. 03(02), pp. 409–413, doi:10.1142/s0218339095000381.
  25. Franck Pommereau, Colin Thomas & Cédric Gaucherel (2022): Petri Nets Semantics of Reaction Rules (RR), a Language for Ecosystems Modelling. In: Proc. 43rd Int. Conf. on Application and Theory of Petri Nets and Concurrency, Bergen, Norway, pp. 1–20, doi:10.1007/978-3-031-06653-5_10.
  26. Adrien Richard (2019): Positive and negative cycles in Boolean networks. Journal of Theoretical Biology 463, pp. 67–76, doi:10.1016/j.jtbi.2018.11.028.
  27. S. Schwoon (2014): The Mole Tool. URL: http://www.lsv.ens-cachan.fr/~schwoon/tools/mole/.
  28. Denis Thieffry & RenĂ© Thomas (1995): Dynamical behaviour of biological regulatory networks—II. Immunity control in bacteriophage lambda. Bulletin of Mathematical Biology 57, pp. 277–297, doi:10.1007/BF02460619.
  29. R. Thomas (1980): On the relation between the logical structure of systems and their ability to generate multiple steady states or sustained oscillations. Springer Series in Synergies 9, pp. 180–193, doi:10.1007/978-3-642-81703-8_24.
  30. René Thomas & Richard d'Ari (1990): Biological Feedback. CRC Press, Boca Raton, Florida, USA.
Comments and questions to: eptcs@eptcs.org
For website issues: webmaster@eptcs.org