248 R. Schwieger and H. Siebert
- De Jong, H., Gouz ́e, J.-L., Hernandez, C., Page, M., Sari, T., Geiselmann, J.:
Qualitative simulation of genetic regulatory networks using piecewise-linear mod-
els. Bull. Math. Biol. 66 (2), 301–340 (2004) - De Jong, H., Page, M., Hernandez, C., Geiselmann, J.: Qualitative simulation of
genetic regulatory networks: method and application. In: IJCAI, pp. 67–73 (2001) - Eisenack, K.: Model ensembles for natural resource management: extensions of
qualitative differential equations using graph theory and viability theory. Unpub-
lished doctoral thesis, Free University Berlin, Germany (2006). Accessed 3 Feb
2008 - John, M., Nebut, M., Niehren, J.: Knockout prediction for reaction networks with
partial kinetic information. In: Giacobazzi, R., Berdine, J., Mastroeni, I. (eds.)
VMCAI 2013. LNCS, vol. 7737, pp. 355–374. Springer, Heidelberg (2013). doi:10.
1007/978-3-642-35873-9 22 - Kein ̈anen, M.: Techniques for solving Boolean equation systems. Ph.D. thesis,
Helsinki University of Technology (2006) - Klarner, H., Streck, A., Siebert, H.: PyBoolNet-a python package for the genera-
tion, analysis and visualisation of boolean networks. Bioinformatics 33 , 770–772
(2016) - Melliti, T., Regnault, D., Richard, A., Sen ́e, S.: Asynchronous simulation of boolean
networks by monotone boolean networks. In: El Yacoubi, S., Was, J., Bandini, S.↪
(eds.) ACRI 2016. LNCS, vol. 9863, pp. 182–191. Springer, Cham (2016). doi:10.
1007/978-3-319-44365-2 18 - Remy,E., Ruet, P., Thieffry, D.: Graphic requirements for multistability and ́
attractive cycles in a boolean dynamical framework. Adv. Appl. Math. 41 (3), 335–
350 (2008) - Streck, A., Thobe, K., Siebert, H.: Data-driven optimizations for model checking
of multi-valued regulatory networks. Biosystems 149 , 125–138 (2016) - Thomas, R.: On the relation between the logical structure of systems and their
ability to generate multiple steady states or sustained oscillations. In: Della, D.J.,
Demongeot, J., Lacolle, B. (eds.) Numerical Methods in the Study of Critical
Phenomena, pp. 180–193. Springer, Heidelberg (1981) - Thomas, R., Kaufman, M.: Multistationarity, the basis of cell differentiation and
memory. I. Structural conditions of multistationarity and other nontrivial behavior.
Chaos 11 (1), 170–179 (2001) - Thomas, R., Kaufman, M.: Multistationarity, the basis of cell differentiation and
memory. II. Logical analysis of regulatory networks in terms of feedback circuits.
Chaos Interdiscip. J. Nonlinear Sci. 11 (1), 180–195 (2001) - Videla, S., Saez-Rodriguez, J., Guziolowski, C., Siegel, A.: caspo: a toolbox for
automated reasoning on the response of logical signaling networks families. Bioin-
formatics 33 , 947–950 (2017) - Wittmann, D.M., Krumsiek, J., Saez-Rodriguez, J., Lauffenburger, D.A., Klamt,
S., Theis, F.J.: Transforming boolean models to continuous models: methodology
and application to T-cell receptor signaling. BMC Syst. Biol. 3 (1), 98 (2009)