Computational Methods in Systems Biology
Temporal Reprogramming of Boolean Networks 191 Validity of the Initial Node:If the initial node is not valid as defined above, t ...
192 H. Mandon et al. To each valid nodeu∈VEorVI of the Peturbation Transition Graph, we associate a setSuof sequences of perturb ...
Temporal Reprogramming of Boolean Networks 193 initial state 1 2 3 ... ... 4 5 6 ... ... ... f∈F IFNg=2 STAT1=1 Fig. 6.Simplific ...
194 H. Mandon et al. References Abou-Jaoud ́e, W., Monteiro, P.T., Naldi, A., Grandclaudon, M., Soumelis, V., Chaouiya, C., Thi ...
Temporal Reprogramming of Boolean Networks 195 Wang, R.-S., Saadatpour, A., Albert, R.: Boolean modeling in systems biology: an ...
Detecting Toxicity Pathways with a Formal Framework Based on Equilibrium Changes Benjamin Miraglio1(B), Gilles Bernot^1 , Jean-P ...
Detecting Toxicity Pathways with a Formal Framework 197 pathway of toxicity, is widely used by regulating authorities to assess ...
198 B. Miraglio et al. can be corseted thanks to constraints expressed in an extended temporal logic. These constraints are usua ...
Detecting Toxicity Pathways with a Formal Framework 199 hormone (TRH), itself produced in the hypothalamus [ 23 ]. Both TSH and ...
200 B. Miraglio et al. TH Metabolism.TH metabolism is mainly carried out by hepatic enzymes. These enzymes are referred to as de ...
Detecting Toxicity Pathways with a Formal Framework 201 Consequently, our domain-oriented formalism represent the evolution of t ...
202 B. Miraglio et al. Definition 3 (Formula). The setFof formulason a signatureE is induc- tively defined by: any atomic formu ...
Detecting Toxicity Pathways with a Formal Framework 203 For short, we will call such rulesE-rules and we will call a “state ofR” ...
204 B. Miraglio et al. Definition 7 (Potential next level).LetRbe anE-action network, letηbe a state ofRandrbe a rule ofRof the ...
Detecting Toxicity Pathways with a Formal Framework 205 In brief, starting from a given state, it is possible to determine which ...
206 B. Miraglio et al. Definition 9 (Temporal formula).Given anE-action networkR, the setTR of temporal formulasonRis inductivel ...
Detecting Toxicity Pathways with a Formal Framework 207 Since properties filter out irrelevant paths from the transition graph, ...
208 B. Miraglio et al. The negative feedback of T4Bon TSH production mediated exclusively by D 2 (as illustrated in Fig. 1 ) is ...
Detecting Toxicity Pathways with a Formal Framework 209 through SE-LTL properties. For instance, we express the fact thatTHactiv ...
210 B. Miraglio et al. π 3 =ΔΔΔΔΔ︸ ︷︷ ︸ η 30 −D−−−−^2 destr→ΔΔΔεΔ ︸ ︷︷ ︸ η 31 −Pit−−−−destr→ΔεΔεΔ ︸ ︷︷ ︸ η 32 TSHsynth −−−−−−−→Δ ...
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