Computational Methods in Systems Biology
A Stochastic Model for the Formation of Spatial Methylation Patterns 171 AL 0 0.2 0.4 0.6 0.8 1 N 0 10 20 30 40 50 60 Dnmt1KODnm ...
172 A. L ̈uck et al. of patterns 0 and 64 (which corresponds to no methylation/full methylation of all sites) in L1 and pattern ...
A Stochastic Model for the Formation of Spatial Methylation Patterns 173 Index of pattern Z 0 102030405060 P(Z) 0 0.1 0.2 0.3 0. ...
174 A. L ̈uck et al. Index of pattern Z 0 102030405060 P(Z) 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1 Wild-typePrediction (^0) 0 1 ...
A Stochastic Model for the Formation of Spatial Methylation Patterns 175 Index of pattern Z 0 102030405060 P(Z) 0 0.1 0.2 0.3 0. ...
176 A. L ̈uck et al. the states of neighboring sites to the left and right [ 14 ]. When these models were tested on double-stran ...
A Stochastic Model for the Formation of Spatial Methylation Patterns 177 References 1.Aij ̈ ̈ o, T., Huang, Y., Mannerstr ̈om, H ...
178 A. L ̈uck et al. Norvil, A.B., Petell, C.J., Alabdi, L., Wu, L., Rossie, S., Gowher, H.: Dnmt3b methylates DNA by a noncoop ...
Temporal Reprogramming of Boolean Networks Hugues Mandon1,2(B), Stefan Haar^1 , and Lo ̈ıc Paulev ́e^2 (^1) LSV, ENS Cachan, INR ...
180 H. Mandon et al. The attractors, or long term dynamics, of qualitative models typically corre- spond to differentiated and s ...
Temporal Reprogramming of Boolean Networks 181 ming, Sect. 4 establishes the identification of temporal reprogramming strate- gi ...
182 H. Mandon et al. 2.2 Cell Reprogramming: The Advantage of Temporal Perturbations Let us consider the following Boolean Netwo ...
Temporal Reprogramming of Boolean Networks 183 Inevitable and existential reprogramming.Thus, this example shows that some attra ...
184 H. Mandon et al. define specific coupled transitions (the simultaneous change of value of several components) to model the c ...
Temporal Reprogramming of Boolean Networks 185 for each clausec∈DNF[¬xi∧fi(x)], there is a transitionti,c∈Tfwith Afsuch that•ti ...
186 H. Mandon et al. Temporary Perturbations.In addition to the places for the BN node values, we addkmutually exclusive places ...
Temporal Reprogramming of Boolean Networks 187 c 1 tc1 c 2 p 0 p 1 t 1 , 1 (^11) (^10) t 2 , 0 (^2120) t 3 , 0 (^31) (^30) (^31) ...
188 H. Mandon et al. M 0 ={ixi|i∈[n]}∪{p 0 ,c 1 } where(Pf,Tf,Af,M 0 ′)=PN(f). Example 3.Figure 4 (bottom) shows part of the t ...
Temporal Reprogramming of Boolean Networks 189 label specifying the performed perturbation. Each node of the original transition ...
190 H. Mandon et al. reachable from(s 0 ,i 0 )usingEandMtransitions, there exists a path from(s, i) to a state inFusingEandMtran ...
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