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Modern tools for the time-discrete dynamics and optimization of gene-environment networks

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dc.contributor.author Defterli, Özlem
dc.contributor.author Fügenschuh, Armin
dc.contributor.author Weber, Gerhard Wilhelm
dc.date.accessioned 2016-08-12T08:24:21Z
dc.date.available 2016-08-12T08:24:21Z
dc.date.issued 2011-12
dc.identifier.citation Defterli, Ö., Fügenschuh, A., Weber, G.W. (2011). Modern tools for the time-discrete dynamics and optimization of gene-environment networks. Communications In Nonlinear Science And Numerical Simulation, 16(12), 4768-4779. http://dx.doi.org/10.1016/j.cnsns.2011.03.003 tr_TR
dc.identifier.issn 1007-5704
dc.identifier.uri http://hdl.handle.net/20.500.12416/1230
dc.description.abstract In this study, we discuss the models of genetic regulatory systems, so-called gene-environment networks. The dynamics of such kind of systems are described by a class of time-continuous ordinary differential equations having a general form (E) over dot = M(E)E, where E is a vector of gene-expression levels and environmental factors and M(E) is the matrix having functional entries containing unknown parameters to be optimized. Accordingly, time-discrete versions of that model class are studied and improved by introducing 3rd-order Heun's method and 4th-order classical Runge-Kutta method. The corresponding iteration formulas are derived and their matrix algebras are obtained. After that, we use nonlinear mixed-integer programming for the parameter estimation in the considered model and present the solution of a constrained and regularized given mixed-integer problem as an example. By using this solution and applying both the new and existing discretization schemes, we generate corresponding time-series of gene-expressions for each method. The comparison of the experimental data and the calculated approximate results is additionally done with the help of the figures to exercise the performance of the numerical schemes on this example tr_TR
dc.language.iso eng tr_TR
dc.publisher Elsevier Science Bv tr_TR
dc.relation.isversionof 10.1016/j.cnsns.2011.03.003 tr_TR
dc.rights info:eu-repo/semantics/closedAccess
dc.subject Gene-networks tr_TR
dc.subject Regulatory Systems tr_TR
dc.subject Dynamical Systems tr_TR
dc.subject Discretization tr_TR
dc.subject Mixed-integer Nonlinear Programming tr_TR
dc.title Modern tools for the time-discrete dynamics and optimization of gene-environment networks tr_TR
dc.type article tr_TR
dc.relation.journal Communications In Nonlinear Science And Numerical Simulation tr_TR
dc.contributor.authorID 31401 tr_TR
dc.identifier.volume 16 tr_TR
dc.identifier.issue 12 tr_TR
dc.identifier.startpage 4768 tr_TR
dc.identifier.endpage 4779 tr_TR
dc.contributor.department Çankaya Üniversitesi, Fen Edebiyat Fakültesi, Matematik Bilgisayar Bölümü tr_TR


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