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Keywords
(9)
Differential Equation
Genetic Network
Genetic Regulatory Network
Inequality Constraint
Mathematical Biology
Measurement Technique
piecewise linear
Qualitative Modeling
Simulation Methods
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Qualitative simulation of genetic regulatory networks using piecewiselinear models
Qualitative simulation of genetic regulatory networks using piecewiselinear models,H. De Jong,J. L. Gouz'e,C. Hernandez,M. Page,T. Sari,J. Geiselman
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Qualitative simulation of genetic regulatory networks using piecewiselinear models
(
Citations: 52
)
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H. De Jong
,
J. L. Gouz'e
,
C. Hernandez
,
M. Page
,
T. Sari
,
J. Geiselmann
Abstract In order to cope with the large amounts of data that have become,available in genomics, mathematical tools for the analysis of networks of interactions between genes, proteins, and other molecules are indispensable. We present a method for the qualitative simulation of genetic regulatory networks, based on a class of piecewiselinear (PL) differential equations that has been wellstudied in mathematical biology. The simulation method,is welladapted to stateoftheart measurement techniques in genomics, which often provide qualitative and coarsegrained descriptions of genetic regulatory networks. Given a qualitative model of a genetic regulatory network, consisting of a system of PL differential equations and inequality constraints on the parameter values, the method produces a graph of qualitative states and transitions between qualitative states, summarizing the qualitative dynamics of the system. The qualitative simulation method has been implemented in Java in the computer tool
Genetic Network
Analyzer.
Published in 2004.
Cumulative
Annual
Citation Context
(2)
...Pioneering work towards automated qualitative analysis and simulation of GRNs has resulted in a computational tool, called GNA[
9
]...
...In the case D Œ Δr, like in traditional QR methods and in GNA[
9
], possible transitions are determined by the signs of & xi .A s &i are defined by linear expressions, such signs are easily determined by exploiting the inequalities that define the parameter space domain...
Liliana Ironi
,
et al.
A computational framework for qualitative simulation of nonlinear dyna...
...A first effort in this direction is given by a qualitative simulator, called GNA [
4
]...
...State Transitions. The possible transitions from D are determined by different strategies according to whether D ∈ ΔR or D ∈ ΔS. In the former case, like in traditional QR methods and in GNA [
4
], transitions are determined by the signs of ˙ xi .A s˙ xi are defined by linear expressions, such signs are easily determined by exploiting the inequalities that define the parameter space domain, and constrain the RSPs to belong to specific ...
Liliana Ironi
,
et al.
An Algorithm for Qualitative Simulation of Gene Regulatory Networks wi...
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