Article (Scientific journals)
An approach for dividing models of biological reaction networks into functional units
Ederer, Michael; Sauter, Thomas; Bullinger, Eric et al.
2003In Simulation, 79 (12), p. 703-716
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Abstract :
[en] Biological reaction networks consist of many substances and reactions between them. Like many other biological systems, they have a modular structure. Therefore, a division of a biological reaction network into smaller units highly facilitates its investigation. The authors propose an algorithm to divide an ordinary differential equation (ODE) model of a biological reaction network hierarchically into functional units. For every compound, an activity function dependent on concentration or concentration change rate is defined. After performing suitable simulations, distances between the compounds are computed by comparing the activities along the trajectories of the simulation. The distance information is used to generate a dendrogram revealing the internal structure of the reaction network. The algorithm identifies functional units in two models of different networks: catabolite repression in Escherichia coli and epidermal growth factor (EGF) signal transduction in mammalian cells.
Disciplines :
Engineering, computing & technology: Multidisciplinary, general & others
Author, co-author :
Ederer, Michael
Sauter, Thomas
Bullinger, Eric ;  Université de Liège - ULiège > Dép. d'électric., électron. et informat. (Inst.Montefiore) > Méthodes computationnelles pour la biologie systémique
Gilles, E. D.
Allgöwer, Frank
Language :
English
Title :
An approach for dividing models of biological reaction networks into functional units
Publication date :
2003
Journal title :
Simulation
ISSN :
0037-5497
eISSN :
1741-3133
Publisher :
SAGE Publications, New York, United States - New York
Volume :
79
Issue :
12
Pages :
703-716
Peer reviewed :
Peer Reviewed verified by ORBi
Available on ORBi :
since 22 June 2009

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