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doi:10.1016/j.tcs.2004.03.063 
Copyright © 2004 Published by Elsevier B.V.
Modeling and querying biomolecular interaction networks
Nathalie Chabrier-Riviera, Marc Chiaverinib, Vincent Danosc, François Fagesd and Vincent Schächter
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Available online 22 April 2004.
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Abstract
We introduce a formalism to represent and analyze protein–protein and protein–DNA interaction networks. We illustrate the expressivity of this language, by proposing a formal counterpart of Kohn's compilation on the mammalian cell-cycle control. This effectively turns an otherwise static knowledge into a discrete transition system incorporating a qualitative description of the dynamics. We then propose to use the computation tree logic (CTL) as a query language for querying the possible behaviors of the system. We provide examples of biologically relevant queries expressed in CTL about the mammalian cell-cycle control and show the effectiveness of symbolic model checking tools to evaluate CTL queries in this context.
