Modeling and querying biomolecular interaction networks

Nathalie Chabrier-Rivier, Marc Chiaverini, Vincent Danos, François Fages, Vincent Schächter

Research output: Contribution to journalArticlepeer-review

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.
Original languageEnglish
Pages (from-to)25 - 44
Number of pages20
JournalTheoretical Computer Science
Volume325
Issue number1
DOIs
Publication statusPublished - Sep 2004

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