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Title:Modelling and querying biomolecular interaction networks
Authors: N Chabrier ; M Chiaverini ; Vincent Danos ; F Fages ; V Schachter
Date:Sep 2004
Publication Title:Theoretical Computer Science
Publication Type:Journal Article Publication Status:Published
Volume No:325 (1) Page Nos:25-44
DOI:10.1016/j.tcs.2004.03.063 ISBN/ISSN:0304-3975
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.
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Bibtex format
author = { N Chabrier and M Chiaverini and Vincent Danos and F Fages and V Schachter },
title = {Modelling and querying biomolecular interaction networks},
journal = {Theoretical Computer Science},
publisher = {Elsevier},
year = 2004,
month = {Sep},
volume = {325 (1)},
pages = {25-44},
doi = {10.1016/j.tcs.2004.03.063},

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