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Minimal intervention strategies in logical signaling networks with ASP

Published online by Cambridge University Press:  25 September 2013

University of Potsdam
University of Potsdam
CNRS - IRISA, Rennes INRIA - Dyliss, Rennes
CNRS - IRISA, Rennes INRIA - Dyliss, Rennes University of Potsdam


Proposing relevant perturbations to biological signaling networks is central to many problems in biology and medicine because it allows for enabling or disabling certain biological outcomes. In contrast to quantitative methods that permit fine-grained (kinetic) analysis, qualitative approaches allow for addressing large-scale networks. This is accomplished by more abstract representations such as logical networks. We elaborate upon such a qualitative approach aiming at the computation of minimal interventions in logical signaling networks relying on Kleene's three-valued logic and fixpoint semantics. We address this problem within answer set programming and show that it greatly outperforms previous work using dedicated algorithms.

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