Boolean Network Identification from Multiplex Time Series Data

Max Ostrowski 1 Loïc Paulevé 2 Torsten Schaub 1 Anne Siegel 3 Carito Guziolowski 4
1 Institut für informatik [Potsdam]
2 LRI - Laboratoire de Recherche en Informatique
3 Dyliss - Dynamics, Logics and Inference for biological Systems and Sequences
Inria Rennes – Bretagne Atlantique , IRISA-D7 - GESTION DES DONNÉES ET DE LA CONNAISSANCE
4 IRCCyN - Institut de Recherche en Communications et en Cybernétique de Nantes
Abstract : Boolean networks (and more general logic models) are useful frameworks to study signal transduction across multiple pathways. Logical models can be learned from a prior knowledge network structure and multiplex phosphoproteomics data. However, most efficient and scal-able training methods focus on the comparison of two time-points and assume that the system has reached an early steady state. In this paper, we generalize such a learning procedure to take into account the time series traces of phosphoproteomics data in order to discriminate Boolean networks according to their transient dynamics. To that goal, we exhibit a necessary condition that must be satisfied by a Boolean network dynamics to be consistent with a discretized time series trace. Based on this condition, we use a declarative programming approach (Answer Set Programming) to compute an over-approximation of the set of Boolean networks which fit best with experimental data. Combined with model-checking approaches, we end up with a global learning algorithm and compare it to learning approaches based on static data.
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Communication dans un congrès
Olivier Roux; Jérémie Bourdon. CMSB 2015 - 13th conference on Computational Methods for Systems Biology, Sep 2015, Nantes, France. Springer International Publishing, 9308, pp.170-181, Lecture Notes in Computer Science. 〈http://cmsb2015.sciencesconf.org/〉. 〈10.1007/978-3-319-23401-4_15〉
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Max Ostrowski, Loïc Paulevé, Torsten Schaub, Anne Siegel, Carito Guziolowski. Boolean Network Identification from Multiplex Time Series Data. Olivier Roux; Jérémie Bourdon. CMSB 2015 - 13th conference on Computational Methods for Systems Biology, Sep 2015, Nantes, France. Springer International Publishing, 9308, pp.170-181, Lecture Notes in Computer Science. 〈http://cmsb2015.sciencesconf.org/〉. 〈10.1007/978-3-319-23401-4_15〉. 〈hal-01164751〉

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