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Authors: Annika Eichler 1 and Gerwald Lichtenberg 2

Affiliations: 1 ETH Zurich, Switzerland ; 2 Hamburg University of Applied Sciences, Germany

Keyword(s): Parameter Identification, Networks, Gene Dynamics, Systems Biology, Boolean Functions, Ternary Logic.

Related Ontology Subjects/Areas/Topics: Dynamical Systems Models and Methods ; Formal Methods ; Simulation and Modeling

Abstract: In gene dynamics modeling, parameters of Boolean networks are identified from continuous data under various assumptions expressed by logical constraints. These constraints may restrict the dynamics of the network to the subclass of canalyzing functions, which are known to be appropriate for genetic networks. This paper introduces a high performance algorithm, which solves the parameter identification problem by so called Zhegalkin identification and exploits the restriction to canalyzing functions resulting in reduced calculation time. The canalyzing constraint is formulated in terms of orthogonal ternary vector lists - which are intrinsically used in a Branch-and-Cut algorithm obeying this constraint. The algorithm is applied to mRNA micro array data from mice under different contaminant conditions and good correspondence to a known apoptotic pathway can be shown.

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Paper citation in several formats:
Eichler, A. and Lichtenberg, G. (2016). Parameter Identification of Canalyzing Boolean Functions with Ternary Vectors for Gene Networks. In Proceedings of the 6th International Conference on Simulation and Modeling Methodologies, Technologies and Applications - SIMULTECH; ISBN 978-989-758-199-1; ISSN 2184-2841, SciTePress, pages 110-118. DOI: 10.5220/0005978701100118

@conference{simultech16,
author={Annika Eichler. and Gerwald Lichtenberg.},
title={Parameter Identification of Canalyzing Boolean Functions with Ternary Vectors for Gene Networks},
booktitle={Proceedings of the 6th International Conference on Simulation and Modeling Methodologies, Technologies and Applications - SIMULTECH},
year={2016},
pages={110-118},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0005978701100118},
isbn={978-989-758-199-1},
issn={2184-2841},
}

TY - CONF

JO - Proceedings of the 6th International Conference on Simulation and Modeling Methodologies, Technologies and Applications - SIMULTECH
TI - Parameter Identification of Canalyzing Boolean Functions with Ternary Vectors for Gene Networks
SN - 978-989-758-199-1
IS - 2184-2841
AU - Eichler, A.
AU - Lichtenberg, G.
PY - 2016
SP - 110
EP - 118
DO - 10.5220/0005978701100118
PB - SciTePress

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