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Authors: Sohei Ito 1 ; Shigeki Hagihara 2 and Naoki Yonezaki 2

Affiliations: 1 National Fisheries University, Japan ; 2 Tokyo Institute of Technology, Japan

ISBN: 978-989-758-012-3

Keyword(s): Gene Regulatory Network, Homeostasis, Temporal Logic, Realisability.

Related Ontology Subjects/Areas/Topics: Agents ; Algorithms and Software Tools ; Artificial Intelligence ; Bioinformatics ; Biomedical Engineering ; Enterprise Information Systems ; Information Systems Analysis and Specification ; Methodologies and Technologies ; Operational Research ; Simulation ; Systems Biology

Abstract: Toward the system level understanding of the mechanisms contributing homeostasis in organisms, a computational framework to model a system and analyse its properties is indispensable. The purpose of this work is to provide a framework which enables testing and validating homeostatic properties on gene regulatory networks in silico. Based on a qualitative analysis framework for gene networks using temporal logic, we proposed a novel formulation of homeostasis by the notion of realisability. This formulation of homeostasis yields a qualitative method to analyse homeostasis of gene networks. In this formulation, homeostasis is captured by a response not for just an instantaneous stimulation such as dose-response relationships but for any input scenario e.g. oscillating or continuous inputs, which is difficult to be captured by quantitative models. Moreover, we can consider any number of inputs from an environment without difficulty. Such flexibility is a notable advantage of our framewor k. We demonstrate the usefulness of our framework in analysing a number of small but tricky networks. (More)

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Paper citation in several formats:
Ito, S.; Hagihara, S. and Yonezaki, N. (2014). A Qualitative Framework for Analysing Homeostasis in Gene Networks.In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2014) ISBN 978-989-758-012-3, pages 5-16. DOI: 10.5220/0004731400050016

@conference{bioinformatics14,
author={Sohei Ito. and Shigeki Hagihara. and Naoki Yonezaki.},
title={A Qualitative Framework for Analysing Homeostasis in Gene Networks},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2014)},
year={2014},
pages={5-16},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0004731400050016},
isbn={978-989-758-012-3},
}

TY - CONF

JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2014)
TI - A Qualitative Framework for Analysing Homeostasis in Gene Networks
SN - 978-989-758-012-3
AU - Ito, S.
AU - Hagihara, S.
AU - Yonezaki, N.
PY - 2014
SP - 5
EP - 16
DO - 10.5220/0004731400050016

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