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Modular analysis of gene networks by linear temporal logic

Ito, Sohei ; Ichinose, Takuma ; Shimakawa, Masaya ; Izumi, Naoko ; Hagihara, Shigeki ; Yonezaki, Naoki

Journal of Integrative Bioinformatics - JIB (ISSN 1613-4516)


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Abstract:
Despite a lot of advances in biology and genomics, it is still difficult to utilise such valuable knowledge and information to understand and analyse large biological systems due to high computational complexity. In this paper we propose a modular method with which from several small network analyses we analyse a large network by integrating them. This method is based on the qualitative framework proposed by authors in which an analysis of gene networks is reduced to checking satisfiability of linear temporal logic formulae. The problem of linear temporal logic satisfiability checking needs exponential time in the size of a formula. Thus it is difficult to analyse large networks directly in this method since the size of a formula grows linearly to the size of a network. The modular method alleviates this computational difficulty. We show some experimental results and see how we benefit from the modular analysis method.


Institution: Faculty of Technology, Research Groups in Informatics
DDC classification: Data processing, computer science, computer systems

Suggested Citation:
Ito, Sohei ; Ichinose, Takuma ; Shimakawa, Masaya ; Izumi, Naoko ; Hagihara, Shigeki ; Yonezaki, Naoki  (2013)  Modular analysis of gene networks by linear temporal logic. Journal of Integrative Bioinformatics - JIB (ISSN 1613-4516), 10(2), 2013

Online-Journal: http://journal.imbio.de/article.php?aid=216
URL: http://biecoll.ub.uni-bielefeld.de/volltexte/2013/5262



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