Timed modelling of gene networks with arbitrarily precise expression discretization

S. Van Goethem, J. M. Jacquet, L. Brim, D. Šafránek

Research output: Contribution to journalArticle

Abstract

In this paper, a novel approach to discrete modeling of gene regulatory networks is presented. The approach is based on timed automata and is new in: (i) reflecting discrete abstraction of gene expression with arbitrary granularity, (ii) combining boolean logic with approximation of Hill kinetics. This is achieved by introducing delays that change dynamically with respect to current activity levels of regulating genes. The approach is implemented in UPPAAL and evaluated on benchmark models and on a biological case study.

Original languageEnglish
Pages (from-to)67-81
Number of pages15
JournalElectronic Notes in Theoretical Computer Science
Volume293
DOIs
Publication statusPublished - 11 Mar 2013

Fingerprint

Gene Networks
Genes
Discretization
Timed Automata
Gene Regulatory Network
Granularity
Modeling
Gene expression
Gene Expression
Kinetics
Logic
Benchmark
Gene
Arbitrary
Approximation
Model
Abstraction

Keywords

  • Boolean logic
  • Discrete modeling
  • gene regulatory network
  • UPAAL

Cite this

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Timed modelling of gene networks with arbitrarily precise expression discretization. / Van Goethem, S.; Jacquet, J. M.; Brim, L.; Šafránek, D.

In: Electronic Notes in Theoretical Computer Science, Vol. 293, 11.03.2013, p. 67-81.

Research output: Contribution to journalArticle

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