title: Inference of Vohradský's models of genetic networks by solving two-dimensional function optimization problems.
abstract: The inference of a genetic network is a problem in which mutual interactions among genes are inferred from time-series of gene expression levels. While a number of models have been proposed to describe genetic networks, this study focuses on a mathematical model proposed by Vohradský. Because of its advantageous features, several researchers have proposed the inference methods based on Vohradský's model. When trying to analyze large-scale networks consisting of dozens of genes, however, these methods must solve high-dimensional non-linear function optimization problems. In order to resolve the difficulty of estimating the parameters of the Vohradský's model, this study proposes a new method that defines the problem as several two-dimensional function optimization problems. Through numerical experiments on artificial genetic network inference problems, we showed that, although the computation time of the proposed method is not the shortest, the method has the ability to estimate parameters of Vohradský's models more effectively with sufficiently short computation times. This study then applied the proposed method to an actual inference problem of the bacterial SOS DNA repair system, and succeeded in finding several reasonable regulations.
authors.affiliation: Graduate School of Engineering, Tottori University, Tottori, Japan.
authors.forename: Shuhei
authors.initials: S
authors.lastname: Kimura
authors.affiliation: National Institute for Basic Biology, Okazaki Institute for Integrative Bioscience, National Institute for Natural Sciences, Okazaki, Japan.
authors.forename: Masanao
authors.initials: M
authors.lastname: Sato
authors.affiliation: RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
authors.forename: Mariko
authors.initials: M
authors.lastname: Okada-Hatakeyama
mesh_terms: D000465:Algorithms; D004269:DNA, Bacterial; D004926:Escherichia coli / Q000235:genetics; D053263:Gene Regulatory Networks; D008957:Models, Genetic; D008962:Models, Theoretical; D015203:Reproducibility of Results; D013014:SOS Response, Genetics
chemical_list: D004269:DNA, Bacterial