title: Inference of S-system models of genetic networks using a cooperative coevolutionary algorithm.
abstract: BACKGROUND
  To resolve the high-dimensionality of the genetic network inference problem in the S-system model, a problem decomposition strategy has been proposed. While this strategy certainly shows promise, it cannot provide a model readily applicable to the computational simulation of the genetic network when the given time-series data contain measurement noise. This is a significant limitation of the problem decomposition, given that our analysis and understanding of the genetic network depend on the computational simulation.
  
  
  RESULTS
  We propose a new method for inferring S-system models of large-scale genetic networks. The proposed method is based on the problem decomposition strategy and a cooperative coevolutionary algorithm. As the subproblems divided by the problem decomposition strategy are solved simultaneously using the cooperative coevolutionary algorithm, the proposed method can be used to infer any S-system model ready for computational simulation. To verify the effectiveness of the proposed method, we apply it to two artificial genetic network inference problems. Finally, the proposed method is used to analyze the actual DNA microarray data.
authors.affiliation: Bioinformatics Group, RIKEN Genomic Sciences Center 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan. skimura@gsc.riken.jp
authors.forename: Shuhei
authors.initials: S
authors.lastname: Kimura
authors.forename: Kaori
authors.initials: K
authors.lastname: Ide
authors.forename: Aiko
authors.initials: A
authors.lastname: Kashihara
authors.forename: Makoto
authors.initials: M
authors.lastname: Kano
authors.forename: Mariko
authors.initials: M
authors.lastname: Hatakeyama
authors.forename: Ryoji
authors.initials: R
authors.lastname: Masui
authors.forename: Noriko
authors.initials: N
authors.lastname: Nakagawa
authors.forename: Shigeyuki
authors.initials: S
authors.lastname: Yokoyama
authors.forename: Seiki
authors.initials: S
authors.lastname: Kuramitsu
authors.forename: Akihiko
authors.initials: A
authors.lastname: Konagaya
mesh_terms: D000465:Algorithms; D001185:Artificial Intelligence; D019143:Evolution, Molecular; D020869:Gene Expression Profiling / Q000379:methods*; D005786:Gene Expression Regulation / Q000502:physiology*; D008957:Models, Genetic; D015233:Models, Statistical; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015398:Signal Transduction / Q000502:physiology*; D012984:Software; D014157:Transcription Factors / Q000502:physiology*
chemical_list: D014157:Transcription Factors