Modeling logic gene networks by means of probabilistic dynamic P systems

Luis Valencia-Cabrera, Manuel García-Quismondo, Mario J. Pérez-Jiménez, Yansen Su, Hui Yu, Linqiang Pan

Research output: Contribution to journalArticle

4 Scopus citations

Abstract

Gene regulatory networks are useful models for biologists to understand the interactions among genes in living organisms. In this work, we consider a special class of gene regulatory networks, called logical networks, where the "links" among genes are inferred by logic analysis of phylogenetic profiles. We provide a formalization of logic networks, and introduce a membrane computing model for reconstructing logical networks and reproducing their dynamics. An example logical network is simulated by using software P-Lingua and MeCoSim. The simulation result shows that membrane computing is a versatile framework for modeling different biological scenarios.

Original languageEnglish (US)
Pages (from-to)445-464
Number of pages20
JournalInternational Journal of Unconventional Computing
Volume9
Issue number5-6 SPEC. ISSUE
StatePublished - Oct 10 2013

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Keywords

  • Gene
  • Genetic network
  • Logic network
  • Membrane computing
  • P system
  • System biology

Cite this

Valencia-Cabrera, L., García-Quismondo, M., Pérez-Jiménez, M. J., Su, Y., Yu, H., & Pan, L. (2013). Modeling logic gene networks by means of probabilistic dynamic P systems. International Journal of Unconventional Computing, 9(5-6 SPEC. ISSUE), 445-464.