title: The effective application of a discrete transition model to explore cell-cycle regulation in yeast.
abstract: BACKGROUND
  Bench biologists often do not take part in the development of computational models for their systems, and therefore, they frequently employ them as "black-boxes". Our aim was to construct and test a model that does not depend on the availability of quantitative data, and can be directly used without a need for intensive computational background.
  
  
  RESULTS
  We present a discrete transition model. We used cell-cycle in budding yeast as a paradigm for a complex network, demonstrating phenomena such as sequential protein expression and activity, and cell-cycle oscillation. The structure of the network was validated by its response to computational perturbations such as mutations, and its response to mating-pheromone or nitrogen depletion. The model has a strong predicative capability, demonstrating how the activity of a specific transcription factor, Hcm1, is regulated, and what determines commitment of cells to enter and complete the cell-cycle.
  
  
  CONCLUSIONS
  The model presented herein is intuitive, yet is expressive enough to elucidate the intrinsic structure and qualitative behavior of large and complex regulatory networks. Moreover our model allowed us to examine multiple hypotheses in a simple and intuitive manner, giving rise to testable predictions. This methodology can be easily integrated as a useful approach for the study of networks, enriching experimental biology with computational insights.
authors.affiliation: School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel.
authors.forename: Amir
authors.initials: A
authors.lastname: Rubinstein
authors.forename: Ofir
authors.initials: O
authors.lastname: Hazan
authors.forename: Benny
authors.initials: B
authors.lastname: Chor
authors.forename: Ron Y
authors.initials: RY
authors.lastname: Pinter
authors.forename: Yona
authors.initials: Y
authors.lastname: Kassir
mesh_terms: D002453:Cell Cycle; D008954:Models, Biological; D012441:Saccharomyces cerevisiae / Q000166:cytology*
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