title: A Bayesian approach to targeted experiment design.
abstract: BACKGROUND
  Systems biology employs mathematical modelling to further our understanding of biochemical pathways. Since the amount of experimental data on which the models are parameterized is often limited, these models exhibit large uncertainty in both parameters and predictions. Statistical methods can be used to select experiments that will reduce such uncertainty in an optimal manner. However, existing methods for optimal experiment design (OED) rely on assumptions that are inappropriate when data are scarce considering model complexity.
  
  
  RESULTS
  We have developed a novel method to perform OED for models that cope with large parameter uncertainty. We employ a Bayesian approach involving importance sampling of the posterior predictive distribution to predict the efficacy of a new measurement at reducing the uncertainty of a selected prediction. We demonstrate the method by applying it to a case where we show that specific combinations of experiments result in more precise predictions.
  
  
  METHODS
  Source code is available at: http://bmi.bmt.tue.nl/sysbio/software/pua.html.
authors.affiliation: Department of BioMedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands. j.vanlier@tue.nl
authors.forename: J
authors.initials: J
authors.lastname: Vanlier
authors.forename: C A
authors.initials: CA
authors.lastname: Tiemann
authors.forename: P A J
authors.initials: PA
authors.lastname: Hilbers
authors.forename: N A W
authors.initials: NA
authors.lastname: van Riel
mesh_terms: D000465:Algorithms; D001499:Bayes Theorem; D053612:Janus Kinases / Q000378:metabolism; D009010:Monte Carlo Method; D011381:Programming Languages; D012107:Research Design; D050791:STAT Transcription Factors / Q000378:metabolism; D015398:Signal Transduction; D049490:Systems Biology / Q000379:methods*; D035501:Uncertainty
chemical_list: D050791:STAT Transcription Factors; D053612:Janus Kinases