title: Automatic detection of changes in the dynamics of delayed stochastic gene networks and in vivo production of RNA molecules in Escherichia coli.
abstract: BACKGROUND
  Production and degradation of RNA and proteins are stochastic processes, difficulting the distinction between spurious fluctuations in their numbers and changes in the dynamics of a genetic circuit. An accurate method of change detection is key to analyze plasticity and robustness of stochastic genetic circuits.
  
  
  RESULTS
  We use automatic change point detection methods to detect non-spurious changes in the dynamics of delayed stochastic models of gene networks at run time. We test the methods in detecting changes in mean and noise of protein numbers, and in the switching frequency of a genetic switch. We also detect changes, following genes' silencing, in the dynamics of a model of the core gene regulatory network of Saccharomyces cerevisiae with 328 genes. Finally, from images, we determine when RNA molecules tagged with fluorescent proteins are first produced in Escherichia coli. Provided prior knowledge on the time scale of the changes, the methods detect them accurately and are robust to fluctuations in protein and RNA levels.
  
  
  BACKGROUND
  Simulator: www.cs.tut.fi/~sanchesr/SGN/SGNSim.html
  
  
  BACKGROUND
  andre.ribeiro@tut.fi
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Computational Systems Biology Research Group, Department of Signal Processing, Tampere University of Technology, FI-33101 Tampere, Finland.
authors.forename: Jarno
authors.initials: J
authors.lastname: Mäkelä
authors.forename: Heikki
authors.initials: H
authors.lastname: Huttunen
authors.forename: Meenakshisundaram
authors.initials: M
authors.lastname: Kandhavelu
authors.forename: Olli
authors.initials: O
authors.lastname: Yli-Harja
authors.forename: Andre S
authors.initials: AS
authors.lastname: Ribeiro
mesh_terms: D000465:Algorithms; D004926:Escherichia coli / Q000235:genetics*; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks / Q000235:genetics*; D020868:Gene Silencing; D006801:Humans; D008957:Models, Genetic; D011506:Proteins / Q000235:genetics*; D012313:RNA / Q000096:biosynthesis* / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D013269:Stochastic Processes
chemical_list: D011506:Proteins; D012313:RNA