title: A method for inverse bifurcation of biochemical switches: inferring parameters from dose response curves.
abstract: BACKGROUND
  Within cells, stimuli are transduced into cell responses by complex networks of biochemical reactions. In many cell decision processes the underlying networks behave as bistable switches, converting graded stimuli or inputs into all or none cell responses. Observing how systems respond to different perturbations, insight can be gained into the underlying molecular mechanisms by developing mathematical models. Emergent properties of systems, like bistability, can be exploited to this purpose. One of the main challenges in modeling intracellular processes, from signaling pathways to gene regulatory networks, is to deal with high structural and parametric uncertainty, due to the complexity of the systems and the difficulty to obtain experimental measurements. Formal methods that exploit structural properties of networks for parameter estimation can help to overcome these problems.
  
  
  RESULTS
  We here propose a novel method to infer the kinetic parameters of bistable biochemical network models. Bistable systems typically show hysteretic dose response curves, in which the so called bifurcation points can be located experimentally. We exploit the fact that, at the bifurcation points, a condition for multistationarity derived in the context of the Chemical Reaction Network Theory must be fulfilled. Chemical Reaction Network Theory has attracted attention from the (systems) biology community since it connects the structure of biochemical reaction networks to qualitative properties of the corresponding model of ordinary differential equations. The inverse bifurcation method developed here allows determining the parameters that produce the expected behavior of the dose response curves and, in particular, the observed location of the bifurcation points given by experimental data.
  
  
  CONCLUSIONS
  Our inverse bifurcation method exploits inherent structural properties of bistable switches in order to estimate kinetic parameters of bistable biochemical networks, opening a promising route for developments in Chemical Reaction Network Theory towards kinetic model identification.
authors.affiliation: BioProcess Engineering Group, IIM-CSIC (Spanish Council for Scientific Research), Eduardo Cabello 6, Vigo, 36208, Spain. ireneotero@iim.csic.es.|Department of Biosystems Science and Engineering, Swiss Federal Institute of Technology (ETH Zurich), Universitatstrasse 19, 8092, Zurich, Switzerland. ireneotero@iim.csic.es.
authors.forename: Irene
authors.initials: I
authors.lastname: Otero-Muras
authors.affiliation: Department of Biosystems Science and Engineering, Swiss Federal Institute of Technology (ETH Zurich), Universitatstrasse 19, 8092, Zurich, Switzerland. pencho.yordanov@bsse.ethz.ch.
authors.forename: Pencho
authors.initials: P
authors.lastname: Yordanov
authors.affiliation: Department of Biosystems Science and Engineering, Swiss Federal Institute of Technology (ETH Zurich), Universitatstrasse 19, 8092, Zurich, Switzerland. joerg.stelling@bsse.ethz.ch.
authors.forename: Joerg
authors.initials: J
authors.lastname: Stelling
mesh_terms: D002468:Cell Physiological Phenomena; D053263:Gene Regulatory Networks / Q000502:physiology*; D007700:Kinetics; D008954:Models, Biological; D015398:Signal Transduction / Q000502:physiology*; D049490:Systems Biology / Q000379:methods*; D035501:Uncertainty