title: Systems modelling methodology for the analysis of apoptosis signal transduction and cell death decisions.
abstract: Systems biology and systems medicine, i.e. the application of systems biology in a clinical context, is becoming of increasing importance in biology, drug discovery and health care. Systems biology incorporates knowledge and methods that are applied in mathematics, physics and engineering, but may not be part of classical training in biology. We here provide an introduction to basic concepts and methods relevant to the construction and application of systems models for apoptosis research. We present the key methods relevant to the representation of biochemical processes in signal transduction models, with a particular reference to apoptotic processes. We demonstrate how such models enable a quantitative and temporal analysis of changes in molecular entities in response to an apoptosis-inducing stimulus, and provide information on cell survival and cell death decisions. We introduce methods for analyzing the spatial propagation of cell death signals, and discuss the concepts of sensitivity analyses that enable a prediction of network responses to disturbances of single or multiple parameters.
authors.affiliation: Centre for Systems Medicine and Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland. mrehm@rcsi.ie
authors.forename: Markus
authors.initials: M
authors.lastname: Rehm
authors.forename: Jochen H M
authors.initials: JH
authors.lastname: Prehn
mesh_terms: D017209:Apoptosis / Q000235:genetics*; D020169:Caspases / Q000235:genetics / Q000378:metabolism; D002470:Cell Survival; D003198:Computer Simulation; D004789:Enzyme Activation; D015870:Gene Expression; D006367:HeLa Cells / Q000378:metabolism* / Q000648:ultrastructure; D006801:Humans; D008954:Models, Biological; D015398:Signal Transduction / Q000235:genetics*; D049490:Systems Biology; D051636:X-Linked Inhibitor of Apoptosis Protein / Q000235:genetics / Q000378:metabolism
chemical_list: D051636:X-Linked Inhibitor of Apoptosis Protein; C496866:XIAP protein, human; D020169:Caspases