2021
Modeling the Nonlinear Dynamics of Intracellular Signaling Networks
Rukhlenko O, Kholodenko B. Modeling the Nonlinear Dynamics of Intracellular Signaling Networks. Bio-protocol 2021, 11: e4089. PMID: 34395728, PMCID: PMC8329461, DOI: 10.21769/bioprotoc.4089.Peer-Reviewed Original ResearchOrdinary differential equationsPartial differential equation systemDifferential equation systemDifferent dynamical regimesBasins of attractionMain qualitative featuresDifferential equationsState trajectoriesEquation systemSystem trajectoriesDynamical regimesNonlinear dynamicsStable steady stateSteady stateBifurcation analysisParameter spaceLimit cyclesMultiple attractorsConstant parametersParametric planePoint dynamicsStandard optimizationIntracellular signaling networksSpatial pointsMultiple steady states
2017
Performance of objective functions and optimisation procedures for parameter estimation in system biology models
Degasperi A, Fey D, Kholodenko BN. Performance of objective functions and optimisation procedures for parameter estimation in system biology models. Npj Systems Biology And Applications 2017, 3: 20. PMID: 28804640, PMCID: PMC5548920, DOI: 10.1038/s41540-017-0023-2.Peer-Reviewed Original ResearchUnknown parametersObjective functionParameter estimationLarge dynamic modelsSpeed of convergenceMathematical modellingSystems biology modelsSimulation approachParameter spaceDynamic systemsOptimization algorithmOptimization procedureParameter estimatesNumber of directionsBiology modelsDynamic modelConvergenceReasonable amountScaling factorsSimulationsAlgorithmApproach increasesNumerous parametersEstimationParameters