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
2002
Control Analysis for Autonomously Oscillating Biochemical Networks
Reijenga K, Westerhoff H, Kholodenko B, Snoep J. Control Analysis for Autonomously Oscillating Biochemical Networks. Biophysical Journal 2002, 82: 99-108. PMID: 11751299, PMCID: PMC1302452, DOI: 10.1016/s0006-3495(02)75377-0.Peer-Reviewed Original ResearchConceptsSummation theoremYeast glycolytic oscillationsLimit cycle oscillationsDynamic systemsControl coefficientsBiochemical networksCycle oscillationsOscillatory propertiesControl analysisMetabolic control analysisTheoremGlycolytic oscillationsTime domainOscillationsModel outputDiscrete Fourier transformFrequency domainSteady stateData setsQualitative way
1996
Control of Dynamics and Steady State: Applications to Multidrug Resistance
Westerhoff H, Bier M, Molenaar D, Spoelstra E, Lankelma J, Jongsma A, Jensen P, Richard P, Kholodenko B. Control of Dynamics and Steady State: Applications to Multidrug Resistance. 1996, 25-31. DOI: 10.1007/978-3-322-85017-1_3.Peer-Reviewed Original Research