2021
Relationship Between Dimensionality and Convergence of Optimization Algorithms: A Comparison Between Data-Driven Normalization and Scaling Factor-Based Methods Using PEPSSBI
Degasperi A, Nguyen L, Fey D, Kholodenko B. Relationship Between Dimensionality and Convergence of Optimization Algorithms: A Comparison Between Data-Driven Normalization and Scaling Factor-Based Methods Using PEPSSBI. Methods In Molecular Biology 2021, 2385: 91-115. PMID: 34888717, PMCID: PMC9446379, DOI: 10.1007/978-1-0716-1767-0_5.Peer-Reviewed Original ResearchConceptsUnknown parametersOrdinary differential equation modelDifferential equation modelMulti-CPU clusterObjective function constructionModel importParameter estimation softwareParameter identifiabilityOptimization algorithmDNS approachPersonal computerFirst softwareConvergence timeEstimation softwareFunction constructionFactor-based methodsDynamic modelAdditional parametersBiological dataData normalizationAlgorithmSoftwareScaling factorsDNSSimulations
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
2005
Mechanistic and modular approaches to modeling and inference of cellular regulatory networks
Kholodenko B, Bruggeman F, Sauro H. Mechanistic and modular approaches to modeling and inference of cellular regulatory networks. Topics In Current Genetics 2005, 13: 143-159. DOI: 10.1007/b136809.Peer-Reviewed Original ResearchReaction-diffusion equationsCellular regulatory networksRegulatory networksSystems biologyMolecular mechanismsBiochemical networksNetwork inferencePhysiological responsesNew insightsModeling approachChemical kineticsInferenceMolecular dynamics simulationsEquationsModelingBiologyComputational modelingNetworkModular approachDynamics simulationsApproachSimulationsNovel approach