2021
Reengineering protein-phosphorylation switches
Kholodenko B, Okada M. Reengineering protein-phosphorylation switches. Science 2021, 373: 25-26. PMID: 34210865, PMCID: PMC8327301, DOI: 10.1126/science.abj5028.Peer-Reviewed Original Research
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 approachInference of signaling and gene regulatory networks by steady-state perturbation experiments: structure and accuracy
Andrec M, Kholodenko B, Levy R, Sontag E. Inference of signaling and gene regulatory networks by steady-state perturbation experiments: structure and accuracy. Journal Of Theoretical Biology 2005, 232: 427-441. PMID: 15572066, DOI: 10.1016/j.jtbi.2004.08.022.Peer-Reviewed Original Research
2002
Modular Response Analysis of Cellular Regulatory Networks
BRUGGEMAN F, WESTERHOFF H, HOEK J, KHOLODENKO B. Modular Response Analysis of Cellular Regulatory Networks. Journal Of Theoretical Biology 2002, 218: 507-520. PMID: 12384053, DOI: 10.1006/jtbi.2002.3096.Peer-Reviewed Original ResearchConceptsRegulatory networksMitogen-activated protein kinase cascadeEpidermal growth factor receptor (EGFR) networkGrowth factor receptor networkProtein kinase cascadeIntermodular interactionsCellular regulatory networksModular Response AnalysisIntracellular regulatory networksAmmonium assimilationKinase cascadeMolecular biological analysisGenetic circuitsInteraction mapSignal transducingEscherichia coliReceptor networkModular organizationMolecular interactionsBiological analysisSignal transferColiTransducingRegulationInteractionModular Interaction Strengths in Regulatory Networks; An Example
Bruggeman F, Kholodenko B. Modular Interaction Strengths in Regulatory Networks; An Example. Molecular Biology Reports 2002, 29: 57-61. PMID: 12241075, DOI: 10.1023/a:1020354302260.Peer-Reviewed Original Research