2021
Can Systems Biology Advance Clinical Precision Oncology?
Rocca A, Kholodenko B. Can Systems Biology Advance Clinical Precision Oncology? Cancers 2021, 13: 6312. PMID: 34944932, PMCID: PMC8699328, DOI: 10.3390/cancers13246312.Peer-Reviewed Original ResearchSignal transduction networksSystems biology studiesGenotype-phenotype relationshipsTransduction networksSystems biology modelsSystems biologyBiological processesEnvironmental perturbationsBiology studiesCancer mutationsNetwork reconstructionPrecision oncologyBiology modelsTumor molecular alterationsBiological systemsArray of techniquesMolecular alterationsIndividual cancer patientsOncological researchBiologyValuable toolMutationsTherapeutic treatment
2019
Mapping connections in signaling networks with ambiguous modularity
Lill D, Rukhlenko O, Mc Elwee A, Kashdan E, Timmer J, Kholodenko B. Mapping connections in signaling networks with ambiguous modularity. Npj Systems Biology And Applications 2019, 5: 19. PMID: 31149348, PMCID: PMC6533310, DOI: 10.1038/s41540-019-0096-1.Peer-Reviewed Original ResearchConceptsModular Response AnalysisProtein abundanceProtein complexesNetwork reconstructionDownstream modulesRetroactive interactionsUpstream moduleComputational restorationNetwork modulesSuite of methodsAbundanceSuch complexesExperimental approachComplexesProteinEnzymePathwaySequestration effectNetwork responseDifferent modules
2018
Impact of measurement noise, experimental design, and estimation methods on Modular Response Analysis based network reconstruction
Thomaseth C, Fey D, Santra T, Rukhlenko OS, Radde NE, Kholodenko BN. Impact of measurement noise, experimental design, and estimation methods on Modular Response Analysis based network reconstruction. Scientific Reports 2018, 8: 16217. PMID: 30385767, PMCID: PMC6212399, DOI: 10.1038/s41598-018-34353-3.Peer-Reviewed Original ResearchConceptsModular Response AnalysisNetwork reconstructionSteady-state response curvesStatistical conceptsMeasurement noisePropagation of noiseNoise settingsEstimation methodNetwork structureTerms of accuracyLarge perturbationsResponse analysisDifferent replicatesPerturbation dataRegression strategyNoiseReconstructing static and dynamic models of signaling pathways using Modular Response Analysis
Santra T, Rukhlenko O, Zhernovkov V, Kholodenko B. Reconstructing static and dynamic models of signaling pathways using Modular Response Analysis. Current Opinion In Systems Biology 2018, 9: 11-21. DOI: 10.1016/j.coisb.2018.02.003.Peer-Reviewed Original ResearchModular Response AnalysisNetwork reconstruction methodsPhysics-based methodBiochemical pathwaysBiological networksNetwork reconstructionTopological modelDynamic modelResponse analysisNetwork modulesCertain conditionsPathwayReconstruction methodMechanistic modelEntire networkModelCore theoryReformulationPerturbationsTheorySufficient numberNetworkGlobal responseDirection