2023
Reversing pathological cell states: the road less travelled can extend the therapeutic horizon
Kholodenko B, Kolch W, Rukhlenko O. Reversing pathological cell states: the road less travelled can extend the therapeutic horizon. Trends In Cell Biology 2023, 33: 913-923. PMID: 37263821, PMCID: PMC10593090, DOI: 10.1016/j.tcb.2023.04.004.Peer-Reviewed Original Research
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 ResearchMeSH KeywordsComputational BiologyComputer SimulationGene Regulatory NetworksModels, BiologicalProtein Interaction MapsProteinsSignal TransductionConceptsModular Response AnalysisProtein abundanceProtein complexesNetwork reconstructionDownstream modulesRetroactive interactionsUpstream moduleComputational restorationNetwork modulesSuite of methodsAbundanceSuch complexesExperimental approachComplexesProteinEnzymePathwaySequestration effectNetwork responseDifferent modules
2015
Silence on the relevant literature and errors in implementation
Bastiaens P, Birtwistle MR, Blüthgen N, Bruggeman FJ, Cho KH, Cosentino C, de la Fuente A, Hoek JB, Kiyatkin A, Klamt S, Kolch W, Legewie S, Mendes P, Naka T, Santra T, Sontag E, Westerhoff HV, Kholodenko BN. Silence on the relevant literature and errors in implementation. Nature Biotechnology 2015, 33: 336-339. PMID: 25850052, DOI: 10.1038/nbt.3185.Peer-Reviewed Original ResearchGene Regulatory NetworksModels, TheoreticalNetwork-based identification of feedback modules that control RhoA activity and cell migration
Kim TH, Monsefi N, Song JH, von Kriegsheim A, Vandamme D, Pertz O, Kholodenko BN, Kolch W, Cho KH. Network-based identification of feedback modules that control RhoA activity and cell migration. Journal Of Molecular Cell Biology 2015, 7: 242-252. PMID: 25780058, DOI: 10.1093/jmcb/mjv017.Peer-Reviewed Original ResearchConceptsRho family GTPasesCancer cell migrationCell migrationRhoA activityControl cell migrationBoolean network modelNetwork-based identificationPotential new targetsRho activationGTPasesSrc inhibitionGenetic backgroundCsk inhibitionMost cancer deathsActivation stateNew targetsNew insightsMigrationCskSrcFAKRewiringInhibitionEGFProtrusion
2013
Complexity of Receptor Tyrosine Kinase Signal Processing
Volinsky N, Kholodenko BN. Complexity of Receptor Tyrosine Kinase Signal Processing. Cold Spring Harbor Perspectives In Biology 2013, 5: a009043. PMID: 23906711, PMCID: PMC3721286, DOI: 10.1101/cshperspect.a009043.Peer-Reviewed Original ResearchConceptsCombinatorial varietySignal processingMathematical modelingSpecific system propertiesSpecific cell fate decisionsSystem propertiesNetwork behaviorReceptor tyrosine kinasesMultiple feedsSpatiotemporal dynamicsComputational approachExcitable responseIntricate landscapeCell fate decisionsSpecific cellular outcomesPathway cross talkOscillationsBistabilityNetwork circuitryDynamicsModelingTranscriptional controlAdapts cellsCellular outcomes