Featured Publications
Untangling the wires: A strategy to trace functional interactions in signaling and gene networks
Kholodenko BN, Kiyatkin A, Bruggeman FJ, Sontag E, Westerhoff HV, Hoek JB. Untangling the wires: A strategy to trace functional interactions in signaling and gene networks. Proceedings Of The National Academy Of Sciences Of The United States Of America 2002, 99: 12841-12846. PMID: 12242336, PMCID: PMC130547, DOI: 10.1073/pnas.192442699.Peer-Reviewed Original ResearchConceptsGene networksFunctional interactionMitogen-activated protein kinase cascadeProtein kinase cascadeProteomic data setsKinase cascadeCellular signalingLarge genomicsUnidentified elementsMechanistic levelCellular networkingSignalingCell systemGenomicsInteractionInteraction routesCascadeComputer-generated responsesNetwork responseCurrent methodologiesResponse
2012
Bimodal Protein Distributions in Heterogeneous Oscillating Systems
Dobrzyński M, Fey D, Nguyen L, Kholodenko B. Bimodal Protein Distributions in Heterogeneous Oscillating Systems. Lecture Notes In Computer Science 2012, 7605: 17-28. DOI: 10.1007/978-3-642-33636-2_3.Peer-Reviewed Original Research
2004
Quantitative analysis of signaling networks
Sauro H, Kholodenko B. Quantitative analysis of signaling networks. Progress In Biophysics And Molecular Biology 2004, 86: 5-43. PMID: 15261524, DOI: 10.1016/j.pbiomolbio.2004.03.002.Peer-Reviewed Original ResearchSignaling switches and bistability arising from multisite phosphorylation in protein kinase cascades
Markevich N, Hoek J, Kholodenko B. Signaling switches and bistability arising from multisite phosphorylation in protein kinase cascades. Journal Of Cell Biology 2004, 164: 353-359. PMID: 14744999, PMCID: PMC2172246, DOI: 10.1083/jcb.200308060.Peer-Reviewed Original ResearchConceptsExtracellular signal-regulated kinaseMultisite phosphorylationProtein kinase cascadeBistable switchSignal-regulated kinaseKinase cascadeMAPK cascadeWidespread mechanismDifferent kinasesSame phosphataseProtein kinasePositive feedback loopProtein activityDephosphorylation reactionsCovalent modificationKinaseMAPK phosphorylationFeedback regulationPhosphorylationKinetic propertiesPhosphataseFeedback loopCascade
2000
Negative feedback and ultrasensitivity can bring about oscillations in the mitogen‐activated protein kinase cascades
Kholodenko B. Negative feedback and ultrasensitivity can bring about oscillations in the mitogen‐activated protein kinase cascades. The FEBS Journal 2000, 267: 1583-1588. PMID: 10712587, DOI: 10.1046/j.1432-1327.2000.01197.x.Peer-Reviewed Original ResearchConceptsMitogen-activated protein kinaseMAPK cascadeProtein kinaseProtein phosphorylation cascadeSlow protein diffusionNegative feedback loopPhosphorylation cascadeSignal transductionFeedback loopCellular targetsProtein diffusionMAPK phosphorylationPhosphorylation levelsCell typesIntracellular wavesKinasePhosphorylationCascadeFunctional organizationUltrasensitivityRecent kinetic dataExternal stimuliTransductionTotal proteinCytoplasmCellular information transfer regarded from a stoichiometry and control analysis perspective
Schuster S, Kholodenko B, Westerhoff H. Cellular information transfer regarded from a stoichiometry and control analysis perspective. Biosystems 2000, 55: 73-81. PMID: 10745111, DOI: 10.1016/s0303-2647(99)00085-4.Peer-Reviewed Original Research
1993
Multiplicity of Control
Westerhoff H, Jensen P, van der Gugten A, Kahn D, Kholodenko B, Schuster S, Oldenburg N, van Dam K, van Heeswijk W. Multiplicity of Control. 1993, 263-268. DOI: 10.1007/978-1-4615-2962-0_41.Peer-Reviewed Original Research