2012
Emergence of bimodal cell population responses from the interplay between analog single-cell signaling and protein expression noise
Birtwistle MR, Rauch J, Kiyatkin A, Aksamitiene E, Dobrzyński M, Hoek JB, Kolch W, Ogunnaike BA, Kholodenko BN. Emergence of bimodal cell population responses from the interplay between analog single-cell signaling and protein expression noise. BMC Systems Biology 2012, 6: 109. PMID: 22920937, PMCID: PMC3484110, DOI: 10.1186/1752-0509-6-109.Peer-Reviewed Original ResearchConceptsProtein expression noiseSingle-cell signalingExtracellular signal-regulated kinaseExpression noiseCell variabilityEpidermal growth factor stimulationProtein abundance variationCell fate decisionsPopulation responsesGrowth factor stimulationSingle cellsSignal-regulated kinaseCell population levelProtein expressionSingle-cell levelERK pathway activationFate decisionsPopulation levelFactor stimulationCell signalingCell population responseERK responseBiological outcomesPathway activationCell level
2008
Domain-oriented reduction of rule-based network models.
Borisov N, Chistopolsky A, Faeder J, Kholodenko B. Domain-oriented reduction of rule-based network models. IET Systems Biology 2008, 2: 342-51. PMID: 19045829, PMCID: PMC2628550, DOI: 10.1049/iet-syb:20070081.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsComputer SimulationGene Expression RegulationMembrane ProteinsModels, BiologicalProteomeSignal TransductionConceptsMulti-domain proteinsAuxiliary proteinsMembrane-bound receptorsTranscriptional regulatorsProgenitor proteinsProtein interactionsComplex assemblyGrowth factor receptorProteinFactor receptorSpeciesCorrect mass balanceEffector functionsHeterodimerisationReceptorsSitesRegulatorAssemblyInteractionDomain
2005
Inference 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 ResearchMeSH KeywordsAlgorithmsAnimalsCell Physiological PhenomenaGene Expression RegulationModels, BiologicalSignal TransductionSystems BiologyThe International Consortium on Systems Biology of Receptor Tyrosine Kinase Regulatory Networks.
Sakaki Y, Kholodenko B, Hatakeyama M, Kitano H, Kolch W, De Meyts P, Yarden Y, Westerhoff H, Wiley H. The International Consortium on Systems Biology of Receptor Tyrosine Kinase Regulatory Networks. IET Systems Biology 2005, 152: 53-4. PMID: 17044231, DOI: 10.1049/ip-syb:20059002.Peer-Reviewed Original Research
2004
Inferring dynamic architecture of cellular networks using time series of gene expression, protein and metabolite data
Sontag E, Kiyatkin A, Kholodenko BN. Inferring dynamic architecture of cellular networks using time series of gene expression, protein and metabolite data. Bioinformatics 2004, 20: 1877-1886. PMID: 15037511, DOI: 10.1093/bioinformatics/bth173.Peer-Reviewed Original Research