2006
Quantifying gene network connectivity in silico: scalability and accuracy of a modular approach.
Yalamanchili N, Zak D, Ogunnaike B, Schwaber J, Kriete A, Kholodenko B. Quantifying gene network connectivity in silico: scalability and accuracy of a modular approach. IET Systems Biology 2006, 153: 236-46. PMID: 16986625, PMCID: PMC2346590, DOI: 10.1049/ip-syb:20050090.Peer-Reviewed Original Research
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 Biology
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
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
1997
Quantification of information transfer via cellular signal transduction pathways
Kholodenko B, Hoek J, Westerhoff H, Brown G. Quantification of information transfer via cellular signal transduction pathways. FEBS Letters 1997, 414: 430-434. PMID: 9315734, DOI: 10.1016/s0014-5793(97)01018-1.Peer-Reviewed Original Research