2005
Dynamic Properties of Network Motifs Contribute to Biological Network Organization
Prill R, Iglesias P, Levchenko A. Dynamic Properties of Network Motifs Contribute to Biological Network Organization. PLOS Biology 2005, 3: e343. PMID: 16187794, PMCID: PMC1239925, DOI: 10.1371/journal.pbio.0030343.Peer-Reviewed Original ResearchConceptsBiological networksRobust dynamical stabilityLarge-scale dynamic systemsNon-random networksBiological network organizationDeep interplayDynamical stabilityDynamical propertiesDynamic systemsSmall perturbationsExhaustive computational analysisSystem dynamicsDynamical implicationsSmaller subnetworksNon-random structureNetwork motifsNetwork structureDynamic propertiesNetworkComputational analysisPropertiesPerturbationsRobustnessDynamicsStabilityComment on "Oscillations in NF-κB Signaling Control the Dynamics of Gene Expression"
Barken D, Wang C, Kearns J, Cheong R, Hoffmann A, Levchenko A. Comment on "Oscillations in NF-κB Signaling Control the Dynamics of Gene Expression". Science 2005, 308: 52a-52a. PMID: 15802586, PMCID: PMC2821939, DOI: 10.1126/science.1107904.Peer-Reviewed Original Research
2004
Regulatory modules that generate biphasic signal response in biological systems.
Levchenko A, Bruck J, Sternberg P. Regulatory modules that generate biphasic signal response in biological systems. IET Systems Biology 2004, 1: 139-48. PMID: 17052124, DOI: 10.1049/sb:20045014.Peer-Reviewed Original Research
2003
Cellerator: extending a computer algebra system to include biochemical arrows for signal transduction simulations
Shapiro B, Levchenko A, Meyerowitz E, Wold B, Mjolsness E. Cellerator: extending a computer algebra system to include biochemical arrows for signal transduction simulations. Bioinformatics 2003, 19: 677-678. PMID: 12651737, DOI: 10.1093/bioinformatics/btg042.Peer-Reviewed Original Research
2002
The IκB-NF-κB Signaling Module: Temporal Control and Selective Gene Activation
Hoffmann A, Levchenko A, Scott M, Baltimore D. The IκB-NF-κB Signaling Module: Temporal Control and Selective Gene Activation. Science 2002, 298: 1241-1245. PMID: 12424381, DOI: 10.1126/science.1071914.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCell LineCell NucleusChemokine CCL5Chemokine CXCL10Chemokines, CXCComputer SimulationCytoplasmDNA-Binding ProteinsElectrophoretic Mobility Shift AssayFeedback, PhysiologicalGene Expression RegulationHumansI-kappa B ProteinsMiceMice, KnockoutModels, BiologicalNF-kappa BNF-KappaB Inhibitor alphaProto-Oncogene ProteinsSignal TransductionTranscriptional ActivationTumor Cells, CulturedTumor Necrosis Factor-alphaConceptsTranscriptional activator NF-kappaBSelective gene activationKnockout cell linesTemporal controlNF-kappaB inhibitor proteinNF-kappaB responseSignaling modulesCoordinated degradationGene activationMammalian cellsNuclear localizationInhibitor proteinGene expressionIkappaB proteinsSignal-processing characteristicsEpsilon functionNF-kappaB activationCell linesNF-kappaB
2000
Scaffold proteins may biphasically affect the levels of mitogen-activated protein kinase signaling and reduce its threshold properties
Levchenko A, Bruck J, Sternberg P. Scaffold proteins may biphasically affect the levels of mitogen-activated protein kinase signaling and reduce its threshold properties. Proceedings Of The National Academy Of Sciences Of The United States Of America 2000, 97: 5818-5823. PMID: 10823939, PMCID: PMC18517, DOI: 10.1073/pnas.97.11.5818.Peer-Reviewed Original ResearchConceptsMitogen-activated protein kinaseScaffold proteinProtein kinaseSpecific cellular contextDifferent subcellular compartmentsDetailed biochemical modelCellular contextSignal transductionSubcellular compartmentsScaffold concentrationsScaffold levelMultimolecular complexesFull activationGeneric scaffoldKinaseProteinBiochemical modelPathwaySignal propagationTransductionComplexesQuantitative computer modelCrosstalkCompartmentsActivation