2024
Spatial–temporal order–disorder transition in angiogenic NOTCH signaling controls cell fate specification
Kang T, Bocci F, Nie Q, Onuchic J, Levchenko A. Spatial–temporal order–disorder transition in angiogenic NOTCH signaling controls cell fate specification. ELife 2024, 12: rp89262. PMID: 38376371, PMCID: PMC10942579, DOI: 10.7554/elife.89262.Peer-Reviewed Original ResearchMeSH KeywordsCell CommunicationCell DifferentiationEndothelial CellsMorphogenesisSignal TransductionConceptsCell fate specificationFate specificationNotch signalingMorphogenic processesCell-cell communicationComplex morphogenic processesCell fateDynamics of spatial patternsDepletion of fibronectinTip cellsSprout extensionAngiogenic morphogenesisHypoxic micro-environmentCell plasticityCellsComputational analysisPre-existing onesCell patternMicro-environmentSpatial patternsLocal enrichmentMorphogenesisEndothelial cellsAngiogenesis modelFibronectin
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
The Systems Biology of Glycosylation
Murrell M, Yarema K, Levchenko A. The Systems Biology of Glycosylation. ChemBioChem 2004, 5: 1334-1347. PMID: 15457533, DOI: 10.1002/cbic.200400143.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCarbohydratesCell CommunicationEukaryotic CellsGlycosylationHumansModels, BiologicalSignal TransductionSystems BiologyConceptsSystems biologyRegulation of differentiationRegulation of glycosylationEukaryotic cellsBiochemical systems analysisCell regulation processesCell decisionsSignal transductionGlycosylationBiologyRegulation processesRegulationTransductionApoptosisDifferentiationProfound influenceCellsNovel research methodologyRegulatory 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
Dynamical and integrative cell signaling: challenges for the new biology
Levchenko A. Dynamical and integrative cell signaling: challenges for the new biology. Biotechnology And Bioengineering 2003, 84: 773-782. PMID: 14708118, DOI: 10.1002/bit.10854.Peer-Reviewed Original ResearchConceptsProtein-centric approachSystems biology approachSignal transduction pathwaysNeural networkHigh-fidelity informationCareful experimental analysisBiology approachStatic worldTransduction pathwaysCell signalingPostgenomic eraHigh-throughput analysisIntracellular networksNetworkComplex networksNew biologyVolatile environmentBiological researchNotion of concentrationStructural viewBiochemical reactionsDynamical viewExperimental analysisPathwayPrimary determinantGSK-3 kinases enhance calcineurin signaling by phosphorylation of RCNs
Hilioti Z, Gallagher D, Low-Nam S, Ramaswamy P, Gajer P, Kingsbury T, Birchwood C, Levchenko A, Cunningham K. GSK-3 kinases enhance calcineurin signaling by phosphorylation of RCNs. Genes & Development 2003, 18: 35-47. PMID: 14701880, PMCID: PMC314273, DOI: 10.1101/gad.1159204.Peer-Reviewed Original ResearchConceptsProtein phosphataseType 1 protein phosphataseGSK-3 kinaseGSK-3 familyConserved serine residueProtein phosphatase activitySerine residuesAnimal cellsConsensus sitesProtein kinaseMuscle developmentPositive feedback loopYeast cellsRCN1CalcineurinMCIP1Phosphatase activityPhosphorylationEndogenous levelsInhibitory formKinaseLarge inductionStimulatory effectHeart growthPhosphataseCellerator: 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-kappaBModels of Eukaryotic Gradient Sensing: Application to Chemotaxis of Amoebae and Neutrophils
Levchenko A, Iglesias P. Models of Eukaryotic Gradient Sensing: Application to Chemotaxis of Amoebae and Neutrophils. Biophysical Journal 2002, 82: 50-63. PMID: 11751295, PMCID: PMC1302448, DOI: 10.1016/s0006-3495(02)75373-3.Peer-Reviewed Original ResearchMeSH KeywordsAmoebaAnimalsChemotaxisChemotaxis, LeukocyteKineticsLigandsModels, BiologicalNeutrophilsSignal TransductionConceptsPersistent signalingBiochemical signal transduction pathwaysSmall G proteinsChemotaxis of amoebaeSignal transduction pathwaysG protein activationEukaryotic cellsGradient sensingEukaryotic gradient sensingG proteinsCell typesSignal gradientExquisite precisionChemoattractant gradientPerfect adaptationSignalingAmoebaeActivatorPositive feedbackSensory systemsContinuous presenceAdaptationShallow gradientsChemoattractantInactivator