Featured Publications
NFBD1/KIAA0170 Is a Chromatin-associated Protein Involved in DNA Damage Signaling Pathways*
Xu X, Stern DF. NFBD1/KIAA0170 Is a Chromatin-associated Protein Involved in DNA Damage Signaling Pathways*. Journal Of Biological Chemistry 2002, 278: 8795-8803. PMID: 12499369, DOI: 10.1074/jbc.m211392200.Peer-Reviewed Original ResearchMeSH KeywordsAdaptor Proteins, Signal TransducingAmino Acid SequenceBase SequenceCell Cycle ProteinsChromatinDNA DamageDNA PrimersDNA ReplicationDNA-Binding ProteinsFluorescent Antibody Technique, IndirectG2 PhaseHeLa CellsHumansMitosisMolecular Sequence DataNuclear ProteinsPhosphorylationSequence Homology, Amino AcidSignal TransductionTrans-ActivatorsConceptsN-terminal FHA domainChromatin-associated proteinsDNA damageDNA Damage Signaling PathwayDNA double-strand breaksDiscrete nuclear fociDNA damage responseNumber of proteinsDouble-strand breaksBRCT domainFHA domainGamma-H2AX fociNuclear fociRad50 fociDamage responseDNA repairNFBD1Signaling pathwaysTandem repeatsProteinNuclear factorUntreated cellsHydroxyurea treatmentPathwayDiffuse nuclear staining
2018
Keeping Tumors Out of the MAPK Fitness Zone
Stern DF. Keeping Tumors Out of the MAPK Fitness Zone. Cancer Discovery 2018, 8: 20-23. PMID: 29311225, DOI: 10.1158/2159-8290.cd-17-1243.Peer-Reviewed Original ResearchConceptsMAPK-targeted therapiesGreater fitnessMAPK signalingTumor cell subclonesMAPK pathwayCell deathERK inhibitorDNA damageTumor cell deathFitness barriersCell subclonesNew therapeutic approachesInhibitor withdrawalResistant clonesTherapeutic approachesTriple combinationMEKSignalingClonesSubclonesFitnessPathwayPatients
2017
GRAPE: a pathway template method to characterize tissue-specific functionality from gene expression profiles
Klein MI, Stern DF, Zhao H. GRAPE: a pathway template method to characterize tissue-specific functionality from gene expression profiles. BMC Bioinformatics 2017, 18: 317. PMID: 28651562, PMCID: PMC5485588, DOI: 10.1186/s12859-017-1711-z.Peer-Reviewed Original ResearchConceptsGene expression profilesExpression profilesIndividual gene expression profilesTissue-specific functionalityEnrichment-based methodsPathway scoresGene expression levelsBatch effectsPathway genesPresent genesPerturbed pathwaysPathway expressionExpression levelsIndividual samplesTissue typesPathwayGenesTCGA subtypesAbnormal pathwaysIndependent datasetsBreast cancer subtypesNon-competitive approachIndividual tumorsCancer subtypesGrapes
2008
NFBD1/MDC1, 53BP1 and BRCA1 have both redundant and unique roles in the ATM pathway
Wilson KA, Stern DF. NFBD1/MDC1, 53BP1 and BRCA1 have both redundant and unique roles in the ATM pathway. Cell Cycle 2008, 7: 3584-3594. PMID: 19001859, PMCID: PMC2763172, DOI: 10.4161/cc.7.22.7102.Peer-Reviewed Original ResearchMeSH KeywordsAdaptor Proteins, Signal TransducingAtaxia Telangiectasia Mutated ProteinsBRCA1 ProteinCell Cycle ProteinsCell LineCheckpoint Kinase 2DNA-Binding ProteinsFibroblastsHumansIntracellular Signaling Peptides and ProteinsNuclear ProteinsPhosphorylationProtein Serine-Threonine KinasesRadiation, IonizingRNA, Small InterferingTrans-ActivatorsTumor Suppressor p53-Binding Protein 1Tumor Suppressor ProteinsConceptsNFBD1/MDC1DNA damage checkpoint proteinsRadiation-induced phosphorylationATM-Chk2 pathwayNormal genetic backgroundBRCT domainCheckpoint responseRedundant functionsPrimary human cellsRedundant rolesATM pathwayNFBD1Checkpoint proteinsMouse cellsHuman cellsGenetic backgroundMDC1Cancer cellsLocalization eventsPhosphorylationBRCA1Unique rolePathwayCellsHuman foreskin
2005
Global analysis of protein phosphorylation in yeast
Ptacek J, Devgan G, Michaud G, Zhu H, Zhu X, Fasolo J, Guo H, Jona G, Breitkreutz A, Sopko R, McCartney RR, Schmidt MC, Rachidi N, Lee SJ, Mah AS, Meng L, Stark MJ, Stern DF, De Virgilio C, Tyers M, Andrews B, Gerstein M, Schweitzer B, Predki PF, Snyder M. Global analysis of protein phosphorylation in yeast. Nature 2005, 438: 679-684. PMID: 16319894, DOI: 10.1038/nature04187.Peer-Reviewed Original ResearchConceptsProtein phosphorylationBasic cellular processesGlobal phosphorylation networksFirst-generation mapYeast kinasesPhosphorylation networksYeast proteinsCellular processesPhosphorylationKinaseYeastSearchable formatGlobal analysisProteinPrime targetEukaryotesNew resourcesProteomicsOrganismsRegulationPathwayChip technologyTargetPhosphoproteomics for oncology discovery and treatment
Stern DF. Phosphoproteomics for oncology discovery and treatment. Expert Opinion On Therapeutic Targets 2005, 9: 851-860. PMID: 16083347, DOI: 10.1517/14728222.9.4.851.Peer-Reviewed Original ResearchConceptsPhosphoproteomic analysisProtein phosphorylationReversible protein phosphorylationSignal transduction pathwaysCellular regulationProtein kinaseTransduction pathwaysHuman cancersDevelopment of drugsPathwayPhosphorylationGood targetImportant insightsCancer therapyCancer drugsPhosphoproteomicsCellsIndividual tumorsPowerful toolKinaseRegulationIntermediary levelDiscoveryTargetIdentification
2004
Establishment of a Cell-Free System to Study the Activation of Chk2
Xu X, Stern DF. Establishment of a Cell-Free System to Study the Activation of Chk2. Methods In Molecular Biology 2004, 280: 165-174. PMID: 15187252, DOI: 10.1385/1-59259-788-2:165.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAtaxia Telangiectasia Mutated ProteinsCell Cycle ProteinsCell-Free SystemCheckpoint Kinase 2DNA DamageDNA-Binding ProteinsGenetic VectorsHumansImmunoblottingPlasmidsPrecipitin TestsProtein BiosynthesisProtein Serine-Threonine KinasesRabbitsReticulocytesTranscription, GeneticTriticumTumor Suppressor ProteinsConceptsActivation of Chk2Cell-free systemVitro transcription/translation systemTranscription/translation systemCheckpoint kinase Chk2Rabbit reticulocyte lysateWheat germ extractKinase Chk2Identification of cofactorsReticulocyte lysateChk2Germ extractDNA damageTranslation systemActivationKinaseCofactorProteinATRLysatesPathway
2003
FHA Domain-Mediated DNA Checkpoint Regulation of Rad53
Schwartz MF, Lee SJ, Duong JK, Eminaga S, Stern DF. FHA Domain-Mediated DNA Checkpoint Regulation of Rad53. Cell Cycle 2003, 2: 381-394. PMID: 12851493, DOI: 10.4161/cc.2.4.457.Peer-Reviewed Original ResearchConceptsDNA damage checkpoint pathwayDamage checkpoint pathwayFHA domainReplication blocksCheckpoint pathwayChromatin assembly factor Asf1Phosphorylation-dependent associationDNA damageDNA replication checkpointActivation of Rad53Phosphopeptide binding domainsReplication checkpointReplicational stressDNA checkpointCheckpoint defectRad53Checkpoint regulationCatalytic domainProtein kinaseFHA1Binding domainsAsf1FHA2Persistent activationPathway
1997
A role for DNA primase in coupling DNA replication to DNA damage response
Marini F, Pellicioli A, Paciotti V, Lucchini G, Plevani P, Stern D, Foiani M. A role for DNA primase in coupling DNA replication to DNA damage response. The EMBO Journal 1997, 16: 639-650. PMID: 9034345, PMCID: PMC1169666, DOI: 10.1093/emboj/16.3.639.Peer-Reviewed Original ResearchMeSH KeywordsBlotting, WesternCell CycleCell Cycle ProteinsCheckpoint Kinase 2DNADNA DamageDNA PrimaseDNA ReplicationEnzyme StabilityFlow CytometryFungal ProteinsGene Expression Regulation, FungalGenes, FungalInterphaseMethyl MethanesulfonateMitosisModels, BiologicalMutagenesis, Site-DirectedMutagensMutationPhosphorylationProtein KinasesProtein Serine-Threonine KinasesRNA NucleotidyltransferasesS PhaseSaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsTemperatureUltraviolet RaysConceptsDNA damage responseDNA replicationDamage responseDNA damageDNA primaseSignal transduction pathwaysS-phase progressionDNA-damaging agentsCell cycle progressionCell cycle delayG1-S transitionRad53p phosphorylationTransduction pathwaysCheckpoint pathwayCycle progressionCycle delayPhase progressionEarly stepsEssential rolePrimaseReplicationPathwayMitosisPhosphorylationOverexpression