2015
Comparative analysis of anti-viral transcriptomics reveals novel effects of influenza immune antagonism
Thakar J, Hartmann BM, Marjanovic N, Sealfon SC, Kleinstein SH. Comparative analysis of anti-viral transcriptomics reveals novel effects of influenza immune antagonism. BMC Immunology 2015, 16: 46. PMID: 26272204, PMCID: PMC4536893, DOI: 10.1186/s12865-015-0107-y.Peer-Reviewed Original ResearchConceptsTranscription factor activityImmune antagonismExpression profilesGenome-wide expression profilesGenome-wide transcriptional profiling dataFactor activityGenome-wide transcriptional profilesTranscription factor SATB1DNA-binding sitesTranscriptional profiling dataHost-pathogen interactionsGene expression profilesISGF3 activityTranscriptional responseTranscription factorsTranscriptional profilesHost interactionsProfiling dataApplication of betaNovel effectMechanistic insightsInfected cellsInfluenza A virusesMechanistic differencesNewcastle disease virus
2013
Reconstruction of regulatory networks through temporal enrichment profiling and its application to H1N1 influenza viral infection
Zaslavsky E, Nudelman G, Marquez S, Hershberg U, Hartmann BM, Thakar J, Sealfon SC, Kleinstein SH. Reconstruction of regulatory networks through temporal enrichment profiling and its application to H1N1 influenza viral infection. BMC Bioinformatics 2013, 14: s1. PMID: 23734902, PMCID: PMC3633009, DOI: 10.1186/1471-2105-14-s6-s1.Peer-Reviewed Original ResearchConceptsRegulatory networksTranscription factorsExtensive genetic reprogrammingUnderlying transcriptional networksGene expression patternsAntiviral responseGene expression changesNovel antiviral factorTranscriptional cascadeTranscriptional networksDendritic cellsPromoter analysisRegulatory connectionsGenetic reprogrammingTranscriptional programsExpression patternsNetwork reconstruction methodsExpression changesCellular responsesExpression kineticsMonocyte-derived human dendritic cellsAntiviral stateHuman monocyte-derived dendritic cellsSuch virus infectionsImmune antagonistsMultiple Transcription Factor Binding Sites Predict AID Targeting in Non-Ig Genes
Duke JL, Liu M, Yaari G, Khalil AM, Tomayko MM, Shlomchik MJ, Schatz DG, Kleinstein SH. Multiple Transcription Factor Binding Sites Predict AID Targeting in Non-Ig Genes. The Journal Of Immunology 2013, 190: 3878-3888. PMID: 23514741, PMCID: PMC3689293, DOI: 10.4049/jimmunol.1202547.Peer-Reviewed Original ResearchConceptsTranscription Factor Binding SitesAID-induced lesionsNon-Ig genesGenome instabilityTranscription factorsAberrant targetingSequence dataCertain genesGenesAID targetingGerminal center B cellsSomatic mutationsLikely targetBinding sitesAID targetsTargetingClassification tree modelMistargetingB cellsLociMechanismTargetMutationsSites
2010
Antiviral Response Dictated by Choreographed Cascade of Transcription Factors
Zaslavsky E, Hershberg U, Seto J, Pham AM, Marquez S, Duke JL, Wetmur JG, tenOever BR, Sealfon SC, Kleinstein SH. Antiviral Response Dictated by Choreographed Cascade of Transcription Factors. The Journal Of Immunology 2010, 184: 2908-2917. PMID: 20164420, PMCID: PMC2856074, DOI: 10.4049/jimmunol.0903453.Peer-Reviewed Original ResearchMeSH KeywordsConserved SequenceDendritic CellsGene Expression Regulation, ViralGenes, OverlappingHumansMonocytesMultigene FamilyNewcastle disease virusOligonucleotide Array Sequence AnalysisPredictive Value of TestsPromoter Regions, GeneticReproducibility of ResultsTranscription FactorsUp-RegulationConceptsCell state transitionsRegulatory networksTranscription factorsGenetic programMost individual genesNovel transcription factorSpecific transcription factorsSingle regulatory networkAntiviral responseGene expression changesCurrent biological knowledgeActivation of RIGChoreographed cascadePromoter analysisIndividual genesGenetic regulatory networksMaster regulatorExpression changesBiological knowledgeExpression kineticsImmune evasion genesAntiviral roleImmune antagonistsHost immune systemNewcastle disease virus