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
2011
Differential Expression of Ly6C and T-bet Distinguish Effector and Memory Th1 CD4+ Cell Properties during Viral Infection
Marshall HD, Chandele A, Jung YW, Meng H, Poholek AC, Parish IA, Rutishauser R, Cui W, Kleinstein SH, Craft J, Kaech SM. Differential Expression of Ly6C and T-bet Distinguish Effector and Memory Th1 CD4+ Cell Properties during Viral Infection. Immunity 2011, 35: 633-646. PMID: 22018471, PMCID: PMC3444169, DOI: 10.1016/j.immuni.2011.08.016.Peer-Reviewed Original ResearchConceptsAcute viral infectionViral infectionEffector cellsTfh cell markersVirus-specific effectorT helper 1Th1 effector cellsT-bet expressionIL-7R expressionMemory precursor cellsTh1 CD4Helper 1Memory TTh1 cellsProliferative responseSecondary infectionEffector typeReliable markerCell markersInfectionPrecursor cellsGene expression profilesLy6CCell featuresCell developmentCell subset prediction for blood genomic studies
Bolen CR, Uduman M, Kleinstein SH. Cell subset prediction for blood genomic studies. BMC Bioinformatics 2011, 12: 258. PMID: 21702940, PMCID: PMC3213685, DOI: 10.1186/1471-2105-12-258.Peer-Reviewed Original ResearchConceptsPeripheral blood mononuclear cellsTotal peripheral blood mononuclear cellsGene signatureSubset-specific genesBlood mononuclear cellsPatient blood samplesPersonalized treatment decisionsSpecific cell subsetsHCV patientsPBMC subsetsNK cellsStandard therapyCell subsetsMononuclear cellsT cellsTreatment decisionsTherapy responseBlood samplesB cellsMyeloid cellsCellular sourceTranscriptional profilingDisease mechanismsGene expression profilesCells