2018
The CAIRR Pipeline for Submitting Standards-Compliant B and T Cell Receptor Repertoire Sequencing Studies to the National Center for Biotechnology Information Repositories
Bukhari SAC, O’Connor M, Martínez-Romero M, Egyedi AL, Willrett D, Graybeal J, Musen MA, Rubelt F, Cheung KH, Kleinstein SH. The CAIRR Pipeline for Submitting Standards-Compliant B and T Cell Receptor Repertoire Sequencing Studies to the National Center for Biotechnology Information Repositories. Frontiers In Immunology 2018, 9: 1877. PMID: 30166985, PMCID: PMC6105692, DOI: 10.3389/fimmu.2018.01877.Peer-Reviewed Original ResearchConceptsMetadata qualityInformation repositoryAdaptive immune receptor repertoiresLarge-scale dataWeb–based templateSoftware frameworkData annotationData standardsEffective sharingAIRR-seq dataReceptor repertoireData submittersCell receptorSequence filesAdaptive immune responsesRepositoryImmune receptor repertoiresMetadataData setsT cell receptorArchive databaseB cell receptorOptimized Threshold Inference for Partitioning of Clones From High-Throughput B Cell Repertoire Sequencing Data
Nouri N, Kleinstein SH. Optimized Threshold Inference for Partitioning of Clones From High-Throughput B Cell Repertoire Sequencing Data. Frontiers In Immunology 2018, 9: 1687. PMID: 30093903, PMCID: PMC6070604, DOI: 10.3389/fimmu.2018.01687.Peer-Reviewed Original Research
2015
Interactive Big Data Resource to Elucidate Human Immune Pathways and Diseases
Gorenshteyn D, Zaslavsky E, Fribourg M, Park CY, Wong AK, Tadych A, Hartmann BM, Albrecht RA, García-Sastre A, Kleinstein SH, Troyanskaya OG, Sealfon SC. Interactive Big Data Resource to Elucidate Human Immune Pathways and Diseases. Immunity 2015, 43: 605-614. PMID: 26362267, PMCID: PMC4753773, DOI: 10.1016/j.immuni.2015.08.014.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsBayes TheoremComputational BiologyGene Regulatory NetworksHost-Pathogen InteractionsHumansImmune SystemImmune System DiseasesInternetProtein Interaction MappingProtein Interaction MapsReproducibility of ResultsSignal TransductionSupport Vector MachineTranscriptomeVirus DiseasesConceptsPublic high-throughput dataGenome-scale experimentsDisease-associated genesHigh-throughput datasetsHigh-throughput dataData-driven hypothesesGenetic studiesImmune pathwaysGenesImmunological diseasesFunctional relationshipBiomedical research effortsImportant interactionsMolecular entitiesImmune systemHuman immune systemProteinExponential growthPathwayData resourcesBayesian integrationRelevant insightsGrowthCompendiumIdentification
2014
High-resolution antibody dynamics of vaccine-induced immune responses
Laserson U, Vigneault F, Gadala-Maria D, Yaari G, Uduman M, Heiden J, Kelton W, Jung S, Liu Y, Laserson J, Chari R, Lee JH, Bachelet I, Hickey B, Lieberman-Aiden E, Hanczaruk B, Simen BB, Egholm M, Koller D, Georgiou G, Kleinstein SH, Church GM. High-resolution antibody dynamics of vaccine-induced immune responses. Proceedings Of The National Academy Of Sciences Of The United States Of America 2014, 111: 4928-4933. PMID: 24639495, PMCID: PMC3977259, DOI: 10.1073/pnas.1323862111.Peer-Reviewed Original Research
2013
Protein array–based profiling of CSF identifies RBPJ as an autoantigen in multiple sclerosis
Querol L, Clark PL, Bailey MA, Cotsapas C, Cross AH, Hafler DA, Kleinstein SH, Lee JY, Yaari G, Willis SN, O'Connor KC. Protein array–based profiling of CSF identifies RBPJ as an autoantigen in multiple sclerosis. Neurology 2013, 81: 956-963. PMID: 23921886, PMCID: PMC3888197, DOI: 10.1212/wnl.0b013e3182a43b48.Peer-Reviewed Original ResearchConceptsCSF of patientsMultiple sclerosisNeurologic diseaseEpstein-Barr virus infectionImmunoglobulin GElevated immunoglobulin GInflammatory neurologic diseasesSubset of patientsLarger validation cohortRecombination signal binding proteinImmunoglobulin kappa J regionCSF autoantibodiesValidation cohortControl subjectsSerum reactivityAutoantigen candidatesHigh prevalenceVirus infectionPatientsAutoantibodiesCSFSclerosisArray-based profilingDiseaseELISA
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