Featured Publications
Benchmarking transcriptional host response signatures for infection diagnosis
Chawla D, Cappuccio A, Tamminga A, Sealfon S, Zaslavsky E, Kleinstein S. Benchmarking transcriptional host response signatures for infection diagnosis. Cell Systems 2022, 13: 974-988.e7. PMID: 36549274, PMCID: PMC9768893, DOI: 10.1016/j.cels.2022.11.007.Peer-Reviewed Original ResearchConceptsInfection diagnosisHost response signatureNon-infectious conditionsClinical applicationResponse signatureChronic infectionPathogen of interestBacterial infectionsInfectionSignature of infectionDisease signaturesDiagnosisTranscriptional profilesStandardized methodologyDevelopment of signaturesDecreased performance
2022
Pan-vaccine analysis reveals innate immune endotypes predictive of antibody responses to vaccination
Fourati S, Tomalin LE, Mulè MP, Chawla DG, Gerritsen B, Rychkov D, Henrich E, Miller HER, Hagan T, Diray-Arce J, Dunn P, Levy O, Gottardo R, Sarwal M, Tsang J, Suárez-Fariñas M, Pulendran B, Kleinstein S, Sékaly R. Pan-vaccine analysis reveals innate immune endotypes predictive of antibody responses to vaccination. Nature Immunology 2022, 23: 1777-1787. PMID: 36316476, PMCID: PMC9747610, DOI: 10.1038/s41590-022-01329-5.Peer-Reviewed Original ResearchConceptsAntibody responsePro-inflammatory response genesToll-like receptor ligandsBlood transcriptional profilesHigher serum antibodyPro-inflammatory responseSerum antibodiesDifferent vaccinesImmune responseImmune stateMetabolism alterationsEndotypesImmune systemVaccinationReceptor ligandsCell proliferationGene expression characteristicsActivation stateDifferential expressionTranscriptional profilesResponse genesExpression characteristicsResponseWide variationAdjuvant
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