2025
Supervised fine-tuning of pre-trained antibody language models improves antigen specificity prediction
Wang M, Patsenker J, Li H, Kluger Y, Kleinstein S. Supervised fine-tuning of pre-trained antibody language models improves antigen specificity prediction. PLOS Computational Biology 2025, 21: e1012153. PMID: 40163503, PMCID: PMC12013870, DOI: 10.1371/journal.pcbi.1012153.Peer-Reviewed Original ResearchConceptsSupervised fine-tuningImmune responseMolecular basis of antigen recognitionSARS-CoV-2 spike proteinLanguage modelSARS-CoV-2 vaccinesAdaptive immune responsesSpecific predictionsMolecular basisSpike proteinAntibody-based therapeuticsFine-tuningAntibody-antigen specificitySpecific to antigensInfluenza hemagglutininVaccine designAntigen recognitionModel embeddingsImmune functionLanguage model embeddingsSARS-CoV-2AntibodiesAntigenInfluenzaVaccine
2024
Evaluation of Strategies for Transitioning to Annual SARS-CoV-2 Vaccination Campaigns in the United States.
Wells C, Pandey A, Moghadas S, Fitzpatrick M, Singer B, Galvani A. Evaluation of Strategies for Transitioning to Annual SARS-CoV-2 Vaccination Campaigns in the United States. Annals Of Internal Medicine 2024, 177: 609-617. PMID: 38527289, PMCID: PMC12051185, DOI: 10.7326/m23-2451.Peer-Reviewed Original ResearchSARS-CoV-2 vaccination campaignSARS-CoV-2Centers for Disease Control and PreventionDisease Control and PreventionSARS-CoV-2 vaccinesHealth care costsVaccine-acquired immunityFood and Drug AdministrationU.S. Food and Drug AdministrationControl and PreventionNational Institutes of HealthVaccination campaignInfluenza vaccineInitial doseInstitutes of HealthSARS-CoV-2 variantsBooster doseImmune evasionDrug AdministrationUnited StatesNotsew Orm Sands FoundationDoseHealthPopulation immunityNational Institute
2023
Immunogenicity and Pre-Clinical Efficacy of an OMV-Based SARS-CoV-2 Vaccine
Grandi A, Tomasi M, Ullah I, Bertelli C, Vanzo T, Accordini S, Gagliardi A, Zanella I, Benedet M, Corbellari R, Di Lascio G, Tamburini S, Caproni E, Croia L, Ravà M, Fumagalli V, Di Lucia P, Marotta D, Sala E, Iannacone M, Kumar P, Mothes W, Uchil P, Cherepanov P, Bolognesi M, Pizzato M, Grandi G. Immunogenicity and Pre-Clinical Efficacy of an OMV-Based SARS-CoV-2 Vaccine. Vaccines 2023, 11: 1546. PMID: 37896949, PMCID: PMC10610814, DOI: 10.3390/vaccines11101546.Peer-Reviewed Original ResearchSARS-CoV-2 vaccinesSARS-CoV-2Outer membrane vesiclesImmune responseSARS-CoV-2 elicitsSARS-CoV-2 variantsPotent immune responsesEffective immune responsePre-clinical efficacyDiverse SARS-CoV-2 variantsInherent adjuvanticityVaccinated miceIntranasal challengeVaccine dosesNeutralization titresEffective vaccineVirus infectionVaccination campaignHeterologous antigensVaccineVirus replicationSpike proteinInfectivity assaysTitresPotential needInfection with alternate frequencies of SARS-CoV-2 vaccine boosting for patients undergoing antineoplastic cancer treatments
Townsend J, Hassler H, Emu B, Dornburg A. Infection with alternate frequencies of SARS-CoV-2 vaccine boosting for patients undergoing antineoplastic cancer treatments. Journal Of The National Cancer Institute 2023, 115: 1626-1628. PMID: 37599438, PMCID: PMC10699797, DOI: 10.1093/jnci/djad158.Peer-Reviewed Original ResearchConceptsReinfection riskAntineoplastic therapyAntibody dataSARS-CoV-2 infectionSARS-CoV-2 vaccinesChemotherapy-immunotherapy combinationsPfizer-BioNTech BNT162b2COVID-19 vaccinationHigh infection riskFrequent boostingRituximab therapyBreakthrough infectionsVaccination scheduleAntibody levelsBooster scheduleVaccination frequencyImmune responseAdditional interventionsReduced riskHigh riskHormonal treatmentGeneral populationNecessitating assessmentPatientsInfection risk
2022
Humoral and Cellular Response of Transplant Recipients to a Third Dose of mRNA SARS-CoV-2 Vaccine: A Systematic Review and Meta-analysis
Bailey A, Maganti H, Cheng W, Shorr R, Buchan C, Allan D. Humoral and Cellular Response of Transplant Recipients to a Third Dose of mRNA SARS-CoV-2 Vaccine: A Systematic Review and Meta-analysis. Transplantation 2022, 107: 204-215. PMID: 36398334, PMCID: PMC9746229, DOI: 10.1097/tp.0000000000004386.Peer-Reviewed Original ResearchConceptsMRNA SARS-CoV-2 vaccineSARS-CoV-2 vaccinesTransplant recipientsThird doseSystematic reviewMeta-analysisNational Institutes of Health Quality Assessment ToolCochrane risk of bias toolAssociated with reduced oddsRisk of bias toolDose of mRNA SARS-CoV-2 vaccineMeta-Analysis reporting guidelinesQuality assessment toolHumoral responseSARS-CoV-2 mRNA vaccinesPreferred Reporting ItemsDerSimonian-Laird random-effects modelRandomized Controlled TrialsAdult transplant recipientsRandom-effects modelLack of controlled studiesClinically relevant thresholdsResponse to vaccinationCochrane riskReporting ItemsAn ELISA Platform for the Quantitative Analysis of SARS-CoV-2 RBD-neutralizing Antibodies As an Alternative to Monitoring of the Virus-Neutralizing Activity
Kostin N, Bobik T, Skryabin G, Simonova M, Knorre V, Abrikosova V, Mokrushina Y, Smirnov I, Aleshenko N, Kruglova N, Mazurov D, Nikitin A, Gabibov A. An ELISA Platform for the Quantitative Analysis of SARS-CoV-2 RBD-neutralizing Antibodies As an Alternative to Monitoring of the Virus-Neutralizing Activity. Acta Naturae 2022, 14: 109-119. PMID: 36348715, PMCID: PMC9611858, DOI: 10.32607/actanaturae.11776.Peer-Reviewed Original ResearchVirus-neutralizing activitySARS-CoV-2Levels of SARS-CoV-2 neutralizing antibodiesSARS-CoV-2 neutralizing antibodiesNeutralizing activity of seraGroup of hospitalized patientsSARS-CoV-2 vaccinesImmunity to SARS-CoV-2Gam-COVID-Vac vaccineActivity of seraHumoral immune responseSARS-CoV-2 infectionGam-COVID-VacNeutralizing antibodiesImmune plasmaSerum immunoglobulinsHospitalized patientsImmune responseELISA platformVirus assayProtective effectAntibodiesHerd immunity to SARS-CoV-2VaccineVirus variantsHumoral Immunogenicity to SARS-CoV-2 Vaccination in Liver Transplant Recipients: A Systematic Review and Meta-Analysis
Yoo J, Yon D, Lee S, Shin J, Kim B. Humoral Immunogenicity to SARS-CoV-2 Vaccination in Liver Transplant Recipients: A Systematic Review and Meta-Analysis. International Journal Of Biological Sciences 2022, 18: 5849-5857. PMID: 36263175, PMCID: PMC9576515, DOI: 10.7150/ijbs.77030.Peer-Reviewed Original ResearchConceptsOrthotopic liver transplant recipientsOrthotopic liver transplantationSARS-CoV-2 vaccinesHumoral immune response rateSolid organ transplant recipientsImmune response rateOrgan transplant recipientsTransplant recipientsOdds ratioAdverse eventsHealthy controlsSARS-CoV-2Response rateLiver transplant recipientsChronic kidney diseaseEvaluate immunogenicityLiver transplantationImmunosuppressive dosesSevere acute respiratory syndrome coronavirus 2Acute respiratory syndrome coronavirus 2Male sexPooled analysisRespiratory syndrome coronavirus 2Kidney diseaseOrgan transplantationEvaluating clinical effectiveness of SARS‐CoV‐2 vaccine in solid organ transplant recipients: A propensity score matched analysis
Tucker M, Azar MM, Cohen E, Gan G, Deng Y, Palacios C, Malinis M. Evaluating clinical effectiveness of SARS‐CoV‐2 vaccine in solid organ transplant recipients: A propensity score matched analysis. Transplant Infectious Disease 2022, 24: e13876. PMID: 35684932, PMCID: PMC9348300, DOI: 10.1111/tid.13876.Peer-Reviewed Original ResearchConceptsSolid organ transplant recipientsSARS-CoV-2 infectionOrgan transplant recipientsCritical COVID-19Clinical effectivenessTransplant recipientsVaccine eraVaccinated solid organ transplant recipientsCOVID-19Propensity score-matched cohortSARS-CoV-2 vaccinationSevere coronavirus disease 2019Cause-specific Cox regression modelsCOVID-19-related mortalitySARS-CoV-2 vaccinesSARS-CoV-2 infection ratesCurrent vaccine recommendationsKey preventative strategiesPrimary vaccine seriesRetrospective cohort studyDoses of mRNACox regression modelCoronavirus disease 2019Poisson regression modelsVaccine seriesModeling of waning immunity after SARS-CoV-2 vaccination and influencing factors
Pérez-Alós L, Armenteros J, Madsen J, Hansen C, Jarlhelt I, Hamm S, Heftdal L, Pries-Heje M, Møller D, Fogh K, Hasselbalch R, Rosbjerg A, Brunak S, Sørensen E, Larsen M, Ostrowski S, Frikke-Schmidt R, Bayarri-Olmos R, Hilsted L, Iversen K, Bundgaard H, Nielsen S, Garred P. Modeling of waning immunity after SARS-CoV-2 vaccination and influencing factors. Nature Communications 2022, 13: 1614. PMID: 35347129, PMCID: PMC8960902, DOI: 10.1038/s41467-022-29225-4.Peer-Reviewed Original ResearchConceptsT cell responsesBNT162b2 vaccineAntibody levelsAntibody responseSARS-CoV-2 vaccinationSARS-CoV-2 vaccinesNatural infectionIgG antibody responseGamma interferon releaseChAdOx1-nCoV19First doseIgA responsesIgG levelsVaccine injectionSecond dosePrior infectionVaccineInfectionImmunityCOVID-19Generalized mixed modelDoseTwo-phase responseAgeSexThrombosis patterns and clinical outcome of COVID-19 vaccine-induced immune thrombotic thrombocytopenia: A Systematic Review and Meta-Analysis
Kim A, Woo W, Yon D, Lee S, Yang J, Kim J, Park S, Koyanagi A, Kim M, Lee S, Shin J, Smith L. Thrombosis patterns and clinical outcome of COVID-19 vaccine-induced immune thrombotic thrombocytopenia: A Systematic Review and Meta-Analysis. International Journal Of Infectious Diseases 2022, 119: 130-139. PMID: 35339716, PMCID: PMC8942584, DOI: 10.1016/j.ijid.2022.03.034.Peer-Reviewed Original ResearchConceptsVaccine-induced immune thrombotic thrombocytopeniaCerebral venous thrombosisChAdOx1 nCoV-19 vaccineSplanchnic vein thrombosisThrombotic thrombocytopeniaVein thrombosisVenous thrombosisClinical outcomesMeta-analysisRate of cerebral venous thrombosisAge of patientsPooled incidence rateAdenoviral vector vaccinesSARS-CoV-2 vaccinesSite of thrombosisChAdOx1 nCoV-19Between-study heterogeneityAnticoagulant treatmentNo significant differenceFemale predominanceClinical manifestationsExtracranial thrombosisIntracranial haemorrhageFatal outcomeOverall mortality
2021
The Use of COVID-19 Vaccines in Patients with SLE
Tang W, Gartshteyn Y, Ricker E, Inzerillo S, Murray S, Khalili L, Askanase A. The Use of COVID-19 Vaccines in Patients with SLE. Current Rheumatology Reports 2021, 23: 79. PMID: 34767100, PMCID: PMC8586600, DOI: 10.1007/s11926-021-01046-2.Peer-Reviewed Original ResearchConceptsAutoimmune inflammatory rheumatic diseasesSystemic lupus erythematosusFood and Drug AdministrationCOVID-19 vaccineRisk of disease flareIncidence of side effectsAdjustment of immunosuppressionSARS-CoV-2 vaccinesInflammatory rheumatic diseasesBooster vaccine dosePhases of vaccine developmentReview current dataImmunosuppressive medicationsDisease flareAIIRD patientsAdministration of vaccinesLupus erythematosusHealthy controlsSummaryThe benefitsBenefits of vaccinationVaccine doseSide effectsImmune responseRheumatic diseasesDrug AdministrationSars-Cov-2 Vaccination in Patients with Pre-Existing Immune Thrombocytopenia
Lee E, Moreira M, Al-Samkari H, Cuker A, DiRaimo J, Gernsheimer T, Kruse A, Kessler C, Kruse C, Leavitt A, Lee A, Liebman H, Newland A, Ray A, Tarantino M, Thachil J, Kuter D, Cines D, Bussel J. Sars-Cov-2 Vaccination in Patients with Pre-Existing Immune Thrombocytopenia. Blood 2021, 138: 586. PMCID: PMC8701617, DOI: 10.1182/blood-2021-152918.Peer-Reviewed Original ResearchSARS-CoV-2 vaccinesITP exacerbationPre-vaccination baselineBristol-Myers SquibbImmune thrombocytopeniaPlatelet countRescue treatmentDose 2Dose 1Second dosePlatelet decreaseSpeakers bureauSpark TherapeuticsConsultancy feesFirst doseCSL BehringSupport associationsNovo NordiskSARS-CoV-2 vaccinationDiagnosis of ITPAdvisory CommitteeData Safety Monitoring BoardConcurrent autoimmune diseasesMore refractory diseasePrior medical treatmentPrevention of host-to-host transmission by SARS-CoV-2 vaccines
Mostaghimi D, Valdez CN, Larson HT, Kalinich CC, Iwasaki A. Prevention of host-to-host transmission by SARS-CoV-2 vaccines. The Lancet Infectious Diseases 2021, 22: e52-e58. PMID: 34534512, PMCID: PMC8439617, DOI: 10.1016/s1473-3099(21)00472-2.Peer-Reviewed Original ResearchConceptsSARS-CoV-2SARS-CoV-2 vaccinesSymptomatic COVID-19Population-level dataVaccine's abilityIntramuscular vaccineImmunological mechanismsVaccine strategiesVaccine capacityPrimary infectionNatural courseClinical trialsObservational studyRespiratory epitheliumReal-world settingViral titresViral replicationVaccineVaccine distributionInfectionCOVID-19Host transmissionTrialsPopulation-level effectsMucosaAntibody‐dependent neutralizing capacity of the SARS‐CoV‐2 vaccine BNT162b2 with and without previous COVID‐19 priming
Hansen C, Jarlhelt I, Hasselbalch R, Hamm S, Fogh K, Pries‐Heje M, Møller D, Heftdal L, Pérez‐Alós L, Sørensen E, Larsen M, Skjoedt M, Ostrowski S, Frikke‐Schmidt R, Bayarri‐Olmos R, Hilsted L, Bundgaard H, Nielsen S, Iversen K, Garred P. Antibody‐dependent neutralizing capacity of the SARS‐CoV‐2 vaccine BNT162b2 with and without previous COVID‐19 priming. Journal Of Internal Medicine 2021, 290: 1272-1274. PMID: 34237190, PMCID: PMC8447364, DOI: 10.1111/joim.13366.Peer-Reviewed Original ResearchA single dose of the SARS-CoV-2 vaccine BNT162b2 elicits Fc-mediated antibody effector functions and T cell responses
Tauzin A, Nayrac M, Benlarbi M, Gong SY, Gasser R, Beaudoin-Bussières G, Brassard N, Laumaea A, Vézina D, Prévost J, Anand SP, Bourassa C, Gendron-Lepage G, Medjahed H, Goyette G, Niessl J, Tastet O, Gokool L, Morrisseau C, Arlotto P, Stamatatos L, McGuire AT, Larochelle C, Uchil P, Lu M, Mothes W, De Serres G, Moreira S, Roger M, Richard J, Martel-Laferrière V, Duerr R, Tremblay C, Kaufmann DE, Finzi A. A single dose of the SARS-CoV-2 vaccine BNT162b2 elicits Fc-mediated antibody effector functions and T cell responses. Cell Host & Microbe 2021, 29: 1137-1150.e6. PMID: 34133950, PMCID: PMC8175625, DOI: 10.1016/j.chom.2021.06.001.Peer-Reviewed Original ResearchConceptsSingle doseEffector functionsCell responsesSARS-CoV-2-naive individualsSARS-CoV-2 vaccinesBNT162b2 mRNA vaccineSARS-CoV-2Public health authoritiesAntibody effector functionsStandard regimenAntibody immunityT helperVaccine efficacyMRNA vaccinesCellular CD4Health authoritiesDoseDosesPotential roleNaive individualsVaccine scarcityVaccineWeeksEfficacyResponseA Single Immunization with Spike-Functionalized Ferritin Vaccines Elicits Neutralizing Antibody Responses against SARS-CoV‑2 in Mice
Powell A, Zhang K, Sanyal M, Tang S, Weidenbacher P, Li S, Pham T, Pak J, Chiu W, Kim P. A Single Immunization with Spike-Functionalized Ferritin Vaccines Elicits Neutralizing Antibody Responses against SARS-CoV‑2 in Mice. ACS Central Science 2021, 7: 183-199. PMID: 33527087, PMCID: PMC7805605, DOI: 10.1021/acscentsci.0c01405.Peer-Reviewed Original ResearchSARS-CoV-2 spikeSelf-assembling ferritin nanoparticlesElicitation of neutralizing antibodiesFerritin-based vaccinesReceptor-binding domainSARS-CoV-2 vaccinesSingle-dose vaccinationImmunization of miceSubunit vaccine candidateVaccine elicitationCOVID-19 patientsEffective SARS-CoV-2 vaccineNeutralization titersClinical trialsConvalescent plasmaPublic health prioritySpike receptor-binding domainAntibody responseNanoparticle platformPseudovirus assayVaccine candidatesMonoclonal antibodiesSARS-CoV-2Ferritin nanoparticlesMice
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