2024
nf-core/airrflow: An adaptive immune receptor repertoire analysis workflow employing the Immcantation framework.
Gabernet G, Marquez S, Bjornson R, Peltzer A, Meng H, Aron E, Lee N, Jensen C, Ladd D, Polster M, Hanssen F, Heumos S, , Yaari G, Kowarik M, Nahnsen S, Kleinstein S. nf-core/airrflow: An adaptive immune receptor repertoire analysis workflow employing the Immcantation framework. PLOS Computational Biology 2024, 20: e1012265. PMID: 39058741, PMCID: PMC11305553, DOI: 10.1371/journal.pcbi.1012265.Peer-Reviewed Original ResearchImmcantation frameworkAIRR-seqAIRR-seq dataAdaptive immune receptor repertoire sequencingSingle-cell sequencing datasetsClonal inferenceSequencing errorsSequencing datasetsNextflow workflowClonal relationshipReceptor sequencesRepertoire sequencingHigh-throughput processingSequenceImmune challengeAnalysis workflowT-cell receptor sequencingNextflowB cellsSARS-CoV-2Experimental toolResponse to SARS-CoV-2Infectious diseases
2021
Mind the gap from research laboratory to clinic: Challenges and opportunities for next-generation assays in human diseases
D'Souza MP, Palin AC, Calder T, Golding H, Kleinstein SH, Milliken EL, O'Connor D, Tomaras G, Warren J, Boggiano C. Mind the gap from research laboratory to clinic: Challenges and opportunities for next-generation assays in human diseases. Vaccine 2021, 39: 5233-5239. PMID: 34366145, PMCID: PMC8343370, DOI: 10.1016/j.vaccine.2021.07.071.Peer-Reviewed Original ResearchConceptsNext-generation assaysSevere acute respiratory syndrome coronavirus type 2Human immunodeficiency virusCoronavirus type 2National InstituteVaccine delivery methodNovel animal modelProtective immunityImmunodeficiency virusLicensed vaccineEffective vaccineModern vaccinologyPowerful adjuvantAnimal modelsImproved vaccinesType 2Immune systemImmunogen designVaccine developmentInfectious diseasesVaccineGeneration assaysTuberculosisDiseaseCritical pathogens
2015
Neutralizing antibodies against West Nile virus identified directly from human B cells by single-cell analysis and next generation sequencing
Tsioris K, Gupta NT, Ogunniyi AO, Zimnisky RM, Qian F, Yao Y, Wang X, Stern JN, Chari R, Briggs AW, Clouser CR, Vigneault F, Church GM, Garcia MN, Murray KO, Montgomery RR, Kleinstein SH, Love JC. Neutralizing antibodies against West Nile virus identified directly from human B cells by single-cell analysis and next generation sequencing. Integrative Biology 2015, 7: 1587-1597. PMID: 26481611, PMCID: PMC4754972, DOI: 10.1039/c5ib00169b.Peer-Reviewed Original ResearchConceptsHumoral responseNext-generation sequencingB cellsWest Nile virus infectionSevere neurological illnessMemory B cellsAntibody-secreting cellsCohort of subjectsWNV-specific antibodiesHuman B cellsMosquito-borne diseaseWest Nile virusAnamnestic responseAntibody responseAvailable treatmentsClinical severityAntibody isotypesNeurological illnessVaccine studiesVirus infectionGeneration sequencingInfectious diseasesPrevious exposureTherapeutic antibodiesAntibodies