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
2023
The Plasma Cell Infiltrate Populating the Muscle Tissue of Patients with Inclusion Body Myositis Features Distinct B Cell Receptor Repertoire Properties
Jiang R, Roy B, Wu Q, Mohanty S, Nowak R, Shaw A, Kleinstein S, O’Connor K. The Plasma Cell Infiltrate Populating the Muscle Tissue of Patients with Inclusion Body Myositis Features Distinct B Cell Receptor Repertoire Properties. ImmunoHorizons 2023, 7: 310-322. PMID: 37171806, PMCID: PMC10579972, DOI: 10.4049/immunohorizons.2200078.Peer-Reviewed Original ResearchConceptsInclusion body myositisMemory B cellsCell infiltrateBody myositisB cellsIBM muscle biopsiesB-cell infiltratesPlasma cell infiltrateClass-switched IgGMuscle tissueAdaptive immune receptor repertoire sequencingHumoral responseHealthy controlsIgA isotypePlasma cellsCell repertoireMuscle biopsyInfiltratesDegenerative disordersDisease pathologyRepertoire sequencingSkeletal muscleDermatomyositisPolymyositisMyositis
2019
Phenotypic and Ig Repertoire Analyses Indicate a Common Origin of IgD−CD27− Double Negative B Cells in Healthy Individuals and Multiple Sclerosis Patients
Fraussen J, Marquez S, Takata K, Beckers L, Montes Diaz G, Zografou C, Van Wijmeersch B, Villar LM, O'Connor KC, Kleinstein SH, Somers V. Phenotypic and Ig Repertoire Analyses Indicate a Common Origin of IgD−CD27− Double Negative B Cells in Healthy Individuals and Multiple Sclerosis Patients. The Journal Of Immunology 2019, 203: 1650-1664. PMID: 31391234, PMCID: PMC6736705, DOI: 10.4049/jimmunol.1801236.Peer-Reviewed Original ResearchConceptsDN B cellsDouble-negative B cellsMultiple sclerosis patientsMS patientsNegative B cellsHealthy controlsClass-switched memoryB cellsAdaptive immune receptor repertoire sequencingSclerosis patientsRepertoire sequencingFrequency of CD95Naive B cellsUnique differentiation pathwayLow CD5Proinflammatory characteristicsImmune agingCD38 expressionHealthy individualsPatientsFlow cytometryLow mutation loadCD27Repertoire analysisMaturation state
2018
AIRR Community Standardized Representations for Annotated Immune Repertoires
Vander Heiden J, Marquez S, Marthandan N, Bukhari SAC, Busse CE, Corrie B, Hershberg U, Kleinstein SH, Matsen F, Ralph DK, Rosenfeld AM, Schramm CA, Community T, Christley S, Laserson U. AIRR Community Standardized Representations for Annotated Immune Repertoires. Frontiers In Immunology 2018, 9: 2206. PMID: 30323809, PMCID: PMC6173121, DOI: 10.3389/fimmu.2018.02206.Peer-Reviewed Original Research