2020
Position-Dependent Differential Targeting of Somatic Hypermutation
Zhou JQ, Kleinstein SH. Position-Dependent Differential Targeting of Somatic Hypermutation. The Journal Of Immunology 2020, 205: 3468-3479. PMID: 33188076, PMCID: PMC7726104, DOI: 10.4049/jimmunol.2000496.Peer-Reviewed Original ResearchMeSH KeywordsAllelesComputer SimulationHumansImmunoglobulin Heavy ChainsModels, GeneticNucleotide MotifsSomatic Hypermutation, ImmunoglobulinConceptsSomatic hypermutationSHM targetingIg sequencesSame DNA motifTranscription start siteAllele-specific effectsInfluence of selectionGene familyVariable gene familiesDNA motifsSequence neighborhoodError-prone repairStart siteAb diversityDNA lesionsDifferential targetingUnique motifMotifSequenceTargetingHypermutationEffective humoral immunityIntrinsic biasesAffinity maturationLarge collection
2018
Optimized 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
2017
Hierarchical Clustering Can Identify B Cell Clones with High Confidence in Ig Repertoire Sequencing Data
Gupta NT, Adams KD, Briggs AW, Timberlake SC, Vigneault F, Kleinstein SH. Hierarchical Clustering Can Identify B Cell Clones with High Confidence in Ig Repertoire Sequencing Data. The Journal Of Immunology 2017, 198: 2489-2499. PMID: 28179494, PMCID: PMC5340603, DOI: 10.4049/jimmunol.1601850.Peer-Reviewed Original Research
2014
Integrating B Cell Lineage Information into Statistical Tests for Detecting Selection in Ig Sequences
Uduman M, Shlomchik MJ, Vigneault F, Church GM, Kleinstein SH. Integrating B Cell Lineage Information into Statistical Tests for Detecting Selection in Ig Sequences. The Journal Of Immunology 2014, 192: 867-874. PMID: 24376267, PMCID: PMC4363135, DOI: 10.4049/jimmunol.1301551.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAntibody AffinityAntibody DiversityB-Lymphocyte SubsetsCell LineageClonal Selection, Antigen-MediatedComputer SimulationConfounding Factors, EpidemiologicGene Rearrangement, B-LymphocyteGenes, ImmunoglobulinHumansMiceModels, ImmunologicalModels, StatisticalROC CurveSequence Analysis, DNASomatic Hypermutation, ImmunoglobulinVDJ ExonsConceptsLineage treesHigh-throughput sequencing technologyLineage tree shapesCell lineage informationIg sequencesRatio of replacementTree-shape analysisStatistical frameworkSequence-based methodsBinomial statistical analysisExperimental data setsIndicators of selectionSequencing technologiesLineage informationSequencing depthNumber of generationsData setsHybrid methodVivo selectionSilent mutationsTree shapeStatistical testsSequenceShape analysisMutations
2012
Quantifying selection in high-throughput Immunoglobulin sequencing data sets
Yaari G, Uduman M, Kleinstein SH. Quantifying selection in high-throughput Immunoglobulin sequencing data sets. Nucleic Acids Research 2012, 40: e134-e134. PMID: 22641856, PMCID: PMC3458526, DOI: 10.1093/nar/gks457.Peer-Reviewed Original ResearchConceptsQuantifying selectionDifferent selection pressuresHigh-throughput immunoglobulinSomatic hypermutationNext-generation sequencing dataDNA mutation patternsSomatic mutation patternsGroups of sequencesAntigen-driven selection processMutation patternsSequence dataSelection pressureSequencing dataB cell affinity maturationB-cell cancersNegative selection
2003
Estimating Hypermutation Rates from Clonal Tree Data
Kleinstein SH, Louzoun Y, Shlomchik MJ. Estimating Hypermutation Rates from Clonal Tree Data. The Journal Of Immunology 2003, 171: 4639-4649. PMID: 14568938, DOI: 10.4049/jimmunol.171.9.4639.Peer-Reviewed Original ResearchWhy are there so few key mutant clones? The influence of stochastic selection and blocking on affinity maturation in the germinal center
Kleinstein SH, Singh JP. Why are there so few key mutant clones? The influence of stochastic selection and blocking on affinity maturation in the germinal center. International Immunology 2003, 15: 871-884. PMID: 12807826, DOI: 10.1093/intimm/dxg085.sgm.Peer-Reviewed Original Research