2019
A linked data graph approach to integration of immunological data
Bukhari SAC, Mandell J, Kleinstein SH, Cheung KH. A linked data graph approach to integration of immunological data. Bioinformatics And Biomedicine 2019, 00: 1742-1749. PMID: 34707915, PMCID: PMC8547546, DOI: 10.1109/bibm47256.2019.8982986.Peer-Reviewed Original ResearchGraph databaseDatabase technologyGraph-based query languageNatural language query interfaceNoSQL database technologyGraph-based databasesNeo4j graph databaseSQL database technologyHeterogeneous biological dataWeb-based dashboardQuery interfaceQuery languageData retrievalData integrationMultiple data typesBiological databasesData repositoryData typesResponse measurement dataGraph approachPathway dataData setsUsersBiological dataScalable method
2018
The CAIRR Pipeline for Submitting Standards-Compliant B and T Cell Receptor Repertoire Sequencing Studies to the National Center for Biotechnology Information Repositories
Bukhari SAC, O’Connor M, Martínez-Romero M, Egyedi AL, Willrett D, Graybeal J, Musen MA, Rubelt F, Cheung KH, Kleinstein SH. The CAIRR Pipeline for Submitting Standards-Compliant B and T Cell Receptor Repertoire Sequencing Studies to the National Center for Biotechnology Information Repositories. Frontiers In Immunology 2018, 9: 1877. PMID: 30166985, PMCID: PMC6105692, DOI: 10.3389/fimmu.2018.01877.Peer-Reviewed Original ResearchConceptsMetadata qualityInformation repositoryAdaptive immune receptor repertoiresLarge-scale dataWeb–based templateSoftware frameworkData annotationData standardsEffective sharingAIRR-seq dataReceptor repertoireData submittersCell receptorSequence filesAdaptive immune responsesRepositoryImmune receptor repertoiresMetadataData setsT cell receptorArchive databaseB cell receptorCEDAR
Musen M, Sansone S, Cheung K, Kleinstein S, Crafts M, Schürer S, Graybeal J. CEDAR. 2018, 427-428. DOI: 10.1145/3184558.3186200.Peer-Reviewed Original ResearchPublic repositoriesScientific data setsLibrary of templatesData annotationExperimental metadataRelevant datasetsMetadataWeb-based methodsOnline datasetsOwn devicesRepositoryDatasetData setsAuthoringScientific ontologyMajor research projectOntologyRetrievalResearch projectAnnotationLack of standardizationScientific communityTechnologyTemplateSet
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