2023
Exploring the impact of clonal definition on B-cell diversity: implications for the analysis of immune repertoires
Pelissier A, Luo S, Stratigopoulou M, Guikema J, Martínez M. Exploring the impact of clonal definition on B-cell diversity: implications for the analysis of immune repertoires. Frontiers In Immunology 2023, 14: 1123968. PMID: 37138881, PMCID: PMC10150052, DOI: 10.3389/fimmu.2023.1123968.Peer-Reviewed Original ResearchConceptsClonal diversityB cell receptorB cellsB cell diversityHigh-throughput sequencing technologyAlignment-free methodsAnalysis of immune repertoiresAlignment-based methodsPatterns of variationB cell receptor sequencesSequencing technologiesClonal clustersClonal identificationB cell repertoireActivated B cellsAdaptive immune responsesDiversity indexHigh-throughput characterizationAdaptive immune systemShort sequencesClonal characterizationClonal familiesClonesRepertoire dataSomatic hypermutation
2022
DECODE: a computational pipeline to discover T cell receptor binding rules
Papadopoulou I, Nguyen A, Weber A, Martínez M. DECODE: a computational pipeline to discover T cell receptor binding rules. Bioinformatics 2022, 38: i246-i254. PMID: 35758821, PMCID: PMC9235487, DOI: 10.1093/bioinformatics/btac257.Peer-Reviewed Original ResearchConceptsT cell receptor bindingT cell receptorComputational pipelineTCR-epitope bindingBlack-box natureSequence motifsSequencing technologiesSupplementary dataBlack-box modelsBiochemical rulesMachine learningVisualization toolsComputational rulesDecodingData abundanceSequenceBioinformaticsEasy-to-useAdaptive immune responsesBindingBinding propertiesT cell-based therapiesT-cell receptor sequencingTCR bindingTCR specificity