2024
Do domain-specific protein language models outperform general models on immunology-related tasks?
Deutschmann N, Pelissier A, Weber A, Gao S, Bogojeska J, Martínez M. Do domain-specific protein language models outperform general models on immunology-related tasks? ImmunoInformatics 2024, 14: 100036. DOI: 10.1016/j.immuno.2024.100036.Peer-Reviewed Original ResearchProtein language modelsDevelopment of bioinformatics pipelinesAmino acid sequenceAntigen recognition capabilitiesBioinformatics pipelineAcid sequenceProtein functionDomain-specific modelsEvolutionary changesB cell receptorAdaptive immune system responsesImmune receptorsT cell receptorB cellsT cellsImmune system responseDownstream analytical tasksVector embeddingsRepresentation capabilityLanguage modelImmune responseEmbedding layerReceptorsAnalytical tasks
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
2020
Computational Model Reveals a Stochastic Mechanism behind Germinal Center Clonal Bursts
Pélissier A, Akrout Y, Jahn K, Kuipers J, Klein U, Beerenwinkel N, Martínez M. Computational Model Reveals a Stochastic Mechanism behind Germinal Center Clonal Bursts. Cells 2020, 9: 1448. PMID: 32532145, PMCID: PMC7349200, DOI: 10.3390/cells9061448.Peer-Reviewed Original ResearchConceptsClonal diversityB cell receptorSequence of nucleotidesEvolutionary phylogenetic treesGC dynamicsIn silico vaccine designPhylogenetic treeClonal dominanceAffinity to antigenB cell differentiationSpecialized compartmentsAntibody genesGenetic eventsInterclonal competitionClonal burstEvolutionary processB cell maturationIntracellular componentsB-cell variantsClonal dynamicsSomatic hypermutationB cellsIncreased affinityAffinity maturationGerminal centers