Epitope-anchored contrastive transfer learning for paired CD8+ T cell receptor–antigen recognition
Zhang Y, Wang Z, Jiang Y, Littler D, Gerstein M, Purcell A, Rossjohn J, Ou H, Song J. Epitope-anchored contrastive transfer learning for paired CD8+ T cell receptor–antigen recognition. Nature Machine Intelligence 2024, 6: 1344-1358. DOI: 10.1038/s42256-024-00913-8.Peer-Reviewed Original ResearchPeptide-major histocompatibility complexT cellsEpitope-specific T cellsImmune responseResidue-level interactionsPredicted binding strengthSpike-specific immune responsesTCR-based immunotherapyTumor-associated antigensT cell antigen recognitionPredicted binding specificityAdaptive immune responsesTCR cross-reactivityTCR repertoireCross-reactivityBinding specificityAutoimmune diseasesImmunodominant epitopesContact residuesAntigen recognitionHistocompatibility complexTCRImmunotherapyDistance matrixT-cell receptor-antigen recognitionSpatially Informed Gene Signatures for Response to Immunotherapy in Melanoma.
Aung T, Warrell J, Martinez-Morilla S, Gavrielatou N, Vathiotis I, Yaghoobi V, Kluger H, Gerstein M, Rimm D. Spatially Informed Gene Signatures for Response to Immunotherapy in Melanoma. Clinical Cancer Research 2024, 30: 3520-3532. PMID: 38837895, PMCID: PMC11326985, DOI: 10.1158/1078-0432.ccr-23-3932.Peer-Reviewed Original ResearchGene signatureResistance to immunotherapyResponse to immunotherapyPrediction of treatment outcomeResistant to treatmentAccurate prediction of treatment outcomePredictive of responseImmunotherapy outcomesMelanoma patientsMelanoma specimensValidation cohortPatient stratificationDiscovery cohortTreatment outcomesImmunotherapyMelanomaTumorPatientsCohortS100BOutcomesGene expression dataGenesCD68+macrophagesExpression data