2023
FLAN: feature-wise latent additive neural models for biological applications
Nguyen A, Vasilaki S, Martínez M. FLAN: feature-wise latent additive neural models for biological applications. Briefings In Bioinformatics 2023, 24: bbad056. PMID: 37031956, PMCID: PMC10199769, DOI: 10.1093/bib/bbad056.Peer-Reviewed Original ResearchConceptsLearning modelsDeep neural networksDeep learning modelsMachine learning modelsBenchmark datasetsLatent spaceNeural modelNeural networkAlgorithmic decisionsEnd-usersBlack-boxComplex datasetsAggregated representationDecision processCritical scenariosImpressive resultsDatasetIndividual featuresRepresentationBiological domainData availabilityCodeUsersDecisionPerformance
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