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 specificityPCfun: a hybrid computational framework for systematic characterization of protein complex function
Sharma V, Fossati A, Ciuffa R, Buljan M, Williams E, Chen Z, Shao W, Pedrioli P, Purcell A, Martínez M, Song J, Manica M, Aebersold R, Li C. PCfun: a hybrid computational framework for systematic characterization of protein complex function. Briefings In Bioinformatics 2022, 23: bbac239. PMID: 35724564, PMCID: PMC9310514, DOI: 10.1093/bib/bbac239.Peer-Reviewed Original ResearchMeSH KeywordsComputational BiologyDatabases, ProteinGene OntologyHumansNatural Language ProcessingProteinsConceptsProtein complex functionGO termsProtein complex databasesGene Ontology (GONatural language processing techniquesRandom forestLanguage processing techniquesNearest neighborsProtein complexesSystematic annotationCellular statesBiological functionsBiological processesQuery vectorComplex queriesWord vectorsUnsupervised approachSupervised approachChild termsProteinMolecular biologySubunit compositionComplex databasesComplex functionsComputational framework
2020
FPGA Accelerated Analysis of Boolean Gene Regulatory Networks
Manica M, Polig R, Purandare M, Mathis R, Hagleitner C, Martínez M. FPGA Accelerated Analysis of Boolean Gene Regulatory Networks. IEEE/ACM Transactions On Computational Biology And Bioinformatics 2020, 17: 2141-2147. PMID: 31494553, DOI: 10.1109/tcbb.2019.2936836.Peer-Reviewed Original ResearchMeSH KeywordsComputational BiologyComputer SimulationGene Regulatory NetworksHumansLeukemia, Large Granular LymphocyticModels, GeneticSoftwareConceptsQualitative models of gene regulatory networksModels of gene regulatory networksAdvanced high-throughput technologiesGene regulatory networksHigh-throughput technologiesComplex molecular networkBoolean modelRegulatory networksBiological insightsT-cell large granular lymphocytic leukemiaMolecular networksAttractor detectionField Programmable Gate ArrayLarge granular lymphocytic leukemiaSoftware simulation toolGranular lymphocytic leukemiaSimulation toolPerformance improvementReconfigurable integrated circuits