2024
Stochastic modeling of a gene regulatory network driving B cell development in germinal centers
Koshkin A, Herbach U, Martínez M, Gandrillon O, Crauste F. Stochastic modeling of a gene regulatory network driving B cell development in germinal centers. PLOS ONE 2024, 19: e0301022. PMID: 38547073, PMCID: PMC10977792, DOI: 10.1371/journal.pone.0301022.Peer-Reviewed Original ResearchMeSH KeywordsB-LymphocytesGene Expression ProfilingGene Regulatory NetworksGerminal CenterHumansSystems BiologyConceptsGene regulatory network structureGene regulatory networksGene expression dataExpression dataB cell differentiationSingle-cellAssociated with cell developmentGC B cell differentiationStages of B-cell differentiationB cell developmentSelection of B cellsGene regulationRegulatory networksTranscriptome dataSystems biologyHigh-affinity antibodiesRegulatory mechanismsCell developmentGenesAdaptive immune systemMRNA distributionPlasmablast stageGerminal centersDifferentiationImmune system
2020
PaccMann: a web service for interpretable anticancer compound sensitivity prediction
Cadow J, Born J, Manica M, Oskooei A, Martínez M. PaccMann: a web service for interpretable anticancer compound sensitivity prediction. Nucleic Acids Research 2020, 48: w502-w508. PMID: 32402082, PMCID: PMC7319576, DOI: 10.1093/nar/gkaa327.Peer-Reviewed Original ResearchMeSH KeywordsAntineoplastic AgentsComputer SimulationDrug RepositioningGene Expression ProfilingInternetNeural Networks, ComputerSirolimusSoftwareConceptsWeb servicesAttention-based neural networkState-of-the-art methodsState-of-the-artOutputs confidence scoresCompound structure informationInteractive editorModel decision makingChemical sub-structuresAttention heatmapsNeural networkWeb-based platformModel interpretationEfficient validationConfidence scoresDrug repositioningCompound structureDrug compoundsWebSource of informationStructural informationCompoundsBiomolecular samplesDecision makingPotential compounds
2012
Quantitative modeling of the terminal differentiation of B cells and mechanisms of lymphomagenesis
Martínez M, Corradin A, Klein U, Álvarez M, Toffolo G, di Camillo B, Califano A, Stolovitzky G. Quantitative modeling of the terminal differentiation of B cells and mechanisms of lymphomagenesis. Proceedings Of The National Academy Of Sciences Of The United States Of America 2012, 109: 2672-2677. PMID: 22308355, PMCID: PMC3289327, DOI: 10.1073/pnas.1113019109.Peer-Reviewed Original ResearchMeSH KeywordsB-LymphocytesCell DifferentiationGene Expression ProfilingHumansImmunologic MemoryLymphomaConceptsB-cell exitTranscriptional regulatory modulesTerminal differentiationTerminal differentiation of B cellsSelf-regulatory interactionsGene expression profiling dataMechanisms of lymphomagenesisExpression profiling dataMature human B cellsRegulatory modulesGene regulationT cell signalingB cellsCellular statesDifferentiation of B cellsHuman B cellsGerminal centersTumorigenic alterationsGenesQuantitative kinetic modelMemory B cellsAssociated with lymphomagenesisFeedback loopLymphomagenesisT cells