2021
Multiscale Modeling of Germinal Center Recapitulates the Temporal Transition From Memory B Cells to Plasma Cells Differentiation as Regulated by Antigen Affinity-Based Tfh Cell Help
Tejero E, Lashgari D, García-Valiente R, Gao X, Crauste F, Robert P, Meyer-Hermann M, Martínez M, van Ham S, Guikema J, Hoefsloot H, van Kampen A. Multiscale Modeling of Germinal Center Recapitulates the Temporal Transition From Memory B Cells to Plasma Cells Differentiation as Regulated by Antigen Affinity-Based Tfh Cell Help. Frontiers In Immunology 2021, 11: 620716. PMID: 33613551, PMCID: PMC7892951, DOI: 10.3389/fimmu.2020.620716.Peer-Reviewed Original ResearchMeSH KeywordsAsymmetric Cell DivisionB-LymphocytesCD40 AntigensCell LineageComputer SimulationGene Regulatory NetworksGerminal CenterHumansImmunologic MemoryInterferon Regulatory FactorsLymphopoiesisModels, ImmunologicalPlasma CellsPositive Regulatory Domain I-Binding Factor 1Proto-Oncogene Proteins c-bcl-6Signal TransductionT Follicular Helper CellsTime FactorsConceptsB cell to plasma cell differentiationAsymmetric divisionRegulatory interactions of transcription factorsPlasma cell differentiationInteraction of transcription factorsCore gene regulatory networkGene regulatory networksCell differentiationCell-fate decisionsTemporal switchB cell receptor affinityGerminal center reactionB cellsCD40 signaling pathwayRegulatory networksRegulatory interactionsTranscription factorsEffective immune protectionCenter reactionSignaling pathwayAdaptive immune systemT follicular helper cellsPlasma cell generationMemory B cellsMolecular modules
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 circuitsComputational 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 centersPaccMann: 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
2010
Messenger RNA fluctuations and regulatory RNAs shape the dynamics of a negative feedback loop
Martínez M, Soriano J, Tlusty T, Pilpel Y, Furman I. Messenger RNA fluctuations and regulatory RNAs shape the dynamics of a negative feedback loop. Physical Review E 2010, 81: 031924. PMID: 20365787, DOI: 10.1103/physreve.81.031924.Peer-Reviewed Original ResearchConceptsSingle-cell levelRegulatory RNAsGene expression variabilityIndividual cellsPost-transcriptional regulationNoncoding regulatory RNAsCell population levelNegative feedback loopSingle-cell experimentsRegulatory networksRNA transcriptsRepress translationRegulatory transcriptsPost-transcriptionallyExpression variabilityRNAStochastic eventsMessenger RNATranscriptionProtein expressionMessengerCell populationsPopulation levelCellsFeedback loop