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
2019
Network-based Biased Tree Ensembles (NetBiTE) for Drug Sensitivity Prediction and Drug Sensitivity Biomarker Identification in Cancer
Oskooei A, Manica M, Mathis R, Martínez M. Network-based Biased Tree Ensembles (NetBiTE) for Drug Sensitivity Prediction and Drug Sensitivity Biomarker Identification in Cancer. Scientific Reports 2019, 9: 15918. PMID: 31685861, PMCID: PMC6828742, DOI: 10.1038/s41598-019-52093-w.Peer-Reviewed Original ResearchConceptsMembrane receptor pathwayDrug sensitivity predictionProtein-protein interaction networkDrug sensitivityGenomics of Drug SensitivityDrug targetsGene expression dataIGFR signaling pathwaysAssignment of high weightsBiomarker identificationExpression dataInteraction networkSensitivity predictionSignaling pathwaySignaling pathway inhibitorsReceptor pathwayTree ensemblesPathway inhibitorPathwayGenomeGenesGDSCNeighborhoods of influenceIdentificationSynthetic datasets
2016
Depletion of FOXM1 via MET Targeting Underlies Establishment of a DNA Damage–Induced Senescence Program in Gastric Cancer
Francica P, Nisa L, Aebersold D, Langer R, Bladt F, Blaukat A, Stroka D, Martínez M, Zimmer Y, Medová M. Depletion of FOXM1 via MET Targeting Underlies Establishment of a DNA Damage–Induced Senescence Program in Gastric Cancer. Clinical Cancer Research 2016, 22: 5322-5336. PMID: 27185371, DOI: 10.1158/1078-0432.ccr-15-2987.Peer-Reviewed Original ResearchConceptsDNA damage-induced senescenceMET inhibitionMET targetingGastric tumorsNegative regulator of senescenceHuman gastric cancer cell linesGastric cancer cell linesInfliction of DNA damageAberrant MET expressionEctopic expression of FoxM1Tumor tissue microarraysCopy number alterationsRegulation of senescenceMET receptor tyrosine kinaseDepletion of FOXM1Receptor tyrosine kinasesGastric tumor cellsExpression of FoxM1Cancer cell linesCancer Genome AtlasDownregulation of FoxM1Deregulated signalingDownstream effectorsNegative regulatorTumor radiosensitivity
2007
Input–output robustness in simple bacterial signaling systems
Shinar G, Milo R, Martínez M, Alon U. Input–output robustness in simple bacterial signaling systems. Proceedings Of The National Academy Of Sciences Of The United States Of America 2007, 104: 19931-19935. PMID: 18077424, PMCID: PMC2148400, DOI: 10.1073/pnas.0706792104.Peer-Reviewed Original Research