2024
Cell-specific gene networks and drivers in rheumatoid arthritis synovial tissues
Pelissier A, Laragione T, Gulko P, Martínez M. Cell-specific gene networks and drivers in rheumatoid arthritis synovial tissues. Frontiers In Immunology 2024, 15: 1428773. PMID: 39161769, PMCID: PMC11330812, DOI: 10.3389/fimmu.2024.1428773.Peer-Reviewed Original ResearchTranscription factorsNatural killer TPhenotypic differencesGene regulatory networksCo-regulatory networkRNA-seq databaseCell typesFibroblast-like synoviocytesRNA-seqRegulatory networksGene networksTF clustersMultiple cell typesB cellsCell regulationKiller TRheumatoid arthritis synovial tissuePhenotypic groupsRA pathogenesisRA synovial tissuePathway changesTissue genesGenesCompare network propertiesComputational approachStochastic 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 ResearchConceptsGene 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
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 ResearchConceptsQualitative 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 circuitsIdentifying the Potential Mechanism of Action of SNPs Associated With Breast Cancer Susceptibility With GVITamIN
Nguyen A, Nicoletti P, Arnol D, Califano A, Martínez M. Identifying the Potential Mechanism of Action of SNPs Associated With Breast Cancer Susceptibility With GVITamIN. Frontiers In Bioengineering And Biotechnology 2020, 8: 798. PMID: 32850701, PMCID: PMC7417307, DOI: 10.3389/fbioe.2020.00798.Peer-Reviewed Original ResearchSingle-nucleotide polymorphismsAssociated with complex traitsCancer-related transcription factorsGenome-wide association studiesGene regulatory networksTranscriptional regulatory programsSystems biology approachBreast cancer-associated single-nucleotide polymorphismsRecombinational repair mechanismsComplex traitsRAD51B geneAssociation studiesRegulatory networksBreast cancer susceptibilityTranscription factorsBiology approachHeritable traitRegulatory programsMolecular phenotypesOncogenic mechanismsRegulatory activityCancer susceptibilityRepair mechanismsTest associationsHomologous recombination repair mechanisms