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 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
2020
COSIFER: a Python package for the consensus inference of molecular interaction networks
Manica M, Bunne C, Mathis R, Cadow J, Ahsen M, Stolovitzky G, Martínez M. COSIFER: a Python package for the consensus inference of molecular interaction networks. Bioinformatics 2020, 37: 2070-2072. PMID: 33241320, PMCID: PMC8337002, DOI: 10.1093/bioinformatics/btaa942.Peer-Reviewed Original ResearchConceptsAdvent of high-throughput technologiesNetwork inferenceMolecular interaction networksHigh-throughput dataHigh-throughput technologiesState-of-the-artSupplementary dataExpression dataInteraction networkPython source codeInference servicesState-of-the-art methodologiesWeb servicesSource codeMolecular networksWeb-based platformRegulatory apparatusBioinformaticsPython packageConsensus strategyNetworkRobust networkInference methodsInferenceIndividual methods
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