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
2023
Computational modelling of immunological mechanisms: From statistical approaches to interpretable machine learning
Martínez M, Barberis M, Niarakis A. Computational modelling of immunological mechanisms: From statistical approaches to interpretable machine learning. ImmunoInformatics 2023, 12: 100029. DOI: 10.1016/j.immuno.2023.100029.Peer-Reviewed Original ResearchHigh-throughput experimental technologiesComputational biologyDevelopment of high-throughput experimental technologiesImmune systemHigh-throughput data analysisImmunological mechanismsMolecular functionsSystems biologyImmune-related diseasesOptimal immunotherapyTherapeutic optionsAutoimmune diseasesComplex disorderInterpretable machine learningMachine learning modelsCellular interactionsGeneration of computational modelsBiologyComputer scienceMachine learningMachine-learning modelsDiverse domainsLearning modelsExperimental technologyInterpretable machine
2021
Diagnostics and correction of batch effects in large‐scale proteomic studies: a tutorial
Čuklina J, Lee C, Williams E, Sajic T, Collins B, Rodríguez Martínez M, Sharma V, Wendt F, Goetze S, Keele G, Wollscheid B, Aebersold R, Pedrioli P. Diagnostics and correction of batch effects in large‐scale proteomic studies: a tutorial. Molecular Systems Biology 2021, 17: msb202110240. PMID: 34432947, PMCID: PMC8447595, DOI: 10.15252/msb.202110240.Peer-Reviewed Original ResearchConceptsBatch effectsProteomic studiesLarge-scale proteomic studiesCorrection of batch effectsMass spectrometry-based proteomicsStep-by-step protocolProteomic datasetsProteomic dataSystems biologyBatch correctionMultiple experimental designsProteomic ChallengeR packageProteomicsClinical proteomicsBiological signalsTechnical variabilityStatistical powerIntensity driftBiology