Featured Publications
Differential regulation of the immune system in a brain-liver-fats organ network during short-term fasting
Huang S, Makhlouf M, AbouMoussa E, Segura M, Mathew L, Wang K, Leung M, Chaussabel D, Logan D, Scialdone A, Garand M, Saraiva L. Differential regulation of the immune system in a brain-liver-fats organ network during short-term fasting. Molecular Metabolism 2020, 40: 101038. PMID: 32526449, PMCID: PMC7339127, DOI: 10.1016/j.molmet.2020.101038.Peer-Reviewed Original ResearchConceptsShort-term fastingGene Ontology enrichment analysisOntology enrichment analysisReactome pathway analysisInnate immune signalingCombination of multivariate analysisImmune systemPriming of adaptive immunityChronic immunological disordersTranscriptional dynamicsGene setsGene OntologyWhite adipose tissueAdipose tissueProtein dataRNA sequencingBrown adipose tissueExpression analysisEnrichment analysisImmune signalingProfiles of miceDifferential regulationBiological pathwaysPathway analysisMolecular mechanismsA transcriptomic atlas of mammalian olfactory mucosae reveals an evolutionary influence on food odor detection in humans
Saraiva L, Riveros-McKay F, Mezzavilla M, Abou-Moussa E, Arayata C, Makhlouf M, Trimmer C, Ibarra-Soria X, Khan M, Van Gerven L, Jorissen M, Gibbs M, O'Flynn C, McGrane S, Mombaerts P, Marioni J, Mainland J, Logan D. A transcriptomic atlas of mammalian olfactory mucosae reveals an evolutionary influence on food odor detection in humans. Science Advances 2019, 5: eaax0396. PMID: 31392275, PMCID: PMC6669018, DOI: 10.1126/sciadv.aax0396.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBiological EvolutionFoodGene Expression ProfilingHumansLigandsMaleMammalsOdorantsOlfactory MucosaOlfactory Receptor NeuronsReceptors, OdorantTranscriptomeConceptsOlfactory sensory neuronsChemosensory receptor gene familiesSpecies-specific adaptationsOlfactory sensory neurons subtypesCanonical olfactory receptorsReceptor gene familyOlfactory mucosa samplesMammalian olfactory mucosaGene familyEcological nichesMammalian evolutionTranscriptomic atlasAnalyzed speciesEvolutionary dynamicsRNA sequencingMammalian olfactory systemEvolutionary influencesOlfactory mucosaHomologous subtypesSensory neuronsOlfactory receptorsMucosa samplesOlfactory systemSubtypesMammalian olfactionHierarchical deconstruction of mouse olfactory sensory neurons: from whole mucosa to single-cell RNA-seq
Saraiva L, Ibarra-Soria X, Khan M, Omura M, Scialdone A, Mombaerts P, Marioni J, Logan D. Hierarchical deconstruction of mouse olfactory sensory neurons: from whole mucosa to single-cell RNA-seq. Scientific Reports 2015, 5: 18178. PMID: 26670777, PMCID: PMC4680959, DOI: 10.1038/srep18178.Peer-Reviewed Original ResearchConceptsMature olfactory sensory neuronsOlfactory sensory neuronsRNA-seqOR genesGene expressionSingle-cell RNA-seqIntact OR genesOlfactory receptorsCell typesSingle-nucleotide polymorphismsOR-expressing OSNsOR gene expressionIntact olfactory receptorsNeuron-one receptor ruleCrude tissue samplesMonoallelic expressionNeuronal cell typesMouse olfactory mucosaMultiple cell typesChemosensory tissuesGenesCellular heterogeneityOlfactory mucosaSensory neuronsNon-neuronal
2023
Genome-Wide RNA Tomography in the Mouse Whole Olfactory Mucosa
Moussa E, Makhlouf M, Mathew L, Saraiva L. Genome-Wide RNA Tomography in the Mouse Whole Olfactory Mucosa. Methods In Molecular Biology 2023, 2710: 19-30. PMID: 37688721, DOI: 10.1007/978-1-0716-3425-7_2.Peer-Reviewed Original Research
2021
SysInflam HuDB, a Web Resource for Mining Human Blood Cells Transcriptomic Data Associated with Systemic Inflammatory Responses to Sepsis
Toufiq M, Huang S, Boughorbel S, Alfaki M, Rinchai D, Saraiva L, Chaussabel D, Garand M. SysInflam HuDB, a Web Resource for Mining Human Blood Cells Transcriptomic Data Associated with Systemic Inflammatory Responses to Sepsis. The Journal Of Immunology 2021, 207: 2195-2202. PMID: 34663591, PMCID: PMC8525868, DOI: 10.4049/jimmunol.2100697.Peer-Reviewed Original ResearchMeSH KeywordsBlood CellsData MiningDatabases as TopicDatasets as TopicGene Expression ProfilingHumansInflammationInternetSepsisSoftwareTranscriptomeUser-Computer InterfaceConceptsPublic transcriptome dataGene expression changesTranscriptome dataTranscriptomic datasetsBlood transcriptome datasetsSystemic inflammatory response to sepsisDisease susceptibilityResponse to infectionBlood gene signaturesExpression changesClinical metadataHost inflammatory responseInflammatory responseSystemic infectionDysregulated host inflammatory responseInflammatory response to sepsisGene signatureSystemic inflammatory responseMechanistic discoveriesSystemic inflammatory diseaseResponse to sepsisHeterogeneous diseaseWeb-based interfaceSepsis biomarkersInflammatory diseases
2017
Variation in olfactory neuron repertoires is genetically controlled and environmentally modulated
Ibarra-Soria X, Nakahara T, Lilue J, Jiang Y, Trimmer C, Souza M, Netto P, Ikegami K, Murphy N, Kusma M, Kirton A, Saraiva L, Keane T, Matsunami H, Mainland J, Papes F, Logan D. Variation in olfactory neuron repertoires is genetically controlled and environmentally modulated. ELife 2017, 6: e21476. PMID: 28438259, PMCID: PMC5404925, DOI: 10.7554/elife.21476.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsGene Expression ProfilingGenetic VariationMiceOlfactory PathwaysOlfactory Receptor NeuronsReceptors, OdorantSequence Analysis, RNAConceptsOlfactory sensory neurons subtypesOlfactory sensory neuronsMouse olfactory sensory neuronsNeuronal diversityOlfactory receptorsOlfactory sensory systemTime-dependent mannerGenetically identical miceRNA sequencing-based methodsSub-stratifiedNeuronal repertoireSensory neuronsSubtype distributionIdentical miceOlfactory stimulationGenetic variationSubtypesMiceEnvironmental factorsDiversityReceptorsRepertoireSensory systemsNeurons
2015
Computational assignment of cell-cycle stage from single-cell transcriptome data
Scialdone A, Natarajan K, Saraiva L, Proserpio V, Teichmann S, Stegle O, Marioni J, Buettner F. Computational assignment of cell-cycle stage from single-cell transcriptome data. Methods 2015, 85: 54-61. PMID: 26142758, DOI: 10.1016/j.ymeth.2015.06.021.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCell CycleCell Line, TumorComputational BiologyEmbryonic Stem CellsGene Expression ProfilingHepatocytesHumansMachine LearningMiceSingle-Cell AnalysisTranscriptomeConceptsCell cycle stageTranscriptomes of single cellsPopulation of cellsSingle-cell transcriptomic dataSingle cellsCell cycle signatureTranscriptome dataCellular statesRNA sequencingCell cycleExpression profilesCell typesTranscriptomePublished datasetsCaptured cellsCustomized predictorCellsComputational approachSupervised machine learning methodsMachine learning methodsNormalisation strategyComputational assignmentLearning methodsPCA-based approach