Featured Publications
A 3D transcriptomics atlas of the mouse nose sheds light on the anatomical logic of smell
Ruiz Tejada Segura M, Abou Moussa E, Garabello E, Nakahara T, Makhlouf M, Mathew L, Wang L, Valle F, Huang S, Mainland J, Caselle M, Osella M, Lorenz S, Reisert J, Logan D, Malnic B, Scialdone A, Saraiva L. A 3D transcriptomics atlas of the mouse nose sheds light on the anatomical logic of smell. Cell Reports 2022, 38: 110547. PMID: 35320714, PMCID: PMC8995392, DOI: 10.1016/j.celrep.2022.110547.Peer-Reviewed Original ResearchDifferential 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 ResearchConceptsOlfactory 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-neuronalHigh-throughput spatial mapping of single-cell RNA-seq data to tissue of origin
Achim K, Pettit J, Saraiva L, Gavriouchkina D, Larsson T, Arendt D, Marioni J. High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin. Nature Biotechnology 2015, 33: 503-509. PMID: 25867922, DOI: 10.1038/nbt.3209.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 ResearchConceptsPublic 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
Heterogeneity of hypothalamic pro-opiomelanocortin-expressing neurons revealed by single-cell RNA sequencing
Lam B, Cimino I, Polex-Wolf J, Kohnke S, Rimmington D, Iyemere V, Heeley N, Cossetti C, Schulte R, Saraiva L, Logan D, Blouet C, O'Rahilly S, Coll A, Yeo G. Heterogeneity of hypothalamic pro-opiomelanocortin-expressing neurons revealed by single-cell RNA sequencing. Molecular Metabolism 2017, 6: 383-392. PMID: 28462073, PMCID: PMC5404100, DOI: 10.1016/j.molmet.2017.02.007.Peer-Reviewed Original ResearchConceptsPOMC neuronsArcuate POMC neuronsControl of body weightUnbiased clustering analysisExpressed low levelsExpressed high levelsArcuate proopiomelanocortinRNA sequencingLeptin receptorAtlas of gene expressionSingle cell RNA sequencingGene expression profilesSingle-cell RNA sequencingCell RNA sequencingNeuronsBody weightLeptinInsulin receptorProopiomelanocortinHeterogeneous populationReceptorsExpression profilesGene expressionExpression
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 ResearchConceptsCell 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 approachMolecular and neuronal homology between the olfactory systems of zebrafish and mouse
Saraiva L, Ahuja G, Ivandic I, Syed A, Marioni J, Korsching S, Logan D. Molecular and neuronal homology between the olfactory systems of zebrafish and mouse. Scientific Reports 2015, 5: 11487. PMID: 26108469, PMCID: PMC4480006, DOI: 10.1038/srep11487.Peer-Reviewed Original ResearchConceptsDegree of molecular conservationYears of evolutionary divergenceVomeronasal organOlfactory mucosaOlfactory organChemosensory receptor genesOlfactory systemTranscriptome of miceDual olfactory systemEvolutionary divergenceMolecular conservationNeuronal homologRepertoire sizeRNA abundanceMolecular relationshipsCell-specific markersClasses of neuronsMolecular basisChemosensory receptorsMarker genesOrgans of rodentsAbsolute abundanceZebrafishReceptor geneVertebrates
2014
The Olfactory Transcriptomes of Mice
Ibarra-Soria X, Levitin M, Saraiva L, Logan D. The Olfactory Transcriptomes of Mice. PLOS Genetics 2014, 10: e1004593. PMID: 25187969, PMCID: PMC4154679, DOI: 10.1371/journal.pgen.1004593.Peer-Reviewed Original ResearchConceptsVomeronasal receptorsVR genesProtein-coding genesProtein coding sequencesDeep RNA sequencingDistribution of abundanceEvidence of expressionCell-specific expressionReference genomeGene annotationMultiple malesMulti-exonQuantitative catalogOlfactory tissueMouse genomeCoding sequenceOR genesOlfactory-mediated behaviorsGenomic techniquesExpression microarraysRNA sequencingGene expressionGenesQuantitative RT-PCRSexual dimorphism