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
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 approach