2021
Gaining Insight into SARS-CoV-2 Infection and COVID-19 Severity Using Self-supervised Edge Features and Graph Neural Networks
Sehanobish A, Ravindra N, Van Dijk D. Gaining Insight into SARS-CoV-2 Infection and COVID-19 Severity Using Self-supervised Edge Features and Graph Neural Networks. Proceedings Of The AAAI Conference On Artificial Intelligence 2021, 35: 4864-4873. DOI: 10.1609/aaai.v35i6.16619.Peer-Reviewed Original ResearchSARS-CoV-2 infectionSingle-cell omics dataCOVID-19 severitySingle-cell RNA sequencing datasetsCell typesRNA sequencing datasetsSARS-CoV-2Transcriptomic patternsSequencing datasetsOmics dataCellular determinantsCellular understandingIndividual cellsBronchoalveolar lavage fluid samplesInfected cellsSevere COVID-19Lavage fluid samplesCOVID-19Lung organoidsDisease statesInfectionTranscriptomeCellsSeverityFluid samples
2019
Histone-Related Genes Are Hypermethylated in Lung Cancer and Hypermethylated HIST1H4F Could Serve as a Pan-Cancer Biomarker
Dong S, Li W, Wang L, Hu J, Song Y, Zhang B, Ren X, Ji S, Li J, Xu P, Liang Y, Chen G, Lou J, Yu W. Histone-Related Genes Are Hypermethylated in Lung Cancer and Hypermethylated HIST1H4F Could Serve as a Pan-Cancer Biomarker. Cancer Research 2019, 79: 6101-6112. PMID: 31575549, DOI: 10.1158/0008-5472.can-19-1019.Peer-Reviewed Original ResearchMeSH KeywordsAdultAgedAged, 80 and overBiomarkers, TumorBronchoalveolar Lavage FluidCell Line, TumorCpG IslandsDatasets as TopicDNA MethylationEarly Detection of CancerFemaleGene Expression Regulation, NeoplasticGenetic LociHistonesHumansLung NeoplasmsMaleMiddle AgedPromoter Regions, GeneticWhole Genome SequencingConceptsHistone-related genesWhole-genome DNA methylation analysisDNA methylation analysisHistone genesCancer Genome AtlasMethylation signaturesMethylation analysisGenesGenome AtlasPan-CancerBronchoalveolar lavage fluid samplesHypermethylationLavage fluid samplesEarly cancer diagnosisTCGA datasetPan-cancer biomarkerLung cancerTCGACancer-related deathsLung cancer cohortMethylationCancer cohortTumor typesTumorigenesisCancer diagnosisA potential role of microvesicle-containing miR-223/142 in lung inflammation
Zhang D, Lee H, Wang X, Groot M, Sharma L, Dela Cruz CS, Jin Y. A potential role of microvesicle-containing miR-223/142 in lung inflammation. Thorax 2019, 74: 865-874. PMID: 31331947, PMCID: PMC7036165, DOI: 10.1136/thoraxjnl-2018-212994.Peer-Reviewed Original ResearchConceptsAcute lung injuryNLRP3 inflammasome activationLung inflammationInflammasome activationMacrophage-mediated inflammatory responsesBronchoalveolar lavage fluid samplesIntratracheal lipopolysaccharide (LPS) instillationUncontrolled lung inflammationInhibition of NLRP3Inflammatory lung responseLavage fluid samplesFunctions of microvesiclesLung injuryLipopolysaccharide instillationLung responseIntratracheal instillationInflammatory responseLung macrophagesMurine lungMacrophage activationMiR-223BALFInflammationLPSMiR-142
2016
Longitudinal analysis of the lung microbiota of cynomolgous macaques during long-term SHIV infection
Morris A, Paulson J, Talukder H, Tipton L, Kling H, Cui L, Fitch A, Pop M, Norris K, Ghedin E. Longitudinal analysis of the lung microbiota of cynomolgous macaques during long-term SHIV infection. Microbiome 2016, 4: 38. PMID: 27391224, PMCID: PMC4939015, DOI: 10.1186/s40168-016-0183-0.Peer-Reviewed Original ResearchConceptsDevelopment of obstructive lung diseaseObstructive lung diseaseNon-human primate modelLung microbiomeSHIV infectionLung microbiotaRibosomal RNALung diseasePrimate modelNon-obstructive groupSHIV-infected animalsResponse to immunosuppressionBronchoalveolar lavage fluid samplesCynomolgous macaquesDevelopment of obstructive diseaseLavage fluid samplesMultiple other speciesSIV-HIVOral anaerobesOral bacteriaTropheryma whippleiObstructive diseaseCommunity compositionBacterial communitiesDisease onset
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