2024
NKX2-2 based nuclei sorting on frozen human archival pancreas enables the enrichment of islet endocrine populations for single-nucleus RNA sequencing
Xie G, Toledo M, Hu X, Yong H, Sanchez P, Liu C, Naji A, Irianto J, Wang Y. NKX2-2 based nuclei sorting on frozen human archival pancreas enables the enrichment of islet endocrine populations for single-nucleus RNA sequencing. BMC Genomics 2024, 25: 427. PMID: 38689254, PMCID: PMC11059690, DOI: 10.1186/s12864-024-10335-w.Peer-Reviewed Original ResearchConceptsSingle-nucleus RNA sequencingRNA sequencingNuclei sortingSnRNA-seqGene expressionEndocrine populationsFluorescence-activated nuclei sortingHuman isletsGene expression librariesNuclei isolation protocolSingle-cell RNA sequencingFrozen archival tissuesIsolated human isletsHuman pancreatic endocrine cellsSingle-cell transcriptomicsTranscriptomic studiesCytoplasmic contaminationTranscriptome profilingConclusionsOur workNKX2-2Isolated nucleiRNA integrityLiving cellsIsolation protocolPancreatic endocrine cells
2023
Integrating genetics and transcriptomics to study major depressive disorder: a conceptual framework, bioinformatic approaches, and recent findings
Hicks E, Seah C, Cote A, Marchese S, Brennand K, Nestler E, Girgenti M, Huckins L. Integrating genetics and transcriptomics to study major depressive disorder: a conceptual framework, bioinformatic approaches, and recent findings. Translational Psychiatry 2023, 13: 129. PMID: 37076454, PMCID: PMC10115809, DOI: 10.1038/s41398-023-02412-7.Peer-Reviewed Original ResearchConceptsBioinformatics approachTranscriptomic dataBrain transcriptomeGenome-wide analysisDynamic transcriptional landscapeBrain gene expression dataGene expression dataTranscriptional landscapeTranscriptomic studiesIntegrating GeneticExpression dataPhenotypic signaturesGenomic driversTranscriptomeMajor depressive disorderValuable resourceRecent findingsEnvironmental influencesTranscriptomicsDepressive disorderGeneticsMultiple approachesPathophysiology of depressionSignaturesDysregulationFive Critical Gene-Based Biomarkers With Optimal Performance for Hepatocellular Carcinoma
Liu Y, Zhang H, Xu Y, Liu Y, Al-Adra D, Yeh M, Zhang Z. Five Critical Gene-Based Biomarkers With Optimal Performance for Hepatocellular Carcinoma. Cancer Informatics 2023, 22: 11769351231190477. PMID: 37577174, PMCID: PMC10413891, DOI: 10.1177/11769351231190477.Peer-Reviewed Original ResearchModel gene-gene interactionsCorrecting batch effectsGene-gene interactionsPublished transcriptomic studiesAnalysis of human cancersGene-based biomarkersWhole-transcriptome datasetsGenomic levelTranscriptome dataTranscriptomic studiesBatch effectsEffective therapeutic targetDEGsHuman cancersDisease etiologyMolecular backgroundCaucasian cohortTherapeutic targetIdentified 5Signature patternsIdentification of biomarkersConceptual advancesMiniaturized setting
2022
Integrated Approaches to Identify miRNA Biomarkers Associated with Cognitive Dysfunction in Multiple Sclerosis Using Text Mining, Gene Expression, Pathways, and GWAS
Prabahar A, Raja K. Integrated Approaches to Identify miRNA Biomarkers Associated with Cognitive Dysfunction in Multiple Sclerosis Using Text Mining, Gene Expression, Pathways, and GWAS. Diagnostics 2022, 12: 1914. PMID: 36010264, PMCID: PMC9406323, DOI: 10.3390/diagnostics12081914.Peer-Reviewed Original ResearchGenome-wide association studiesGenome-wide association study signalsGenome-wide association study catalogECM-receptor signaling pathwayPathway analysisSignaling pathwaySusceptibility genetic lociSusceptibility genetic variantsReceptor Signaling PathwayAssociation signalsGenetic lociGenomic etiologyAssociation studiesGene regulationTranscriptomic studiesGenetic variantsPI3K/Akt Signaling PathwayGene expressionComprehensive repositoryGenetic riskPathwayHsa-miR-148b-3pGenesExperimental associationsAssociation networks
2021
G2S3: A gene graph-based imputation method for single-cell RNA sequencing data
Wu W, Liu Y, Dai Q, Yan X, Wang Z. G2S3: A gene graph-based imputation method for single-cell RNA sequencing data. PLOS Computational Biology 2021, 17: e1009029. PMID: 34003861, PMCID: PMC8189489, DOI: 10.1371/journal.pcbi.1009029.Peer-Reviewed Original ResearchConceptsSingle-cell transcriptomic datasetsTranscriptomic datasetsGene expressionSingle-cell RNA sequencing technologySingle-cell transcriptomic studiesSingle-cell RNA sequencing dataRNA sequencing technologyRNA sequencing dataSingle-cell resolutionGene expression profilesAdjacent genesTranscriptomic studiesSequencing technologiesSequencing dataExpression profilesGene graphDownstream analysisGenesCell trajectoriesDropout eventsCell subtypesExpressionHigh data sparsityCells
2019
Elevated CO2 regulates the Wnt signaling pathway in mammals, Drosophila melanogaster and Caenorhabditis elegans
Shigemura M, Lecuona E, Angulo M, Dada LA, Edwards MB, Welch LC, Casalino-Matsuda SM, Sporn PHS, Vadász I, Helenius IT, Nader GA, Gruenbaum Y, Sharabi K, Cummins E, Taylor C, Bharat A, Gottardi CJ, Beitel GJ, Kaminski N, Budinger GRS, Berdnikovs S, Sznajder JI. Elevated CO2 regulates the Wnt signaling pathway in mammals, Drosophila melanogaster and Caenorhabditis elegans. Scientific Reports 2019, 9: 18251. PMID: 31796806, PMCID: PMC6890671, DOI: 10.1038/s41598-019-54683-0.Peer-Reviewed Original ResearchConceptsLarge-scale transcriptomic studyAvailable transcriptomic datasetsCell linesWnt pathway genesOrganismal functionDrosophila melanogasterElevated CO2Different tissue originsTranscriptomic studiesBronchial cell lineCO2 elevationTranscriptomic datasetsGenomic responsesHuman bronchial cell linePathway genesGene expressionDifferent tissuesGenesHigh CO2Tissue originMammalsSkeletal musclePathwayCaenorhabditisMelanogasterAtopic Dermatitis Is an IL-13–Dominant Disease with Greater Molecular Heterogeneity Compared to Psoriasis
Tsoi L, Rodriguez E, Degenhardt F, Baurecht H, Wehkamp U, Volks N, Szymczak S, Swindell W, Sarkar M, Raja K, Shao S, Patrick M, Gao Y, Uppala R, Perez White B, Getsios S, Harms P, Maverakis E, Elder J, Franke A, Gudjonsson J, Weidinger S. Atopic Dermatitis Is an IL-13–Dominant Disease with Greater Molecular Heterogeneity Compared to Psoriasis. Journal Of Investigative Dermatology 2019, 139: 1480-1489. PMID: 30641038, PMCID: PMC6711380, DOI: 10.1016/j.jid.2018.12.018.Peer-Reviewed Original ResearchConceptsTranscriptomic studiesPaired-end readsRNA sequencing samplesPathophysiology of ADPaired-endHigh-resolution viewStudies of ADAD transcriptomeDrug target predictionRNA sequencingLong noncoding RNAsRNA samplesDysregulated genesNoncoding RNAsRNAPsoriasis transcriptomeTranscriptomeCellular featuresGenesMolecular heterogeneityDisease heterogeneityTranslational impactIL-4 expressionAD skinGlobal architecture
2018
Impact of Transcriptomics on Our Understanding of Pulmonary Fibrosis
Vukmirovic M, Kaminski N. Impact of Transcriptomics on Our Understanding of Pulmonary Fibrosis. Frontiers In Medicine 2018, 5: 87. PMID: 29670881, PMCID: PMC5894436, DOI: 10.3389/fmed.2018.00087.Peer-Reviewed Original ResearchTranscriptomic studiesImpact of transcriptomicsGenome-scale profilingSingle-cell RNAseqRole of microRNAsIdiopathic pulmonary fibrosisNovel genesTranscriptomic analysisEpithelial genesIPF lungsRNA transcriptsDevelopmental pathwaysWnt pathwayBulk tissueMolecular analysisPulmonary fibrosisSpatial heterogeneityAnimal modelsTranscriptomicsGenesLethal fibrotic lung diseaseHuman IPF lungsImpact of lungPathwayFibrotic lung diseaseFibrosis: Lessons from OMICS analyses of the human lung
Yu G, Ibarra GH, Kaminski N. Fibrosis: Lessons from OMICS analyses of the human lung. Matrix Biology 2018, 68: 422-434. PMID: 29567123, PMCID: PMC6015529, DOI: 10.1016/j.matbio.2018.03.014.Peer-Reviewed Original ResearchConceptsIdiopathic pulmonary fibrosisDramatic phenotypic alterationsTranscriptomic studiesOmics analysisOmics profilingOmics technologiesPulmonary fibrosisNumerous aberrationsPhenotypic alterationsMechanistic understandingHuman idiopathic pulmonary fibrosisIPF lung tissueEpithelial cellsCentral roleHuman tissuesIPF samplesNew insightsMolecular featuresIPF lungsInflammatory cellsPatient cohortLung tissueAnimal modelsLethal disorderHuman lung
2017
Evolution of Gene Expression in the Uterine Cervix related to Steroid Signaling: Conserved features in the regulation of cervical ripening
Wagner GP, Nnamani MC, Chavan AR, Maziarz J, Protopapas S, Condon J, Romero R. Evolution of Gene Expression in the Uterine Cervix related to Steroid Signaling: Conserved features in the regulation of cervical ripening. Scientific Reports 2017, 7: 4439. PMID: 28667298, PMCID: PMC5493687, DOI: 10.1038/s41598-017-04759-6.Peer-Reviewed Original ResearchConceptsGene expressionComparative transcriptomic studyEutherian mammalsPlacental mammalsCervical ripeningTranscriptomic studiesEutherian speciesSteroid signalingUterine cervixChange expressionTiming of parturitionMammalsPremature cervical ripeningFunctional progesterone withdrawalDecreased expressionMaintenance of pregnancyExpressionSpeciesRipeningPutative mechanismsPreterm birthProgesterone withdrawalProgesterone receptorMouse cervixCervixEnvironment Tunes Propagation of Cell-to-Cell Variation in the Human Macrophage Gene Network
Martins A, Narayanan M, Prüstel T, Fixsen B, Park K, Gottschalk R, Lu Y, Andrews-Pfannkoch C, Lau W, Wendelsdorf K, Tsang J. Environment Tunes Propagation of Cell-to-Cell Variation in the Human Macrophage Gene Network. Cell Systems 2017, 4: 379-392.e12. PMID: 28365150, PMCID: PMC8392141, DOI: 10.1016/j.cels.2017.03.002.Peer-Reviewed Original ResearchConceptsGene networksCellular adaptationCell variationSingle-cell transcriptomic studiesGene-gene correlationsUnderlying regulatory mechanismsDegree of phosphorylationPhenotypic diversityTranscriptomic studiesEnvironmental adaptationMultiple molecular parametersGene expressionRegulatory mechanismsCellular heterogeneityDistinct environmentsSingle cellsHuman macrophagesQuantitative tuningCell populationsNatural perturbationsGenesDifferent environmentsSuch variationCellsStochastic simulation analysis
2013
On the outside, looking in: A review and evaluation of the comparability of blood and brain “‐omes”
Tylee DS, Kawaguchi DM, Glatt SJ. On the outside, looking in: A review and evaluation of the comparability of blood and brain “‐omes”. American Journal Of Medical Genetics Part B Neuropsychiatric Genetics 2013, 162: 595-603. PMID: 24132893, DOI: 10.1002/ajmg.b.32150.Peer-Reviewed Original ResearchConceptsCpG island methylation levelsCross-tissue correlationBlood-based biomarker studiesTranscriptomic studiesDNA methylationOmics analysisGene expressionMethylation levelsBlood tissue samplesExpression levelsProtein expressionProfiling methodExpressionEpigenomeTranscriptomeProteomeGenesMethylationTranscriptsTissue samplesValidation of biomarkersBetter understandingCritical precursorPatternsParticular subset
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