2025
Differential gene expression study in whole blood identifies candidate genes for psychosis in African American individuals
Knowles E, Peralta J, Rodrigue A, Mathias S, Mollon J, Leandro A, Curran J, Blangero J, Glahn D. Differential gene expression study in whole blood identifies candidate genes for psychosis in African American individuals. Schizophrenia Research 2025, 280: 85-94. PMID: 40267851, PMCID: PMC12107465, DOI: 10.1016/j.schres.2025.04.018.Peer-Reviewed Original ResearchConceptsGene expressionGenome-wide associationDifferential gene expression studiesGene co-expression network analysisWeighted gene co-expression network analysisCo-expression network analysisGene expression phenotypesIndividuals of European descentOverrepresentation of biological processesGene expression studiesGene expression analysisAfrican American ancestryGenomic regionsPsychosis-spectrum disordersRNA-seqAfrican American individualsPopulation stratificationAssociated with psychosisEtiology of psychosisSignificant genesCellular functionsExpression phenotypesExpression studiesAmerican ancestryExpression analysisAge-invariant genes: multi-tissue identification and characterization of murine reference genes
González J, Thrush-Evensen K, Meer M, Levine M, Higgins-Chen A. Age-invariant genes: multi-tissue identification and characterization of murine reference genes. Aging 2025, 17: 170-202. PMID: 39888841, PMCID: PMC11810059, DOI: 10.18632/aging.206195.Peer-Reviewed Original ResearchRNA-seq datasetsReference genesRNA-seqHallmarks of agingPathway enrichment analysisGenes-thoseCpG islandsShorter transcriptRT-qPCRMolecular functionsExpression studiesGene normalizationTissue-specificEnrichment analysisMouse tissuesGenesMurine tissuesAged tissuesHallmarksYoung organismsLifespanTranscriptionCpGTissuePathwayAge-invariant genes: multi-tissue identification and characterization of murine reference genes
González J, Thrush-Evensen K, Meer M, Levine M, Higgins-Chen A. Age-invariant genes: multi-tissue identification and characterization of murine reference genes. Aging 2025, 17: 170-202. PMID: 39873648, PMCID: PMC11810070, DOI: 10.18632/aging.206192.Peer-Reviewed Original ResearchConceptsRNA-seq datasetsReference genesRNA-seqHallmarks of agingPathway enrichment analysisGenes-thoseCpG islandsShorter transcriptRT-qPCRMolecular functionsExpression studiesGene normalizationTissue-specificEnrichment analysisMouse tissuesGenesMurine tissuesAged tissuesHallmarksYoung organismsLifespanTranscriptionCpGTissuePathway
2024
Genomic insights into the comorbidity between type 2 diabetes and schizophrenia
Arruda A, Khandaker G, Morris A, Smith G, Huckins L, Zeggini E. Genomic insights into the comorbidity between type 2 diabetes and schizophrenia. Schizophrenia 2024, 10: 22. PMID: 38383672, PMCID: PMC10881980, DOI: 10.1038/s41537-024-00445-5.Peer-Reviewed Original ResearchBody mass indexType 2 diabetesType 2 diabetes riskEffect of body mass indexPutative effector genesN-methyl-D-aspartatePublic health challengeIncreased Body Mass IndexLipid-related pathwaysRisk-increasing effectMulti-omics dataMendelian randomizationPotential causal relationshipGene expression studiesDirection of effectMental healthDrug repurposing opportunitiesAssociation signalsGenomic lociGenomic insightsHealth challengesEffector genesGenetic liabilityMass indexExpression studies
2022
Advances in Pigmentation Management: A Multipronged Approach.
Widgerow A, Wang J, Ziegler M, Fabi S, Garruto J, Robinson D, Bell M. Advances in Pigmentation Management: A Multipronged Approach. Journal Of Drugs In Dermatology 2022, 21: 1206-1220. PMID: 36342738, DOI: 10.36849/jdd.7013.Peer-Reviewed Original ResearchConceptsGene expression profilesCell linesExpression profilesProduction of pigmentsGene expression studiesMultiple cell linesProduction of melaninAffecting pigmentationPigment productionCellular pathwaysExpression studiesEndothelial cellsSynthesize melaninDistribute melaninMelanocyte linesIndependent pathwaysInhibitor of melanogenesisHuman skin pigmentationNeighboring keratinocytesCell typesHexapeptide-11Inflammation-related factorsGenesPathwayEndothelial cell interactionsOMiCC: An expanded and enhanced platform for meta-analysis of public gene expression data
Liu C, Guo Y, Vrindten K, Lau W, Sparks R, Tsang J. OMiCC: An expanded and enhanced platform for meta-analysis of public gene expression data. STAR Protocols 2022, 3: 101474. PMID: 35880119, PMCID: PMC9307621, DOI: 10.1016/j.xpro.2022.101474.Peer-Reviewed Original ResearchMeSH KeywordsGene Expression
2021
Roles of Bone Morphogenetic Protein Receptor 1A in Germinal Centers and Long-Lived Humoral Immunity
Tomayko MM, Karaaslan S, Lainez B, Conter LJ, Song E, Venkatesan S, Mishina Y, Shlomchik MJ. Roles of Bone Morphogenetic Protein Receptor 1A in Germinal Centers and Long-Lived Humoral Immunity. ImmunoHorizons 2021, 5: 284-297. PMID: 33975878, DOI: 10.4049/immunohorizons.2100019.Peer-Reviewed Original ResearchConceptsBone marrow-resident plasma cellsBone morphogenetic protein receptor 1AMemory B cellsMultiple stem cell populationsGene deletionStrong selective pressureGC B cellsStem cell populationGerminal centersB cellsReceptor 1aSelective pressureExpression studiesResultant establishmentNovel roleClass-switched memory B cellsEGFP reporter miceSynaptic recognition molecules in development and disease
Chowdhury D, Watters K, Biederer T. Synaptic recognition molecules in development and disease. Current Topics In Developmental Biology 2021, 142: 319-370. PMID: 33706921, PMCID: PMC8632550, DOI: 10.1016/bs.ctdb.2020.12.009.ChaptersConceptsSingle-cell expression studiesRecognition moleculesRecognition factorsKey protein familiesPost-translational modificationsLeucine-rich repeatsCell expression studiesSemaphorin/PlexinAlternative splicingProtein familyProteomic approachCombinatorial actionMolecular playersPartner recognitionExpression studiesMolecular themesSpecific expressionDisease relevanceSynapse specificationVertebrate brainImmunoglobulin SuperfamilyRich repertoireAppropriate brain regionsNeuron type-specific expressionSynaptic wiring
2020
Gene X environment: the cellular environment governs the transcriptional response to environmental chemicals
Burman A, Garcia-Milian R, Whirledge S. Gene X environment: the cellular environment governs the transcriptional response to environmental chemicals. Human Genomics 2020, 14: 19. PMID: 32448403, PMCID: PMC7247264, DOI: 10.1186/s40246-020-00269-1.Peer-Reviewed Original ResearchConceptsTranscriptional responseCellular environmentCellular contextGenetic sexUnique gene networksGene regulatory networksEnvironment interactionEnvironmental chemicalsGene expression studiesUnique transcriptional profileGene expression array dataExpression array dataPhenotype of cellsGene networksRegulatory networksTranscriptional profilesBiological functionsCellular organizationExpression studiesFemale cellsCellular responsesPhysiological cuesHuman gene expression studiesMolecular pathwaysGenetic results
2018
Epigenetics and autism spectrum disorder: A report of an autism case with mutation in H1 linker histone HIST1H1E and literature review
Duffney LJ, Valdez P, Tremblay MW, Cao X, Montgomery S, McConkie‐Rosell A, Jiang Y. Epigenetics and autism spectrum disorder: A report of an autism case with mutation in H1 linker histone HIST1H1E and literature review. American Journal Of Medical Genetics Part B Neuropsychiatric Genetics 2018, 177: 426-433. PMID: 29704315, PMCID: PMC5980735, DOI: 10.1002/ajmg.b.32631.Peer-Reviewed Original ResearchConceptsLinker proteinH1 linker histonesLinker histone proteinFamily member EChromatin organizationEpigenetic machineryHistone proteinsEpigenetic regulationLinker histonesNucleosome packagingLoss of functionDeleterious mutationsCandidate genesExpression studiesHistone writersWhole-exome sequencingHuman diseasesGenesProteinMutationsProtein expressionExome sequencingGenetic mutationsMember EHIST1H1E
2017
Characteristics of allelic gene expression in human brain cells from single-cell RNA-seq data analysis
Zhao D, Lin M, Pedrosa E, Lachman HM, Zheng D. Characteristics of allelic gene expression in human brain cells from single-cell RNA-seq data analysis. BMC Genomics 2017, 18: 860. PMID: 29126398, PMCID: PMC5681780, DOI: 10.1186/s12864-017-4261-x.Peer-Reviewed Original ResearchConceptsMonoallelic expressionHuman brain cellsGene expressionMonoallelic gene expressionAllelic gene expressionGenome-wide levelSingle-cell RNA-seq datasetsRNA-seq data analysisAllelic expression studiesSingle-cell RNA-seq data analysisRNA-seq datasetsSingle nucleotide variantsBrain cellsCellular identityAutosomal genesNeuronal diversityExpression studiesNucleotide variantsCorrelated expressionGenesIndividual cellsHuman psychiatric disordersNeuronal cellsSingle cellsCell functionTranscriptome Alterations in Posttraumatic Stress Disorder
Girgenti MJ, Duman RS. Transcriptome Alterations in Posttraumatic Stress Disorder. Biological Psychiatry 2017, 83: 840-848. PMID: 29128043, DOI: 10.1016/j.biopsych.2017.09.023.Peer-Reviewed Original ResearchConceptsPosttraumatic stress disorderNext-generation sequencing technologiesAberrant gene expressionGene expression changesAmount of transcriptsGene expression studiesGene profiling studiesAlternative splicingTranscriptome alterationsTranscriptomic technologiesRNA sequencingSequencing technologiesTranscript identificationExpression studiesGene expressionExpression changesStress disorderBlood of patientsCellular mechanismsPeripheral blood cellsProfiling studiesHuman peripheral bloodPeripheral bloodLifetime prevalenceGeneral populationTranscriptome profiles in sarcoidosis and their potential role in disease prediction
Schupp JC, Vukmirovic M, Kaminski N, Prasse A. Transcriptome profiles in sarcoidosis and their potential role in disease prediction. Current Opinion In Pulmonary Medicine 2017, 23: 487-492. PMID: 28590292, PMCID: PMC5637542, DOI: 10.1097/mcp.0000000000000403.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsGenome-wide expression studiesWide expression studiesTranscriptome profilesTranscriptomic dataRNA sequencingExpression studiesGene expressionMolecular mechanismsLarge prospective followTh1 immune responseTranscriptomeNonnecrotizing granulomasProspective followSystemic diseaseDisease progressionTreatment outcomesImmune responseSarcoidosisPotential roleControl tissuesProgressive sarcoidosisKey roleDiseaseTranscriptomicsGranulomas
2016
Gene Expression Correlated with Severe Asthma Characteristics Reveals Heterogeneous Mechanisms of Severe Disease
Modena BD, Bleecker ER, Busse WW, Erzurum SC, Gaston BM, Jarjour NN, Meyers DA, Milosevic J, Tedrow JR, Wu W, Kaminski N, Wenzel SE. Gene Expression Correlated with Severe Asthma Characteristics Reveals Heterogeneous Mechanisms of Severe Disease. American Journal Of Respiratory And Critical Care Medicine 2016, 195: 1449-1463. PMID: 27984699, PMCID: PMC5470748, DOI: 10.1164/rccm.201607-1407oc.Peer-Reviewed Original ResearchConceptsWeighted gene coexpression network analysisGene coexpression network analysisCoexpression network analysisGene expressionBiological processesAirway epithelial cell gene expressionEpithelial cell gene expressionNetwork of genesGene expression networksGene network modulesAsthma susceptibility lociT2 gene expressionCell gene expressionGene expression studiesNeuronal functionEpithelial growthMultiple molecular mechanismsExpression networksT2 genesGene networksUnderlying biological processesHub genesExpression studiesBiological insightsNetwork analysisOptimization of techniques for multiple platform testing in small, precious samples such as human chorionic villus sampling
Pisarska MD, Akhlaghpour M, Lee B, Barlow GM, Xu N, Wang ET, Mackey AJ, Farber CR, Rich SS, Rotter JI, Chen Y, Goodarzi MO, Guller S, Williams J. Optimization of techniques for multiple platform testing in small, precious samples such as human chorionic villus sampling. Prenatal Diagnosis 2016, 36: 1061-1070. PMID: 27718505, PMCID: PMC5142835, DOI: 10.1002/pd.4936.Peer-Reviewed Original ResearchConceptsGenome-wide methylation profilingRNA-seq librariesSystems biology approachGene expression studiesBiology approachEpigenetic modificationsLow DNA yieldRNA sequencingMethylation profilingExpression studiesGene expressionPurification of DNAQuality DNAGlobal changeHighest RNA yieldDNA yieldRNA yieldRNADNAIsolation kitRNAlater samplesRNAlaterGenesChorionic villiMultiple testingRNA sequencing of transformed lymphoblastoid cells from siblings discordant for autism spectrum disorders reveals transcriptomic and functional alterations: Evidence for sex‐specific effects
Tylee DS, Espinoza AJ, Hess JL, Tahir MA, McCoy SY, Rim JK, Dhimal T, Cohen OS, Glatt SJ. RNA sequencing of transformed lymphoblastoid cells from siblings discordant for autism spectrum disorders reveals transcriptomic and functional alterations: Evidence for sex‐specific effects. Autism Research 2016, 10: 439-455. PMID: 27529825, DOI: 10.1002/aur.1679.Peer-Reviewed Original ResearchConceptsTranscriptomic differencesGenome-wide expression studiesGene co-expression network analysisCo-expression network analysisTranscriptomic signaturesGene-set analysisStructural genetic variantsIdentified transcriptsGenomic studiesExpression studiesLymphoblastoid cell linesGenetic variantsCell linesExpression valuesNetwork analysisSignificant overlapGenesTranscriptsRNAASD studiesAutism spectrum disorderMale samplesLarge numberSignaturesFemales
2015
Toxicogenomic Screening of Replacements for Di(2-Ethylhexyl) Phthalate (DEHP) Using the Immortalized TM4 Sertoli Cell Line
Nardelli TC, Erythropel HC, Robaire B. Toxicogenomic Screening of Replacements for Di(2-Ethylhexyl) Phthalate (DEHP) Using the Immortalized TM4 Sertoli Cell Line. PLOS ONE 2015, 10: e0138421. PMID: 26445464, PMCID: PMC4596883, DOI: 10.1371/journal.pone.0138421.Peer-Reviewed Original ResearchConceptsTM4 Sertoli cell lineUpregulated genesSertoli cell lineMajor signal transduction pathwaysCholesterol biosynthesisSignal transduction pathwaysERK/MAPKGene expression studiesCell linesToxicogenomic screeningTransduction pathwaysDNA repairRho signalingDEHP/MEHPExpression studiesGene expressionStress responseGenesToxicogenomic profilesAltered expressionButanediol dibenzoateBiosynthesisMultiple commercial applicationsDioctyl succinateExpressionPervasive and opposing effects of Unpredictable Chronic Mild Stress (UCMS) on hippocampal gene expression in BALB/cJ and C57BL/6J mouse strains
Malki K, Mineur YS, Tosto MG, Campbell J, Karia P, Jumabhoy I, Sluyter F, Crusio WE, Schalkwyk LC. Pervasive and opposing effects of Unpredictable Chronic Mild Stress (UCMS) on hippocampal gene expression in BALB/cJ and C57BL/6J mouse strains. BMC Genomics 2015, 16: 262. PMID: 25879669, PMCID: PMC4412144, DOI: 10.1186/s12864-015-1431-6.Peer-Reviewed Original ResearchConceptsWeighted gene coexpression network analysisGene networksGene expressionStress responseHippocampal gene expressionGene coexpression network analysisNumber of genesCandidate gene selectionCoexpression network analysisUbiquitin C geneGene expression studiesGenomic levelGENDEP projectGene pathwaysCandidate genesExpression studiesPathway analysisMolecular mechanismsC geneEnvironmental stressorsGenesGene selectionCREB1 geneBALB/cJAdverse environments
2014
Evolving toward a human-cell based and multiscale approach to drug discovery for CNS disorders
Schadt E, Buchanan S, Brennand K, Merchant K. Evolving toward a human-cell based and multiscale approach to drug discovery for CNS disorders. Frontiers In Pharmacology 2014, 5: 252. PMID: 25520658, PMCID: PMC4251289, DOI: 10.3389/fphar.2014.00252.Peer-Reviewed Original ResearchBiology approachNeurological disease pathwaysSpecific neural cell typesSystems biology approachPatient-derived hiPSCsDrug discoveryGeneration of hiPSCsInduced pluripotent stem cellsRepresentative neurological diseasesHuman induced pluripotent stem cellsNeural cell typesPluripotent stem cellsSingle geneGlobal epigeneticExpression studiesFrequent clinical failuresDrug screening strategiesNeurodegenerative diseases Alzheimer's diseaseHuman diseasesPsychiatric disorders schizophreniaCell typesCNS disordersHiPSC linesDisease pathwaysBiological networksSurvival and Integration of Neurons Derived from Human Embryonic Stem Cells in MPTP-Lesioned Primates
Wakeman DR, Weiss S, Sladek JR, Elsworth JD, Bauereis B, Leranth C, Hurley PJ, Roth RH, Redmond DE. Survival and Integration of Neurons Derived from Human Embryonic Stem Cells in MPTP-Lesioned Primates. Cell Transplantation 2014, 23: 981-994. PMID: 23562290, DOI: 10.3727/096368913x664865.Peer-Reviewed Original ResearchConceptsHuman embryonic stem cell linesEmbryonic stem cell linesHuman embryonic stem cellsEmbryonic stem cellsGene expression studiesStem cell linesGFP lentiviral vectorExpression studiesDifferentiated cellsDifferentiation protocolsDopamine neuronal survivalIntegration of neuronsNeuronal cellsNeuronal phenotypeTyrosine hydroxylaseStem cellsExtension of processesBiochemical analysisDopaminergic marker tyrosine hydroxylaseHESCCell linesIII-tubulinMidbrain of MPTPPhenotypeMembrane depolarization
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