2024
EpiGePT: a pretrained transformer-based language model for context-specific human epigenomics
Gao Z, Liu Q, Zeng W, Jiang R, Wong W. EpiGePT: a pretrained transformer-based language model for context-specific human epigenomics. Genome Biology 2024, 25: 310. PMID: 39696471, PMCID: PMC11657395, DOI: 10.1186/s13059-024-03449-7.Peer-Reviewed Original ResearchConceptsTranscription factor activityChromatin interactionsEpigenomic signalsGenomic interactionsHuman epigenomeGene regulationVariant impactBiological sequencesCellular contextInteraction predictionFactor activityGenomeChromatinEpigenomeTranscriptionGenesHttp://healthSequenceRegulationTransformer-based modelsInteractionAnti-neuroinflammatory effects of the KIOM -patented Polygonum multiflorum maximized root tuber against LPS-stimulated BV2 Cells
Oh T, Ban Y, Kang Y. Anti-neuroinflammatory effects of the KIOM -patented Polygonum multiflorum maximized root tuber against LPS-stimulated BV2 Cells. Applied Biological Chemistry 2024, 67: 71. DOI: 10.1186/s13765-024-00928-0.Peer-Reviewed Original ResearchHigher content of active ingredientP. multiflorumMouse microglial BV-2 cellsLPS-stimulated BV2 cellsContent of active ingredientsTranscription factor activityAnti-neuroinflammatory effectsMitogen-activated protein kinaseMechanisms of neurodegenerationActivation of p38Pathological mechanisms of neurodegenerationMicroglial BV-2 cellsHigher contentIncreased biomassRoot tubersBV2 cellsAntioxidant effectsCultivation conditionsProtein kinaseOriental medicinal herbRegulation mechanismBV-2 cellsInducible NO synthaseMAPK phosphorylationMedicinal herbsTemporal coordination of the transcription factor response to H2O2 stress
Jose E, March-Steinman W, Wilson B, Shanks L, Parkinson C, Alvarado-Cruz I, Sweasy J, Paek A. Temporal coordination of the transcription factor response to H2O2 stress. Nature Communications 2024, 15: 3440. PMID: 38653977, PMCID: PMC11039679, DOI: 10.1038/s41467-024-47837-w.Peer-Reviewed Original ResearchConceptsGroup of transcription factorsTranscription factorsResponse to H2O2 stressTranscription factor activityCell cycle arrestDose-dependent outcomeRepair oxidative damageOxidative stressDose-dependent activationTime-lapse imagingH2O2 stressCell deathRestoring redox balanceDose-dependentlyTranscriptionRedox balanceGlucose oxidase enzymeNF-kBFactor activity
2023
Single-cell multiomic understanding of HIV-1 reservoir at epigenetic, transcriptional, and protein levels
Wong M, Wei Y, Ho Y. Single-cell multiomic understanding of HIV-1 reservoir at epigenetic, transcriptional, and protein levels. Current Opinion In HIV And AIDS 2023, 18: 246-256. PMID: 37535039, PMCID: PMC10442869, DOI: 10.1097/coh.0000000000000809.Peer-Reviewed Original ResearchConceptsSurface protein expressionMultiomics approachATAC-seqProtein expressionTranscription factor activityProtein levelsRNA mappingRNA-seqBioinformatics analysisHIV-1-infected cellsFalse positive discoveriesBiological insightsBulk transcriptomeFactor activityDNA amplificationExpressionCellsTranscriptomeTherapeutic strategiesEpigeneticsDiscoveryDNA PCRRNADNAHIV-1
2021
High Throughput Single-Cell Simultaneous Genotyping and Chromatin Accessibility Reveals Genotype to Phenotype Relationship in Human Myeloproliferation
Myers R, Izzo F, Prieto T, Mimitou E, Raviram R, Chaligne R, Hoffman R, Stahl M, Abdel-Wahab O, Marcellino B, Smibert P, Landau D. High Throughput Single-Cell Simultaneous Genotyping and Chromatin Accessibility Reveals Genotype to Phenotype Relationship in Human Myeloproliferation. Blood 2021, 138: 678. DOI: 10.1182/blood-2021-149226.Peer-Reviewed Original ResearchChromatin accessibilityMotif accessibilityFitness advantageTranscription factor (TFGenotype to phenotype relationshipsSomatic mutationsGenotype-to-phenotype mapCopy number inferenceChromatin accessibility profilesSingle-cell multi-omicsCell-type specific effectsPseudo-temporal orderingCell line identityTarget gene transcriptionTranscription factor activityMyeloproliferative neoplasmsJAK2 V617FCell fractionClonal outgrowthStages of erythroid maturationEntity's Board of DirectorsGenome coverageGenotyping accuracyGenomic locationsMPN samples
2015
Comparative analysis of anti-viral transcriptomics reveals novel effects of influenza immune antagonism
Thakar J, Hartmann BM, Marjanovic N, Sealfon SC, Kleinstein SH. Comparative analysis of anti-viral transcriptomics reveals novel effects of influenza immune antagonism. BMC Immunology 2015, 16: 46. PMID: 26272204, PMCID: PMC4536893, DOI: 10.1186/s12865-015-0107-y.Peer-Reviewed Original ResearchConceptsTranscription factor activityImmune antagonismExpression profilesGenome-wide expression profilesGenome-wide transcriptional profiling dataFactor activityGenome-wide transcriptional profilesTranscription factor SATB1DNA-binding sitesTranscriptional profiling dataHost-pathogen interactionsGene expression profilesISGF3 activityTranscriptional responseTranscription factorsTranscriptional profilesHost interactionsProfiling dataApplication of betaNovel effectMechanistic insightsInfected cellsInfluenza A virusesMechanistic differencesNewcastle disease virus
2013
Promoter Sequence Determines the Relationship between Expression Level and Noise
Carey LB, van Dijk D, Sloot PM, Kaandorp JA, Segal E. Promoter Sequence Determines the Relationship between Expression Level and Noise. PLOS Biology 2013, 11: e1001528. PMID: 23565060, PMCID: PMC3614515, DOI: 10.1371/journal.pbio.1001528.Peer-Reviewed Original ResearchMeSH KeywordsAlcohol DehydrogenaseBacterial ProteinsBase SequenceBinding SitesCation Transport ProteinsEnzyme InductionGene ExpressionGene Expression Regulation, FungalGene LibraryGenes, ReporterKineticsLuminescent ProteinsModels, GeneticPromoter Regions, GeneticProtein BindingSaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsTranscription FactorsConceptsTranscriptional burstsUnique transcriptional statesTranscription factor activitySingle target geneExpression levelsMechanism of repressionAbility of cellsTF activityGene expression levelsExtracellular cuesTranscriptional statesTranscriptional regulationPromoter DNAPromoter sequencesSingle TFCell variabilityTarget genesRegulatory mechanismsExpression changesZap1Diverse mechanismsNative targetsFactor activityExpression increasesGenes
2006
Non-conducting functions of voltage-gated ion channels
Kaczmarek LK. Non-conducting functions of voltage-gated ion channels. Nature Reviews Neuroscience 2006, 7: 761-771. PMID: 16988652, DOI: 10.1038/nrn1988.Peer-Reviewed Original ResearchConceptsMitogen-activated protein kinaseΒ-subunitProtein kinaseIntrinsic protein kinase activityTRP familyΑ-subunitNon-conducting functionCell-cell adhesionTranscription factor activityDependent protein kinase IIProtein kinase activityLarge extracellular domainCell proliferationSynaptic release machineryTranscription factor CREBProtein kinase IIVoltage-gated ion channelsKey PointsIn additionMAPK/ERKIntrinsic enzyme activityNon-selective cation channelsCell adhesion moleculeReductase functionC-terminusKinase activity
2001
Friend of GATA-1 Represses GATA-3–dependent Activity in CD4+ T Cells
Zhou M, Ouyang W, Gong Q, Katz S, White J, Orkin S, Murphy K. Friend of GATA-1 Represses GATA-3–dependent Activity in CD4+ T Cells. Journal Of Experimental Medicine 2001, 194: 1461-1471. PMID: 11714753, PMCID: PMC2193678, DOI: 10.1084/jem.194.10.1461.Peer-Reviewed Original ResearchConceptsFOG-1Friend of GATATranscription factor activityActivator of transcriptionIL-5 promoterHematopoietic developmentMegakaryocyte differentiationSignal transducerGATA-3Dependent inductionFactor activityNaive T cellsTh2 developmentT cellsOverexpressionAutoactivationCellsGATA-3 expressionPrimary activationActivationInductionTranscriptionPromoterGATAProtein
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