2023
Integrative analysis of transcriptome dynamics during human craniofacial development identifies candidate disease genes
Yankee T, Oh S, Winchester E, Wilderman A, Robinson K, Gordon T, Rosenfeld J, VanOudenhove J, Scott D, Leslie E, Cotney J. Integrative analysis of transcriptome dynamics during human craniofacial development identifies candidate disease genes. Nature Communications 2023, 14: 4623. PMID: 37532691, PMCID: PMC10397224, DOI: 10.1038/s41467-023-40363-1.Peer-Reviewed Original ResearchConceptsGene co-expression analysisSingle-cell RNA-seqCraniofacial disordersSet of genesCo-expression analysisTranscriptome dynamicsDevelopmental enhancersRegulatory hubEpigenomic dataCraniofacial developmentRNA-seqDe novo mutationsDisease genesGene expressionIntegrative analysisCraniofacial tissuesGenesNovo mutationsHuman tissuesMutationsDevelopment identifiesCommon congenital defectsWeeks post conceptionPost conceptionCraniofacial region
2020
Epigenomic and Transcriptomic Dynamics During Human Heart Organogenesis
VanOudenhove J, Yankee T, Wilderman A, Cotney J. Epigenomic and Transcriptomic Dynamics During Human Heart Organogenesis. Circulation Research 2020, 127: e184-e209. PMID: 32772801, PMCID: PMC7554226, DOI: 10.1161/circresaha.120.316704.Peer-Reviewed Original ResearchMeSH KeywordsChromatinEnhancer Elements, GeneticEpigenomicsGene Expression ProfilingGene Expression Regulation, DevelopmentalGene Regulatory NetworksGenetic VariationHeartHeart Defects, CongenitalHistone CodeHomeobox Protein Nkx-2.5HumansNAV1.5 Voltage-Gated Sodium ChannelOrganogenesisRegulatory Sequences, Ribonucleic AcidT-Box Domain ProteinsTranscriptomeConceptsRegulatory sequencesHeart enhancersHeart organogenesisGene expression network analysisWeighted gene coexpression networkGene expression dynamicsGene expression networksPutative disease genesWhole-genome sequencing dataGene coexpression networksExpression network analysisDisease-relevant genesGenome sequencing dataRare sequence alterationsHeart-specific expressionClear genetic componentChromatin stateTranscriptomic dynamicsHistone modificationsFunctional annotationExpression networksExpression dynamicsGene modulesCoexpression networkGenetic variation