2020
A curated benchmark of enhancer-gene interactions for evaluating enhancer-target gene prediction methods
Moore J, Pratt H, Purcaro M, Weng Z. A curated benchmark of enhancer-gene interactions for evaluating enhancer-target gene prediction methods. Genome Biology 2020, 21: 17. PMID: 31969180, PMCID: PMC6977301, DOI: 10.1186/s13059-019-1924-8.Peer-Reviewed Original ResearchMeSH KeywordsBenchmarkingData CurationEnhancer Elements, GeneticGene Expression RegulationGenomicsMachine LearningConceptsEnhancer-gene interactionsTarget genesGene prediction methodsGenome-wide collectionCis-regulatory elementsCell typesEpigenomic dataDevelopment of computational methodsPredicted target genesGenomic interactionsPublished computational methodsTargetFinderComputational methodsGenesConclusionsOur resultsCCREsDistance methodCellsResultsToInteractionConclusionsOurTypePEPPrediction method
2018
Differential analysis of chromatin accessibility and histone modifications for predicting mouse developmental enhancers
Fu S, Wang Q, Moore J, Purcaro M, Pratt H, Fan K, Gu C, Jiang C, Zhu R, Kundaje A, Lu A, Weng Z. Differential analysis of chromatin accessibility and histone modifications for predicting mouse developmental enhancers. Nucleic Acids Research 2018, 46: 11184-11201. PMID: 30137428, PMCID: PMC6265487, DOI: 10.1093/nar/gky753.Peer-Reviewed Original ResearchConceptsPeak callersH3K27ac peaksDevelopmental enhancersHistone modificationsDistal cis-regulatory elementsAnalysis of chromatin accessibilityChIP-seq peaksPeak-calling algorithmsDepleted of nucleosomesCis-regulatory elementsModulate gene expressionTransgenic mouse assaysF-SeqDNase-seqHeart enhancersChromatin accessibilityH3K27ac signalH3K27acDNaseGene expressionHistoneDNase peakMouse assayPredicted enhancersDistant tissues