2022
Building integrative functional maps of gene regulation
Xu J, Pratt HE, Moore JE, Gerstein MB, Weng Z. Building integrative functional maps of gene regulation. Human Molecular Genetics 2022, 31: r114-r122. PMID: 36083269, PMCID: PMC9585680, DOI: 10.1093/hmg/ddac195.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsGene regulationRegulatory mapSame genetic informationNon-coding genesSuch regulatory elementsEvolutionary analysisHuman genomeRegulatory elementsGenetic informationGene expressionType diversityRegulatory roleGenomeBase pairsIndividual cellsFunctional assaysSpecific functionsRegulationCellsFunctional mapsGenesDNADiversityCopiesSequence
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 ResearchConceptsEnhancer-gene interactionsTarget genesGene prediction methodsGenome-wide collectionCis-regulatory elementsCell typesEpigenomic dataDevelopment of computational methodsPredicted target genesGenomic interactionsPublished computational methodsTargetFinderComputational methodsGenesConclusionsOur resultsCCREsDistance methodCellsResultsToInteractionConclusionsOurTypePEPPrediction method