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
2021
Integration of high-resolution promoter profiling assays reveals novel, cell type-specific transcription start sites across 115 human cell and tissue types
Moore J, Zhang X, Elhajjajy S, Fan K, Pratt H, Reese F, Mortazavi A, Weng Z. Integration of high-resolution promoter profiling assays reveals novel, cell type-specific transcription start sites across 115 human cell and tissue types. Genome Research 2021, 32: gr.275723.121. PMID: 34949670, PMCID: PMC8805725, DOI: 10.1101/gr.275723.121.Peer-Reviewed Original ResearchConceptsTranscription start site annotationTranscription start siteGenome-wide association studiesStart siteAccurate transcription start siteCell type-specific usageMapping of promotersPaired-end informationPaired-end readsAnalysis of gene expressionTranscriptomic data setsGENCODE genesRNA annotationGWAS genesPaired-endGenomic positionsGene collectionTissue typesAssociation studiesTranscriptional regulationTranscription assaysBiological communitiesGene expressionHuman diseasesHuman cellsFactorbook: an updated catalog of transcription factor motifs and candidate regulatory motif sites
Pratt H, Andrews G, Phalke N, Huey J, Purcaro M, van der Velde A, Moore J, Weng Z. Factorbook: an updated catalog of transcription factor motifs and candidate regulatory motif sites. Nucleic Acids Research 2021, 50: d141-d149. PMID: 34755879, PMCID: PMC8728199, DOI: 10.1093/nar/gkab1039.Peer-Reviewed Original ResearchConceptsChIP-seqHT-SELEXTranscription factorsDNA-binding transcription factorsHT-SELEX experimentsChIP-seq dataChIP-seq experimentsAnnotation of variantsTF binding sitesCis-regulatory elementsTranscriptional regulatory proteinsDatabase of annotationsIntegrated analysisENCODE projectHuman genomeMotif modelsTrait heritabilityRegulatory proteinsBinding specificityGene expressionMotifBinding sitesCell typesRegulatory effectsComprehensive collectionInvestigating the Potential Roles of SINEs in the Human Genome
Zhang X, Pratt H, Weng Z. Investigating the Potential Roles of SINEs in the Human Genome. Annual Review Of Genomics And Human Genetics 2021, 22: 1-20. PMID: 33792357, DOI: 10.1146/annurev-genom-111620-100736.Peer-Reviewed Original ResearchConceptsShort interspersed nuclear elementsHuman genomePol II-transcribed genesFunctional regulatory elementsGene-rich regionsRNA polymerase IIIProximity to genesInterspersed nuclear elementsRegulate gene expressionPotential regulatory functionsSINE RNAsNonautonomous retrotransposonsPolymerase IIIGene regulationRegulatory elementsAutonomous retroelementsGenomeNuclear elementsGene expressionGenesRNARNA levelsPolPotential roleRetrotransposons
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
2013
Genome-wide Analysis of Immune System Genes by Expressed Sequence Tag Profiling
Giallourakis C, Benita Y, Molinie B, Cao Z, Despo O, Pratt H, Zukerberg L, Daly M, Rioux J, Xavier R. Genome-wide Analysis of Immune System Genes by Expressed Sequence Tag Profiling. The Journal Of Immunology 2013, 190: 5578-5587. PMID: 23616578, PMCID: PMC3703829, DOI: 10.4049/jimmunol.1203471.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCluster AnalysisComputational BiologyDatabases, Nucleic AcidDNA-Binding ProteinsExpressed Sequence TagsGene Expression ProfilingGene Regulatory NetworksGenome-Wide Association StudyGenomicsHumansImmune SystemImmune System DiseasesLymphoma, B-CellMiceMolecular Sequence AnnotationReproducibility of ResultsRNA, Long NoncodingTranscription FactorsTranscriptomeConceptsExpressed sequence tagsExpressed sequence tag profilingEncyclopedia of DNA ElementsHuman expressed sequence tagsGenome-wide analysisIdentification of transcriptsMicroarray-based studiesImmune system genesRNA sequencing analysisStudies of mRNADNA elementsSequence tagsNovel genesMetabolic gene signatureNoncoding genesSequence analysisTranscriptome analysisImmune systemMicroarray studiesOverexpressed genesSystem genesGene expressionGenesFunctional studiesNoncoding RNAs