2020
Expanded encyclopaedias of DNA elements in the human and mouse genomes
Moore J, Purcaro M, Pratt H, Epstein C, Shoresh N, Adrian J, Kawli T, Davis C, Dobin A, Kaul R, Halow J, Van Nostrand E, Freese P, Gorkin D, Shen Y, He Y, Mackiewicz M, Pauli-Behn F, Williams B, Mortazavi A, Keller C, Zhang X, Elhajjajy S, Huey J, Dickel D, Snetkova V, Wei X, Wang X, Rivera-Mulia J, Rozowsky J, Zhang J, Chhetri S, Zhang J, Victorsen A, White K, Visel A, Yeo G, Burge C, Lécuyer E, Gilbert D, Dekker J, Rinn J, Mendenhall E, Ecker J, Kellis M, Klein R, Noble W, Kundaje A, Guigó R, Farnham P, Cherry J, Myers R, Ren B, Graveley B, Gerstein M, Pennacchio L, Snyder M, Bernstein B, Wold B, Hardison R, Gingeras T, Stamatoyannopoulos J, Weng Z. Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature 2020, 583: 699-710. PMID: 32728249, PMCID: PMC7410828, DOI: 10.1038/s41586-020-2493-4.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsChromatinDatabases, GeneticDeoxyribonuclease IDNADNA FootprintingDNA MethylationDNA Replication TimingGenomeGenome, HumanGenomicsHistonesHumansMiceMice, TransgenicMolecular Sequence AnnotationRegistriesRegulatory Sequences, Nucleic AcidRNA-Binding ProteinsTranscription, GeneticTransposasesConceptsMouse genomeCandidate cis-regulatory elementsCis-regulatory elementsDNA Elements (ENCODE) projectMouse fetal developmentChromatin structureGene regulationRespective genomesCellular contextDNA elementsDNA methylationENCODE dataTranscription factorsRNA transcriptionWeb-based serverGenomeExpansive resourceRNAEncyclopediaProteinFetal developmentChromatinTranscriptionHumansMethylation
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