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
2018
Decoding the non-coding genome: Opportunities and challenges of genomic and epigenomic consortium data
Pratt H, Weng Z. Decoding the non-coding genome: Opportunities and challenges of genomic and epigenomic consortium data. Current Opinion In Systems Biology 2018, 11: 82-90. DOI: 10.1016/j.coisb.2018.09.002.Peer-Reviewed Original ResearchGenome-wide chromatin structureNext-generation sequencing dataCellular responses to stimuliFeatures of gene regulationUniform data processingNon-coding genomeTranscription factor bindingCell type differentiationIntegrated analysisGene expression changesSequence dataChromatin structureFactor bindingGene regulationOrganismal developmentTranscriptional activityExpression changesPhenotypic changesResponse to stimuliConsortium dataDisease mechanismsType differentiationComputational analysisInternational consortiumGenome