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Showing 1–18 of 18 results
Advanced filters: Author: Pouya Kheradpour Clear advanced filters

  • This overview of the ENCODE project outlines the data accumulated so far, revealing that 80% of the human genome now has at least one biochemical function assigned to it; the newly identified functional elements should aid the interpretation of results of genome-wide association studies, as many correspond to sites of association with human disease.

    • Ian Dunham
    • Anshul Kundaje
    • Ewan Birney
    ResearchOpen Access
    Nature
    Volume: 489, P: 57-74

  • This study describes the integrative analysis of 111 reference human epigenomes, profiled for histone modification patterns, DNA accessibility, DNA methylation and RNA expression; the results annotate candidate regulatory elements in diverse tissues and cell types, their candidate regulators, and the set of human traits for which they show genetic variant enrichment, providing a resource for interpreting the molecular basis of human disease.

    • Anshul Kundaje
    • Wouter Meuleman
    • Manolis Kellis
    ResearchOpen Access
    Nature
    Volume: 518, P: 317-330

  • By generating maps of histone modifications at promoters and enhancers in several different human cell lines, it has been possible to determine that although modification patterns at promoters are largely invariant between cell types, the patterns at most enhancers are specific to a single cell type and correlate well with cell-type-specific gene expression.

    • Nathaniel D. Heintzman
    • Gary C. Hon
    • Bing Ren
    Research
    Nature
    Volume: 459, P: 108-112

  • As part of the modENCODE initiative, which aims to characterize functional DNA elements in D. melanogaster and C. elegans, this study created a map of the regulatory part of the fruitfly genome. On the basis of the developmental dynamics of chromatin modifications, polymerase and transcription factor occupancy this work defines a vast array of putative regulatory elements, such as enhancers, promoters, insulators and silencers. This resource represents the first attempt at a comprehensive annotation of cis-regulatory elements in a metazoan genome.

    • Nicolas Nègre
    • Christopher D. Brown
    • Kevin P. White
    Research
    Nature
    Volume: 471, P: 527-531

  • Breschi et al. investigated proteomic profiles from the Project Baseline Health Study cohort to identify whether there are differential plasma profiles associated with type 2 diabetes. They find that integration of proteomic and clinical data could enable a more refined risk-based stratification of individuals with normoglycemia or prediabetes.

    • Alessandra Breschi
    • Yuliang Wang
    • Charles C. Kim
    ResearchOpen Access
    Communications Medicine
    Volume: 5, P: 1-14

  • The authors summarize the data produced by phase III of the Encyclopedia of DNA Elements (ENCODE) project, a resource for better understanding of the human and mouse genomes.

    • Federico Abascal
    • Reyes Acosta
    • Zhiping Weng
    ResearchOpen Access
    Nature
    Volume: 583, P: 699-710

  • A map of genome-wide binding locations of 165 human, 93 worm and 52 fly transcription-regulatory factors (almost 50% presented for the first time) from diverse cell types, developmental stages, or conditions reveals that gene-regulatory properties previously observed for individual factors may be general principles of metazoan regulation that are well preserved.

    • Alan P. Boyle
    • Carlos L. Araya
    • Michael Snyder
    ResearchOpen Access
    Nature
    Volume: 512, P: 453-456

  • An international consortium reports the genomic sequence for ten Drosophila species, and compares them to two other previously published Drosophila species. These data are invaluable for drawing evolutionary conclusions across an entire phylogeny of species at once.

    • Andrew G. Clark
    • Michael B. Eisen
    • Iain MacCallum
    Research
    Nature
    Volume: 450, P: 203-218

  • Platypuses are monotremes and combine aspects of both reptilian and mammalian behaviour. An international consortium reports the genome sequence and analysis of Ornithorhynchus anatinus and as expected, parts of the genome look more like mammals, whereas other parts more like reptiles or even chickens.

    • Wesley C. Warren
    • LaDeana W. Hillier
    • Richard K. Wilson
    ResearchOpen Access
    Nature
    Volume: 453, P: 175-183

  • The authors summarize the history of the ENCODE Project, the achievements of ENCODE 1 and ENCODE 2, and how the new data generated and analysed in ENCODE 3 complement the previous phases.

    • Federico Abascal
    • Reyes Acosta
    • Richard M. Myers
    Reviews
    Nature
    Volume: 583, P: 693-698