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Showing 1–17 of 17 results
Advanced filters: Author: Michael Zaleski Clear advanced filters

  • 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

  • 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

  • A description is given of the ENCODE effort to provide a complete catalogue of primary and processed RNAs found either in specific subcellular compartments or throughout the cell, revealing that three-quarters of the human genome can be transcribed, and providing a wealth of information on the range and levels of expression, localization, processing fates and modifications of known and previously unannotated RNAs.

    • Sarah Djebali
    • Carrie A. Davis
    • Thomas R. Gingeras
    ResearchOpen Access
    Nature
    Volume: 489, P: 101-108

  • As part of the modENCODE initiative, which aims to characterize functional DNA elements in D. melanogaster and C. elegans, this study uses RNA-Seq, tiling microarrays and cDNA sequencing to explore the transcriptome in 30 distinct developmental stages of the fruitfly. Among the results are scores of new genes, coding and non-coding transcripts, as well as splicing and editing events.

    • Brenton R. Graveley
    • Angela N. Brooks
    • Susan E. Celniker
    Research
    Nature
    Volume: 471, P: 473-479

  • The Mouse ENCODE Consortium has mapped transcription, DNase I hypersensitivity, transcription factor binding, chromatin modifications and replication domains throughout the mouse genome in diverse cell and tissue types; these data were compared with those from human to confirm substantial conservation in the newly annotated potential functional sequences and to reveal pronounced divergence of other sequences involved in transcriptional regulation, chromatin state and higher order chromatin organization.

    • Feng Yue
    • Yong Cheng
    • Bing Ren
    ResearchOpen Access
    Nature
    Volume: 515, P: 355-364

  • Neutrophils are the first responders in acute inflammatory events such as acute respiratory distress syndrome and tend to home to lung capillaries during acute inflammation, where they can cause tissue damage by diapedesis and secretion of specific molecules. Here the authors show that nanoparticles coated with agglutinated proteins selectively target activated neutrophils in inflamed lungs and can be used for imaging and therapeutic purposes.

    • Jacob W. Myerson
    • Priyal N. Patel
    • Jacob S. Brenner
    Research
    Nature Nanotechnology
    Volume: 17, P: 86-97

  • White-tailed deer are an important reservoir of SARS-CoV-2 in the USA and continued monitoring of the virus in deer populations is needed. In this genomic epidemiology study from Ohio, the authors show that the virus has been introduced multiple times to deer from humans, and that it has evolved faster in deer.

    • Dillon S. McBride
    • Sofya K. Garushyants
    • Andrew S. Bowman
    ResearchOpen Access
    Nature Communications
    Volume: 14, P: 1-15

  • Uniform processing and detailed annotation of human, worm and fly RNA-sequencing data reveal ancient, conserved features of the transcriptome, shared co-expression modules (many enriched in developmental genes), matched expression patterns across development and similar extent of non-canonical, non-coding transcription; furthermore, the data are used to create a single, universal model to predict gene-expression levels for all three organisms from chromatin features at the promoter.

    • Mark B. Gerstein
    • Joel Rozowsky
    • Robert Waterston
    ResearchOpen Access
    Nature
    Volume: 512, P: 445-448

  • The analysis of mammalian transcriptomes could provide new insights into human biology. Here the authors carry out RNA sequencing in a large collection of mouse tissues and compare these data to human transcriptome profiles, identifying a set of constrained genes that carry out basic cellular functions with remarkably constant expression levels across tissues and species.

    • Dmitri D. Pervouchine
    • Sarah Djebali
    • Thomas R. Gingeras
    ResearchOpen Access
    Nature Communications
    Volume: 6, P: 1-11

  • 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

  • In this Review, the authors describe the molecular profile of bladder cancer progression associated with the subtypes of this disease and comment on their potential diagnostic, prognostic and therapeutic importance.

    • Charles C. Guo
    • Sangkyou Lee
    • Bogdan Czerniak
    Reviews
    Nature Reviews Urology
    Volume: 21, P: 391-405

  • Development of large-scale offshore wind farms in Californian offshore waters may alter local wind stress curl and lead to reduced inshore upwelling and increased offshore upwelling, according to numerical simulations from an atmospheric-ocean circulation model.

    • Kaustubha Raghukumar
    • Timothy Nelson
    • Jesse Roberts
    ResearchOpen Access
    Communications Earth & Environment
    Volume: 4, P: 1-12