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Showing 1–7 of 7 results
Advanced filters: Author: Rupali P Patwardhan Clear advanced filters

  • Two groups describe approaches for synthesizing and assaying the function of thousands of variants of mammalian DNA regulatory elements. Melnikov et al. use their results to engineer short optimized regulatory elements in human cells, whereas Patwardhan et al. study enhancers hundreds of bases long in mice.

    • Rupali P Patwardhan
    • Joseph B Hiatt
    • Jay Shendure
    Research
    Nature Biotechnology
    Volume: 30, P: 265-270

  • Patwardhan et al. describe a high-throughput approach for analyzing at single-nucleotide resolution the DNA regulatory sequences that control gene expression. Characterizing these sequences in a massively parallel manner will be useful for deciphering the regulatory logic of the cell and for synthetic biology.

    • Rupali P Patwardhan
    • Choli Lee
    • Jay Shendure
    Research
    Nature Biotechnology
    Volume: 27, P: 1173-1175

  • Short sequence reads are grouped based on the long genomic fragments from which they derive, enabling efficient local assembly of the long fragments and therefore accurate de novo genome assembly and metagenome sequencing.

    • Joseph B Hiatt
    • Rupali P Patwardhan
    • Jay Shendure
    Research
    Nature Methods
    Volume: 7, P: 119-122

  • Sequencing a human genome using next-generation methods does not distinguish between the two copies of each chromosome. Kitzman et al. determine a haplotype-resolved genome sequence by efficiently constructing and sequencing long-insert clones that cover the diploid genome with a low likelihood of overlap.

    • Jacob O Kitzman
    • Alexandra P MacKenzie
    • Jay Shendure
    Research
    Nature Biotechnology
    Volume: 29, P: 59-63

  • Nadav Ahituv and colleagues use a massively parallel reporter assay to test 4,970 synthetic regulatory element sequences, containing patterns of 12 known liver transcription factor binding sites, in mice and in HepG2 cells. They systematically test the impact of binding site copy number, spacing, combination and order on gene expression.

    • Robin P Smith
    • Leila Taher
    • Nadav Ahituv
    Research
    Nature Genetics
    Volume: 45, P: 1021-1028