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Showing 1–6 of 6 results
Advanced filters: Author: Sourya Bhattacharyya Clear advanced filters

  • Immune cells are important in the pathogenesis of COVID-19. Here the authors assessed the effects of COVID-19-risk variants on gene expression in a range of immune cell types, highlighting their potential to impact the function of diverse immune cell types and influence severe disease.

    • Benjamin J. Schmiedel
    • Job Rocha
    • Pandurangan Vijayanand
    ResearchOpen Access
    Nature Communications
    Volume: 12, P: 1-12

  • Here, the authors present an HiChIP dataset on naïve CD4 T cells from 30 donors. They investigate genotype-dependent and allele-specific variation of chromatin loops between active regulatory elements, reporting loop-associated variants linked to dynamic changes in gene expression.

    • Sourya Bhattacharyya
    • Ferhat Ay
    ResearchOpen Access
    Nature Communications
    Volume: 15, P: 1-22

  • HiChIP/PLAC-seq assay is popular for profiling 3D genome interactions among regulatory elements at kilobase resolution. Here the authors describe FitHiChIP an empirical null-based, flexible computational method for statistical significance estimation and loop calling from HiChIP data.

    • Sourya Bhattacharyya
    • Vivek Chandra
    • Ferhat Ay
    ResearchOpen Access
    Nature Communications
    Volume: 10, P: 1-14

  • In multiple myeloma, a 4;14 translocation induces overexpression of histone methyltransferase NSD2, resulting in expansion of H3K36me2 and shrinkage of H3K27me3 domains. Here the authors find that CTCF, H3K27ac and gene expression changes cluster within a subset of insulated domains implicating 3D chromosome organization as a key factor in the NSD2-mediated phenotype.

    • Priscillia Lhoumaud
    • Sana Badri
    • Jane A. Skok
    ResearchOpen Access
    Nature Communications
    Volume: 10, P: 1-18

  • Fit-Hi-C is a computational tool for identifying statistically significant contacts from Hi-C data. This protocol describes how to apply the new version, called FitHiC2, on high-resolution Hi-C data, demonstrating the added functionalities.

    • Arya Kaul
    • Sourya Bhattacharyya
    • Ferhat Ay
    Protocols
    Nature Protocols
    Volume: 15, P: 991-1012