Genomic analysis articles within Nature Communications

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  • Article |

    Prostate cancer often does not progress to invasive disease and thus markers predicting the course of the disease progression are critical for optimal treatment choices. Here the authors show that variants at two genetic loci correlate with the aggressiveness of prostate cancer.

    • Sonja I. Berndt
    • , Zhaoming Wang
    •  & Stephen J. Chanock

  • Article |

    Artifacts caused by whole-genome amplification bias are a recurrent challenge in single-cell sequencing analysis. Here, the authors develop statistical models and demonstrate an efficient strategy for controlling amplification errors by a joint analysis of single cell genomes.

    • Cheng-Zhong Zhang
    • , Viktor A. Adalsteinsson
    •  & J. Christopher Love

  • Article
    | Open Access

    Basal cell carcinoma is a common cancer among people of European ancestry, with associated high economic costs to monitor and treat. Here Stacey et al.conduct a genome-wide association study on Icelandic and other European populations, identifying four novel loci associated with cancer susceptibility.

    • Simon N. Stacey
    • , Hannes Helgason
    •  & Kari Stefansson

  • Article |

    Genes are often transcribed in random bursts followed by long periods of inactivity. Here the authors show, by a light-inducible transcription system in Neurospora, that refractory promoters carry a physical memory of their previous transcription history.

    • François Cesbron
    • , Michael Oehler
    •  & Michael Brunner

  • Article |

    As important post-transcriptional regulators of gene expression, microRNAs play a key role in the generation of complex phenotypes. Here, Huan et al.identify miR-eQTLs in whole blood samples to create a roadmap linking regulation of microRNA expression to complex diseases.

    • Tianxiao Huan
    • , Jian Rong
    •  & Jane E. Freedman

  • Article |

    ADAR1 is an adenosine deaminase that converts adenosine to inosine (A-to-I) mostly on Alu repeats in human RNA. Here by analysing transcriptome-wide ADAR1–RNA interactions, the authors show that ADAR1 also binds non-Alusequences to regulate alternative 3′ UTR usage and miRNA biogenesis in the nucleus.

    • Jae Hoon Bahn
    • , Jaegyoon Ahn
    •  & Xinshu Xiao

  • Article
    | Open Access

    Levels of circulating thyrotropin and free thyroxine reflect thyroid function, however, their genetic underpinnings remain poorly understood. Taylor et al. take advantage of whole-genome sequence data from cohorts within the UK10K project to identify novel variants associated with these traits.

    • Peter N. Taylor
    • , Eleonora Porcu
    •  & Pingbo Zhang

  • Article
    | Open Access

    Multiple regulatory elements distant from their targets on the linear genome can influence gene expression through chromatin looping. Here, the authors report an improved chromosome conformation capture approach that can be used to identify long-range chromatin interactions in cancer risk loci.

    • Roland Jäger
    • , Gabriele Migliorini
    •  & Richard S. Houlston

  • Article
    | Open Access

    Common variants account for only a small amount of the heritable risk for developing asthma. Using a meta-analysis approach, Igartua et al. identify one low-frequency missense mutation and two genes with functional variants that are associated with asthma, but only in specific ethnic groups.

    • Catherine Igartua
    • , Rachel A. Myers
    •  & Carole Ober

  • Article |

    Ampullary organs are involved in electroreception, but whether these are derived from placodes, thickened ectoderm, is unclear. In this study, the ampullary organs of the primitive ray-finned fish,Polyodon spathula, are shown to develop from lateral line placodes, suggesting that this is the ancestral state in bony fishes.

    • Melinda S. Modrell
    • , William E. Bemis
    •  & Clare V.H. Baker

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