Analysis methods for studying the 3D architecture of the genome

Ferhat Ay*, William S. Noble

*Corresponding author for this work

    Research output: Contribution to journalReview articlepeer-review

    110 Scopus citations


    The rapidly increasing quantity of genome-wide chromosome conformation capture data presents great opportunities and challenges in the computational modeling and interpretation of the three-dimensional genome. In particular, with recent trends towards higher-resolution high-throughput chromosome conformation capture (Hi-C) data, the diversity and complexity of biological hypotheses that can be tested necessitates rigorous computational and statistical methods as well as scalable pipelines to interpret these datasets. Here we review computational tools to interpret Hi-C data, including pipelines for mapping, filtering, and normalization, and methods for confidence estimation, domain calling, visualization, and three-dimensional modeling.

    Original languageEnglish (US)
    Article number183
    JournalGenome biology
    Issue number1
    StatePublished - Sep 2 2015


    • Chromatin conformation capture
    • Genome architecture
    • Three-dimensional genome
    • Three-dimensional modeling

    ASJC Scopus subject areas

    • Genetics
    • Ecology, Evolution, Behavior and Systematics
    • Cell Biology


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