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Shili Lin, Ohio State

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Random Effect Modeling of Whole Genome Chromatin 3D Structure
29 March 2018 from 4:00 PM to 5:00 PM
104 Thomas Building
Contact Name
Lorey Burghard
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The expression of a gene is usually controlled by the regulatory elements in its promoter region. However, it has long been hypothesized that, in complex genomes such as that of the human, a gene may also be controlled by distal enhancers and repressors. Globally, the chromatin structure is closely linked to the biological function of the genome and has great implications in human health and disease.  A recently developed molecular technique is able to detect physical contacts between distant genomic loci, validating the theory that communications between such elements are achieved through spatial organization of chromosomes to bring genes and their regulatory elements into close proximity. Such a molecular technique, coupled with the Next Generation Sequencing (NGS) technology, enables genome-wide detection of physical contacts. The availability of these data makes it possible to reconstruct the underlying three-dimensional (3D) spatial chromatin structure of a genome and to study spatial gene regulation in genomics. However, several special features of the NGS-based high-throughput data have posed challenges for statistical modeling and inference. I will discuss a random effect modeling strategy for addressing such features, including dependency, sparsity, and over-dispersion. Compounded with the sheer size of the data, the problem is even more challenging when the whole genome structure is considered. The question of how to tackle the sparse nature of single-cell Hi-C data will also be touched upon, but a viable solution remains elusive.

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