the bioinformatics chat

#61 3D genome organization and GRiNCH with Da-Inn Erika Lee

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In this episode, Jacob Schreiber interviews Da-Inn Erika Lee about

data and computational methods for making sense of 3D genome structure. They
begin their discussion by talking about 3D genome structure at a high level
and the challenges in working with such data. Then, they discuss a method
recently developed by Erika, named GRiNCH, that mines this data to
identify spans of the genome that cluster together in 3D space and
potentially help control gene regulation.

Links:

  • GRiNCH: simultaneous smoothing and detection of topological units of genome organization from sparse chromatin contact count matrices with matrix factorization (Da-Inn Lee and Sushmita Roy)
  • GRiNCH Project Page
  • In silico prediction of high-resolution Hi-C interaction matrices (Shilu Zhang, Deborah Chasman, Sara Knaack, and Sushmita Roy)

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    the bioinformatics chatBy Roman Cheplyaka
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