the bioinformatics chat

A podcast about computational biology, bioinformatics, and next generation sequencing.

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


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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 2021-06-23  1h9m