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

<p>In this episode, <a href="https://jmschrei.github.io/">Jacob Schreiber</a> interviews <a href="https://dyneofdata.github.io/">Da-Inn Erika Lee</a> 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 <a href="https://roy-lab.github.io/grinch/">GRiNCH</a>, that mines this data to identify spans of the genome that cluster together in 3D space and potentially help control gene regulation.</p> <p>Links:</p> <ul> <li><a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02378-z">GRiNCH: simultaneous smoothing and detection of topological units of genome organization from sparse chromatin contact count matrices with matrix factorization</a> (Da-Inn Lee and Sushmita Roy)</li> <li><a href="https://roy-lab.github.io/grinch/">GRiNCH Project Page</a></li> <li><a href="https://www.nature.com/articles/s41467-019-13423-8">In silico prediction of high-resolution Hi-C interaction matrices</a>(Shilu Zhang, Deborah Chasman, Sara Knaack, and Sushmita Roy)</li> </ul>