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#61 3D genome organization and GRiNCH with Da-Inn Erika Lee
Manage episode 295693293 series 1537951
Content provided by Roman Cheplyaka. All podcast content including episodes, graphics, and podcast descriptions are uploaded and provided directly by Roman Cheplyaka or their podcast platform partner. If you believe someone is using your copyrighted work without your permission, you can follow the process outlined here https://player.fm/legal.
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)
If you enjoyed this episode, please consider supporting the podcast on Patreon.
70 episodes
Share
Manage episode 295693293 series 1537951
Content provided by Roman Cheplyaka. All podcast content including episodes, graphics, and podcast descriptions are uploaded and provided directly by Roman Cheplyaka or their podcast platform partner. If you believe someone is using your copyrighted work without your permission, you can follow the process outlined here https://player.fm/legal.
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)
If you enjoyed this episode, please consider supporting the podcast on Patreon.
70 episodes
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Similar to the bioinformatics chat
How many organs could you donate and remain alive? How many planet Earths could fit inside the Sun? How high is a giraffe's blood pressure? Why is the sea blue? To find out, Ask The Naked Scientists!
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…
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This Week in Microbiology is a podcast about unseen life on Earth hosted by Vincent Racaniello and friends. Following in the path of his successful shows 'This Week in Virology' (TWiV) and 'This Week in Parasitism' (TWiP), Racaniello and guests produce an informal yet informative conversation about microbes which is accessible to everyone, no matter what their science background.
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