the bioinformatics chat

#51 Basset and Basenji with David Kelley

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In this episode, Jacob Schreiber interviews David Kelley about

machine learning models that can yield insight into the consequences of
mutations on the genome. They begin their discussion by talking about
Calico Labs, and then delve into a series of papers that David has
written about using models, named Basset and Basenji, that connect genome
sequence to functional activity and so can be used to quantify the effect of
any mutation.

Links:

  • Calico Labs
  • Basset: Learning the regulatory code of the accessible genome with deep convolutional neural networks (David R. Kelley, Jasper Snoek, and John Rinn)
  • Sequential regulatory activity prediction across chromosomes with convolutional neural networks (David R. Kelley, Yakir A. Reshef, Maxwell Bileschi, David Belanger, Cory Y. McLean, and Jaspar Snoek)
  • Cross-species regulatory sequence activity prediction (David R. Kelley)
  • Basenji GitHub Repo

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