[FRIAM] More on levels of sequence organization

[Marcus Daniels]

Cool!

“For synthetic biology, iteratively querying a model of the mutational fitness landscape could help efficiently guide the introduction of mutations to enhance protein function (Romero & Arnold, 2009), inform protein design using a combination of activating mutants (Hu et al., 2018), and make rational substitutions to optimize protein properties such as substrate specificity (Packer et al., 2017), stability (Tan et al., 2014), and binding (Ricatti et al., 2019).”

Get a few billion people to get full genome sequencing, and let the TPUs discover how we work!    Everyone gets a custom cocktail to improve stamina, fight off cancer, etc. etc.

Marcus

From: Friam <friam-bounces at redfish.com> on behalf of Roger Critchlow <rec at elf.org>
Reply-To: The Friday Morning Applied Complexity Coffee Group <Friam at redfish.com>
Date: Tuesday, April 30, 2019 at 8:49 PM
To: The Friday Morning Applied Complexity Coffee Group <Friam at redfish.com>
Subject: [FRIAM] More on levels of sequence organization

This just turned up on hacker news:

   https://www.biorxiv.org/content/10.1101/622803v1

[...] To this end we use unsupervised learning to train a deep contextual language model on 86 billion amino acids across 250 million sequences spanning evolutionary diversity. The resulting model maps raw sequences to representations of biological properties without labels or prior domain knowledge. The learned representation space organizes sequences at multiple levels of biological granularity from the biochemical to proteomic levels. [...]

Don't know if I have the energy to plow through the text.

-- rec --
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