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Do you need a billion parameters and millions of sequences for #proteindesign? Maybe not! See our paper: shorturl.at/novMO
We show that interpretable, non-autoregressive structure-based protein design can work!
Original thread: shorturl.at/cdgCP
David Ding retweeted
Check out our last pub. from @mfgrp lab! We discovered that skin commensal microbes induce systemic and local B cell responses upon colonization and took advantage of this knowledge to create topical vaccines using engineered skin microbes. Please read the thread for details.
Today we report that an engineered skin bacterium, swabbed gently on the head of a mouse, can unleash a potent antibody response against a pathogen. Could lead to topical vaccines that are applied in a cream. @DjenetBousbaine led the charge... @Nature 1/55
David Ding retweeted
Excited to share our new preprint on the Taxol pathway!
We developed a strategy to systematically activate and identify gene sets in non-model organisms and used it to find 8 new genes in the Taxol pathway, allowing us to biosynthesize Taxol precursors de novo.
Surprisingly, this required a new protein (FoTO1) that helps the first Taxol P450 oxidase produce the correct product. more here: biorxiv.org/content/10.1101/… congrats to coauthors
@Sattely_lab
@ctliu629 @fordycelab
David Ding retweeted
What limits rubisco function? Is it the chemical mechanism? Evolution? In an updated pre-print @prywes et. al explore this question by assaying >99% of single amino acid mutants in Form II rubisco (1/7)
So we are blowing past 1.5C, and expecting hundreds of millions of global south folks with forced migration and newly poverty in the coming years. #ipcc
Really enjoyed this summary of recent AI progress and possible implications: youtu.be/xoVJKj8lcNQ?si=8oI0… thanks Carlo amadei
Thanks to the team @ecolienthusiast, @samsinai, @_nathanrollins, @NoamPrywes, @dfsavage, @michael_laub8, @deboramarks. Thanks also to @chloehsu0 + @SteffanPaul3, and 2 anonymous reviewers for great suggestions.
The 5050 program is giving me the tools to turn my research into a startup, everything from how to move fast to the secrets of fundraising to how to build a team around you. If you want to learn about deep tech startups, and build one, go apply!
xitter.cf/sethbannon/status/1757…
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That’s why we built 5050, “a cheat code for starting a deep tech startup.” (quote from an alumni)
Applications open!
fiftyyears.com/5050
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David Ding retweeted
@MafaldaFigDias & @Jonnygfrazer lab is looking for someone who loves model building and is keen on studying disease from an evolutionary perspective.
Experience in statistics, deep learning, or transcriptomics is desirable but not essential.
David Ding retweeted
New preprint out!
Babies are born to breastfeed.
While 50% of lactating persons struggle to make enough milk, there are no FDA-approved drugs to enhance lactation.
We engineered a long-acting prolactin, Prolactin-XL,
to enhance milk production.
bit.ly/prolactin-XL
1/14
David Ding retweeted
Excited to share our preprint on cyanobacterial communities and their core microbiome, with @Dr__Diamond as corresponding author and incredible help from @jkzorz, @K_BoumaGregson, @catacruanas, @BanfieldLab. #microbiome #Genomics #WomenInSTEM
biorxiv.org/content/10.1101/…
Do you need a billion parameter protein language model to make the right mutations?
Turns out: Learning residue mutation preferences from structure enables designing protein variants better than autoregressive methods.
biorxiv.org/content/10.1101/…
1/7
So maybe most that expensive & uninterpretable sequence models are learning is just the local structural context. Building models directly on structure can be more powerful.
6/7
More info here: youtube.com/watch?v=OaOj3znH…
This was great teamwork with @ecolienthusiast, @samsinai, @_nathanrollins, @NoamPrywes, @dfsavage, @michael_laub8, @deboramarks. Thanks also to @chloehsu0 + @SteffanPaul3.
7/7
David Ding retweeted
Watch this mother react the moment she sees her baby move
This newborn baby boy was born at Sedgwick County Zoo via c section on November 15 and was put on oxygen,
here is mum and baby reunited
David Ding retweeted
Here at @SavageCatsOnly we are thrilled to present a review on rubisco. We focused on structure, mechanism, evolution and engineering attempts. We try, and fail, to conclusively answer the question "What exactly is holding this enzyme back?" 1/10
arxiv.org/abs/2207.10773















