Brian Naughton

2.6K posts

Brian Naughton

Brian Naughton

@btnaughton

genetics/data/programming. ex-Hexagon ex-Stanford ex-23andMe ex-TCD https://t.co/77VRsi7znN 🇮🇪

Katılım Ocak 2015
2K Takip Edilen3.6K Takipçiler
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Brian Naughton
Brian Naughton@btnaughton·
Great, I'd love to save money by buying 100 copies of this book. (Really good (audio)book btw)
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Dr. Shelby
Dr. Shelby@shelbynewsad·
Lead, microplastics, forever chemicals, poor air quality are amongst us all. Folks like lead lady have built large followings around that one thing. excited for our generation to reckon with all the toxic things we’ve been subjected too and create some in vivo detox products!
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Brian Naughton
Brian Naughton@btnaughton·
@draparente @brad_woolf In general, there is a nice alignment between variants that are imputable and variants that are interpretable. So imputation works great, but it kind of defeats the purpose of whole genome sequencing, which in my mind is finding rare de novos.
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Bradley Woolf
Bradley Woolf@brad_woolf·
i have now sequenced my own DNA 5x at home and learned so much about myself i wrote out the protocol here so anyone can follow it and talk to their DNA: bradleywoolf.com/links-1/sequen… a lot of people helped with this, they are all mentioned below
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Brian Naughton
Brian Naughton@btnaughton·
@brad_woolf @draparente I think swabs are just low volume. Can you not use the same prep as for the swab? One little known fact is that saliva is up to 80% white blood cells.
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Bradley Woolf
Bradley Woolf@brad_woolf·
@draparente 3-5x on MinION, but my earliest learning runs were 0.2-1x so 1. next batch is focused on increasing quantity of DNA (blood) 2. i think the coverage can increase exponentially from software inference rather than chemistry 3. i don’t think this is ready as a consumer technology
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Aaron Ring
Aaron Ring@aaronmring·
I took OpenDDE for a spin. Parenthetically, the name is terrible and should be changed: "OpenDDE" has zero relationship to DDE. Anyway, it seems to be a decent model. I ran predictions for ~550 unpublished VHH against their target and a decoy. Slight edge vs Protenix-v2.
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Bradley Woolf
Bradley Woolf@brad_woolf·
@SethSHowes @btnaughton @eryney_ok @JayLikesGenomes @0xCF88 @ThatMrE Genetic variants from first principles: x.com/adibvafa/statu… Pass your genome + RNA to any of these models: biotender.online/bio-model-inst… Take it to a doctor if you metabolize particular drugs differently: x.com/parmita/status… @patrickc Claude post: x.com/patrickc/statu…
Patrick Collison@patrickc

I'm lucky enough to have a great doctor and access to excellent Bay Area medical care. I've taken lots of standard screening tests over the years and have tried lots of "health tech" devices and tools. With all this said, by far the most useful preventative medical advice that I've ever received has come from unleashing coding agents on my genome, having them investigate my specific mutations, and having them recommend specific follow-on tests and treatments. Population averages are population averages, but we ourselves are not averages. For example, it turns out that I probably have a 30x(!) higher-than-average predisposition to melanoma. Fortunately, there are both specific supplements that help counteract the particular mutations I have, and of course I can significantly dial up my screening frequency. So, this is very useful to know. I don't know exactly how much the analysis cost, but probably less than $100. Sequencing my genome cost a few hundred dollars. (One often sees papers and articles claiming that models aren't very good at medical reasoning. These analyses are usually based on employing several-year-old models, which is a kind of ludicrous malpractice. It is true that you still have to carefully monitor the agents' reasoning, and they do on occasion jump to conclusions or skip steps, requiring some nudging and re-steering. But, overall, they are almost literally infinitely better for this kind of work than what one can otherwise obtain today.) There are still lots of questions about how this will diffuse and get adopted, but it seems very clear that medical practice is about to improve enormously. Exciting times!

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Brian Naughton
Brian Naughton@btnaughton·
@brad_woolf Nice work!! At one point I made it half-way through making a video tutorial but it was brutally slow to make...
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Brian Naughton
Brian Naughton@btnaughton·
@DerekCroote I agree! The rest of the paragraph tries to say this. My only pause is: why does carrageenan reduce infection duration? It's solely a barrier. It sucks that the test is gone already. Weird timing. There are others I could replace it with but they are probably all ephemeral...
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Derek Croote
Derek Croote@DerekCroote·
Fun read! Sadly the 10-in-1 Alibaba kit has been taken down already. I wonder about the timing. "Once you have identified HMPV as the virus, then you would spray the peptide in your nose" - but if you have sufficient symptoms to prompt you to take the test to identify the virus, wouldn't it already be too late for a nasal spray intervention?
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Nima Alidoust
Nima Alidoust@nalidoust·
Today we are introducing Tara. Biological datasets are a source of insights and a means to train biological AI models. As the ability to reason at scale emerges, they take on a new role: the ground truth for testing what reasoning models produce, and the environment in which those models operate, get feedback, and improve. Tara, our autonomous research agent, is embedded in our ever-expanding datasets, lab-generated and synthetic, and built to test and evolve the hypotheses frontier models generate, matching the pace at which they produce new ideas. By keeping those models grounded in a vast space of high-precision biological data, we believe we can compound biological reasoning and close the impedance mismatch between hypothesis generation and validation.
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Aaron Ring
Aaron Ring@aaronmring·
I've been really impressed with ESMFold2's design capabilities. To make it easier to run locally, as well as to support structural templates, multichain targets, hotspots, Protenix-v2 validation, and automated MSA handling, I created this project: github.com/cytokineking/e…
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Ryan Bethencourt
Ryan Bethencourt@RyanBethencourt·
@btnaughton Very interesting and novel idea Brian! Have you thought of playing around with other ideas like this that go deeper (lung level)? Lots of pretty serious viral/bacterial/fungal infections that this strategy might work on too!
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