Come check out Cera’s poster (4106) today at 2:30pm! Pre-print: www.medrxiv.org/content/10.1...
17.10.2025 17:23
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Come check out Cera’s poster (4106) today at 2:30pm! Pre-print: www.medrxiv.org/content/10.1...
ASHG25 Poster 4106 Today at 2:30pm! Whole-genome long-read sequencing from 10 NANOGRAMS, not micrograms! ULI-HiFi delivers:
✅ 99.82% F1 for SNVs
✅ 98.9% TR accuracy
✅ Discovered LIMD1 TR expansion progressively increasing from normal→polyp→adenocarcinoma, with evidence of function
At ASHG25 RIGHT NOW: Deep-coverage PacBio HiFi sequencing reveals hotspots of tandem repeat variation in the male germline. 12 men, paired blood/sperm, 1.7M repeats analyzed. What we found about mutational bias will surprise you! Poster 6044W, 2:30-4:30pm today. Lucas Finot presenting.
Just trying to follow in your footsteps, Kara!
Absolutely!! Thanks David :)
Proud to announce that we received the NIH Director's New Innovator Award to develop a new class of genome editing tools!
A follow-up to my quote of the day this morning:
A short Bluetorial about Vannevar Bush and his legacy
Interested in modern grant writing in the age of AI? Join us this summer through Stanford Continuing Studies! continuingstudies.stanford.edu/courses/prof...
Big: The final version of a randomized, controlled World Bank study finds using a GPT-4 tutor with teacher guidance in a six week afterschool program in Nigeria had "more than twice the effect of some of the most effective interventions in education" ("equating to 1.5 to 2 years" of standard school)
I had such a powerful experience at BCM SKY Retreat this weekend led by @grahamerwin.bsky.social and met so many amazing people!
It was a thought-provoking and reflective weekend with lessons that I will carry with me!
What a privilege to partake in such a transformative experience! 🥰
A first in human genomics: a 4-generation pedigree reference, now in Nature.
Built with #PacBio HiFi, it maps de novo mutation rates, reveals paternal bias, and captures high mutation rates in tandem repeats—even in Y and repeat-rich regions.
Paper here: go.nature.com/4lGMPlP
#TheresHiFiForThat
Here is the output in case there are issues with the link.
Prompt: Do research. find peer-reviewed publications of pyrrole-imidazole polyamides used to activate gene expression (transcriptional activators). Expected output: an exhaustive list of references to the original publication.
The only tool to capture both so far has been ChatGPT Deep Research and o3 (new model from OpenAI released today. It also captures 2 other important papers from Sugiyama and Kodadek. (3/3)
bit.ly/LLMtaste
The two more important papers on polyamide-based transcriptional activators would be Mapp et al PNAS 2000 (the OG on the topic) and our 2017 Science paper (one of the most convincing in a disease model). (2/3)
There are a number of tools (Elicit, Perplexity, Google's Deep Research, Consensus within ChatGPT) to find references. One of the complaints from academics is these tools don't find "the right papers".
So far, ChatGPT Deep Research and their o3 model have the best "taste" that I have found. (1/3)
Caveat: The authors didn't perform a statistical test comparing these groups, but the trend is the same on bot top-1 and top-10 accuracy.
Table 1 Top-1 and top-10 accuracy of DDx lists produced with AMIE and Search assistance
The LLM (AMIE in this case) performs higher (59.1% top-10 accuracy) than the clinician with the LLM (51.7%).
Another study consistent with what @emollick.bsky.social has been sharing for a while now.
www.nature.com/articles/s41...
Yes! Benchmarks aside, 3.7 Sonnet and Gemini 2.5 Pro have been performing well for me.
Updated this chart with the newest Gemini. It shows the rapid progress in AI over less than two years: costs for GPT-4 class models has dropped 99.7% and even the most advanced models (beating PhDs at the GPQA) are still 82% cheaper than GPT-4.
Probably not worth betting on this trend ending soon.
A new means of selectively imaging the inner mycolate of mycobacteria using a compound that covalently modifies an enzyme intercepts to create a new intermediate with the Kim lab, @thebrysonlab.bsky.social and the Bernhardt lab. #TB
Congratulations, Harriet. This will be a valuable resource for us!
The strchive.org paper is out!!
The paper describes STRchive as a resource to improve the diagnosis of tandem repeat disorders, then goes beyond it to consider what can be learned about childhood onset and population prevalence of these diseases.
🖥️ 🧬
link.springer.com/article/10.1...
A new article from Laurel Hiatt and @hdashnow.bsky.social describing STRchive is now available at Genome Medicine. genomemedicine.biomedcentral.com/articles/10....
Check out the database resource, as STRchive "streamlines TR variant interpretation at disease-associated loci."
strchive.org
Evidence that a well prompted LLM can help learning from a (small, single-subject) randomized controlled trial at Harvard: “here we show that students learn more than twice as much in less time with an AI tutor compared to an active learning classroom, while also being more engaged and motivated.”
We don't spend a penny on marketing. It's all word of mouth for @costplusdrugs.com
That's how we keep prices so low. Please spread the word !
The first bifunctional protein degrader to deliver Phase III data! It seems to work, but people were definitely expecting more:
5 yr anniversary of the day I started my COVID ICU visit
Spectacular news this morning for CRISPR gene editing to treat genetic disease from Beam Therapeutics.
This method was developed by David Liu's lab at the Broad.
= "academic" science produces innovations that enables the biotech sector to build medicines
investors.beamtx.com/news-release...
Excited to share the peer-reviewed version of our paper, which is out today!!
Bispecific antibodies targeting the N-terminal and receptor binding domains potently neutralize SARS-CoV-2 variants of concern | Science Translational Medicine www.science.org/doi/10.1126/...
