Whole-genome variant detection in long-read sequencing data from ultra-low input patient samples Long-read sequencing provides a more complete view of the genome than short-read sequencing, with advantages in the detection of structural variants, tandem repeats, and small variants (single nucleot...

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 cartoon says hey everybody an old man 's talking while bart simpson looks on ALT: a cartoon says hey everybody an old man 's talking while bart simpson looks on

A follow-up to my quote of the day this morning:

A short Bluetorial about Vannevar Bush and his legacy

Modern Grant Writing with AI AI is transforming grant writing—turning a time-intensive task into a more strategic, efficient process that elevates both research and storytelling. This hands-on course explores how to integrate AI ...

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.

ChatGPT A conversational AI system that listens, learns, and challenges

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

ChatGPT A conversational AI system that listens, learns, and challenges

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)

ChatGPT A conversational AI system that listens, learns, and challenges

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!

STRchive: a dynamic resource detailing population-level and locus-specific insights at tandem repeat disease loci - Genome Medicine Approximately 8% of the human genome consists of repetitive elements called tandem repeats (TRs): short tandem repeats (STRs) of 1–6 bp motifs and variable number tandem repeats (VNTRs) of 7 + bp moti...

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...

STRchive: a dynamic resource detailing population-level and locus-specific insights at tandem repeat disease loci - Genome Medicine Approximately 8% of the human genome consists of repetitive elements called tandem repeats (TRs): short tandem repeats (STRs) of 1–6 bp motifs and variable number tandem repeats (VNTRs) of 7 + bp moti...

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 !

A Bifunctional Degrader Reads Out in Phase 3

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...

Bispecific antibodies targeting the N-terminal and receptor binding domains potently neutralize SARS-CoV-2 variants of concern Bispecific antibodies incorporating a cross-reactive NTD-specific antibody are resilient to SARS-CoV-2 variants of concern.

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/...

Mutations to transcription factor MAX allosterically increase DNA selectivity by altering folding and binding pathways - Nature Communications In this work, high-throughput microfluidic assays reveal how allosteric substitutions that alter folding-and-binding pathways shape DNA specificity and selectivity landscapes in the human…

Researchers from @pollyfordyce.bsky.social lab explore what makes some transcription factors more or less selective for their DNA ligands. This work could guide the design of more selective DNA-binding proteins for many bioengineering applications: