Excited to share this preprint that describes my latest work on using GPUs to accelerate processing of RNA-seq data.
The title says it all: "RNA-seq analysis in seconds using GPUs" now on biorxiv www.biorxiv.org/content/10.6... and github github.com/pachterlab/k...
Figure 1 shows they key result
🧬New today!
📄Inclusion bias affects common variant discovery and replication in a health-system linked biobank
🧑🤝🧑 @loldeloo.bsky.social @apimplaskar.bsky.social @bpasaniuc.bsky.social & colleagues
Happy to see this work out now in Genome Biology! Check out the final version here for your FACS DMS needs: link.springer.com/article/10.1...
Great work by Albert from my lab! Albert has a few more papers coming shortly and will be graduating soon. Then off to a PD! He is a great PD catch and you should consider him :) bsky.app/profile/albe...
My preprint on keju, a statistical tool for Massively Parallel Reporter Assay (MPRA) data, is out! keju improves sensitivity, calibration, and reliability over previous methods by closely modeling important uncertainty sources in MPRAs. Check it out: www.biorxiv.org/content/10.6... (1/n)
"Vegan protein options: mushrooms"
god, this is so bad it's kind of funny
Destroying the earth to make shit memes with GPT:
(the idea was not mine, fortunately)
@jbenning.bsky.social @jedidiahcarlson.com
et al. exemplify how confounding can lead to flawed inference on genetic causality. In studies of human behavior and social outcomes, the cost of downplaying this problem can be steep. royalsocietypublishing.org/doi/epdf/10.... bsky.app/profile/jben...
You win some, you lose some. WELP
One can hope
I'm so tired.
Illustration of Burrows-Wheeler Transform and many auxiliary structures from the input string how$now$brown$cow$#
New tool "bwt-svg" for making illustrations of the BWT and the many auxiliary arrays and other structures related to it. Pyodide-based no-installation-necessary interface here: benlangmead.github.io/bwt-svg/. (H/t to @robert.bio for pointing me to pyodide!) Full repo: github.com/benlangmead/....
The proteasome-substrate-shuttle protein UBQLN2 contains—like other quality control system proteins—a long region devoid of lysine (a lysine desert)
Martin Grønbæk-Thygesen (from @rhp-lab.bsky.social) et al show that introducing K here causes ubiquitylation and degradation
doi.org/10.1101/2025...
🤣
yikes... sorry...
my only advice is to proactively carry a 5lb bag of rice with your laptop
The first (of hopefully many) reports to come from our collaboration with @hjp.bsky.social
We present a new type of cell fitness assay that allows you to both quantify and explain differences across human donors in cell proliferation and sensitivity to environmental toxicants.
Thanks!
Thank you!
Huge congrats to my student Chloe who led the computational side, and Mike's student Tim who led the experimental side. Both worked diligently on the analysis. And of course, many congrats to my collaborator and friend @mfwells.bsky.social and his lab who did all the experimental work
Stay tuned -- much more in queue
3. we apply these experimental and computational advances along with 'GWAS in a dish' approaches to find genetic variants associated with NPC proliferation. further, we find genetic variants associated with response to lead in NPCs
2. develop computational models that model the nuance in cell villages, including the compositional nature, small sample sizes, and structure of the variance
Super excited to get this out. This collab started a few years ago and is the first paper from it. Here, with experimental and computational approaches we:
1. establish that cell villages can be just as accurate (one might argue more accurate!) than arrayed-based designs
bsky.app/profile/bior...
😭
Color me surprised that the same people who don't believe solid epi over decades (like those guiding nutritional guidelines) believe this. Unreal.
Super excited to have this out. Thanks very much to the reviewers who helped improve this manuscript. Congrats to @jingyour.bsky.social!
bsky.app/profile/bioi...
Pretty sure that’s the point bsky.app/profile/josh...
5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 IN THE UNITED STATES DISTRICT COURT FOR THE NORTHERN DISTRICT OF CALIFORNIA GAVIN NEWSOM, et al., Plaintiffs, Case No. 25-cv-04870-CRB OPINION GRANTING INJUNCTIVE RELIEF V. DONALD J. TRUMP, et al., Defendants. Congress spoke clearly in 1878 when it passed the Posse Comitatus Act, prohibiting the use of the U.S. military to execute domestic law. Nearly 140 years later, Defendants President Trump, Secretary of Defense Hegseth, and the Department of Defense deployed the National Guard and Marines to Los Angeles, ostensibly to quell a rebellion and ensure that federal immigration law was enforced. There were indeed protests in Los Angeles, and some individuals engaged in violence. Yet there was no rebellion, nor was civilian law enforcement unable to respond to the protests and enforce the law. Nevertheless, at Defendants' orders and contrary to Congress's explicit instruction, federal troops executed the laws. The evidence at trial established that Defendants systematically used armed soldiers (whose identity was often obscured by protective armor) and military vehicles to set up protective perimeters and traffic blockades, engage in crowd control, and otherwise demonstrate a military presence in and around Los Angeles. In short, Defendants violated the Posse Comitatus Act.
BREAKING: Trump, Hegseth violated the Posse Comitatus Act with their troop deployment to Los Angeles, Judge Charles Breyer rules after trial. storage.courtlistener.com/recap/gov.us...
