Harold Pimentel

We will be hosting 4th Full Circle Symposium for Native Biologists hosted at UCSF in May 2027! We aim to build community and provide meaningful opportunities for Native scientists. If you are a Native biologist at any training stage who wants to speak, plz fill this out by this 1/31: bit.ly/4kh5GFx

🚨New preprint! Ligands at the same GPCR can produce wildly different signaling outputs. Why? We built a mutational scanning platform to measure ~10,000 µOR variants across 15 opioids, yielding ~400k measurements of how sequence and ligand chemistry set signaling. www.biorxiv.org/content/10.6... 1/10

Happy GRFP letter day for all those who celebrate!

Come be my colleague at UCSF! Our department BTS (like the K-pop band, but aka Bioengineering and Therapeutic Sciences) is searching for TWO new faculty members. Links, timeline, and why two searches in this thread 🧵

Is this a joke? Yes. Is it also an opportunity to demonstrate how extrapolations that incorporate uncertainty are far better behaved than those that don't? Absolutely.

Please repost: My department at USC is hiring for a teaching-track faculty position. We are looking for someone principally to teach statistics for biologists, but there will be opportunities for other courses in statistics & algorithms applied to biology usccareers.usc.edu/job/los-ange...

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)

@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...

I'm so tired.

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...

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.

Radical transparency 🎁 www.nytimes.com/2025/09/23/h...

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...

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...

You’re not dropping a single, asshole. If you’re actually knew anything, it would be criminal not to reveal it now. But of course, this is a bullshit publicity stunt.

From @jxtxfoundation.bsky.social | JXTX + CSHL 2025 Genome Informatics Scholarships | Up to $750 for domestic or $1,250 for international travel | Application deadline is September 15, 2025 | #OpenScience 🧬 🖥️ 🧪 ⬇️ jxtxfoundation.org/news/2025-6-...

Yesterday the Supreme Court issued a convoluted, 36-page emergency order about NIH grant terminations. Two main takeaways: -$2 billion (not the government # of $780 million) in NIH grants will likely be re-terminated -future legal challenges will be much harder w/ @maxkozlov.bsky.social:

Very proud of @ytchang11.bsky.social for her first publication from her doctoral research! She conducted very meticulous genomic analyses that uncovered novel isoform-specific mechanistic hypotheses underlying genetic loci associated with multiple cancers. www.nature.com/articles/s41...

Very excited to have this out! Here, we take inspiration from model selection MR to decouple direct and indirect effects in DMS experiments. Check out Jingyou's explainer and paper below: bsky.app/profile/jing...

It is depressing, but all too predictable, how swiftly we’ve gone from the Social Science Genetic Association Consortium offering reassurances about the uses of behavioural polygenic scores to one of their lead authors marketing embryo selection for IQ

Suspension of all grants to UCLA www.latimes.com/california/s...

Super proud of my first student, @jingyour.bsky.social! Well done! Looking forward to the amazing work you will do in the future 🥲 bsky.app/profile/jing...

Super excited to see this out. What started as some math in a grant in 2020, to a student deciding to take this on in 2022, to published in 2025. These things can take time and patience is key!

New preprint! Deacon is a versatile tool for filtering FASTA/FASTQ files and streams at hundreds of megabases per second using minimizers, built with rapid metagenomic host depletion in mind, but equally useful for search. github.com/bede/deacon

Very excited to have this work out by @jeromics.bsky.social ! Please check it out. I think my favorite story from the supplement is how impactful normalization can be in this context. bsky.app/profile/jero...

Qapla’! A great ending to a wonderful talk on science engagement and learning with students from @jasonwilliamsny.bsky.social

St. Jude researchers and international collaborators developed a more affordable and accessible technique of single-cell RNA analysis that combines microscopy with RNA detection. ow.ly/Er0i50WaQnv

Powerful statement by Sen. Alex Padilla. Please notice that anytime senators or representatives try to conduct oversight, they’re blocked. In this case, a sitting US senator was tackled to the ground and handcuffed—for asking a question. Where the hell has Chuck Schumer been on this?

And then they attempted to block the Senator's staff from recording his apparent arrest: bsky.app/profile/demo...

🚨 Applications are open for the UCLA Postdoct Training Program in Neurobehavioral Genetics 🧠🧬 Deadline: 6/30 👉 neurogen.semel.ucla.edu/curriculum/ Contact me if you're interested to write a proposal together combining genetics + functional genomics + digital phenotypes from wearables/smartphones!