Harold Pimentel
Assistant prof at UCLA using the Bayes for the genomes https://pimentellab.com
- Destroying the earth to make shit memes with GPT: (the idea was not mine, fortunately)
- god, this is so bad it's kind of funny
- Reposted by Harold Pimentel@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...
- We're excited to share the final version of our paper, where we demonstrate how confounding remains a thorny problem for claims about causal genetic influences on human behavioral and socioeconomic outcomes. (w/ @jedidiahcarlson.com @oliviarxiv.bsky.social Ruth Shaw @arbelharpak.bsky.social) 🧵👇
- I'm so tired.
- Reposted by Harold PimentelNew 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/....
- Reposted by Harold PimentelThe 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 importance of UBQLN2 ubiquitylation for its turnover and localization biorxiv.org/content/10.1101/202…
- Reposted by Harold PimentelThe 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.
- Cell villages and Dirichlet modeling map human cell fitness genetics biorxiv.org/content/10.1101/202…
- 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...
- Cell villages and Dirichlet modeling map human cell fitness genetics biorxiv.org/content/10.1101/202…
- 2. develop computational models that model the nuance in cell villages, including the compositional nature, small sample sizes, and structure of the variance
- 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
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View full threadHuge 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
- Reposted by Harold PimentelRadical 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...
- 🧩 Recently published in Bioinformatics Advances: “Rosace-AA: Enhancing interpretation of deep mutational scanning data with amino acid substitution and position-specific insights” Full article available: doi.org/10.1093/bioadv/vbaf218
- Pretty sure that’s the point bsky.app/profile/josh...
- "Losses of significant research and other federal funding would devastate UC and inflict real, long-term harm on our students, faculty, staff, patients, and all Californians. It would also end life-saving research from which all Americans benefit." www.universityofcalifornia.edu/press-room/l...
- Reposted by Harold PimentelBREAKING: 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...
- Reposted by Harold PimentelYou’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.
- Reposted by Harold Pimentel[This post could not be retrieved]
- Reposted by Harold PimentelFrom @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-...
- Reposted by Harold PimentelY'all The ICE building in Portland is painting a line in front of their building But they don't even know how to spell government
- Reposted by Harold PimentelScience will always be political when it tries to help people who the political establishment doesn't center as the default American. Health disparities? Climate change? Public health? Have always been political, will always be political.
- Reposted by Harold PimentelYesterday 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:
- Reposted by Harold PimentelVery 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...
- How do we decouple the effects of two functional phenotypes in protein deep mutational scanning (DMS)? Meet Cosmos, our new statistical framework for causal inference in multi-phenotype DMS. www.biorxiv.org/content/10.1... [1/n]
- Reposted by Harold Pimentel
- Reposted by Harold PimentelIt 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
- Reposted by Harold PimentelSuspension 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...
- Thrilled to share that I just successfully defended my PhD! Thanks to my committee, collaborators, and everyone who’d supported me throughout my seven years at UCLA. A special thank you to my PI Harold for his incredible mentorship! @hjp.bsky.social
- Reposted by Harold PimentelSuper 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!
- 📢OUT TODAY @natgenet.nature.com 📰Improved multiancestry fine-mapping identifies cis-regulatory variants underlying molecular traits and disease risk. By @zeyunlu.bsky.social, @nmancuso.bsky.social and colleagues. ⬇️ www.nature.com/articles/s41...
- Reposted by Harold PimentelNew 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
- Deacon: fast sequence filtering and contaminant depletion biorxiv.org/content/10.1101/202…
- 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...
- Reposted by Harold PimentelQapla’! A great ending to a wonderful talk on science engagement and learning with students from @jasonwilliamsny.bsky.social
- Reposted by Harold PimentelSt. 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
- Reposted by Harold PimentelPowerful 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?
- Reposted by Harold PimentelAnd then they attempted to block the Senator's staff from recording his apparent arrest: bsky.app/profile/demo...
- Reposted by Harold Pimentel🚨 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!
- Reposted by Harold PimentelCheck out the latest from me, Steve Cha, @sarahd1.bsky.social & @cspinet.org's @drpeterlurie.bsky.social. Whatever one thinks of the merits of FDA's decision, the process by which decisions (and policies) are made matters. And the process here spells trouble for public health and innovation.
- Reposted by Harold PimentelThe 2026 Probabilistic Modeling in Genomics (ProbGen) meeting will be held at UC Berkeley, March 25-28, 2026. We have an amazing list of keynote speakers and session chairs: probgen2026.github.io Please help spread the news.
- Reposted by Harold PimentelWhen everything is "normal", writing and administering an NIH T32 program is crazy. Despite being an immense amount of work (probably the single most effort-demanding grant one can direct), it comes with no salary for the PI...
- Reposted by Harold PimentelWant to write to your community about the importance of science funding? Join me on zoom this Friday at 12pm ET / 9am PT to learn to write an op-ed as part of the #McClintockLetters initiative! Sign up to write a letter and register for the workshop here: blogs.cornell.edu/asap/events-...
- Reposted by Harold PimentelLots of colorful and revealing language in here about the new NIH Director from NIH staff speaking to @walkerbragman.bsky.social www.importantcontext.news/p/out-of-his...
- Reposted by Harold PimentelThrilled to announce that I am joining DTU in Copenhagen in the fall, as an assistant professor of chemistry. My research group will focus on fundamental methodology in machine learning for molecules.
- Reposted by Harold PimentelNew paper from our lab joint with Val Arboleda @val-arboleda.bsky.social
- Reposted by Harold PimentelHow can one efficiently simulate phylodynamics for populations with billions of individuals, as is typical in many applications, e.g., viral evolution and cancer genomics? In this work with M. Celentano, @wsdewitt.github.io , & S. Prillo, we provide a solution. doi.org/10.1073/pnas... 1/n
- Recasting the perils of phylodynamic non-identifiability as a feature not a bug, we show that a unique forward-equivalent process enables exact and efficient simulation from arbitrarily large populations. With M Celentano, S Prillo, @yun-s-song.bsky.social www.pnas.org/doi/10.1073/pnas.2412978122
- Reposted by Harold PimentelLast call—hiring for my lab moving to UCLA!
- I’m super honored to be selected, and immensely grateful. Huge thanks, @hypothesisfund.bsky.social! We are looking forward to doing some fun science! bsky.app/profile/hypo...
- 3/ Leveraging large population studies & small scale lab experiments, Awardee @hjp.bsky.social will integrate diverse datasets to strengthen our ability to interpret rare genetic🧬 variants in disease. 🤯 🥳 Congrats Dr. Pimentel! 🙏 #HFScout Kay Tye
- Reposted by Harold Pimentel
- Reposted by Harold Pimentel[This post could not be retrieved]
- The biggest downside I've seen on bluesky is I accidentally type 'bk [enter]' and end up searching burger king
- Reposted by Harold PimentelThe Department of Human Genetics at the University of Utah is sponsoring the Rising Stars in Genetics and Genomics symposium! - We are seeking nominations bu June 1. - September 18-19, 2025 - Please share with the star postdocs that you know. docs.google.com/forms/d/e/1F...
- Reposted by Harold PimentelPostdocs: Human Genetics at Utah will be hosting our annual Rising Stars in Genetics and Genomics Symposium in Sept. Apply here: shorturl.at/wBMg2 There will be sessions on developmental, evolutionary and disease genetics. A chance be invited to SLC to network here and with peers! Please share.
- Sometimes my 7yo and I talk about me growing up without iPad screens and things I’d do. Today he asked if we had toilet paper when I was growing up…
- Reposted by Harold PimentelAMERICA: we want more babies ALSO AMERICA: but not those babies
- *deep breath* Okay, I remember all the GRE discussions on Twitter. Our program is considering adding back our GRE requirement. Has anyone who removed it and considered adding back (or actually added back) the GRE requirement in computational/quantitative programs? TIA
- Reposted by Harold PimentelI wrote about how we must stand and fight against the threat of eugenics. Fueled by white nationalism and scientific racism, these beliefs are factually wrong and ethically abhorrent. This fight includes supporting efforts to diversify our workforce & science. To stop now would be a deep betrayal.
- Reposted by Harold PimentelBefore, we had quite a lot of academic freedom. Now, amidst the cancellation of grants based on improper keywords, deprioritized topics, and target institutions, I suppose we are going to get a lot of "academic freedom": www.nih.gov/about-nih/wh...
- It’s interesting how the number of times salad mix is commercially washed is the same number as acceptable biological replicates. People get food poisoning from salad mixes, right?
- people who reverse into one way parking spots…
- Reposted by Harold Pimentel
[This post could not be retrieved] - Reposted by Harold Pimentelsuper excited to share the newest from my lab: a tool that can securely process RNA-seq reads to quantify gene expression. Huge congrats to the dream team Seungwan, @BioConorWalker, and Annie! We developed a new gene expression quantification algorithm 1/2 www.nature.com/articles/s41...
- Go follow my dear friend and colleague, @loldeloo.bsky.social. She’s trying to recover from the site we shall not mention bsky.app/profile/lold...
- Love this post. But real talk, the most troubling outcome of all of this for me is the soon to be reality of super fucked up designer dogs. Goddammit. bsky.app/profile/urno...
- Super sad to hear. I've been blissfully ignorant about this. MARC gave me my start in science. It literally was a choice between doing research or continuing at an internship to pay for school [which would have led to a job and no science] bsky.app/profile/rdhe...
- Reposted by Harold PimentelJust received the email that my recent appointment to a BSC, which was supposed to be until June 2029, was terminated effective immediately.
- Reposted by Harold PimentelThe advert is officially live and you can apply online here: tinyurl.com/yd5bsvfb
- Not pointing fingers, but recent LLM prompted me to think about emissions of training one of these things and the number of groups that are starting to do it. ChatGPT estimates about 55K cars on the road for an entire year. Something to think about.
- Reposted by Harold PimentelI am extra mad because of this from literally this month? bsky.app/profile/kali...
