Harold Pimentel
@hjp.bsky.social
📤 2565
📥 766
📝 109
Assistant prof at UCLA using the Bayes for the genomes
https://pimentellab.com
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Harold Pimentel
Needhi Bhalla 💅🏽
13 days ago
tech capture of the NSF: “it allows NSF to make awards to nontraditional recipients such as a limited partnership or a venture capital firm, some of which might have been created solely for the purpose of receiving the NSF award.”
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Michael "Shapes Dude" Betancourt
17 days ago
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.
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Harold Pimentel
Doc Edge
2 months ago
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...
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Full-Time, Teaching-Track Faculty Position in Quantitative and Computational Biology at USC
Learn more about applying for Full-Time, Teaching-Track Faculty Position in Quantitative and Computational Biology at USC
https://usccareers.usc.edu/job/los-angeles/full-time-teaching-track-faculty-position-in-quantitative-and-computational-biology/1209/94300113920
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Páll Melsted
4 months ago
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
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The American Journal of Human Genetics
4 months ago
🧬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
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Inclusion bias affects common variant discovery and replication in a health-system linked biobank
We quantify inclusion bias in a health-system-linked biobank using classification models to distinguish enrolled individuals from the background population. To evaluate its impact on genetic findings ...
https://www.cell.com/ajhg/fulltext/S0002-9297(26)00075-3
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Jerome
4 months ago
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...
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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...
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4 months ago
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Harold Pimentel
4 months ago
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...
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https://www.biorxiv.org/content/10.64898/2026.02.24.707790v1
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Destroying the earth to make shit memes with GPT: (the idea was not mine, fortunately)
8 months ago
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Harold Pimentel
Arbel Harpak
8 months ago
@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...
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I'm so tired.
9 months ago
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Harold Pimentel
Ben Langmead
9 months ago
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/...
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Harold Pimentel
Kresten Lindorff-Larsen
9 months ago
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...
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Harold Pimentel
The Wells Lab of UCLA
9 months ago
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.
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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...
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9 months ago
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Joshua Weitz
9 months ago
Radical transparency 🎁
www.nytimes.com/2025/09/23/h...
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Harvard Dean Was Paid $150,000 as an Expert Witness in Tylenol Lawsuits
https://www.nytimes.com/2025/09/23/health/harvard-dean-autism-tylenol-lawsuits-payment.html?unlocked_article_code=1.oU8.7zw_.lNMONV-PFO8E&smid=url-share
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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...
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10 months ago
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Pretty sure that’s the point
bsky.app/profile/josh...
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10 months ago
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Harold Pimentel
Chris Geidner
10 months ago
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...
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Carl T. Bergstrom
10 months ago
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.
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BF Francis Ouellette
10 months ago
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-...
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JXTX + CSHL 2025 Genome Informatics Scholarship
JXTX + CSHL 2025 Genome Informatics Scholarships
https://jxtxfoundation.org/news/2025-6-09-gi
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Harold Pimentel
unlawful whatever 🐝
11 months ago
Y'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
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Harold Pimentel
Gen Wojcik
11 months ago
Science 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.
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Harold Pimentel
Dan Garisto
11 months ago
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
:
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US Supreme Court allows NIH to cut $2 billion in research grants
The decision will hinder lawsuits against grant terminations, legal specialists say.
https://www.nature.com/articles/d41586-025-02721-5
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Arjun Bhattacharya
11 months ago
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...
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Isoform-level analyses of 6 cancers uncover extensive genetic risk mechanisms undetected at the gene-level - British Journal of Cancer
British Journal of Cancer - Isoform-level analyses of 6 cancers uncover extensive genetic risk mechanisms undetected at the gene-level
https://www.nature.com/articles/s41416-025-03141-y
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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...
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11 months ago
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Harold Pimentel
Rosa Lafer-Sousa
11 months ago
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Graham Coop
11 months ago
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
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Alicia Izquierdo
11 months ago
Suspension of all grants to UCLA
www.latimes.com/california/s...
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Trump freezes $200 million in UCLA science and medical research funding, citing antisemitism
The Trump administration has frozen roughly $200 million in National Science Foundation, National Institutes of Health and other federal agency-funded research at UCLA, citing allegations the school d...
https://www.latimes.com/california/story/2025-07-31/trump-freezes-nih-nsf-funding-ucla
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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...
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12 months ago
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Harold Pimentel
Nicholas Mancuso
12 months ago
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!
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Harold Pimentel
Bede Constantinides
about 1 year ago
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
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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...
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about 1 year ago
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Harold Pimentel
Nate Coraor
about 1 year ago
Qapla’! A great ending to a wonderful talk on science engagement and learning with students from
@jasonwilliamsny.bsky.social
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Harold Pimentel
St. Jude Research
about 1 year ago
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
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Harold Pimentel
Christopher Webb
about 1 year ago
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?
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Harold Pimentel
BWJones
about 1 year ago
And then they attempted to block the Senator's staff from recording his apparent arrest:
bsky.app/profile/demo...
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Harold Pimentel
Brunilda Balliu
about 1 year ago
🚨 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!
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Curriculum – UCLA Center for Neurobehavioral GeneticsAccessibility ToolsIncrease TextDecrease TextGrayscaleHigh ContrastNegative ContrastLight BackgroundLinks UnderlineReadable FontReset
https://neurogen.semel.ucla.edu/curriculum/
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Harold Pimentel
Patti Zettler
about 1 year ago
Check 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.
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Harold Pimentel
Yun S. Song
about 1 year ago
The 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.
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Home - ProbGen 2026
Your Site Description
https://probgen2026.github.io
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about 1 year ago
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Harold Pimentel
J. David Jentsch 🏳️🌈
about 1 year ago
When 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...
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Harold Pimentel
Katherine Xue
about 1 year ago
Want 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-...
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Harold Pimentel
Brian Wasik
about 1 year ago
Lots 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...
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“Out Of His Depth,” “Sold His Soul,” “Clueless”: NIH Staffers Speak Out About Director Bhattacharya
Widespread dissatisfaction over the NIH’s “continuous free fall” has people speaking out.
https://www.importantcontext.news/p/out-of-his-depth-sold-his-soul-clueless
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Harold Pimentel
Eli Weinstein
about 1 year ago
Thrilled 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.
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Harold Pimentel
Keri Backus
about 1 year ago
New paper from our lab joint with Val Arboleda
@val-arboleda.bsky.social
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Harold Pimentel
Yun S. Song
about 1 year ago
How 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...
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Amy Goldberg
over 1 year ago
Last call—hiring for my lab moving to UCLA!
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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...
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about 1 year ago
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