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Harold Pimentel

@hjp.bsky.social

2.5K followers 740 following 100 posts

Assistant prof at UCLA using the Bayes for the genomes https://pimentellab.com

pimentellab.com

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Reposted by Harold Pimentel

Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 1d

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...

Fig. 1 – UBQLN2 is a conserved lysine-depleted protein. (A) Sequence comparison of
UBQLN2 orthologs in the indicated species. Intrinsically disordered regions in human
UBQLN2 based on MobiDB are shown as a blue bar. The domain organization based on the
SMART database is marked. Lysine residues are marked as black squares. (B) ESM-2
predictions of all possible single amino acid substitutions of human UBQLN2 presented as a
heat map. The wild-type residues are marked in blue. ESM-2 scores close to zero (light
yellow colors) indicate that the amino acid substitution is compatible with the ESM-2
language model, whereas negative scores (dark orange colors) indicate that the variant is
incompatible with the ESM-2 model. The domain organization (based on SMART) is aligned
above the map. Note that substitutions to lysine or cysteine in general appear detrimental, in
particular downstream of the UBL domain. (C) The AlphaFold2 predicted structured of
human UBQLN2 (AF-Q9UHD9-F1) (left panel). The UBL domain is colored blue, and the
UBA domain is colored orange and the STI1 regions green. Zoom in on the UBL domain
(right panel) with the lysine residues highlighted as stick representations and colored based
on the relative accessible surface area (rASA, dark red exposed; grey, buried).

Harold Pimentel @hjp.bsky.social · 7d

🤣

Harold Pimentel @hjp.bsky.social · 7d

yikes... sorry...

my only advice is to proactively carry a 5lb bag of rice with your laptop

Reposted by Harold Pimentel

The Wells Lab of UCLA @wellslab.bsky.social · 8d

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.

bioRxiv Genetics @biorxiv-genetic.bsky.social · 9d

Cell villages and Dirichlet modeling map human cell fitness genetics https://www.biorxiv.org/content/10.1101/2025.09.26.678880v1

Harold Pimentel @hjp.bsky.social · 9d

Thanks!

Harold Pimentel @hjp.bsky.social · 9d

Thank you!

Harold Pimentel @hjp.bsky.social · 9d

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

Harold Pimentel @hjp.bsky.social · 9d

Stay tuned -- much more in queue

Harold Pimentel @hjp.bsky.social · 9d

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

Harold Pimentel @hjp.bsky.social · 9d

2. develop computational models that model the nuance in cell villages, including the compositional nature, small sample sizes, and structure of the variance

Harold Pimentel @hjp.bsky.social · 9d

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...

bioRxiv Genetics @biorxiv-genetic.bsky.social · 9d

Cell villages and Dirichlet modeling map human cell fitness genetics https://www.biorxiv.org/content/10.1101/2025.09.26.678880v1

Harold Pimentel @hjp.bsky.social · 14d

😭

Harold Pimentel @hjp.bsky.social · 14d

Color me surprised that the same people who don't believe solid epi over decades (like those guiding nutritional guidelines) believe this. Unreal.

Reposted by Harold Pimentel

Joshua Weitz @joshuasweitz.bsky.social · 14d

Radical transparency

🎁
www.nytimes.com/2025/09/23/h...

Harvard Dean Was Paid $150,000 as an Expert Witness in Tylenol Lawsuits

www.nytimes.com

Harold Pimentel @hjp.bsky.social · 16d

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...

Bioinformatics Advances @bioinfoadv.bsky.social · 16d

🧩 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: https://doi.org/10.1093/bioadv/vbaf218

Harold Pimentel @hjp.bsky.social · 23d

Pretty sure that’s the point bsky.app/profile/josh...

Joshua Weitz @joshuasweitz.bsky.social · 23d

"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 Pimentel

Chris Geidner @chrisgeidner.bsky.social · Sep 2

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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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.

Reposted by Harold Pimentel

Carl T. Bergstrom @carlbergstrom.com · Aug 27

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.

THE HILL
HEALTH CARE
RFK Jr. says agency will reveal causes of autism in September
BY JOSEPH CHOI - 08/26/25 4:01 PM ET

Reposted by Harold Pimentel

David Kaye @davidakaye.bsky.social · Aug 26

i imagine this implicitly anti-newsom flyer is showing up on doorsteps across california.

'visit protectfairelections.org to learn more,' it says. 'paid for by Right Path Coalition'.

which is . . . led by the chairperson of the california republican party

it's a flyer: 'gerrymandering is wrong - no matter who does it', framed as a 'power grab'.

Reposted by Harold Pimentel

BF Francis Ouellette @bffo.bsky.social · Aug 26

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-...

JXTX + CSHL 2025 Genome Informatics Scholarship

JXTX + CSHL 2025 Genome Informatics Scholarships

jxtxfoundation.org

Reposted by Harold Pimentel

Gen Wojcik @genandgenes.bsky.social · Aug 23

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.

Needhi Bhalla 💅🏽 @needhibhalla.bsky.social · Aug 23

Insisting on expertise over ideology is not “politicizing” science. The ideologues installing scientific and governmental policy that is contradicted by evidence and data are.

By emphasizing ideology over expertise, THEY have made arguing for expertise and evidence-based decision making partisan.

Scientists Are Caught in a Political Trap

Fighting back against the Trump administration means they start to look more like activists.

www.theatlantic.com

Reposted by Harold Pimentel

Dan Garisto @dangaristo.bsky.social · Aug 22

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:

US Supreme Court allows NIH to cut $2 billion in research grants

The decision will hinder lawsuits against grant terminations, legal specialists say.

Harold Pimentel @hjp.bsky.social · Aug 20

Well deserved. Congrats, Arjun!

Reposted by Harold Pimentel

Arjun Bhattacharya @arjunbhattac.bsky.social · Aug 20

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...

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