iiinova — where your digital self keeps evolving

Reposted by Harold Pimentel

Gregory Kohn @kohngregory.bsky.social · 15/08/2026

In the wake of Arday's death, Nathan Cofnas (who led the X mob against him) states his motivation. Beyond whistleblowing, he states that after a 'revolution' removes professors like Arday, it will open opportunities for him to become 'head of the department of eugenics and race science at Harvard'.

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Needhi Bhalla 💅🏽 @needhibhalla.bsky.social · 22/06/2026

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 @betanalpha.bsky.social · 18/06/2026

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.

Posterior predictions that extrapolate Messi's goals per game to the 2042 world cup using an extremely simple model of scoring rate evolution.

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Doc Edge @docedge.bsky.social · 28/04/2026

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...

usccareers.usc.edu

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

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Páll Melsted @pmelsted.bsky.social · 06/03/2026

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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Harold Pimentel @hjp.bsky.social · 04/03/2026

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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albertsxue.bsky.social @albertsxue.bsky.social · 02/03/2026

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)

biorxiv.org

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Harold Pimentel @hjp.bsky.social · 18/11/2025

Destroying the earth to make shit memes with GPT: (the idea was not mine, fortunately)

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Arbel Harpak @arbelharpak.bsky.social · 07/11/2025

@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...

royalsocietypublishing.org

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Ben Langmead @benlangmead.bsky.social · 14/10/2025

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/....

Illustration of Burrows-Wheeler Transform and many auxiliary structures from the input string how$now$brown$cow$#

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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 07/10/2025

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).

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The Wells Lab of UCLA @wellslab.bsky.social · 30/09/2025

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.

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Harold Pimentel @hjp.bsky.social · 29/09/2025

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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Harold Pimentel @hjp.bsky.social · 22/09/2025

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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Harold Pimentel @hjp.bsky.social · 15/09/2025

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

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Chris Geidner @chrisgeidner.bsky.social · 02/09/2025

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.

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Carl T. Bergstrom @carlbergstrom.com · 27/08/2025

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

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Reposted by Harold Pimentel

BF Francis Ouellette @bffo.bsky.social · 26/08/2025

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-...

jxtxfoundation.org

JXTX + CSHL 2025 Genome Informatics Scholarship

JXTX + CSHL 2025 Genome Informatics Scholarships

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unlawful whatever 🐝 @inlovewthemooon.bsky.social · 23/08/2025

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

Image shows a DHS agent watching somebody in a blue shirt painting on the ground the words is goverment

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Gen Wojcik @genandgenes.bsky.social · 23/08/2025

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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Dan Garisto @dangaristo.bsky.social · 22/08/2025

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:

nature.com

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

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

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Arjun Bhattacharya @arjunbhattac.bsky.social · 20/08/2025

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...

nature.com

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

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Harold Pimentel @hjp.bsky.social · 15/08/2025

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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Reposted by Harold Pimentel

Graham Coop @gcbias.bsky.social · 02/08/2025

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

Text from an FAQ in Okbay et al 20222:
https://www.nature.com/articles/s41588-022-01016-z
a similar same statement is made in an FAQ in 2025: https://www.biorxiv.org/content/10.1101/2025.05.14.653986v1.supplementary-material
Text reads:
"The results of SSGAC studies have sometimes been used by online platforms, including some companies, to predict individual outcomes. We recognize that returning individual genomic “results” can be a fun way to engage people in research and other projects and to feed or stoke their interest in genomics. But it is important that participants/users understand that these individual results are not meaningful predictions and should be regarded essentially as entertainment. Failure to make this point clear risks sowing confusion and undermining trust in genetics research"

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Harold Pimentel @hjp.bsky.social · 22/07/2025

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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Reposted by Harold Pimentel

Nicholas Mancuso @nmancuso.bsky.social · 21/07/2025

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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Bede Constantinides @bede.im · 13/06/2025

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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Harold Pimentel @hjp.bsky.social · 02/07/2025

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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Nate Coraor @nate.foo · 26/06/2025

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

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St. Jude Children's Research Hospital @stjuderesearch.bsky.social · 17/06/2025

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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Christopher Webb @cwebbonline.com · 12/06/2025

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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BWJones @bwjones.bsky.social · 12/06/2025

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

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Brunilda Balliu @brunildaballiu.bsky.social · 10/06/2025

🚨 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!

neurogen.semel.ucla.edu

Curriculum – UCLA Center for Neurobehavioral GeneticsAccessibility ToolsIncrease TextDecrease TextGrayscaleHigh ContrastNegative ContrastLight BackgroundLinks UnderlineReadable FontReset

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Patti Zettler @pzettler.bsky.social · 09/06/2025

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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Yun S. Song @yun-s-song.bsky.social · 06/06/2025

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.

probgen2026.github.io

Home - ProbGen 2026

Your Site Description

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J. David Jentsch 🏳️‍🌈 @jdavidjentsch.bsky.social · 05/06/2025

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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Katherine Xue @ksxue.bsky.social · 03/06/2025

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-...

A flyer with the heading McClintock Letter-Writing Workshop. Details are Friday, June 6th, 12pm ET and 9am PT, virtual.

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Eli Weinstein @eliweinstein.bsky.social · 29/05/2025

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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Keri Backus @keribackus.bsky.social · 24/05/2025

New paper from our lab joint with Val Arboleda @val-arboleda.bsky.social

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Yun S. Song @yun-s-song.bsky.social · 23/05/2025

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... 1/n

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Amy Goldberg @amygoldberg.bsky.social · 13/03/2025

Last call—hiring for my lab moving to UCLA!

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