Harold Pimentel
@hjp.bsky.social
Assistant prof at UCLA using the Bayes for the genomes https://pimentellab.com
Reposted by Harold Pimentel
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 🧵
October 10, 2026 at 7:32 PM
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 🧵
Reposted by Harold Pimentel
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'.
August 14, 2026 at 11:23 PM
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'.
Reposted by Harold Pimentel
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.”
Been wondering why NSF isn't spending most of its FY26 appropriation? A $1.5B tech initiative may be the reason. And big cuts to hundreds of research programs could be just the beginning of the bad news. www.science.org/content/arti...
Exclusive: NSF slashes research programs to support new tech initiative, insiders say
Unexpected shift in funds has meant sharp drop in grants this fiscal year
www.science.org
June 22, 2026 at 3:50 PM
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.”
Reposted by Harold Pimentel
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.
Is it also an opportunity to demonstrate how extrapolations that incorporate uncertainty are far better behaved than those that don't? Absolutely.
June 18, 2026 at 1:45 AM
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.
Is it also an opportunity to demonstrate how extrapolations that incorporate uncertainty are far better behaved than those that don't? Absolutely.
Reposted by Harold Pimentel
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...
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
usccareers.usc.edu
April 28, 2026 at 5:09 AM
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...
Reposted by Harold Pimentel
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
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
March 6, 2026 at 7:32 PM
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
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
Reposted by Harold Pimentel
🧬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
📄Inclusion bias affects common variant discovery and replication in a health-system linked biobank
🧑🤝🧑 @loldeloo.bsky.social @apimplaskar.bsky.social @bpasaniuc.bsky.social & colleagues
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 ...
www.cell.com
March 10, 2026 at 3:07 PM
🧬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
📄Inclusion bias affects common variant discovery and replication in a health-system linked biobank
🧑🤝🧑 @loldeloo.bsky.social @apimplaskar.bsky.social @bpasaniuc.bsky.social & colleagues
Reposted by Harold Pimentel
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...
February 26, 2026 at 11:21 PM
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)
www.biorxiv.org
March 4, 2026 at 4:42 PM
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...
Reposted by Harold Pimentel
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)
www.biorxiv.org
March 2, 2026 at 6:59 PM
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)
Destroying the earth to make shit memes with GPT:
(the idea was not mine, fortunately)
(the idea was not mine, fortunately)
November 18, 2025 at 3:48 AM
Destroying the earth to make shit memes with GPT:
(the idea was not mine, fortunately)
(the idea was not mine, fortunately)
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...
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...
November 7, 2025 at 8:07 PM
@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...
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...
Reposted by Harold Pimentel
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/....
October 14, 2025 at 8:48 PM
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/....
Reposted by Harold Pimentel
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...
Martin Grønbæk-Thygesen (from @rhp-lab.bsky.social) et al show that introducing K here causes ubiquitylation and degradation
doi.org/10.1101/2025...
October 7, 2025 at 9:20 PM
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...
Martin Grønbæk-Thygesen (from @rhp-lab.bsky.social) et al show that introducing K here causes ubiquitylation and degradation
doi.org/10.1101/2025...
Reposted by Harold Pimentel
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.
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 https://www.biorxiv.org/content/10.1101/2025.09.26.678880v1
September 30, 2025 at 7:17 PM
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.
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.
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...
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 https://www.biorxiv.org/content/10.1101/2025.09.26.678880v1
September 29, 2025 at 4:47 PM
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...
1. establish that cell villages can be just as accurate (one might argue more accurate!) than arrayed-based designs
bsky.app/profile/bior...
Reposted by Harold Pimentel
Harvard Dean Was Paid $150,000 as an Expert Witness in Tylenol Lawsuits
www.nytimes.com
September 24, 2025 at 1:29 AM
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...
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: https://doi.org/10.1093/bioadv/vbaf218
Full article available: https://doi.org/10.1093/bioadv/vbaf218
September 22, 2025 at 5:35 PM
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...
bsky.app/profile/bioi...
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...
www.universityofcalifornia.edu/press-room/l...
September 15, 2025 at 6:26 PM
Pretty sure that’s the point bsky.app/profile/josh...
Reposted by Harold Pimentel
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...
September 2, 2025 at 1:50 PM
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...
Reposted by Harold Pimentel
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.
If you’re actually knew anything, it would be criminal not to reveal it now. But of course, this is a bullshit publicity stunt.
August 27, 2025 at 2:41 AM
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.
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
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/news/2025-6-...
JXTX + CSHL 2025 Genome Informatics Scholarship
JXTX + CSHL 2025 Genome Informatics Scholarships
jxtxfoundation.org
August 26, 2025 at 2:13 PM
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/news/2025-6-...
Reposted by Harold Pimentel
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
The ICE building in Portland is painting a line in front of their building
But they don't even know how to spell government
August 23, 2025 at 6:25 PM
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
The ICE building in Portland is painting a line in front of their building
But they don't even know how to spell government