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Harold Pimentel

@hjp.bsky.social

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

109 Posts2573 Follower766 Folgt
Needhi Bhalla 💅🏽@needhibhalla.bsky.social · last mo.

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.”

Jeffrey Mervis@policyhound.bsky.social · last mo.

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...

Doc Edge@docedge.bsky.social · 3mo 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...

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

The American Journal of Human Genetics@ajhgnews.bsky.social · 5mo 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

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 ...

cell.com

Jerome@jeromics.bsky.social · 5mo 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...

Accurate variant effect estimation in FACS-based deep mutational scanning data with Lilace - Genome Biology

Deep mutational scanning (DMS) coupled with fluorescence-activated cell sorting (FACS) provides a high-throughput method to link genetic variants with quantitative molecular phenotypes. Analysis of th...

link.springer.com

Jerome@jeromics.bsky.social · last yr.

Check out our new preprint on Lilace, a statistical tool for scoring FACS-based deep mutational scanning experiments! Lilace directly models the shift between variant fluorescence distributions and provides score uncertainty estimates to better assess reliability and reproducibility. (1/3)

Harold Pimentel@hjp.bsky.social · 5mo ago

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...

@albertsxue.bsky.social · 5mo 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... (1/n)

Arbel Harpak@arbelharpak.bsky.social · 9mo 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...

royalsocietypublishing.org

John Benning@jbenning.bsky.social · 9mo ago

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) 🧵👇

Kresten Lindorff-Larsen@lindorfflarsen.bsky.social · 10mo 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...

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).
bioRxivpreprint@biorxivpreprint.bsky.social · 10mo ago

The importance of UBQLN2 ubiquitylation for its turnover and localization https://www.biorxiv.org/content/10.1101/2025.10.02.679934v1

The Wells Lab of UCLA@wellslab.bsky.social · 10mo 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.

bioRxiv Genetics@biorxiv-genetic.bsky.social · 10mo ago

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 · 10mo ago

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 · 10mo ago

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 · 11mo ago

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 · 11mo ago

🧩 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

Gen Wojcik@genandgenes.bsky.social · 12mo 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.

Needhi Bhalla 💅🏽@needhibhalla.bsky.social · 12mo ago

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.

Dan Garisto@dangaristo.bsky.social · 12mo 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:

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

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

nature.com

Arjun Bhattacharya@arjunbhattac.bsky.social · 12mo 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...

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

nature.com

Harold Pimentel@hjp.bsky.social · 12mo ago

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...

Jingyou Rao@jingyour.bsky.social · last yr.

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]

Graham Coop@gcbias.bsky.social · last yr.

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"