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...

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...

Happy to see the ENCODE4 long-read RNA tracks now up on UCSC! Thank you to Jeltje, Mark, and any others at UCSC for working to make this happen 🤩 👉 Read the preprint: www.biorxiv.org/content/10.1...

Suspension of all grants to UCLA www.latimes.com/california/s...

Many proteins bind RNA, yet we still don’t know what RNAs most bind because methods map one RBP at a time. In @cp-cell.bsky.social, with the Jovanovic lab, we describe SPIDR – a method for mapping the RNA binding sites of dozens of RBPs in a single experiment. www.sciencedirect.com/science/arti...

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...

Nature research paper: Mapping and engineering RNA-driven architecture of the multiphase nucleolus https://go.nature.com/44Tib11

I wrote a review of a recent paper on false discovery and multiple testing correction. liorpachter.wordpress.com/2025/06/16/r...

Congratulations to Anne Kil on successful defense of her PhD! Her thesis focused on engineering solutions for saliva as a biomedical diagnostic, from improved collection asmedigitalcollection.asme.org/medicaldevic... to assessing the potential of saliva multiomics www.biorxiv.org/content/10.1...

Congratulations to @delaneyksull.bsky.social on successfully defending his PhD (photo below with his committee: Barbara Wold, @mitchguttman.bsky.social, and another of my former students @hjp.bsky.social). His thesis is on software, tools, and methods development for single-cell transcriptomics.

Very excited to finally see this out! 🦠🧬 Huge thanks to all of my amazing co-authors! @lpachter.bsky.social @delaneyksull.bsky.social Original paper thread: x.com/neuroluebber... Free access link to the paper: rdcu.be/eiIWC

New preprint out! This is probably my most important paper. To my deep chagrin, it has no math. XIST is a non-coding RNA exclusive to XX females. It silences one of the X chromosomes. So what is it doing in male heart Schwann cells?

New lawsuit filed today in Massachusetts aginst NIH from many state Attorneys General First, plaintiffs seek relief for the unreasonable and intentional delays currently plaguing the grant-application process 1/n

🚨 BREAKING: I'm suing #RFKJr @ #HHS & #JayBhattacharya @ #NIH Canceling medical research grants threatens innovations benefiting ALL Americans, no matter your politics! 🇺🇸 Thanks to my lawyers @aclu.org @aclum.bsky.social @protectdemocracy.org & @cspi.bsky.social Long 🧵 on why I'm suing 👇 1/

Revoking Congressionally appropriated funds based on political ideology is not just undemocratic, it's illegal. It's a gross misuse of American tax dollars, and it recklessly endangers everyone. Grateful to my colleagues for standing against this. Enough is enough.

F mechanisms (New and Competitive renewals) Oof! 3/n

I am livid that my student who submitted a diversity F31 and received an outstanding score, near the top of the fundable range, was told to submit again. Refusing to fund F31s from URMs while funding regular F31s from white/privileged students with worse scores is blatant discrimination.

Just wanted to give a shoutout to @marimo.io (cc @akshaykagrawal.bsky.social ). If u have been using Jupyter Notebooks, u should REALLY try Marimo. It is such an upgrade. We have been actively developing on it in the lab (integration with NLP LLMs) as well & are huge fans. Strongly recommend.

More great reporting from Judd Legum at Popular...Great in terms of getting the receipts, definitely not great in terms of what is happening... popular.info/p/update-nih...

New York Times article now up on Federal Register stuff. www.nytimes.com/2025/02/21/s... 1/n

for any others who applied to diversity-related NIH grants that are being affected by the DEIA ban, if you'd like to join a whatsapp group (for support + looking into legal options) reply to this post & i'll DM you a join link!

And now back to our regularly scheduled $hitshow The dismantling of NIH programs to increase diversity in the biomedical workforce and the abhorrent treatment of talented young scientists

ATTENTION If you are someone who had an F31-Diversity (or similar) application submitted this cycle, please DM me here, contact me on signal (jeremymberg.78), or email me at [email protected]. I will keep all information confidential. 2/n

I have learned from several sources that NIH staff tried to find out how to transfer F31-diversity applications to other program announcements for funding but were not able to do this. I don't know whether this was technical (regulations) or ideological. 1/n

Very excited to announce that the single cell/nuc. RNA/ATAC/multi-ome resource from ENCODE4 is now officially public. This includes raw data, processed data, annotations and pseudobulk products. Covers many human & mouse tissues. 1/ www.encodeproject.org/single-cell/...

After 4y in the making, I am super excited that my main PhD project is published 🎉🥳🎉🎉🥳 www.nature.com/articles/s41... LEMUR is a tool to analyze multi-condition single-cell data and model differential expression as a continuous function of the cell-state space. Some highlights⬇️

Our ChromBPNet preprint out! www.biorxiv.org/content/10.1... Huge congrats to Anusri! This was quite a slog (for both of us) but we r very proud of this one! It is a long read but worth it IMHO. Methods r in the supp. materials. Bluetorial coming soon below 1/

Brisk: Exact resource-efficient dictionary for k-mers https://www.biorxiv.org/content/10.1101/2024.11.26.625346v1

Gene regulation involves thousands of proteins that bind DNA, yet comprehensively mapping these is challenging. Our paper in Nature Genetics describes ChIP-DIP, a method for genome-wide mapping of hundreds of DNA-protein interactions in a single experiment. www.nature.com/articles/s41...

🤩 Congrats to the team!