Delaney Sullivan

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

Version 3 is out, read it at www.biorxiv.org/content/10.1...! New additions:
• Human genomics
• Pig transcriptomics
• Bottom-up reanalysis of long-read human data

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...

Congrats to @jingyour.bsky.social !

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...

Trump freezes $200 million in UCLA science and medical research funding, citing antisemitism The Trump administration has frozen roughly $200 million in National Science Foundation, National Institutes of Health and other federal agency-funded research at UCLA, citing allegations the school d...

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...

Congrats!!!!!

Mapping and engineering RNA-driven architecture of the multiphase nucleolus - Nature Spatially segregated rRNA processing dictates nucleolar morphology and drives outward progression of pre-ribosomal RNA through nucleolar phases.

Nature research paper: Mapping and engineering RNA-driven architecture of the multiphase nucleolus

https://go.nature.com/44Tib11

Reply to: Reply to: False positives in the study of memory-related gene expression In the Nature paper “Spatial transcriptomics reveal neuron–astrocyte synergy in long-term memory” published on March 14th, 2024, authors Sun et al. claimed to identify cell-type specifi…

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

Thanks Harold! :)

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

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🚨 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 👇

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ACLU sues National Institutes of Health for ‘ideological purge’ of research projects The lawsuit says that NIH has canceled more than 670 research grants, which were due more than $1.1 billion in funding.

www.nbcnews.com/health/healt...

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!

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Same situation with me :/ Literally was just one step away from the NOA. Can’t resubmit b/c of my graduation timeline.

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.

UPDATE: NIH reimposes "DEI" funding freeze despite court order The National Institutes of Health (NIH) is still blocking most ongoing scientific funding over concerns about "diversity, equity and inclusion" (DEI), according to NIH sources and internal NIH corresp...

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...

@jeremymberg.bsky.social Just now, they removed the funding opportunity page (PA-23-271) and updated grants.gov page to have a closing date of Feb 21 and an archive date of Feb 22. Wtf is going on?

Trump Administration Stalls Scientific Research Despite Court Ruling (Gift Article) Using an arcane law, officials have effectively delayed funding from the National Institutes of Health, leaving medical studies in jeopardy.

New York Times article now up on Federal Register stuff.

www.nytimes.com/2025/02/21/s...

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I had one submitted last April; no NOA after JIT, but at least it hasn’t disappeared from era commons.