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Delaney Sullivan

@delaneyksull.bsky.social
412 followers 158 following 13 posts

UCLA-Caltech MD/PhD student Stanford ‘16

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Reposted by Delaney Sullivan
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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Gennady Gorin @goringennady.bsky.social · 25/01/2026
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
biorxiv.org
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Reposted by Delaney Sullivan
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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Fairlie Reese @fairlie.bsky.social · 18/07/2025
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...
biorxiv.org
The ENCODE4 long-read RNA-seq collection reveals distinct classes of transcript structure diversity
The majority of mammalian genes encode multiple transcript isoforms that result from differential promoter use, changes in exonic splicing, and alternative 3’ end choice. Detecting and quantifying tra...
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Reposted by Delaney Sullivan
Alicia Izquierdo @aliciaizquierdo.bsky.social · 01/08/2025
Suspension of all grants to UCLA www.latimes.com/california/s...
latimes.com
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...
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Mitch Guttman @mitchguttman.bsky.social · 26/07/2025
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...
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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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Nature @nature.com · 08/07/2025
Nature research paper: Mapping and engineering RNA-driven architecture of the multiphase nucleolus go.nature.com/44Tib11
go.nature.com
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.
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Reposted by Delaney Sullivan
Lior Pachter @lpachter.bsky.social · 16/06/2025
I wrote a review of a recent paper on false discovery and multiple testing correction. liorpachter.wordpress.com/2025/06/16/r...
liorpachter.wordpress.com
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…
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Lior Pachter @lpachter.bsky.social · 05/05/2025
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...
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Lior Pachter @lpachter.bsky.social · 05/05/2025
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.
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Laura Luebbert @handle.invalid · 22/04/2025
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
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Gennady Gorin @goringennady.bsky.social · 15/04/2025
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?
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Jeremy Berg @jeremymberg.bsky.social · 04/04/2025
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
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Brittany Charlton @britshmit.bsky.social · 02/04/2025
🚨 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/
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Jeremy Berg @jeremymberg.bsky.social · 03/04/2025
www.nbcnews.com/health/healt...
nbcnews.com
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.
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Angie Rasmussen @angierasmussen.bsky.social · 02/04/2025
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.
Header of complaint linked here: https://storage.courtlistener.com/recap/gov.uscourts.mad.282821/gov.uscourts.mad.282821.1.0.pdf
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Jeremy Berg @jeremymberg.bsky.social · 29/03/2025
F mechanisms (New and Competitive renewals) Oof! 3/n
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Anita Devineni @anitadevineni.bsky.social · 18/03/2025
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.
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Anshul Kundaje @anshulkundaje.bsky.social · 05/03/2025
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.
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Jeremy Berg @jeremymberg.bsky.social · 24/02/2025
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...
popular.info
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...
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Jeremy Berg @jeremymberg.bsky.social · 21/02/2025
New York Times article now up on Federal Register stuff. www.nytimes.com/2025/02/21/s... 1/n
nytimes.com
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.
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cameronleroux.bsky.social @cameronleroux.bsky.social · 07/02/2025
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!
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Reposted by Delaney Sullivan
Jeremy Berg @jeremymberg.bsky.social · 09/02/2025
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
media.tenor.com
a cartoon of homer simpson holding a card
ALT: a cartoon of homer simpson holding a card
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Jeremy Berg @jeremymberg.bsky.social · 07/02/2025
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 jeremymberg@gmail.com. I will keep all information confidential. 2/n
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Jeremy Berg @jeremymberg.bsky.social · 07/02/2025
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
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Anshul Kundaje @anshulkundaje.bsky.social · 07/01/2025
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/...
encodeproject.org
Single cell – ENCODEHomo sapiens clickable body map
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Constantin Ahlmann-Eltze @const-ae.bsky.social · 03/01/2025
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⬇️
Overview of the LEMUR steps: (1) subspace alignment, (2) differential expression, (3) DE neighborhoods, (4) pseudobulking.
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Anshul Kundaje @anshulkundaje.bsky.social · 25/12/2024
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/
biorxiv.org
ChromBPNet: bias factorized, base-resolution deep learning models of chromatin accessibility reveal cis-regulatory sequence syntax, transcription factor footprints and regulatory variants
Despite extensive mapping of cis-regulatory elements (cREs) across cellular contexts with chromatin accessibility assays, the sequence syntax and genetic variants that regulate transcription factor (T...
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Reposted by Delaney Sullivan
bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 29/11/2024
Brisk: Exact resource-efficient dictionary for k-mers www.biorxiv.org/content/10.1101/202…
biorxiv.org
Brisk: Exact resource-efficient dictionary for k-mers https://www.biorxiv.org/content/10.1101/2024.11.26.625346v1
The rapid advancements in DNA sequencing technology have led to an unprecedented increase in the gen
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Mitch Guttman @mitchguttman.bsky.social · 27/11/2024
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...
nature.com
ChIP-DIP maps binding of hundreds of proteins to DNA simultaneously and identifies diverse gene regulatory elements - Nature Genetics
ChIP-DIP (ChIP done in parallel) is a highly multiplex assay for protein–DNA binding, scalable to hundreds of proteins including modified histones, chromatin regulators and transcription factors, offe...
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Delaney Sullivan @delaneyksull.bsky.social · 27/11/2024
🤩 Congrats to the team!
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