Delaney Sullivan @delaneyksull.bsky.social · 29/07/2026Thanks and congrats on this cool work! @daniel-c0deb0t.bsky.social told me about antisequence a while back; nice to see how performant it is in practice! :) 120
Reposted by Delaney SullivanPáll Melsted @pmelsted.bsky.social · 06/03/2026Excited 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 618887
Reposted by Delaney SullivanGennady Gorin @goringennady.bsky.social · 25/01/2026Version 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 databiorxiv.org 051
Reposted by Delaney SullivanHarold Pimentel @hjp.bsky.social · 29/09/2025Super 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... 24021
Reposted by Delaney SullivanHarold Pimentel @hjp.bsky.social · 22/09/2025Super 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... 1205
Reposted by Delaney SullivanFairlie Reese @fairlie.bsky.social · 18/07/2025Happy 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.orgThe ENCODE4 long-read RNA-seq collection reveals distinct classes of transcript structure diversityThe 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... 0114
Reposted by Delaney SullivanAlicia Izquierdo @aliciaizquierdo.bsky.social · 01/08/2025Suspension of all grants to UCLA www.latimes.com/california/s...latimes.comTrump freezes $200 million in UCLA science and medical research funding, citing antisemitismThe 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... 21157112
Reposted by Delaney SullivanMitch Guttman @mitchguttman.bsky.social · 26/07/2025Many 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... 19937
Reposted by Delaney SullivanHarold Pimentel @hjp.bsky.social · 22/07/2025Super 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... 0317
Reposted by Delaney SullivanNature @nature.com · 08/07/2025Nature research paper: Mapping and engineering RNA-driven architecture of the multiphase nucleolus go.nature.com/44Tib11go.nature.comMapping and engineering RNA-driven architecture of the multiphase nucleolus - NatureSpatially segregated rRNA processing dictates nucleolar morphology and drives outward progression of pre-ribosomal RNA through nucleolar phases. 03310
Reposted by Delaney SullivanLior Pachter @lpachter.bsky.social · 16/06/2025I wrote a review of a recent paper on false discovery and multiple testing correction. liorpachter.wordpress.com/2025/06/16/r...liorpachter.wordpress.comReply to: Reply to: False positives in the study of memory-related gene expressionIn 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… 714342
Reposted by Delaney SullivanLior Pachter @lpachter.bsky.social · 05/05/2025Congratulations 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... 1656
Reposted by Delaney SullivanLior Pachter @lpachter.bsky.social · 05/05/2025Congratulations 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. 2341
Reposted by Delaney SullivanLaura Luebbert @handle.invalid · 22/04/2025Very 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 02711
Reposted by Delaney SullivanGennady Gorin @goringennady.bsky.social · 15/04/2025New 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? 11811
Reposted by Delaney SullivanJeremy Berg @jeremymberg.bsky.social · 04/04/2025New 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 3316113
Reposted by Delaney SullivanBrittany 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/ 18493011951
Reposted by Delaney SullivanJeremy Berg @jeremymberg.bsky.social · 03/04/2025www.nbcnews.com/health/healt...nbcnews.comACLU sues National Institutes of Health for ‘ideological purge’ of research projectsThe lawsuit says that NIH has canceled more than 670 research grants, which were due more than $1.1 billion in funding. 216143
Reposted by Delaney SullivanAngie Rasmussen @angierasmussen.bsky.social · 02/04/2025Revoking 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. 10580170
Reposted by Delaney SullivanJeremy Berg @jeremymberg.bsky.social · 29/03/2025F mechanisms (New and Competitive renewals) Oof! 3/n 119554
Delaney Sullivan @delaneyksull.bsky.social · 18/03/2025Same situation with me :/ Literally was just one step away from the NOA. Can’t resubmit b/c of my graduation timeline. 110
Reposted by Delaney SullivanAnita Devineni @anitadevineni.bsky.social · 18/03/2025I 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. 514143
Reposted by Delaney SullivanAnshul Kundaje @anshulkundaje.bsky.social · 05/03/2025Just 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. 1387
Reposted by Delaney SullivanJeremy Berg @jeremymberg.bsky.social · 24/02/2025More 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.infoUPDATE: NIH reimposes "DEI" funding freeze despite court orderThe 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... 16633
Delaney Sullivan @delaneyksull.bsky.social · 22/02/2025@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? 010
Reposted by Delaney SullivanJeremy Berg @jeremymberg.bsky.social · 21/02/2025New York Times article now up on Federal Register stuff. www.nytimes.com/2025/02/21/s... 1/nnytimes.comTrump 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. 17647354
Delaney Sullivan @delaneyksull.bsky.social · 11/02/2025I had one submitted last April; no NOA after JIT, but at least it hasn’t disappeared from era commons. 000
Reposted by Delaney Sullivancameronleroux.bsky.social @cameronleroux.bsky.social · 07/02/2025for 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! 7107
Reposted by Delaney SullivanJeremy Berg @jeremymberg.bsky.social · 09/02/2025And 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 scientistsmedia.tenor.coma cartoon of homer simpson holding a cardALT: a cartoon of homer simpson holding a card 521964
Reposted by Delaney SullivanJeremy Berg @jeremymberg.bsky.social · 07/02/2025ATTENTION 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 8193269
Reposted by Delaney SullivanJeremy Berg @jeremymberg.bsky.social · 07/02/2025I 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 4252118
Delaney Sullivan @delaneyksull.bsky.social · 07/02/2025So many got screwed over. Existing apps (whether submitted in Dec or already approved for funding) SHOULD be treated like standard F31s. Rly hoping someone comes to their senses & it happens. 0122
Delaney Sullivan @delaneyksull.bsky.social · 07/02/2025Many MD/PhD students applied F31-D b/c it actually funds part of med school (standard F31 can't, for whatever reason). There is also an F30 mechanism for MD/PhD students but institutions like NHGRI don't even participate in them! So to get funding for MD+PhD, the ONLY choice was the F31-D. 1112
Reposted by Delaney SullivanAnshul Kundaje @anshulkundaje.bsky.social · 07/01/2025Very 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.orgSingle cell – ENCODEHomo sapiens clickable body map 628786
Reposted by Delaney SullivanConstantin Ahlmann-Eltze @const-ae.bsky.social · 03/01/2025After 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⬇️ 815435
Reposted by Delaney SullivanAnshul Kundaje @anshulkundaje.bsky.social · 25/12/2024Our 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.orgChromBPNet: bias factorized, base-resolution deep learning models of chromatin accessibility reveal cis-regulatory sequence syntax, transcription factor footprints and regulatory variantsDespite 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... 723189
Reposted by Delaney SullivanbioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 29/11/2024Brisk: Exact resource-efficient dictionary for k-mers www.biorxiv.org/content/10.1101/202… biorxiv.orgBrisk: 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 0147
Reposted by Delaney SullivanMitch Guttman @mitchguttman.bsky.social · 27/11/2024Gene 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.comChIP-DIP maps binding of hundreds of proteins to DNA simultaneously and identifies diverse gene regulatory elements - Nature GeneticsChIP-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... 9382150