Dems are considering caving and getting nothing. The “deal” they keep talking about gives the Rs exactly what they want: continued lawlessness from the executive, millions of Americans costed out of healthcare, and all they are giving is a “promise” to hold a vote. Their promises are nothing.

Guaranteed funding for five years and a 20% increase in a $39K base stipend if you haul in a fellowship. World class facilities and faculty in metabolism, structural biology, epigenetics, and beyond. Grand Rapids is half the cost of living of California or Boston. Apply by December 1st if interested

Stop scrolling and post two characters who bring you happiness 😀

Finally, someone has solved a real problem with AI! No more having to take a paper in the format for a journal that rejected you, and reformat it for a new journal. Well done!! formatmypaper.com

🦒Long read giraffe is out!🦒 Mapping long reads to pangenome graphs is ~10x faster than with GraphAligner, with veeery slightly better mapping accuracy, short variant calling, and SV genotyping than GraphAligner or Minimap2

We want to congratulate our President, Dr. Tony Letai, on his appointment as Director of the NCI. This announcement marks an historic moment for cancer research. Dr. Letai has been a tireless advocate and visionary leader for functional precision medicine 🧵 www.nih.gov/news-events/...

Good news for @alice.soragnilab.com, SFPM, and rare disease models. Bad news for mouse cancer enthusiasts (humans are unreliable models of mouse disease).

Mathematical models in biology are powerful, but often hard to run, visualise, or reuse without specialist skills. Menelmacar is a new platform that makes biological models interactive and easy to explore directly in the browser: biomodels.bacpop.org 🧬💻

Post a perfect album from the 90s that isn’t Nirvana, Pearl Jam, Soundgarden, or Alice In Chains

What gif pops up for your name?

Our paper benchmarking foundation models for perturbation effect prediction is finally published 🎉🥳🎉 www.nature.com/articles/s41... We show that none of the available* models outperform simple linear baselines. Since the original preprint, we added more methods, metrics, and prettier figures! 🧵

So this happened... Useful if you want to make economic (and health) arguments about the importance of NIH.

An intuitive visualization of the regulatory layers influencing the stoichiometry of a protein complex. pmc.ncbi.nlm.nih.gov/articles/PMC...

Everyone can go home now, scholarly Bluesky has peaked

Excited to share a new preprint from the lab with @ryandhindsa.bsky.social ! www.biorxiv.org/content/10.1... Led by @sherrynyeo.bsky.social, @erinmayc.bsky.social, and friends, we continue our journey to find viral DNA in our favorite place-- the overlooked and discarded reads in existing data! 1/

Academic job search guide

Me examining a new follower:

“But why should I learn statistics? AI can handle it for me!” Not if you don’t know how to ask questions. It’s the intuition about probability that we want people to walk away with: how to make decisions under uncertainty where information can be wrong. Why does this matter? Here’s a thread.

I am paw-sitively thrilled to say that out latest work is out in Nature today! #Virology #Genomics #Coronavirus #AnimalHealth #InfectiousDisease #Sequencing #FIP #FCoV23 www.nature.com/articles/s41...

I'm proud to announce the latest release of 🧬 #Oxbow 🏹, with new features to make NGS data analysis more powerful, efficient, and "composable". Learn more at: oxbow.readthedocs.io

Excited to share our latest by my postdoc Ben KS: we use statistical physics & Bayesian inference to model genome-wide perturbation outcomes. Remarkably, perturbation responses are encoded in gene "chatter" even before the perturbation–a fundamental insight with broad implications shorturl.at/2LHbw

I am incredibly honored to be named a 2025 Jane Coffin Childs Fellow! Grateful for my mentors, supporters, and the stability this award provides! Very excited to join this community of outstanding scientists.

Now published! Note that since Vikram's original post (quoted here), he's made it easy to dynamically update a set of multi-MUMs (e.g. when more genomes are added to a pangenome) and to find multi-MUMs for huge collections like HPRCv2 genomebiology.biomedcentral.com/articles/10....

As grant money starts drying up, it's more important than ever not to waste it on paying publishers' open access "article processing fees" when we can host PDFs for free. Tom Morgan and I wrote a paper on this, forthcoming at Science and Public Policy. Accepted draft here: osf.io/preprints/os...

Finally, something AI can do just as well as real "researchers". www.nature.com/articles/d41...

New preprint with the Shendure lab @jshendure.bsky.social ! We apply the DNA Typewriter lineage recorder to mouse 3D gastruloids, a powerful model of early mammalian development. Led by Sam Regalado and CX Qiu @cxqiu.bsky.social : www.biorxiv.org/content/10.1... (1/13)

Atul Butte died yesterday. The world lost a giant. A big bear of a man. With a huge smile. With love for everyone. With energy that could power a room. I loved everything about Atul. I loved how he was always happy. I loved how excited he was about science and helping people.

My HemeSky feed is now also picking up #EHA2025! bsky.app/profile/dpas...

Attention @bloodjournals.hematology.org and #hemesky : the singularity has arrived.

EPIGENETIC HULK READY TO SMASH AGAIN! GET IN LOSERS!

Pedixplorer: a Bioconductor package to streamline pedigree design and visualization. #PedigreeDesign #PedigreeVisualization #Bioconductor #Bioinformatics 🧬 🖥️ academic.oup.com/bioinformati... louislenezet.github.io/Pedixplorer/

A Developer Engagement position for the BIoconductor community is open for applications, based at the University of Limerick. Applications close on July 4th. universityvacancies.com/university-l... #rstats #bioconductor #bioinformatics

"a fascinating case study on the limits of AI in biology and the harms of current publishing incentives" rachel.fast.ai/posts/2025-0...

Everyone should watch and share. Thank you David. youtu.be/8YhJM6zxYDw

Axolotls are the "moopsy" of model organisms, they do all the things humans wish we could and look great doing them. Here is how, at a cellular level, they do their magic! Starting to think that @nature.com might have some solid editors 🤔

Time for a short thread! We developed HiddenFoot, a biophysics-inspired approach to decode single-molecule footprinting data and infer TF, nucleosome, and RNA Pol II binding profiles on individual DNA molecules. One molecule at a time! www.biorxiv.org/content/10.1... 1/6

@sonalish25.bsky.social your recent nature paper is fantastic! www.nature.com/articles/s41...

Just to be clear, this is a violation of the fundamental ethical principle in clinical trial design called "equipoise." Equipoise means that no-one is exposed to excess risk just to test the therapy. That's specifically *why* vaccine trials don't use placebo arms. Ethical violation as POLICY.

genomebiology.biomedcentral.com/articles/10.... Quite an indictment of some of the current single cell "virtual cell" foundation models. Even for the relatively mundane applications, cell labeling, batch correction etc, they are poor compared to much simpler & cheaper methods.

If I was doing a postdoc, this is where I'd do it. Note that Germany is now the safe haven for persecuted scientists, in a mildly ironic twist. Amazing team.

EMBO workshop on Single cell Lineage Tracing! Sept 18-21 in Sant Feliu, Girona, Spain. Registration OPEN!!!!! Tons of opportunities for talks (including some full length ones). You don’t want to miss it! meetings.embo.org/event/25-lin...

Stand up with ASH and #Fight4Hematology! 🩸💪 As executive orders threaten hematologic research and care of patients, ASH has created a new #Fight4Hematology Action Hub to keep you informed and involved. Learn how to protect #hematology: www.hematology.org/a...#Fight4Hematology!#Fight4Hematology#hematology:#HemeSky #MedSky

If you are serious about mathematical oncology and/or malignant evolution, you really must apply to this masterclass.

Register here: www.iseh.org/2025MiniSymp... Membership is only $30 (ASH members, take note) and the community is super inclusive (will nudge you to participate)

miniprot-0.14 was released two weeks ago. It now supports chromosomes longer than 2Gb.

@slotkin.senate.gov hi Senator Slotkin, I've tried calling your offices and they all respond with "high call volume". If I have time I'll visit your Grand Rapids office today. But my request is very simple: Please for the love of god vote against cloture and the CR until and unless it is amended.

Post a meme made by you

Research support for rare diseases, which cumulatively affect ~30 million Americans, is primarily derived from NIH. Such work is exemplified by Prof Anna Greka @broadinstitute.org in a new Ground Truths podcast. Open-access, w/ transcript, video, no ads erictopol.substack.com/p/anna-greka...