🧬NEW PAPER🧬 To what extent is cancer development deterministic? Does the germline genome affect that predictability? Find out in our #StrainDifferences paper @nature.com "Genetic background sets the trajectory of experimental cancer evolution" www.nature.com/articles/s41... 🧵[1/14]

Genetic background sets the trajectory of experimental cancer evolution - Nature

Experimentally replaying tumour evolution in divergent mouse strains reveals the importance of interactions between genetic ancestry and acquired cancer-driving mutations in shaping the earliest stage...

nature.com

I missed it at the time, but it looks like the July PyTorch 2.13 release introduced FlexAttention to Apple Silicon, which means that models with Flash Attention dependencies (for ex Evo2) have an easier path to be forked + deployed on Apple Silicon. Just a PSA for anyone else who missed this!

I love close.city and I used it to pick the first neighborhood I lived in when I moved to Seattle. Thanks for putting so much love into this effort @nathenry.com !

Close - Travel Time Map

Close travel time map. Find neighborhoods where you can walk, bike, or take public transit to the amenities that matter most to you.

close.city

Nat Henry@nathenry.com · 3w ago

Not enough room to describe all the new features that just released on Close today—go check them out! close.city Three more major updates coming this week 👀

i think all raccoons should be shaped like that actually

Yes, self promotion sucks, academics, but if you don’t do it nobody will find out about your work. The point is to publish and be read, not publish and hope you are discovered by fate, lifted out of a humble and pure obscurity so that you may be both famous and retiring

salmon 2.0 (the rust re-write) is now live! It's also the version you get if you install via bioconda. This is a from-scratch rewrite in rust, and the base for future development. I'll post a more detailed thread tomorrow, but you can read the docs here combine-lab.github.io/salmon/

Russell Vought, Director of the OMB, has issued a set of proposed changes that would dramatically alter federal grant funding. However, we can each take action to prevent these from taking effect. Here's how, a 🧵 🧪 1/n www.science.org/content/arti...

White House seeks to tighten political oversight of grantmaking

Sweeping proposed rule, now open for comments, would also restrict foreign collaborations and remove federal funding for open-access fees

science.org

Painting Zucks megayacht on Lake Union last night 🔥

If you are going to comment on the proposed changes to how science is done in the US, please use this guide. The rules specify that you have to mention the number associated with the proposed changes, and this blog has those. Here is where to comment: www.federalregister.gov/documents/20...

Regulation for Federal Financial Assistance

The Office of Management and Budget (OMB) proposes to revise the Guidance for Federal Financial Assistance to improve government- wide policies and requirements related to the management of grants, co...

federalregister.gov

Susana Wadgymar🌿🔬@smwadgymar.bsky.social · 2mo ago

Here's a summary of what is being proposed: elizabethginexi.substack.com/p/summary-of...

Dear colleagues, PLEASE submit a comment against OMB's proposed rule. Elizabeth wrote great guide on drafting a comment. To submit it, go to www.regulations.gov/search and search for OMB-2026-0034. It will take time & effort to write a good comment, but a worthwhile effort to save our profession.

elizabethginexi.bsky.social@elizabethginexi.bsky.social · 2mo ago

Calling all Scientists! Research Administrators! Deans! Fans of Science! No one is coming to save us. Here is your assignment. I have written a step by step, easy to understand "how-to" document to help you comment on the proposed OMB rule. elizabethginexi.substack.com/p/what-we-ne...

If you are interested in volunteering as a mentor, please apply ASAP at forms.gle/mBEZs98z4XMU... and no later than Friday, May 22. (We really appreciate early applications as we are actively matching mentors to mentees based on needs/expertise.) (4/n)

MERIT Mentor Interest Form 2026

Hey there, Thanks for your interest in serving as a mentor for the MERIT (Mentorship and Research Individualized Training) program between Stanford and the Tanzania Human Genetics Organization. The go...

forms.gle

tinyurl.com/reuxynmc Very excited to see this work I was a small part of published! We analysed two large scale colocalisation datasets: OpenTargets data and an analysis of immune-mediated disease GWAS/immune cell eQTLs seeking to understand the "colocalisation gap". Some highlights:

Design and interpretation of eQTL-GWAS colocalisation studies: Lessons from a large-scale evaluation

Author summary Most of the genetic variants associated with complex traits are located outside genes, limiting functional interpretation. Genetic colocalisation helps identify candidate causal genes b...

journals.plos.org

Incredibly disappointing to hear that this is even being considered.

Michael Hoffman@michaelhoffman.bsky.social · 3mo ago

ASHG (@geneticssociety.bsky.social) is proposing bylaw changes that include removing its commitment to diversity in committee appointments. A sad day.

If you want to know what 3′UTRs with long conserved sequence stretches do, check out our BioRxiv preprint doi.org/10.64898/202.... They form functional intermolecular 3′UTR-3′UTR interactions that enable co-folding of proteins to rapidly induce transcriptional programs.

Population geneticists! Come work at 23andMe! New role just posted. 23andme.wd5.myworkdayjobs.com/23/job/Palo-...

(1/15) Thrilled to share new Evo-Devo work where we address the molecular, cellular & morphometric basis of an extreme axis segmentation program in the Japanese eel — an animal that forms 120 vertebrae.

Site-specific, multi-kilobase insertions and over-writes in mammalian cells, without DSBs, HDR, recombinases, integrases, transposases, or active cell cycling? Using fully or predominantly single-stranded DNA donors? 1/15

there goes the central dogma, i guess. is nothing sacred anymore?

Maxim Greenberg@maxvcg.bsky.social · 4mo ago

There are Science papers and then there are *I just dropped and shattered my mug of coffee Usual Suspects style* Science papers www.science.org/doi/10.1126/...

Original image from 2011 of what I just had seen under the microscope when I ran into @oliverrocks.bsky.social’s office to show him. Turned out he’d observed this too, had no idea what it was either, but was just as stunned and curious as I was. This is how it all started... /1

Oliver Rocks@oliverrocks.bsky.social · 4mo ago

Check out our new release on BioRxiv co-lead by @pm-mueller.bsky.social 👉 rb.gy/lnrizk special🙏 to Severine Kunz #MDC @leventallab.bsky.social @andimicroscopy.bsky.social @ewerslab.bsky.social and Kedar Narayan @NCI CCR VolumeEM Are the days of discovering new cellular structures over?? /1

Buckle up 'So let’s finally talk about peptides. And I don’t mean peptides as chemists and biologists understand them (short chains of amino acids) I mean “Peptides!”, the hot new wonder drugs that you can order by mail. Oh man.' www.science.org/content/blog...

Ah, Peptides. Where to Begin?

Ah, Peptides. Where to Begin?

science.org

Reporting for duty 🫡

Nick@nicksattele.bsky.social · 4mo ago

Our YIMBY in chief 🫡

If you use GitHub (especially if you pay for it!!) consider doing this *immediately* Settings -> Privacy -> Disallow GitHub to train their models on your code. GitHub opted *everyone* into training. No matter if you pay for the service (like I do). WTH github.com/settings/cop...

I’ve been resistant to calling Americans/developed world more broadly politicans/voters “decadent”, but like if you keep knocking loadbearing pillars out of your economy for aesthetic reasons because you don’t care about the consequences - then there really isn’t any other word to use for it

I just had surgery to remove an orange-sized cyst from inside my chest, and the thoracic surgeon and absolutely every RN & NAC has been an immigrant or child/grandchild of immigrants. The U.S. would have no healthcare system without immigration. We’re so fortunate these people made America home.

How do immune disease-relevant variants rewire gene regulation in CD4+ T cells? In a collaboration led by Daniel Schraivogel and Lars Steinmetz at @embl.org, we combined two large-scale CRISPRi screens (4.1M cells) to map the downstream cascades of thousands of SNPs.

I wrote a primer on AI antibody design, published on Asimov press. www.asimov.press/p/antibody-d...

How to Design Antibodies

A step-by-step guide to making de novo binders.

asimov.press

Some molecular machines, like ribosomes, can persist for long periods of time in cells. Could molecular aging of ribosomes shape how proteins are made? In our new preprint we track ribosomes as they age in cells and uncover unexpected effects on translation (1/10) www.biorxiv.org/content/10.6...

When someone says „Scientists do not want you to know“ you can dismiss everything from there on. Scientists want you to know. They are desperate that you know. They can’t shut up about what they found out and want you to know.

The main project of my PhD 🧬🔬 is out: we developed single-cell lentiMPRA, a lentivirus-based method to measure enhancer activity and transcriptomes at single-cell resolution. We then applied sc-lentiMPRA to fully synthetic enhancers 🧩... 🔗 doi.org/10.64898/202...