The most beautiful data is on the horizon!

This is truly an incredible breakthrough IMO. Really exemplifies what you get when deep domain expertise (popgen/evolution/disease genetics in this case) fuses with cleverly crafted ML. What u get r sleek, well thought out architectures that absolutely destroy the behemoths. Wow!! 1/

Most of the #EurIPS workshops now have their websites online 🙌 A lot of them have active call for participation and/or papers, so if you see something relevant to your field of research please consider submitting! Links for most workshops are available at: eurips.cc/workshops/

We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics. www.biorxiv.org/content/10.1... (1/n)

Excited for a major milestone in our efforts to map enhancers and interpret variants in the human genome: The E2G Portal! e2g.stanford.edu This collates our predictions of enhancer-gene regulatory interactions across >1,600 cell types and tissues. Uses cases 👇 1/

NeurIPS 2025 financial assistance and volunteer applications are now open for both San Diego and Mexico City! The deadline for both applications is 1 Oct AoE. See neurips.cc/Conferences/... for more details.

Many of the most complex and useful functions in biology emerge at the scale of whole genomes. Today, we share our preprint “Generative design of novel bacteriophages with genome language models”, where we validate the first, functional AI-generated genomes 🧵

Exciting to see our protein binder design pipeline BindCraft published in its final form in @Nature ! This has been an amazing collaborative effort with Lennart, Christian, @sokrypton.org, Bruno and many other amazing lab members and collaborators. www.nature.com/articles/s41...

I'm hoping to take 1 MSc & 1 PhD student next year in the areas of Phylogenetic, Computational, and/or Evolutionary Paleobiology. Please reach out if you are interested in joining the @oupaleobiology.bsky.social, especially if interested in working on fossil echinoderms. Link for more info below. 🧪

Excited / nervous to share the “magnum opus” of my postdoc in Andreas Wagner’s lab! "De-novo promoters emerge more readily from random DNA than from genomic DNA" This project is the accumulation of 4 years of work, and lays the foundation for my future group. In short, we… (1/4)

@jengreitz.bsky.social l & my lab want to co-hire a computational biologist/biostatistician with project management expertise to help map the regulatory code of the human genome and discover genetic mechanisms of disease. Details below careersearch.stanford.edu/jobs/computa... Plz RT

New paper out today in PLOS Comp Biol: journals.plos.org/ploscompbiol... Intrinsically disordered regions make variant prediction deceptively easy for benign changes but very hard for pathogenic ones. Our work shows why current tools struggle here, and why disorder-aware approaches are needed.

I am absolutely delighted to share our work describing a new *recessive* condition caused by variants in #RNU4-2. Yes, that #RNU4-2! tinyurl.com/3j9r56s8 @rociorius.bsky.social @yuyangchen.bsky.social @gregfindlay.bsky.social @dgmacarthur.bsky.social @cassimons.bsky.social @nickywhiffin.bsky.social

🧪 A generative AI framework designed new antibiotics by exploring uncharted chemical space. The approach yielded two lead compounds effective against multidrug-resistant N.gonorrhoeae and S.aureus in mouse models of infection. 🧬💻 #MLSky

❗New Preprint w/ C Bueno (‪@cabb99.bsky.social‬), IE Sánchez (@nachoquique.bsky.social‬), PG Wolynes & DU Ferreiro (@diegulise.bsky.social‬) We define the Protein Dark Energy and use it to localize and quantify the functional evolutionary constraints on natural proteins arxiv.org/abs/2508.08109

A common takeaway from "the bitter lesson" is we don't need to put effort into encoding inductive biases, we just need compute. Nothing could be further from the truth! Better inductive biases mean better scaling exponents, which means exponential improvements with computation.

This is not just HHMI. All Chan Zuckerberg Initiative funding calls are CLOSED. The Gates Foundation has no Grand Challenges funding opportunities. I've never seen anything like this. Private foundations have just decided to stop supporting biomedical research.

🧬🧬🧬 New review from the lab: Evolution of comparative transcriptomics: biological scales, phylogenetic spans, and modeling frameworks authors.elsevier.com/sd/article/S... By @mattezambon.bsky.social & @fedemantica.bsky.social, together with @jonnyfrazer.bsky.social & Mafalda Dias.

The 2026 Probabilistic Modeling in Genomics (ProbGen) meeting will be held at UC Berkeley, March 25-28, 2026. We have an amazing list of keynote speakers and session chairs: probgen2026.github.io Please help spread the news.

I'm excited to share work on a research direction my team has been advancing: connecting machine learning derived genetic variant embeddings to downstream tasks in human genetics. This work was led by the amazing Divyanshi Srivastava! www.biorxiv.org/content/10.1...

*Easter egg alert* NOT in the published paper. We also benchmarked Evo 2 and while it did better than other gLMs (consistent that scale can improve gLMs), it still falls short of a basic CNN trained using one-hot sequences and far short of supervised SOTA

Excited to be presenting my paper "Deep Learning is Not So Mysterious or Different" tomorrow at ICML, 11 am - 1:30 pm, East Exhibition Hall A-B, E-500. I made a little video overview as part of the ICML process (viewable from Chrome): recorder-v3.slideslive.com#/share?share...

EurIPS is coming! 📣 Mark your calendar for Dec. 2-7, 2025 in Copenhagen 📅 EurIPS is a community-organized conference where you can present accepted NeurIPS 2025 papers, endorsed by @neuripsconf.bsky.social and @nordicair.bsky.social and is co-developed by @ellis.eu eurips.cc

What if AI isn’t about building solo geniuses, but designing social systems? Michael Jordan advocates blending ML, economics, and uncertainty management to prioritize social welfare over mere prediction. A must-read rethink. arxiv.org/abs/2507.062...

Check out our latest work on the evolution of animal genome regulation out today in @nature.com. Nicely summarized below by @ianakim.bsky.social. www.nature.com/articles/s41... This is a major output from our ERC-StG project Evocellmap @erc.europa.eu at @crg.eu

One thing that really bothers me with the new "virtual cell" terminology is that it is currently largely focused on a very narrow definition of models that can predict effects of trans perturbations (gene dosage, drugs etc) on gene expression. 1/

New preprint - collab with the groups of @mehurles.bsky.social and @dr-appie.bsky.social. We imputed missing fluid intelligence test scores into ~170k @ukbiobank.bsky.social indivs & showed how this reduces bias and increases power for rare+common variant analyses. www.medrxiv.org/content/10.1...

🚨 New paper 🚨 RNA modeling just got its own Gym! 🏋️ Introducing RNAGym, large-scale benchmarks for RNA fitness and structure prediction. 🧵 1/9

There are many domain-specific noise processes for discrete diffusion, but masking dominates! Why? We show masking exploits a key property of discrete diffusion, which we use to unlock the potential of those structured processes and beat masking! w/ Nate Gruver and @andrewgwils.bsky.social 1/7

It's great to see some new notices of funding opportunities from NIH, but here's a reminder that Harvard researchers remain ineligible to apply for any federal grants. "Harvard should no longer seek GRANTS from the federal government, since none will be provided." www.harvard.edu/research-fun...

“The search is on for 25 researchers from around the world in Lund University’s largest ever international recruitment drive. The main focus will be on AI research and other areas in which the University has a strategic focus.” www.lunduniversity.lu.se/article/lund...

🚨 Internship Alert! 🚨 Exciting opportunity @Genentech for a Computational Biology intern in Aging Research! 🧬 Work on #single-cell transcriptomics & imaging data to advance #aging biology insights with @mkoutrouli.bsky.social & me. Applications due June 26: lnkd.in/dBE28Wtk

✈️ 𝐓𝐫𝐚𝐯𝐞𝐥 𝐆𝐫𝐚𝐧𝐭𝐬: 𝐁𝐫𝐢𝐧𝐠𝐢𝐧𝐠 𝐆𝐥𝐨𝐛𝐚𝐥 𝐕𝐨𝐢𝐜𝐞𝐬 𝐭𝐨 #ESEB2025 🌍 At #ESEB2025, we believe great science should be accessible to all, regardless of geography or background. 📅 𝐄𝐱𝐩𝐥𝐨𝐫𝐞 𝐚𝐯𝐚𝐢𝐥𝐚𝐛𝐥𝐞 𝐠𝐫𝐚𝐧𝐭𝐬:  🔗 https://lnkd.in/dXRzeUks

End-to-end differentiable homology search for protein fitness prediction. @yaringal.bsky.social @deboramarks.bsky.social @pascalnotin.bsky.social arxiv.org/abs/2506.089...

Average zero-shot mutation effect predictions across related sequences to reduce noise and improve accuracy. @cwjpugh.bsky.social @paulinanunezv.bsky.social @jonnyfrazer.bsky.social Mafalda Dias www.biorxiv.org/content/10.1...

Also, Charlie's #VariantEffect25 talk is available here www.youtube.com/watch?v=johJ...

Reminder that the MSCA postdoctoral program exists. If you have a PhD and want to work in a European lab, you have until September to apply. Just contact them now. ec.europa.eu/info/funding...

📣 Latest from the lab: Performance of deep-learning-based approaches to improve polygenic scores www.nature.com/articles/s41... Its thought deep learning will substantially improve PGS but the reality is MANY have tried but no/little gain has been seen so far. Here we report our negative results.

We have updated our preprint about 850,000 person UK-Danish haplotype sharing - sheding light on the rich history each person carries with them in their DNA and comparing this to historical records. Xiaolei Zhang postdoc in my group led this work. www.biorxiv.org/content/10.1...

Do protein language models store different structural elements in factorizable subnetworks? To find out, we masked out PLM weights to suppress performance on CATH subcategories or secondary structure elements while maintaining performance on other sequences or residues.

1 plant hormone receptor ☘️ 3,500 mutants, to single-site saturation 🧬 >45,000 binding and abundance measurements 📶 Very happy to present our latest work – where deep mutational scanning meets the world of small molecules.

 www.biorxiv.org/content/10.1...

 With @benlehner.bsky.social [1/7]

I have an opportunity to hire a staff scientist for my lab. Looking for someone with outstanding skillset in ML/statistics, genomics applications; interest in mentoring, strong publication record, PD experience required. Email CV to me+cc my assistant (see 'contact' on my website). Ad to follow.

We're thrilled to introduce PromoterAI — a tool for accurately identifying promoter variants that impact gene expression. 🧵 (1/)

If I was applying for PhD positions, Eli’s group would be at the top of my list.

NIH funding supporting the HMMER and Infernal software projects has been terminated. NIH states that our work, as well as all other federally funded research at Harvard, is of no benefit to the US.

Both translational and fundamental curiosity-driven research are needed to fuel the incredible progress we're seeing in genomic medicine; an important message in this article and and some lovely quotes from @sarahlwynn.bsky.social www.ft.com/content/25dd...

Thank you so much!

Want to improve your protein or genomic language model’s performance at zero-shot variant effect prediction? We propose a simple adjustment to likelihood-based predicton

Recasting the perils of phylodynamic non-identifiability as a feature not a bug, we show that a unique forward-equivalent process enables exact and efficient simulation from arbitrarily large populations. With M Celentano, S Prillo, @yun-s-song.bsky.social www.pnas.org/doi/10.1073/pnas.2412978122

🚨With some delay, we're excited to announce that our proposal for a MSCA Doctoral Network on Evolutionary Medical Genomics (EvoMG-DN) got funded! 🎉 🧬 14 labs and 2 companies across 7 European countries will be coordinated by the EvoMG Joint Program at @crg.eu & @upf.edu. europa.eu/!NNq63m