First time on Bsky and first big announcement! I am excited to announce that our new study explaining the missing heritability of many phenotypes using WGS data from ~347,000 UK Biobank participants has just been published in @Nature. Our manuscript is here: www.nature.com/articles/s41....

(1/N) Thrilled to share that our paper HiPoNet (High dimensional Point cloud Network) to be presented at NeurIPS 2025! HiPoNet treats an entire high-dimensional point cloud as a datapoint! It captures multi-scale geometry and topology of the cloud perform classification and regression tasks.

More than two decades have passed since we discovered that rare disruptions of the FOXP2 gene disturb development of proficient speech/language skills. Today we know of multiple FOXP genes that are directly implicated in distinct brain-related conditions with differences in symptoms & severity.🧪 1/n

Our review is out in Nature Reviews Genetics! rdcu.be/d5AY2 We show how phylogeny-based methods can resolve the problem of non-independence in genomic datasets. These methods must be considered an essential part of the comparative genomics toolkit. @lauriebelch.bsky.social @stuwest.bsky.social

Now online @nature.com! Want to change the consequences of receptor activation? Small molecules binding the GPCR-transducer interface change G protein subtype preference in predictable ways, enabling rational drug design 💥 So many new possibilities! 🧪🧠🟦 www.nature.com/articles/s41... 🧵👇

Applications are open for the @crg_eu PhD Programme! 20 fully funded positions — including one in our group through the Evolutionary Medical Genomics ITN. Join us to develop deep generative models of cross-species data to tackle open questions in disease genetics. www.crg.eu/en/content/t...

Announcing our new protein design server evedesign.bio: • End-to-end protein design for everyone! • Analyze your generated library interactively and on 3D structures • Export codon-optimized DNA sequences for experimental testing.

The second session (Thr 09/10, morning) was dedicated to the Genomic Basis & History of Disease.

I adored writing this piece. It brings together several of the things preoccupying me right now, like chromatin organization and gene regulation. There's so much more to be said on that. Also, these marine critters look gorgeous. www.quantamagazine.org/loops-of-dna...

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]