Meet evedesign: open-source AI, accessible protein design ✅Combine models for multiobjective optimization ✅Integrate experimental data ✅ Run on your own infrastructure 📄Paper: www.biorxiv.org/content/10.6... 💻Code: github.com/evedesignbio 🌐Webserver: evedesign.bio Collaborate: hello@evedesign.bio

evedesign: accessible biosequence design with a unified framework

Unified protein design for computational researchers and experimentalists

deboramarkslab.substack.com

New paper “Proteome-wide model for human disease genetics” is now live at Nature Genetics: rdcu.be/eRu7K popEVE (pop.evemodel.org) finds the needles in the haystacks of human genetic variation:

Try it! Give feedback -and be kind, it's beta ...

Martin Steinegger 🇺🇦@martinsteinegger.bsky.social · 10mo ago

End-to-end protein design in the browser through evedesign. Generate and interactively explore designs in 2D/3D and export them as codon-optimized DNA. The underlying open source framework (released soon) is build to easily add new methods, more on that soon. 🌐 evedesign.bio

My new paper "Deep Learning is Not So Mysterious or Different": arxiv.org/abs/2503.02113. Generalization behaviours in deep learning can be intuitively understood through a notion of soft inductive biases, and formally characterized with countable hypothesis bounds! 1/12

RNA, RNA, RNA -> RNAGym! read all about it! biorxiv.org/content/10.110… Been a long time goal of @deboramarks.bsky.social We tried a million years ago, sciencedirect.com/science/articl��� Now total refresh led by Rohit Arora and Murphy Angelo and Pascal Notin for pulling together!!

Which RNAs are functional? Been a long time goal of @deboramarks.bsky.social to start an RNA sequence —> function and structure mapping. Huge thx to team for pushing on this when - led by Rohit Arora and Murphy Angelo for seeing this thru and Pascal Notin for pulling together!!!

Pascal Notin@pascalnotin.bsky.social · last yr.

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

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

This, by Michael Lynch. I'd include AI techbros as well. www.pnas.org/doi/10.1073/...

Weekly: Great papers across the centuries and subjects! Relaxing! fermatslibrary.com/journal_club

Fermat's Library | Home

Fermat’s Library is a platform for illuminating academic papers. A new scientific paper annotated every week.

fermatslibrary.com

Just under a week until the #MLCB2025 paper/abstract deadline on June 1st! In-person registration is full but you can join the wait list forms.gle/gnj6AAV7oWj6... or watch online at youtube.com/@mlcbconf. Sept 10-11 at @nygenome.org. Full deets at mlcb.org! Please RP.

Machine Learning in Computational Biology

Youtube channel for the Machine Learning in Computational Biology conference.

youtube.com

New preprint in collaboration with @paulinanunezv.bsky.social supervised by @jonnyfrazer.bsky.social and Mafalda Dias – we propose a simple approach to improving zero-shot variant effect prediction in pre-existing protein and genome language models: 🧶 1/n www.biorxiv.org/content/10.1...

From Likelihood to Fitness: Improving Variant Effect Prediction in Protein and Genome Language Models

Generative models trained on natural sequences are increasingly used to predict the effects of genetic variation, enabling progress in therapeutic design, disease risk prediction, and synthetic biolog...

biorxiv.org

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

Charlie Pugh@cwjpugh.bsky.social · last yr.

New preprint in collaboration with @paulinanunezv.bsky.social supervised by @jonnyfrazer.bsky.social and Mafalda Dias – we propose a simple approach to improving zero-shot variant effect prediction in pre-existing protein and genome language models: 🧶 1/n www.biorxiv.org/content/10.1...

From Likelihood to Fitness: Improving Variant Effect Prediction in Protein and Genome Language Models https://www.biorxiv.org/content/10.1101/2025.05.20.655154v1

Is a photo subversive? NSF staff overcome obstacles to 75th anniversary portrait | Science | AAAS www.science.org/content/arti...

Is a photo subversive? NSF staff overcome obstacles to 75th anniversary portrait

Management tried to quash outpouring of support for beleaguered agency

science.org

And now, the final talk of #VariantEffect25. @roseorenbuch-art.bsky.social from Harvard Medical School presents work from our long-standing collaboration, and one that’s very close to my heart: Proteome-wide model for human disease genetics