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1/n I'm excited to share our preprint *Large-scale clinical interpretation of genetic variants using evolutionary data and deep learning* biorxiv.org/content/10.110… from a great collab with Pascal Notin Mafalda Dias @AidanNGomez Dr. Kelly Brock Yarin (OATML_Oxford) Debora Marks 🧵

Our code for making EVE models is now public! Code: github.com/OATML/EVE Preprint: biorxiv.org/content/10.110… Website (update coming soon!): evemodel.org Recent MIA talk with Mafalda Dias: broadinstitute.org/talks/large-sc… Tweetorial: x.com/Jonnygfrazer/s…

Also in nature this week: a computational method called EVE (evolutionary model of variant effect) which predicts the functional effects of genetic variants based on evolutionary conservation and sequence context without clinical labels and supervision go.nature.com/3ElVPpT

Fab collaboration with OATML_Oxford - our paper out today nature.com/articles/s4158…

I think we have barely scratched the surface of what sequencing diverse organisms can teach us about the genetics of disease. I'm very happy to say our paper out in nature this week shows that unsupervised deep learning can aid in this pursuit. nature.com/articles/s4158…

An AI model called EVE shows remarkable capacity to interpret the meaning of gene variants in humans as benign or disease-causing hms.harvard.edu/news/all-about…

A brief overview of our new NeurIPS paper:

A brief overview of our new preprint, which Alan Amin, will grathwohl, Daniel Kassler, and Jean-Jean all contributed to:

This October I drew 1 #pdb molecule a day following an official #inktober2021 prompt list. Picking proteins as my theme was risky but rewarding. Lesson learned: proteins are so versatile! See my 31 entries below and let me know your favorite. A thread. Protein Data Bank rcsb pdb 💉🧬💻🔬💊🌱🧠🦠

What a honour to be sketched by Alex Cagan at #VariantEffect22. Has already been such a great workshop

So great to see this out! Ensembl is such a crazy valuable resource. It’s an honour to have our scores included.

Thrilled: Learning Meaningful Representations of Life was accepted for NeurIPS Conference 2022. For lots of reasons, we'll be virtual -- hope that makes it easy and safe for you to attend! Pre-register for workshop updates at LMRL.org and join the Slack, follow on Twitter, etc. Thanks for sharing!

A few updates for our Tranception paper with Marks Lab and OATML_Oxford: 1) We have just pushed major upgrades to our GitHub repo, including a PyTorch implementation of Tranception, example scripts and access to model checkpoints via our servers and the Hugging Face hub

Can one anticipate viral evolution enough to support timely intervention? Check out our new preprint on forecasting antibody escape biorxiv.org/content/10.110… With Sarah Gurev Pascal Notin Noor Youssef Nathanael Rollins Chris Sander aka cscbio Yarin (OATML_Oxford), Debora Marks, 🧵1/10

It is happening! Jonathan Frazer and I are starting our group at Centre for Genomic Regulation (CRG) this Autumn! We will be developing deep generative models to map genetic variation to phenotypic change. Super excited!

Introducing scPerturb, a collection of 44 single cell perturbation datasets with unified annotations available at scperturb.org (1/5)

We are happy to announce the next edition of our journal club! Join us on Friday September 2nd at 5 PM CEST as Jonathan Frazer, Pascal Notin and Mafalda Dias present "Disease variant prediction with deep generative models of evolutionary data" (nature.com/articles/s4158…)!

Very excited to share our latest work on ML powered genetics with the fantastic Rose Orenbuch and other members, past and present, of Debora Marks lab!

🚨The new version of ProteinGym is out!🚨 biorxiv.org/content/10.110… #NeurIPS2023 #GenBio #Proteins #Benchmark #MAVE

Want to tackle big problems in disease and evolution with statistical modelling/ ML? Open PhD position in our group, joint with Manuel Irimia ! Amazing science, amazing people, amazing city.