Hey Bluesky 🦋✨ It’s been a while! 👋🏽

As a small update, a preprint I’m on was posted to bioRxiv! 📑 It was great to work with Ke on analyzing the Butterfly scRNA-seq data, and teach him bioinformatics over multiple boba runs! 🧬 💻 🧪

Seurat has also changed SO, SO MUCH since I last used it ~2020 🫣

The premier conference on Machine Learning for Computational Biology is Sep 9-10 at the NY Genome Center in NYC!

Submission deadline is June 1 for 2-page abstracts and 8-page papers (eligible for proceedings track).

Registration is now open! (Link below)

Please retweet!

We were just notified that our contract to UCSD and Scripps Research to support wastewater surveillance in San Diego (searchcovid.info) was terminated immediately for the same reasons 👇.

That means no more genomic wastewater surveillance, and our proposed extensions to measles, Hep A, others, gone.

We have released the weights of our model, Decima, that predicts pseudobulk scRNA counts from DNA sequence. Use it for variant effect prediction, interpretation, design and more!
Preprint: www.biorxiv.org/content/10.1...
Code: github.com/Genentech/de...
Original tweetorial: x.com/lal_avantika...

Can DNA sequence models predict mutations affecting human traits?

We introduce TraitGym, a curated benchmark of causal regulatory variants for 113 Mendelian & 83 complex traits, and evaluate functional genomics and DNA language models. Joint work w/ Gökcen Eraslan and @yun-s-song.bsky.social 🧵👇

Excited to announce our preprint describing SUPERB-SEQ 🦸, a new method to measure Cas9 edits and their effects on gene expression in single cells. Led by @micklorenzini.bsky.social and @bradbalderson.bsky.social www.biorxiv.org/content/10.1...

[SAVE THE DATE] MLCB 2025 is happening Sept 10-11 at the NY Genome Center in NYC!

Attend the premier conference at the intersection of ML & Bio, share your research and make lasting connections!

Submission deadline: June 1
More details: mlcb.github.io

Help spread the word—please RT! #MLCB2025

0/ Essential reading for anyone training or using sequence-function models trained on genomic sequences! 🚨 In our new preprint, we explore the ways homology within genomes can cause leakage when training sequence-based models and ways to prevent it

I wanted to write briefly about a very pleasant experience we recently had coordinating and collaborating closely on competing publications with 2 other teams. 1/