New work from the lab trying to wrap our heads around the massive complexity of the human transcriptome revealed by long-read RNA-seq! Fun collab with Gloria Sheynkman. www.biorxiv.org/content/10.1...

We have updated our protein lanuage model trained on structure dynamics. Our new models show significant better zero-shot performance on mutation effects of designed and viral proteins compared to ESM2. check the new preprint here: www.biorxiv.org/content/10.1...

Some encouraging news for cross-gene generalization of allele effects in S2F models. www.biorxiv.org/content/10.1...

An engineered Cas12a enables higher-order combinatorial functional genomic screens using CRISPR interference go.nature.com/3UTnSXM rdcu.be/ef95k

1/10 Excited to share our latest - the first whole-body map of both DNA methylation and 3D genome at single-cell resolution.

Biorxiv seems to be really slow nowadays. Is it just me? Curious whether it's due to some infra change or there are some AI Agents crawling the data...

For decades, government funding “has positioned the United States as a global leader” in science, says scientist Tom Maniatis of @zuckermanbrain.bsky.social and the New York Genome Center. He highlights how a new #NIH policy cutting money for research “jeopardizes” this, in Cell tinyurl.com/ubw6uphe

Can someone send this to the NIH Director nominee who said yesterday under oath that he doesn’t know where the indirects go.

We are crowd sourcing reductions in graduate admissions and hiring freezes across biomedical research and higher ed in response to pauses in NIH funding and EO’s. If you have information if you could add to this spreadsheet, it would be greatly appreciated!: docs.google.com/spreadsheets...

This is very cool work (where I was fortunate to play a small part), providing creative and crucial solutions for secure and federated eQTL mapping. Bigger functional genetic studies with less administrative and legal hassle! 💪

Combinatorial mapping of E3 ubiquitin ligases to their target substrates www.cell.com/molecular-ce...

Deep learning models (@chromozz.bsky.social) trained only on yeast chromosomes predict nucleosome positioning, RNA Poll II and cohesin tracks along foreign DNA, based on the sequence alone. This implies that the behavior of any DNA in a host cell follows deterministic sequence-based rules.

[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

Lars Steinmetz and @seczmarta.bsky.social put together a wonderful perspective on these two studies. www.science.org/doi/10.1126/...

The "kitchen sink" of omics to solve the basis for an undiagnosed disease: long read genome , transcriptome, methytome, epigenome, all synchronized (a first) www.nature.com/articles/s41...

Super excited to share our new study from the @jbuenrostro.bsky.social Lab in @nature.com! We developed a computational method for tracking transcription factor and nucleosome binding using single-cell ATAC-seq and deep learning. Paper: www.nature.com/articles/s41...

The most senior cell typing expert should and always have been the evolution

@anusri.bsky.social first author & developer of ChromBPNet is looking for opportunities in industry in ML for bio/genomics. She is an excellent rigorous scientist (as u can see from the paper). Very strongly recommend her. Plz reach out to her if u have openings. Plz forward.

The human genome encodes more than 20,000 proteins. Missense variants in nearly 5,000 of these proteins cause Mendelian diseases. Most variants compatible with life are likely present in someone currently alive. The study marks an important step in understanding the functional consequences.

GET is finally published! - Paper: t.ly/iQct_ (new validations, dry and wet) - Model: t.ly/4jnUI (new tutorial on PBMC 10x Multiome data, and yes you can even fine-tune it on a Macbook) - Analysis package: t.ly/OqLAL - Demo: t.ly/rbFQB - Docker: t.ly/86n_i

Our ChromBPNet preprint out! www.biorxiv.org/content/10.1... Huge congrats to Anusri! This was quite a slog (for both of us) but we r very proud of this one! It is a long read but worth it IMHO. Methods r in the supp. materials. Bluetorial coming soon below 1/

What do GWAS and rare variant burden tests discover, and why? Do these studies find the most IMPORTANT genes? If not, how DO they rank genes? Here we present a surprising result: these studies actually test for SPECIFICITY! A 🧵on what this means... (🧪🧬) www.biorxiv.org/content/10.1...