Shiny new probabilistic model, gruyere 🧀, for powering up rare variant associations w/ DL effect prediction! We find novel associations for Alzheimer's disease, e.g. nuclear pore protein NUP93 in microglia. Big thanks to NIH/NIA/ADSP and Anjali for the hard work! authors.elsevier.com/a/1ldzwgeXDzHj

Last week I released bpnet-lite v0.5.0.

BPNet/ChromBPNet are powerful models for understanding regulatory genomics from @anshulkundaje.bsky.social's group, and now it's way easier to go from raw data to trained models and analysis + results in PyTorch

Try it out with `pip install bpnet-lite`

This looks very interesting

Textbooks: “Enhancers are just a bunch of TFBSs”

But how do they REALLY work?

New paper with many contributors here @berkeleylab.lbl.gov, @anshulkundaje.bsky.social, @anusri.bsky.social

A 🧵 (1/n)

Free access link: rdcu.be/erD22

Industry friends, now is the time for MUCH more speaking out on behalf of academic colleagues under duress. Here are core open source methods that many of your products doubtlessly depend on either directly or indirectly (see en.wikipedia.org/wiki/HMMER) being abruptly defunded. Make noise.

Our new contribution to the quest to find causal GWAS genes! Sam Ghatan from my lab at @nygenome.org led a systematic comparison of eQTLs and CRISPRi+scRNA-seq screens. TL;DR: they provide highly complementary insights, with ortogonal pros and cons. 🧵👇
www.biorxiv.org/content/10.1...

It is impossible to put into words what a force of nature Sayan Mukherjee was. The field of TDA is better for having him as a part of it. The world lost a wonderful person this week.

We are proud to announce Bing Ren, PhD, as the new Scientific Director & CEO of the New York Genome Center

Dr. Ren brings his expertise in the fields of genomics & epigenetics to the NYGC & Columbia University, where he will hold a joint appointment.

For more on Dr. Ren: bit.ly/3DJXtah

Masaki Kashiwara has won the 2025 Abel Prize “for his fundamental contributions to algebraic analysis and representation theory.”

Wow. "NIH" canceled my co-mentored (with Dave Sulzer) PhD student's F31 funding. His work is on understanding the genetics and neuroscience of language learning disorders. F31 provides no indirect $ to Columbia, just pays his salary. Not that it should matter, but he's an American citizen. W.T.F.

In our updated TraitGym preprint (w/ @gonzalobenegas.bsky.social & Gökcen Eraslan), we evaluate Evo 2 on regulatory variants associated with human traits. We see marked performance gains with scale on Mendelian traits, although still a bit behind alignment-based methods.
doi.org/10.1101/2025...
1/n

Selective State Space Models Outperform Transformers at Predicting RNA-Seq Read Coverage https://www.biorxiv.org/content/10.1101/2025.02.13.638190v1 🧬🖥️🧪 https://github.com/ihh/bilby