This is the preprint write up of my sabbatical work with Dave Kelley’s group at Calico. We tried out several transformer replacements for multi-task learning in functional genomics (i.e. what Borzoi does). Mamba, in particular, seems to outperform a mini version of Borzoi, especially when “striped”.

Comprehensive dissection of cis-regulatory elements in a 2.8 Mb topologically associated domain in six human cancers www.nature.com/articles/s41...

Our new paper about rare variant contributions to sex differences in autism is out at AJHG, led by Mahmoud Koko with @vw1234.bsky.social and Kyle Satterstrom. Biggest analysis of exome data in autism to date including SPARK and ASC. www.sciencedirect.com/science/arti...

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...

“The distribution of highly deleterious variants across human ancestry groups”. Preprint with Anastasia Stolyarova and @gcbias.bsky.social: www.biorxiv.org/content/10.1...

Excited to present our work on developing jaxQTL, a fast single-cell eQTL mapping tool that improves power and robustness in identifying sc-eQTLs using count-based models. See details in threads 🧵 www.medrxiv.org/content/10.1...

Excited to share our first foray into (noncoding) rare variant association testing: a probabilistic model that learns functional annotation importance and finds associations missed by existing methods. Anjali did a fantastic job with model assessment and scaling! www.medrxiv.org/content/10.1...