We are excited to share our pan-pangenome paper! This is a long time coming work of my postdoc with the incredible @psudmant.bsky.social, and a stellar group of people! I hope you enjoy reading it! And I am excited to talk more more about it this week at #PEQG26!! www.biorxiv.org/content/10.6...

We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics. www.biorxiv.org/content/10.1... (1/n)

I am thrilled to announce that in January 2026 I will be starting my own lab at NYU Biology! Soon enough I will be recruiting postdocs and students! Please reach out if you are interested with a CV and description of your research interests, or if you know of people who could be interested! 🧬🗽 🦊

How can one efficiently simulate phylodynamics for populations with billions of individuals, as is typical in many applications, e.g., viral evolution and cancer genomics? In this work with M. Celentano, @wsdewitt.github.io , & S. Prillo, we provide a solution. doi.org/10.1073/pnas... 1/n

Thrilled to see my digital art on the cover of Trends Genet. The two binary strings represent reverse-complementary DNA sequences (00=A, 01=C, 10=G, 11=T) and the connecting rectangles represent “embeddings” learned by DNA language models. Pls check out our article as well: doi.org/10.1016/j.ti...

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

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 🧵👇

Benchmarking DNA Sequence Models for Causal Regulatory Variant Prediction in Human Genetics https://www.biorxiv.org/content/10.1101/2025.02.11.637758v1

Our work, which shows statistical issues with the previous claim of a severe ancient bottleneck in the ancestry of African populations, has been selected as a Featured article in Genetics. doi.org/10.1093/gene...

Coincidentally, another article from my lab on DNA language models got published on the same day as GPN-MSA. It's freely available for 50 days from this link: authors.elsevier.com/a/1kNCscQbJB... Genomic language models: opportunities and challenges Please share with your colleagues.

Happy New Year! Our GPN-MSA paper is finally published, under a slightly different title from the preprint. Please check it out and share it with your colleagues: doi.org/10.1038/s415... 1/4

A DNA language model based on multispecies alignment predicts the effects of genome-wide variants - @yun-s-song.bsky.social go.nature.com/4gWppWg

Large protein language models can learn complex epistatic interactions, but how much does that help with predicting variant effects? In this NeurIPS article, we show that classical independent-sites phylogenetic models can outperform pLMs on this task. 1/7 openreview.net/forum?id=H7m...