An open-rank faculty search in AI + Engineering (Bioengineering included) at UC Berkeley. Due date: Monday, Nov 3, 2025 at 11:59pm (PT) Please help spread the news. aprecruit.berkeley.edu/JPF05144

This is truly an incredible breakthrough IMO. Really exemplifies what you get when deep domain expertise (popgen/evolution/disease genetics in this case) fuses with cleverly crafted ML. What u get r sleek, well thought out architectures that absolutely destroy the behemoths. Wow!! 1/

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)

SINGER, our ARG inference method, is finally published and freely available online: doi.org/10.1038/s415... It was a long journey – 16 months from initial submission to acceptance. Is it just me, or has peer review gotten more arduous lately? 4+ rounds of review isn't so unusual these days...

Hi Bluesky — Dedicating my first post to this work and software, led by the incredibly meticulous and capable @fandingzhou.bsky.social! An earlier version of this was shared at the 2022 Bioconductor Conference (bioc2022.bioconductor.org/schedule/).

Gene expression changes aren’t just about mean shifts — variability shifts matter too, especially for aging. We're thrilled to introduce QRscore, a flexible non-parametric framework for detecting shifts in mean and variance across conditions. doi.org/10.1016/j.cr...

In a new preprint we use deep learning on lineage trees to infer the functional form of the relationship between affinity and fitness that controls antibody evolution in germinal centers: arxiv.org/abs/2508.09871 🧵

Antibodies are highly diverse, but most possible sequences are unstable or polyreactive. In this work, just published in Cell Syst., we propose a new source of data for modeling constraints from these properties. Our models show clear improvements in predicting Ab dysfunction. (1/n) t.co/qCZERPUMPF

(1/4) 🧬 Why Sequence the Genomes of Earth’s Biodiversity? The Earth BioGenome Project 🌍 is a global network of initiatives working together to create a complete genome library for all Eukaryotic life—from mushrooms 🍄 to mammals 🐘. #biodiversity #genomes #sequence #earthbiogenome #education #stem

Germinal center clonal diversity trees as a musical score, a great image to start @victora.bsky.social's CCII seminar, "Replaying germinal center evolution on a quantified affinity landscape" #GerminalCenter #Immunology www.ccii.med.kyoto-u.ac.jp/en/event/the...

In vivo mapping of mutagenesis sensitivity of human enhancers www.nature.com/articles/s41...

The 2026 Probabilistic Modeling in Genomics (ProbGen) meeting will be held at UC Berkeley, March 25-28, 2026. We have an amazing list of keynote speakers and session chairs: probgen2026.github.io Please help spread the news.

Wanted to highlight our latest preprint--a huge effort by multiple people and labs, but led primarily by @wsdewitt.github.io, Tatsuya Araki, and Ashni Vora, in a very close wet-dry collaboration with @matsen.bsky.social’s lab at the Hutch www.biorxiv.org/content/10.1...

Check out CRISPRpedia, our resource on all things #CRISPR! The latest chapter is on CRISPR & ethics: innovativegenomics.org/crisprpedia/... CRISPRpedia features 85+ original illustrations that are free to download & use for non-commercial purposes! #STEMeducation #STEMed #bioethics #SciArt

How well can deep learning models predict the effect of modifying chromatin on gene expression??? Our work -- led by Sanjit Batra and Alan Cabrera when they were in @yun-s-song.bsky.social ’s and Isaac Hilton’s labs -- tries to answer this. 🧵🧬🧪 elifesciences.org/reviewed-pre...

New preprint in collaboration with @paulinanunezv.bsky.social supervised by @jonnyfrazer.bsky.social and Mafalda Dias – we propose a simple approach to improving zero-shot variant effect prediction in pre-existing protein and genome language models: 🧶 1/n www.biorxiv.org/content/10.1...

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

In a medical breakthrough, a team including IGI’s @urnov.bsky.social & @giannikopoulosp.bsky.social created an on-demand #CRISPR therapy for an infant with a deadly gene mutation — developed, approved, and delivered to the patient in just 6 months. Read more: ow.ly/G0Bg50VTonC #RareDisease 🧬

Jennifer Doudna @jenniferdoudna.bsky.social @doudna-lab.bsky.social speaks with Cleo Abrams on the history and future of #CRISPR 🧬. Watch here: youtu.be/0OXaanDHENI?...

Overfitting is among the conceptually most interesting problems in machine learning. I am happy of several new phenomena we began to understand with Pierfrancesco Urbani. Alert: mostly non-rigorous! (Celebrating Jorge Kurchan) web.stanford.edu/~montanar/OT...

If you want to check if a human gene has copy-number changes or lands in a complex region, try pangene.bioinweb.org. Recently updated with more and better assemblies.

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 🧵👇

A month ago we @vevotherapeutics.bsky.social announced that we have generated the largest single-cell perturbation atlas in history, Tahoe-100M. Today, we announce that we will fully open-source Tahoe-100M in Feb, as part of a collaboration with NVidia health to train cell state models.

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

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...

Just had a thesis meeting with Yun Deng, finishing his PhD in @yun-s-song.bsky.social’s lab and beginning a postdoc with @jkpritch.bsky.social. His SINGER software for MCMC inference of ancestral recombination graphs is a really impressive contribution to the field www.biorxiv.org/content/10.1...

Thrilled to share our approach for language model-guided discovery of unknown mammalian metabolites: DeepMet. We’ve now used this approach to discover ~50 new human and mouse metabolites! www.biorxiv.org/content/10.1...

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...