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GPN-Star, a genomic language model with a phylogeny-aware architecture for whole-genome alignment data, is shown to be a scalable and flexible tool for genetic variant effect prediction across species...

UC Berkeley and UCSF have launched a joint program called the Bakar Computational Biomedicine Initiative to develop the frontier of AI and biomedicine, tremendously accelerating advances in clinical c...

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A five year collaboration with the Victora lab is bearing fruit for evolutionary biology.

Intragenomic conflict with selfish genetic elements spurs adaptive changes in subunits of essential multiprotein complexes. Whether and how these adaptive changes disrupt interactions within such comp...

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...

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SINGER is a method for creating ancestral recombination graphs to understand the genealogical history of genomes. The method has increased speed, and thus scalability, without sacrificing accuracy.

B cells and the antibodies they produce are vital to health and survival, motivating research on the details of the mutational and evolutionary processes in the germinal centers (GC) from which mature...

Human enhancers contain a high density of sequence features that are required for their normal in vivo function.

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Darwinian evolution of immunoglobulin genes within germinal centers (GC) underlies the progressive increase in antibody affinity following antigen exposure. Whereas the mechanics of how competition be...

Generative models trained on natural sequences are increasingly used to predict the effects of genetic variation, enabling progress in therapeutic design, disease risk prediction, and synthetic biolog...

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Hu et al. (Science, 2023) recently inferred a severe ancient bottleneck around 900 thousand years (kya) ago in African ancestry but found no similar eviden

A language model predicts the effects of genetic variants in the human genome.

Standard genome-wide association studies (GWAS) and rare variant burden tests are essential tools for identifying trait-relevant genes. Although these methods are conceptually similar, we show by anal...

Despite decades of study, large parts of the mammalian metabolome remain unexplored. Mass spectrometry-based metabolomics routinely detects thousands of small molecule-associated peaks within human ti...

Amino acid substitution rate matrices are fundamental to statistical phylogenetics and evolutionary biology. Estimating them typically requires reconstructed trees for massive amounts of aligned...