[R] AlphaGenome: DeepMind’s unified DNA sequence model predicts regulatory variant effects across 11 modalities at single-bp resolution (Nature 2026)

Key results: - Takes 1M base pairs of DNA as input, predicts thousands of functional genomic tracks at single-base-pair resolution - Matches or exceeds best specialized models in 25 of 26 variant effect prediction evaluations - U-Net backbone with CNN + transformer layers, trained on human and mouse genomes - 1Mb context captures 99% of validated enhancer-gene pairs - Training took 4 hours (half the compute of Enformer) on TPUv3, inference under 1 second on H100 - Demonstrates cross-modal variant interpretation on TAL1 oncogene in T-ALL I wrote a detailed explainer for a general tech audience: https://rewire.it/blog/alphagenome-one-model-for-the-other-98-percent-of-your-dna/ Paper: https://www.nature.com/articles/s41586-025-10014-0 bioRxiv preprint: https://www.biorxiv.org/content/10.1101/2025.06.25.661532v1 DeepMind blog: https://deepmind.google/blog/alphagenome-ai-for-better-understanding-the-genome/ GitHub: https://github.com/google-deepmind/alphagenome