holy shit, it’s here!
deepmind just released AlphaGenome.
an AI model that reads 1 million bases of DNA and predicts how any mutation changes molecular function
not just in single genes but across the entire regulatory genome.
DNA is code, and you are software
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Jun 25, 2025 · 2:32 PM UTC
oh yeah, and it's an API
github.com/google-deepmind/a…
the human genome is 3 billion letters.
but less than 2% codes for proteins.
the other 98% is the regulatory machinery:
expression timing, chromatin architecture, RNA splicing, 3D folding etc
until now, we've been functionally blind to how it works.
AlphaGenome changes that
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the core breakthrough: they solved a fundamental tradeoff.
old models had to choose:
- long-range vision, low resolution (blurred)
- sharp resolution, tiny context (myopic)
AlphaGenome does both.
1 million base context
1 bp resolution
simultaneously
3/
this isn’t academic abstraction.
they tested it on TAL1 mutations in T-ALL leukemia.
AlphaGenome predicted:
- creation of a MYB motif
- enhancer activation
- increased H3K27ac
- gene upregulation
a single base change → full regulatory cascade
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this is the first model that:
- understands splicing at junction, site, and isoform levels
- sees regulatory interactions across 1Mbp windows
- predicts impact of variants in the non-coding genome
- resolves cause → mechanism → consequence
at single-nucleotide granularity
7/
use cases
- identify root causes of rare disease
- simulate mutations before testing
- design synthetic DNA with tissue-specific control
- prioritize therapeutic targets from GWAS
- predict off-target effects at the regulatory layer
the new backend for genomics
8/
obv there are limits:
- 100kb distal interactions still weak
- not calibrated for personal genomes (yet)
- doesn’t predict full phenotypes, only molecular outputs
- not clinical-grade (yet)
but this is version 1. trained in 4 hours. on half the compute of Enformer
9/
every failed therapy. every rare disease. every complex trait.
all of them start with misinterpreted DNA.
now we can finally see the system
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and when you can see a system clearly, you can begin to design it.
biology stops being mysterious. it starts becoming programmable.
this is the transition from description → control. AlphaGenome is the turning point
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