Evidence map›Paper›PMID 39541441›Full record

ArticleScience (New York, N.Y.)2024

Sequence modeling and design from molecular to genome scale with Evo.

Eric Nguyen, Michael Poli, Matthew G Durrant, Brian Kang, Dhruva Katrekar, David B Li, Liam J Bartie, Armin W Thomas, Samuel H King, Garyk Brixi and 10 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Science (New York, N.Y.), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 257 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
257citing papers in PubMed, 1 pooled it
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

257 citing papers in PubMed, 1 synthesis or guideline pooled it.

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197 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

20 authors.

Eric Nguyen *Arc Institute, Palo Alto, CA, USA.ORCID 0009-0008-6593-0707
Michael Poli *Department of Computer Science, Stanford University, Stanford, CA, USA.
Matthew G Durrant *Arc Institute, Palo Alto, CA, USA.
Brian Kang *Arc Institute, Palo Alto, CA, USA.
Dhruva Katrekar *Arc Institute, Palo Alto, CA, USA.ORCID 0000-0002-8028-3244
David B Li *Arc Institute, Palo Alto, CA, USA.ORCID 0000-0002-8921-5168
Liam J BartieArc Institute, Palo Alto, CA, USA.
Armin W ThomasStanford Data Science, Stanford University, Stanford, CA, USA.
Samuel H KingArc Institute, Palo Alto, CA, USA.ORCID 0000-0002-1260-5045
Garyk BrixiArc Institute, Palo Alto, CA, USA.ORCID 0000-0002-1253-0522
Jeremy SullivanArc Institute, Palo Alto, CA, USA.
Madelena Y NgStanford Center for Biomedical Informatics Research, Stanford, CA, USA.ORCID 0000-0003-3824-9349
Ashley LewisDepartment of Biomedical Data Science, Stanford University, Stanford, CA, USA.
Aaron LouDepartment of Computer Science, Stanford University, Stanford, CA, USA.
Stefano ErmonDepartment of Computer Science, Stanford University, Stanford, CA, USA.ORCID 0000-0003-0039-2887
Stephen A BaccusDepartment of Neurobiology, Stanford University, Stanford, CA, USA.ORCID 0000-0001-8692-5685
Tina Hernandez-BoussardDepartment of Biomedical Data Science, Stanford University, Stanford, CA, USA.ORCID 0000-0001-6553-3455
Christopher RéDepartment of Computer Science, Stanford University, Stanford, CA, USA.
Patrick D HsuArc Institute, Palo Alto, CA, USA.ORCID 0000-0002-9380-2648
Brian L HieArc Institute, Palo Alto, CA, USA.ORCID 0000-0003-3224-8142

Funding

Stanford Center for Clinical & Translational Education and Research (Spectrum)UL1TR003142 · NCATS · STANFORD UNIVERSITY · PI O'HARA, RUTH M · 2019 to 2023
$45.0M
Stanford Center for Clinical and Translational Research and EducationUM1TR004921 · NCATS · STANFORD UNIVERSITY · PI MANISHA DESAI, DEAN W FELSHER · 2024 to 2026
$30.1M
Training CoreU54EB020405 · NIBIB · STANFORD UNIVERSITY · PI DELP, SCOTT L · 2014 to 2018
$11.6M
NCATS NIH HHS UL1 TR003142NCATS NIH HHS UM1 TR004921NIBIB NIH HHS U54 EB020405
6 · The paper itself

Abstract

The genome is a sequence that encodes the DNA, RNA, and proteins that orchestrate an organism's function. We present Evo, a long-context genomic foundation model with a frontier architecture trained on millions of prokaryotic and phage genomes, and report scaling laws on DNA to complement observations in language and vision. Evo generalizes across DNA, RNA, and proteins, enabling zero-shot function prediction competitive with domain-specific language models and the generation of functional CRISPR-Cas and transposon systems, representing the first examples of protein-RNA and protein-DNA codesign with a language model. Evo also learns how small mutations affect whole-organism fitness and generates megabase-scale sequences with plausible genomic architecture. These prediction and generation capabilities span molecular to genomic scales of complexity, advancing our understanding and control of biology.

Indexed as

DNAGenomicsHigh-Throughput Nucleotide SequencingModels, GeneticCRISPR-Cas SystemsDNA Transposable ElementsGenome, ArchaealGenome, BacterialGenome, ViralMutagenesisMutationRNADNADNA Transposable ElementsRNA

Identifiers

PMID39541441
PMCPMC12057570

What Socratic holds

Textmetadata
LicenceTDM
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.