Evidence map›Paper›PMID 41325770›Full record

ArticleNucleic acids research2025

Generating functional plasmid origins with OriGen.

Jamie Irvine, Jonathan N V Martinson, Jigyasa Arora, Sarah I Hasham, Jaymin R Patel, Emily T Qi, Brady F Cress, Benjamin E Rubin

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nucleic acids research, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
–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

3 citing papers in PubMed.

  1. Article
  2. Article
  3. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

8 authors.

Jamie IrvineInnovative Genomics Institute, University of California, Berkeley, CA 94720, United States.
Jonathan N V MartinsonInnovative Genomics Institute, University of California, Berkeley, CA 94720, United States.
Jigyasa AroraInnovative Genomics Institute, University of California, Berkeley, CA 94720, United States.
Sarah I HashamInnovative Genomics Institute, University of California, Berkeley, CA 94720, United States.
Jaymin R PatelInnovative Genomics Institute, University of California, Berkeley, CA 94720, United States.
Emily T QiInnovative Genomics Institute, University of California, Berkeley, CA 94720, United States.
Brady F CressInnovative Genomics Institute, University of California, Berkeley, CA 94720, United States.ORCID 0000-0002-2948-2846
Benjamin E RubinInnovative Genomics Institute, University of California, Berkeley, CA 94720, United States.ORCID 0000-0001-8684-2417

Funding

Anne Wojcicki FoundationCH FoundationEmerson Collective, Mike Schroepfer and Erin Hoffman Family FundHastings/Quillin FundInnovative Genomics Institute Genomic Tool Discovery Program at UC BerkeleyInnovative Genomics Institute; Leona M. and Harry B. Helmsley Charitable Trust G-2302-06692Laura and Gary Lauder and FamilyLyda Hill Philanthropiesm-CAFEs Microbial Community Analysis & Functional EvaluationSea Grape FoundationShurl and Kay Curci FoundationSilicon Valley Community FoundationU.S. Department of Energy DE-AC02-05CH11231Valhalla Foundation
6 · The paper itself

Abstract

While generative artificial intelligence has shown promise for biological design, no computational system has yet created sequences proven capable of replication. Focusing on plasmids as minimal replicating systems, we develop OriGen, a language model that generates novel plasmid origins of replication while maintaining essential functional elements. We experimentally validate OriGen's ability to create active origins in Escherichia coli that diverge from existing wild types, demonstrating the model's capacity to capture the complex and often enigmatic mechanisms of biological replication. Further, we directed OriGen to produce functional origins that avoid common restriction sites, demonstrating the model's potential for automated controllable design of vectors with desirable properties.

Indexed as

PlasmidsReplication OriginDNA ReplicationEscherichia coliProgramming Languages

Identifiers

PMID41325770
PMCPMC12663086

What OpenQuestion holds

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Registered trials

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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 OpenQuestion graph.