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Generating functional plasmid origins with OriGen
Open accessPreprint — published as 10.1093/nar/gkaf1198 · Paper page
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 functional origins that diverge from existing wild types, demonstrating the model’s capacity to capture the complex and often enigmatic mechanisms of biological replication.
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Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764
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Metadata
- Authors
- Irvine, J., Arora, J., Martinson, J. N. V., Patel, J. R., Hasham, S. I., Cress, B. F., & Rubin, B. E.
- Affiliations
- Innovative Genomics Institute (US)
- Corresponding author
- Rubin, Benjamin E.
- Venue
- Nucleic Acids Research
- Publisher
- openRxiv
- Published
- 2025-02-04
- Volume
- 53
- Issue
- 22
- ISSN
- 0305-1048 (ISSN-L)
- PMC
- PMC12663086
- OpenAlex
- W4416838960
- Cited by
- 4
- References
- 1
- Citations by year
- 2026: 2 · 2025: 2
- FWCI
- 2.34
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nucleic Acids Research (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nd)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed (publishedVersion)
- eScholarship (California Digital Library) (submittedVersion, cc-by)
- Funders
- U.S. Department of Energy (DE AC02 05CH11231)
- Silicon Valley Community Foundation
- CH Foundation
- Lyda Hill Foundation
- Shurl and Kay Curci Foundation
- Valhalla Foundation
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
- Keywords
- Origen, generative AI, language models, Escherichia coli, DNA replication, restriction sites
- MeSH terms
- DNA Replication, Escherichia coli, Plasmids, Programming Languages, Replication Origin
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