Author

Alexandra L. Hoffman

Duke University

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Synthetic Biology· 1

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Organism:bacteria (other)· 1 Research Focus:benchmarking· 1 Approach:deep learning· 1 Assay:metagenomics· 1

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Allison J. LopatkiniD· 1 shared Ashwini R. Shende· 1 shared César A. Villalobos· 1 shared Daniel Mark ShapiroiD· 1 shared Dongheon LeeiD· 1 shared Emma J. ChoryiD· 1 shared Emrah ŞimşekiD· 1 shared Feilun WuiD· 1 shared

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1 shared paperSynthetic Biology

Allison J. LopatkinORCID

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1 paper

Recent·Most cited

A foundation model for microbial growth dynamics

Zachary A. Holmes, Irida Shyti, Alexandra L. Hoffman, Katherine E. Duncker, Helena R. Ma, Zhengqing Zhou, Dongheon Lee, Rohan Maddamsetti, Kyeri Kim, Emrah Şimşek, Grayson S. Hamrick, Hye-In Son, César A. Villalobos, Jia Grace Lu, Yuanchi Ha, , Lingchong You

This paper develops a foundation model for microbial growth dynamics using self-supervised learning on diverse datasets, enabling accurate reconstruction and prediction of growth patterns and antibiotic responses.

bioRxiv · Dec 3, 2025 · PreprintSynthetic Biology