Author

Shaoze Yuan

California Institute of TechnologyORCID 0009-0004-0257-9818Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioengineering· 1 Synthetic Biology· 1

Signature Assays, Organisms & Methods

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Assay:protein sequence· 2 Research Focus:sequence-to-function modeling· 2 Approach:deep learning· 1 Approach:machine learning (classical)· 1 Research Focus:protein design· 1 Assay:protein structure· 1 Approach:transformer / foundation model· 1

Frequent Co-Authors

Alec L. Lourenço· 1 shared Alex Toftgaard NielseniD· 1 shared Arjuna M. SubramanianiD· 1 shared Bjarke Erichsen· 1 shared Jinbei LiiD· 1 shared Kenan JijakliiD· 1 shared Lei YangiD· 1 shared Matt Thomson· 1 shared

Activity by Year

2023-2025 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 21 mutual co-author links

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1 shared paperBioengineering

Alec L. Lourenço

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2 papers

Recent·Most cited

Synthetic BiologybioRxivPreprintOct 24, 2025

MillionFull enables massive, full-length enzyme sequence-fitness data collection at low cost for machine learning-guided enzyme engineering

Jinbei Li, Bjarke Erichsen, Simon R Krarup…·Alex Toftgaard Nielsen

MillionFull collects large-scale sequence-fitness data for enzymes at low cost, enabling machine learning for enzyme engineering.

DOI 10.1101/2025.10.24.684421

protein sequencemachine learning (classical)

𝕏 PostBluesky

BioengineeringbioRxivPreprintDec 22, 2023

Unexplored regions of the protein sequence-structure map revealed at scale by a library of foldtuned language models

Arjuna M. Subramanian, Zachary A. Martinez, Alec L. Lourenço…·Matt Thomson

This paper introduces foldtuning, a method to generate novel protein sequences with target structures, bypassing evolutionary barriers and enabling synthetic biology applications.

DOI 10.1101/2023.12.22.573145

protein sequenceprotein structure

𝕏 PostBluesky