Author

Yan He

Westlake UniversityORCID 0000-0002-3879-4091Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Assay:protein sequence· 3 Approach:deep learning· 2 Research Focus:protein design· 2 Approach:contrastive learning· 1 Approach:large language model· 1 Approach:machine learning (classical)· 1 Assay:protein structure· 1 Research Focus:protein structure prediction· 1

Frequent Co-Authors

Fajie YuaniD· 3 shared Jin SuiD· 3 shared Xing ChangiD· 3 shared An‐Ping ZengiD· 2 shared Chenchen HaniD· 2 shared Fengyuan Dai· 2 shared Hongyuan LuiD· 2 shared Shiyang You· 2 shared

Activity by Year

2025-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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3 shared papersBioinformatics

Fajie YuanORCID

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Author profile →

3 papers

Recent·Most cited

Toward De Novo Protein Design from Natural Language

Fengyuan Dai, Shiyang You, Yudian Zhu, Yuan Gao, Lihao Fu, Xibin Zhou, Jin Su, Chentong Wang, Yuliang Fan, Qingsong Tan, Xiaoxiao Ma, Xianjun Deng, Letong Yu, Hui Qian, Yan He, , Fajie Yuan

This paper introduces Pinal, a foundation model that designs proteins from natural language descriptions, achieving functional alignment and experimental success in four design tasks.

Nature · Oct 21, 2026Peer-reviewedBioengineering

Democratizing Protein Language Model Training, Sharing and Collaboration

Jin Su, Zhikai Li, Tianli Tao, Chenchen Han, Yan He, Fengyuan Dai, Qingyan Yuan, Yuan Gao, Tong Si, Xuting Zhang, Yuyang Zhou, Junjie Shan, Xibin Zhou, Xing Chang, Shiyu Jiang, , Sergey Ovchinnikov

The paper introduces SaprotHub, a platform that simplifies training and sharing of protein language models, enabling non-experts to build and collaborate on customized models.

Nature Biotechnology · Oct 24, 2025Peer-reviewedBioinformatics

ProTrek: Navigating the Protein Universe through Tri-Modal Contrastive Learning

Jin Su, Yan He, Shiyang You, Shiyu Jason Jiang, Xibin Zhou, Xuting Zhang, Yuxuan Wang, Xining Su, Igor Tolstoy, Xing Chang, Hongyuan Lu, Fajie Yuan

ProTrek introduces a tri-modal contrastive learning model for protein sequence, structure, and function, achieving significant improvements in speed and accuracy over existing tools.

Nature Biotechnology · Oct 2, 2025Peer-reviewedBioinformatics