Author

Shiyang You

The Hong Kong University of Science and Technology (Guangzhou)

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

Click to filter author papers

Bioinformatics· 3 Bioengineering· 1 Synthetic Biology· 1

Signature Assays, Organisms & Methods

Click to filter · or open tag

Approach:deep learning· 4 Assay:protein sequence· 4 Research Focus:drug response / drug discovery· 2 Research Focus:protein design· 2 Research Focus:protein structure prediction· 2 Approach:contrastive learning· 1 Approach:experimental assay· 1 Approach:large language model· 1

Frequent Co-Authors

Fajie YuaniD· 3 shared Jin SuiD· 3 shared Fengyuan Dai· 2 shared Hongyuan LuiD· 2 shared Renju LIU· 2 shared Xianjun Deng· 2 shared Xiaoxiao Ma· 2 shared Xibin ZhouiD· 2 shared

Activity by Year

2025-2026 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 40 mutual co-author links

Click any collaborator node to inspect or filter shared papers

Focal author (center)Selected co-authorORCID co-authorUnlinked name

Curved chords = mutual co-authorship

3 shared papersBioinformatics

Fajie YuanORCID

Mutual co-authors in cluster

Author profile →

5 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

Pathogen context reshapes antimicrobial peptide generation

Shiyang You, C H I Zhang, Yingchun Han, Qiuyun Jiang, X S Guo, Moran Li, Yongxin Su, Xiyang Dong, Menglin Yang, Hongyuan Lu

This paper introduces AMPHORA, a pathogen-conditioned generator of antimicrobial peptides, showing that incorporating pathogen-specific features improves peptide design and potency.

bioRxiv · Jul 3, 2026 · PreprintBioinformatics

A coupled fluorescence assay for high-throughput screening of polyurethane-degrading enzymes

Liujun YANG, Xianjun DENG, Renju LIU, Jianyang Li, Junyao ZHAI, Xiaoxiao MA, Shiyang YOU, He Qinghao, Arthur K.L. LIN, Zongze Shao, LU Hongyuan

This paper introduces a high-throughput screening assay for polyurethane-degrading enzymes using a synthetic substrate and fluorescence detection to quantify enzymatic activity.

Journal of Hazardous Materials · Feb 1, 2026Peer-reviewedSynthetic Biology

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

Decoding the Molecular Language of Proteins with Evolla

Xibin Zhou, Chenchen Han, Yingqi Zhang, Huan Du, Jiayuan Tian, Jin Su, Renju Liu, Kai Zhuang, Shiyu Jiang, Anthony Gitter, Li Liu, Huayu Li, Meiqi Wu, Shiyang You, Zichen Yuan, , Fajie Yuan

Evolla, a protein-language model, improves functional inference and discovers novel proteins through natural language queries and benchmarking.

bioRxiv · Jan 5, 2025 · PreprintBioinformatics