Author

Junjie Shan

Harvard University

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

Biology Disciplines

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Bioinformatics· 2

Signature Assays, Organisms & Methods

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Assay:protein sequence· 2 Research Focus:software / tool· 2 Approach:deep learning· 1 Approach:machine learning (classical)· 1 Assay:protein structure· 1 Approach:transformer / foundation model· 1 Research Focus:variant effect prediction· 1

Frequent Co-Authors

Fajie YuaniD· 2 shared Jin SuiD· 2 shared An‐Ping ZengiD· 1 shared Anthony GitteriD· 1 shared Anum Azam GlasgowiD· 1 shared Caixia GaoiD· 1 shared Chenchen HaniD· 1 shared Chenchen HaniD· 1 shared

Activity by Year

2023-2025 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 38 mutual co-author links

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2 shared papersBioinformatics

Fajie YuanORCID

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2 papers

Recent·Most cited

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

SaProt: Protein Language Modeling with Structure-aware Vocabulary

Jin Su, Chenchen Han, Yuyang Zhou, Junjie Shan, Xibin Zhou, Fajie Yuan

Pairing each residue with its Foldseek 3D-structure token and pre-training an ESM-2-sized model on about 40 million AlphaFold2 structures beat ESM-2 and structure-based baselines on variant-effect and function tasks.

bioRxiv · Oct 1, 2023 · PreprintBioinformatics✦ In-depth digest