Author

Yong He

Alibaba Group (China)ORCID 0000-0002-1585-2009Unclaimed ORCID profile · follow to get notified of new preprints

Additional preprints under this name without ORCID

Yong He4 papers · Alibaba Group (China)

Biology Disciplines

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Microbiology· 2 Bioinformatics· 1

Signature Assays, Organisms & Methods

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Approach:deep learning· 2 Assay:metagenomics· 2 Approach:statistical model· 2 Research Focus:cell type annotation· 1 Research Focus:chromatin & epigenetic regulation· 1 Assay:DNA methylation· 1 Research Focus:ecology & biodiversity· 1 Research Focus:gene regulatory network inference· 1

Frequent Co-Authors

Zhaorong LiiD· 3 shared Mǎng ShīiD· 2 shared Xiyang DongiD· 2 shared Andrew S. LangiD· 1 shared Chuwen ZhangiD· 1 shared Edward Charles HolmesiD· 1 shared Federico BaltariD· 1 shared Feng ZhuiD· 1 shared

Activity by Year

2025-2025 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 24 mutual co-author links

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3 shared papersMicrobiology

Zhaorong LiORCID

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3 papers

Recent·Most cited

Generalized Biological Foundation Model with Unified Nucleic Acid and Protein Language

Yong He, Pan Fang, Yongtao Shan, Yuanfei Pan, Yanhong Wei, Yichang Chen, Yihao Chen, Yi Liu, Zhenyu Zeng, Zhan Mei Zhou, Feng Zhu, Edward Charles Holmes, Jieping Ye, Jun Li, Yuelong Shu, , Zhaorong Li

This paper introduces LucaOne, a foundation model trained on nucleic acid and protein sequences, demonstrating understanding of biological principles and performing well on related tasks.

Nature Machine Intelligence · Jun 18, 2025Peer-reviewedBioinformatics

Illuminating microbial phosphorus cycling in deep-sea cold seep sediments using protein language models

Chuwen Zhang, Yong He, Jieni Wang, Tengkai Chen, Federico Baltar, Minjie Hu, Jing Liao, Xi Xiao, Zhaorong Li, Xiyang Dong

This study uses a protein language model to discover new phosphorus-cycling protein families in deep-sea cold seep sediments, revealing novel microbial processes and ecological roles.

Nature Communications · May 26, 2025Peer-reviewedMicrobiology

Uncovering the hidden RNA virus diversity in Lake Nam Co: evolutionary insights from an extreme high-altitude environment

Lilin Wu, Yongqin Liu, Wenqing Shi, Tianyi Chang, Pengfei Liu, Keshao Liu, Yong He, Zhaorong Li, Mǎng Shī, Nianzhi Jiao, Andrew S. Lang, Xiyang Dong, Qiang Zheng

This study identifies 742 RNA virus species in Lake Nam Co, revealing novel viral groups and evolutionary adaptations in an extreme high-altitude environment.

Proceedings of the National Academy of Sciences · Feb 4, 2025Peer-reviewedMicrobiology