Author

Ningyu Zhang

Zhejiang UniversityORCID 0000-0002-1970-0678Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Approach:deep learning· 2 Approach:large language model· 2 Research Focus:benchmarking· 1 Assay:bulk RNA-seq· 1 Research Focus:cell type annotation· 1 Research Focus:deconvolution· 1 Organism:mouse· 1 Research Focus:protein design· 1

Frequent Co-Authors

Huajun CheniD· 3 shared Jinlu ZhangiD· 2 shared Xiang ZhuangiD· 2 shared Xiaohui FaniD· 2 shared Xin ShaoiD· 2 shared Binbin CheniD· 1 shared Dan WuiD· 1 shared Fang YiniD· 1 shared

Activity by Year

2022-2024 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 33 mutual co-author links

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3 shared papersBioinformatics

Huajun ChenORCID

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3 papers

Recent·Most cited

Multi-purpose controllable protein generation via prompted language models

Zeyuan Wang, Binbin Chen, Keyan Ding, Jiawen Cao, Ming Qin, Yadan Niu, Xiang Zhuang, Xiaotong Li, Kehua Feng, Tong Xu, Ningyu Zhang, Haoran Yu, Qiang Zhang, Huajun Chen

This paper introduces PROPEND, a protein design method using prompted language models to directly control multiple properties, achieving higher functional recovery than traditional pipelines.

bioRxiv · Nov 17, 2024 · PreprintSynthetic Biology

Exploring the Potential of Large Language Models in Molecular Tasks: An Insightful Evaluation with GPT-4

Jinlu Zhang, Yin Fang, Ningyu Zhang, Xin Shao, Huajun Chen, Xiaohui Fan

This study evaluates GPT-4 and GPT-3.5 in molecular tasks, showing their strengths in molecular optimization but challenges in generating complex molecules.

bioRxiv · Nov 28, 2023 · PreprintBioinformatics

De novo analysis of bulk RNA-seq data at spatially resolved single-cell resolution

Jie Liao, Jingyang Qian, Fang Yin, Zhuo Chen, Xiang Zhuang, Ningyu Zhang, Xin Shao, Yining Hu, Penghui Yang, Junyun Cheng, Yang Hu, Lingqi Yu, Haihong Yang, Jinlu Zhang, Xiaoyan Lu, , Xiaohui Fan

Bulk2Space deconvolves bulk RNA-seq data to reveal spatial and cellular heterogeneity using single-cell and spatial transcriptomics references, identifying immune cell spatial variance and novel gene patterns in mouse brain regions.

Nature Communications · Oct 30, 2022Peer-reviewedBioinformatics