Author

Yaxuan Cui

University of Tsukuba

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· 3

Signature Assays, Organisms & Methods

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Organism:human· 3 Research Focus:clustering· 2 Approach:deep learning· 2 Research Focus:differential expression· 2 Assay:spatial transcriptomics· 2 Assay:bulk RNA-seq· 1 Approach:diffusion model· 1 Research Focus:dimensionality reduction· 1

Frequent Co-Authors

Kenta NakaiiD· 2 shared Leyi WeiiD· 2 shared Ruheng WangiD· 2 shared Tetsuya SakuraiiD· 2 shared Xiucai YeiD· 2 shared Yang CuiiD· 2 shared Zheyong Zhu· 2 shared Feifei CuiiD· 1 shared

Activity by Year

2024-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 36 mutual co-author links

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2 shared papersBioinformatics

Kenta NakaiORCID

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3 papers

Recent·Most cited

A Hierarchy-aware Gene Exploration Platform for Multi-layered Toxicogenomic Analysis: A Case Study on Acetaminophen-induced Hepatotoxicity

M Kim, Yaxuan Cui, Myeong Gyu Kim

The paper introduces a hierarchy-aware gene exploration platform that improves functional coherence in transcriptomic analysis of acetaminophen-induced hepatotoxicity.

bioRxiv · Apr 14, 2026 · PreprintBioinformatics

DiffusionST: A deep generative diffusion model-based framework for enhancing spatial transcriptomics data quality and identifying spatial domains

Yaxuan Cui, Yang Cui, Ruheng Wang, Zheyong Zhu, Xin Zeng, Kenta Nakai, Feifei Cui, Zilong Zhang, Hua Wang Shi, Yan Chen, Xiucai Ye, Tetsuya Sakurai, Leyi Wei

DiffusionST improves spatial transcriptomics data quality and identifies spatial domains through a diffusion model and graph convolutional network.

bioRxiv · Jun 12, 2025 · PreprintBioinformatics

DenoiseST: A dual-channel unsupervised deep learning-based denoising method to identify spatial domains and functionally variable genes in spatial transcriptomics

Yaxuan Cui, Ruheng Wang, Xin Zeng, Yang Cui, Zheyong Zhu, Kenta Nakai, Xiucai Ye, Tetsuya Sakurai, Leyi Wei

DenoiseST is a deep learning method for spatial transcriptomics that improves data imputation, clustering, and identification of functionally variable genes by reducing dropout noise.

bioRxiv · Mar 4, 2024 · PreprintBioinformatics