I am a Ph.D. student in the Laboratory of Functional Analysis in Silico at the University of Tokyo, supervised by Professor Kenta Nakai. My research interests include bioinformatics, single-cell and spatial multi-omics, and oncology. I am seeking collaboration opportunities as well as postdoctoral positions. Feel free to reach out via email for more details.
📝 Publications
Articles
STAIG: Spatial transcriptomics analysis via image-aided graph contrastive learning for domain exploration and alignment-free integration
Yang, Y., Cui, Y., Zeng, X., Zhang, Y., Loza, M., Park, S. J., & Nakai, K. (2025)
Nature Communications, 16(1), 1067.
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Comparative single-cell transcriptomic analysis reveals putative differentiation drivers and potential origin of vertebrate retina
Zeng, X., Gyoja, F., Cui, Y., Loza, M., Kusakabe, T. G., & Nakai, K. (2024)
NAR Genomics and Bioinformatics6(4), lqae149 (2024).
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Computational analysis of the functional impact of MHC-II-expressing triple-negative breast cancer
Cui, Y., Zhang, W., Zeng, X., Yang, Y., Park, S. J., & Nakai, K. (2024)
Frontiers in Immunology, 15, 1497251.
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Diffusionst: A diffusion model-based framework for enhancing spatial transcriptomics data quality and identifying spatial domains
Cui, Y.*, Cui, Y.*, Wang, R., Nakai, K., Ye, X., Sakurai, T., & Wei, L. (2024)
Preprint, 2024-07.
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DenoiseST: A dual-channel unsupervised deep learning-based denoising method to identify spatial domains and functionally variable genes in spatial transcriptomics
Cui, Y., Wang, R., Zeng, X., Cui, Y., Zhu, Z., Nakai, K., ... & Wei, L. (2024)
Preprint, 2024-03.
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HyGAnno: hybrid graph neural network–based cell type annotation for single-cell ATAC sequencing data
Zhang, W., Cui, Y., Liu, B., Loza, M., Park, S. J., & Nakai, K. (2024)
Briefings in Bioinformatics, 25(3), bbae152.
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Posters
Computational Transcriptomic Analysis Reveals MHC-II Expressing Tumor Cells Influence Immune Surveillance and Prognostic Outcomes in the Tumor Microenvironment of Triple-Negative Breast Cancer
Cui, Y., Zhang, W., Zeng, X., Yang, Y., Park, S. J., & Nakai, K.
Poster presented at: 1st Asia & Pacific Bioinformatics Joint Conference (APBJC2024), 2024 Oct22-25, Japan, Okinawa. |
Computational Transcriptomic Analysis Identifies a Novel Immune-dysregulated TNBC Subtype Regulated by STAT3
Cui, Y., Nakai, K.
Poster presented at: MBSJ2023, 2023 Dec.6-8, Japan, Kobe. |
Unveiling a Distinct Immunological Characteristic and a Prognostic Prediction Model in Breast Cancer through Integrated Transcriptomic Analysis
Cui, Y., Nakai, K.
Poster presented at: The 21st Awaji International Forum on Infection and Immunity, 2023 Sep.3-6, Japan, Karuizawa. |
🎓 Education
Apr 2022 - Present:
PhD Student
Department of Computational Biology and Medical Sciences
Graduate School of Frontier Sciences
The University of Tokyo
Laboratory of Functional Analysis in Silico
Supervised by Professor Kenta Nakai
Apr 2020 - Mar 2022:
Master’s Degree
Department of Immunology
Graduate School of Medical and Dental Sciences
Tokyo Medical and Dental University
Supervised by Professor Tsubata Takeshi
Sep 2013 - Jul 2017:
Bachelor’s Degree
Department of Biotechnology
School of Bioengineering
East China University of Science and Technology
🏆 Award
May 2024 - Present SPRING GX Fellowship (JST)
