Publications
Zhang, W., Cui, Y., Liu, B., Loza, M., Park, S. J., & Nakai, K. (2024). HyGAnno: hybrid graph neural network–based cell type annotation for single-cell ATAC sequencing data. Briefings in Bioinformatics, 25(3), bbae152. [Link]
Cui, Y., Wang, R., Zeng, X., Cui, Y., Zhu, Z., Nakai, K., … & Wei, L. (2024). DenoiseST: A dual-channel unsupervised deep learning-based denoising method to identify spatial domains and functionally variable genes in spatial transcriptomics. Preprint, 2024-03. [Link]
Cui, Y., Cui, Y., Wang, R., Nakai, K., Ye, X., Sakurai, T., & Wei, L. (2024). Diffusionst: A diffusion model-based framework for enhancing spatial transcriptomics data quality and identifying spatial domains. Preprint, 2024-07. [Link]
Cui, Y., Zhang, W., Zeng, X., Yang, Y., Park, S. J., & Nakai, K. (2024). Computational analysis of the functional impact of MHC-II-expressing triple-negative breast cancer. Frontiers in immunology, 15, 1497251. [Link]
Zeng, X., Gyoja, F., Cui, Y., Loza, M., Kusakabe, T. G., & Nakai, K. (2024). Comparative single-cell transcriptomic analysis reveals putative differentiation drivers and potential origin of vertebrate retina. NAR Genomics and Bioinformatics6(4), lqae149 (2024). [Link]
Yang, Y., Cui, Y., Zeng, X., Zhang, Y., Loza, M., Park, S. J., & Nakai, K. (2025). STAIG: Spatial transcriptomics analysis via image-aided graph contrastive learning for domain exploration and alignment-free integration. Nature communications, 16(1), 1067. [Link]
Poster Presention
- Cui, Y., Nakai, K., Unveiling a Distinct Immunological Characteristic and a Prognostic Prediction Model in Breast Cancer through Integrated Transcriptomic Analysis, Poster presented at: The 21st Awaji International Forum on Infection and Immunity, 2023 Sep.3-6, Japan, Karuizawa.
- Cui, Y., Nakai, K., Computational Transcriptomic Analysis Identifies a Novel Immune-dysregulated TNBC Subtype Regulated by STAT3, Poster presented at: MBSJ2023, 2023 Dec.6-8, Japan, Kobe.
- Cui, Y., Zhang, W., Zeng, X., Yang, Y., Park, S. J., & Nakai, K., Computational Transcriptomic Analysis Reveals MHC-II Expressing Tumor Cells Influence Immune Surveillance and Prognostic Outcomes in the Tumor Microenvironment of Triple-Negative Breast Cancer, Poster presented at: 1st Asia & Pacific Bioinformatics Joint Conference (APBJC2024), 2024 Oct22-25, Japan, Okinawa.