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]

• Yang, Y., Cui, Y., Zeng, X., Zhang, Y., Loza, M., Park, S. J., & Nakai, K. (2023). STAIG: Spatial Transcriptomics Analysis via Image-Aided Graph Contrastive Learning for Domain Exploration and Alignment-Free Integration. bioRxiv, 2023-12. [Link]

• Zeng, X., Gyoja, F., Cui, Y., Loza, M., Kusakabe, T. G., & Nakai, K. (2023). Comparative single-cell transcriptomic analysis reveals key differentiation drivers and the potential origin of the vertebrate retina. bioRxiv, 2023-12. [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. bioRxiv, 2024-03. [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 21th Awaji International Forum on Infection and Immunity, 2023. Sep3-6, 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.