YANG CUI, Ph.D

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.

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.

NAR Genomics and Bioinformatics, 6(4), lqae149 (2024).

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.

Frontiers in Immunology, 15, 1497251 (2024).

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.

Preprint, July 2024.

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.

Preprint, March 2024.

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.

Briefings in Bioinformatics, 25(3), bbae152 (2024).