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Shen, Wenjun.; Hu, Yunfei.; Lei, Yuanfang.; Wong, Hau-San.; Liu, Cheng.; Wu, Si.; Zhou, Xin Maizie. (2026). CSsingle: A unified tool for robust decomposition of bulk and spatial transcriptomic data across diverse single-cell references. Nucleic Acids Research, 54(8). https://doi.org/10.1093/nar/gkag410 Measuring which cell types are present in a tissue… Read More

Zhu, Junchao; Deng, Ruining; Guo, Junlin; Yao, Tianyuan; Xiong, Juming; Qu, Chongyu; Yin, Mengmeng; Wang, Yu; Zhao, Shilin; Yang, Haichun; Xu, Daguang; Tang, Yucheng; & Huo, Yuankai. (2025). Img2ST-Net: Efficient high-resolution spatial omics prediction from whole-slide histology images via fully convolutional image-to-image learning. Journal of Medical Imaging, 12(6), 61410. https://doi.org/10.1117/1.JMI.12.6.061410… Read More

Liu, Qi; Wang, Yu; Hsu, Chihyuan; Wanjalla, Celestine N.; Lau, Ken S.; & Shyr, Yu. (2026). Microenvironment-aware spatial modeling for accurate inference of cell identity. Nucleic Acids Research, 54(1). https://doi.org/10.1093/nar/gkaf1477 Spatial omics technologies make it possible to measure many molecular features in cells while also preserving information about… Read More

Loberg, Matthew A.; Chen, Sheauchiann; Chen, Huachang; Wahoski, Claudia C.; Caroland, Kailey; Tigue, Megan L.; Hartmann, Heather A.; Gallant, Jean Nicolas; Phifer, Courtney J.; Ocampo, Andres A.; Wang, Dayle K.; Fankhauser, Reilly G.; Karunakaran, Kirti A.; Wu, Chiachin; Tarabichi, Maxime; Shaddy, Sophia M.; Netterville, James L.; Rohde, Sarah… Read More

Hu, Yunfei., Lin, Zhenhan., Xie, Manfei., Yuan, Weiman., Li, Yikang., Rao, Mingxing., Liu, Yichen Henry., Shen, Wenjun., Zhang, Lu., & Zhou, Xin Maizie. (2025). MaskGraphene: an advanced framework for interpretable joint representation for multi-slice, multi-condition spatial transcriptomics. Genome Biology, 26(1), 380. https://doi.org/10.1186/s13059-025-03850-w Recent advances in spatial transcriptomics (ST),… Read More

Srivastava, Aruesha., Shaik, Neha., Lu, Yunrui., Chan, Matthew., Diallo, Alos B., Zavras, John P., Han, Serin., Punshon, Tracy., Jackson, Brian Phillip., Vahdat, Linda T., Liu, Xiaoying., Mittal, Vivek., Lau, Ken S., Gui, Jiang., Vaickus, Louis J., Hoopes, Jack., Kolling, Fred W., Perreard, Laurent., Marotti, Jonathan Douglas., & Levy,… Read More

Wang, Yu, Yang, Haichun, Deng, Ruining, Huo, Yuankai, Liu, Qi, Shyr, Yu, & Zhao, Shilin. (2025). StImage: A versatile framework for optimizing spatial transcriptomic analysis through customizable deep histology and location informed integration. Briefings in Bioinformatics, 26(5), bbaf429. https://doi.org/10.1093/bib/bbaf429 Spatial transcriptomics (ST) is a… Read More

Shui, Lan, Maitra, Anirban, Yuan, Ying, Lau, Ken S., Kaur, Harsimran, Li, Liang, & Li, Ziyi. (2025). “PoweREST: Statistical power estimation for spatial transcriptomics experiments to detect differentially expressed genes between two conditions.” PLOS Computational Biology, 21(7), e1013293. https://doi.org/10.1371/journal.pcbi.1013293 Recent advances in spatial transcriptomics (ST)—a… Read More