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Junchao Zhu; Ruining Deng; Junlin Guo; Tianyuan Yao; Siqi Lu; Chongyu Qu; Juming Xiong; Yanfan Zhu; Zhengyi Lu; Yuechen Yang; Marilyn Lionts; Yucheng Tang; Daguang Xu; Yu Wang; Shilin Zhao; Haichun Yang; Yuankai Huo. (2026).聽A comprehensive survey of computer vision methods for spatial transcriptomics.聽Briefings in Bioinformatics, 27(3),… Read More

Shen, Wenjun.; Hu, Yunfei.; Lei, Yuanfang.; Wong, Hau-San.; Liu, Cheng.; Wu, Si.; Zhou, Xin Maizie. (2026).聽CSsingle: A unified tool for robust decomposition of bulk and spatial transcriptomic data across diverse single-cell references.聽Nucleic Acids Research, 54(8).聽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).聽Img2ST-Net: Efficient high-resolution spatial omics prediction from whole-slide histology images via fully convolutional image-to-image learning.聽Journal of Medical Imaging,聽12(6), 61410.聽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).聽Microenvironment-aware spatial modeling for accurate inference of cell identity.聽Nucleic Acids Research,聽54(1).聽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).聽MaskGraphene: an advanced framework for interpretable joint representation for multi-slice, multi-condition spatial transcriptomics.聽Genome Biology,聽26(1), 380.聽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). 鈥淧oweREST: Statistical power estimation for spatial transcriptomics experiments to detect differentially expressed genes between two conditions.鈥� PLOS Computational Biology, 21(7), e1013293. https://doi.org/10.1371/journal.pcbi.1013293 Recent advances in聽spatial transcriptomics (ST)鈥攁… Read More