Spatial Transcriptomics
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A comprehensive survey of computer vision methods for spatial transcriptomics
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 MoreJune 17, 2026
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CSsingle: a unified tool for robust decomposition of bulk and spatial transcriptomic data across diverse single-cell references
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 MoreMay 27, 2026
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Img2ST-Net: efficient high-resolution spatial omics prediction from whole-slide histology images via fully convolutional image-to-image learning
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 MoreJanuary 28, 2026
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Microenvironment-aware spatial modeling for accurate inference of cell identity
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 MoreJanuary 28, 2026
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An integrated single-cell and spatial transcriptomic atlas of thyroid cancer progression identifies prognostic fibroblast subpopulations
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 MoreJanuary 28, 2026
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MaskGraphene: an advanced framework for interpretable joint representation for multi-slice, multi-condition spatial transcriptomics
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 MoreNovember 23, 2025
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Integration of elemental imaging and spatial transcriptomic profiling for proof-of-concept metals-based pathway analysis of colon tumor microenvironment
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 MoreNovember 23, 2025
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StImage: A versatile framework for optimizing spatial transcriptomic analysis through customizable deep histology and location informed integration
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 MoreSeptember 26, 2025
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PoweREST: Statistical power estimation for spatial transcriptomics experiments to detect differentially expressed genes between two conditions
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 MoreAugust 25, 2025