Spatial Transcriptomics
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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 MoreJan. 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 MoreJan. 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 MoreJan. 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 MoreNov. 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 MoreNov. 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 MoreSep. 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 MoreAug. 25, 2025