SpaGCN: Integrating gene expression, spatial location and histology to identify spatial domains and spatially variable genes by graph convolutional network

Hu, Jian, Li, Xiangjie, Coleman, Kyle, Schroeder, Amelia, Ma, Nan, Irwin, David J., Lee, Edward B., Shinohara, Russell T. +1 more·2021·Nature Methods

Cited by (1,117)

Items 301–400 of 1,117

  1. spatiAlign: an unsupervised contrastive learning model for data integration of spatially resolved transcriptomics
    Chao Zhang, Lin Liu, Ying Zhang, Mei Li, Qiang Kang, Qiang Kang, Ao Chen, Xun Xu, Yong Zhang, Yuxiang Li · 2024 · GigaScience
  2. Spatially Informed Graph Structure Learning Extracts Insights from Spatial Transcriptomics
    Wan Nie, Yingying Yu, Xueying Wang, Ruohan Wang, Shuai Cheng Li · 2024 · Advanced Science
  3. Statistical batch-aware embedded integration, dimension reduction, and alignment for spatial transcriptomics
    Yanfang Li, Shihua Zhang · 2024 · Bioinformatics
  4. StereoSiTE: a framework to spatially and quantitatively profile the cellular neighborhood organized iTME
    Xing Liu, Chi Qu, Chuandong Liu, Na Zhu, Huaqiang Huang, Fei Teng, Caili Huang, Bingying Luo, Xuanzhu Liu, Min Xie et al. · 2024 · GigaScience
  5. Spatial Transcriptomics: Biotechnologies, Computational Tools, and Neuroscience Applications
    Qianwen Wang, Hongyuan Zhu, Linhong Deng, Shuangbin Xu, Wenqin Xie, Ming Li, Rui Wang, Liang Tie, Li Zhan, Guangchuang Yu · 2025 · Small Methods
  6. LEGEND: Identifying Co-expressed Genes in Multimodal Transcriptomic Sequencing Data
    Tao Deng, Mengqian Huang, Kaichen Xu, Yan Lu, Yucheng Xu, Siyu Chen, Nina Xie, Qiuyue Tao, Hao Wu, Xiaobo Sun · 2025 · Genomics Proteomics & Bioinformatics
  7. The automated computational workflow QUICHE reveals structural definitions of antitumor responses in triple-negative breast cancer
    Jolene S. Ranek, Noah F. Greenwald, Mako Goldston, Christine Camacho Fullaway, Cameron Sowers, Alex Kong, Silvana Andrea Mouron, Miguel Quintela-Fandiño, Robert B. West, Sean C. Bendall et al. · 2026 · Nature Cancer
  8. stGCL: a versatile cross-modality fusion method based on multi-modal graph contrastive learning for spatial transcriptomics
    Na Yu, Daoliang Zhang, Wen Zhang, Zhiping Liu, Xu Qiao, Chuanyuan Wang, Miaoqing Zhao, 晁宝婷, Wei Li, Yang Z. De Marinis et al. · 2026 · Genome biology
  9. Single-Cell Informatics for Tumor Microenvironment and Immunotherapy
    Jiabao Tian, Xinyu Bai, Camelia Y. J. Quek · 2024 · International Journal of Molecular Sciences
  10. Computational modeling for deciphering tissue microenvironment heterogeneity from spatially resolved transcriptomics
    Chuanchao Zhang, Lequn Wang, Qianqian Shi · 2024 · Computational and Structural Biotechnology Journal
  11. ST-SCSR: identifying spatial domains in spatial transcriptomics data via structure correlation and self-representation
    Min Zhang, Wensheng Zhang, Xiaoke Ma · 2024 · Briefings in Bioinformatics
  12. A graph self-supervised residual learning framework for domain identification and data integration of spatial transcriptomics
    Jinjin Huang, Xiaoqian Fu, Zhuangli Zhang, Yinfeng Xie, Shangkun Liu, Yarong Wang, Zhihong Zhao, Youmei Peng · 2024 · Communications Biology
  13. SpaGRA: Graph augmentation facilitates domain identification for spatially resolved transcriptomics
    Xue Gang Sun, Wei Zhang, Wenrui Li, Na Yu, Daoliang Zhang, Qi Zou, Qiongye Dong, Xianglin Zhang, Zhi‐Ping Liu, Zhiyuan Yuan et al. · 2024 · Journal of genetics and genomics/Journal of Genetics and Genomics
  14. Bridging cell morphological behaviors and molecular dynamics in multi-modal spatial omics with MorphLink
    Jing Huang, Chenyang Yuan, Jiahui Jiang, Jianfeng Chen, Sunil Badve, Yesim Gökmen‐Polar, Rossana N. Lazcano Segura, Xinmiao Yan, Alexander J. Lazar, Jianjun Gao et al. · 2025 · Nature Communications
  15. Benchmarking LLM-based agents for single-cell omics analysis
    Yang Liu, Lu Zhou, Xiawei Du, Ruikun He, Xuguang Zhang, Rongbo Shen, Yixue Li · 2026 · Genome biology
  16. Tissue and cellular spatiotemporal dynamics in colon aging
    Aidan C. Daly, Francesco Cambuli, Tarmo Äijö, Britta Lötstedt, Nemanja Despot Marjanovic, Sara Fernandez, Olena Kuksenko, Matthew Smith-Erb, Daniel Domovic, Nicholas Van Wittenberghe et al. · 2025 · Nature Biotechnology
  17. A classification method of gastric cancer subtype based on residual graph convolution network
    Can Liu, Yuchen Duan, Qingqing Zhou, Yongkang Wang, Yong Gao, Hongxing Kan, Jili Hu · 2023 · Frontiers in Genetics
  18. Harnessing computational spatial omics to explore the spatial biology intricacies
    Zhiyuan Yuan, Jianhua Yao · 2023 · Seminars in Cancer Biology
  19. Transforming drug discovery with a high-throughput AI-powered platform: A 5-year experience with Patrimony
    François-Xavier Blaudin de Thé, Claire Baudier, Renan Andrade Pereira, Céline Lefèbvre, Philippe E. Moingeon · 2023 · Drug Discovery Today
  20. ScribbleDom: using scribble-annotated histology images to identify domains in spatial transcriptomics data
    Mohammad Nuwaisir Rahman, Abdullah Al Noman, Abir Mohammad Turza, Mohammed Abid Abrar, Md. Abul Hassan Samee, Mohammad Saifur Rahman · 2023 · Bioinformatics
  21. Multi-modal domain adaptation for revealing spatial functional landscape from spatially resolved transcriptomics
    Lequn Wang, Yaofeng Hu, Kai Xiao, Chuanchao Zhang, Qianqian Shi, Luonan Chen · 2024 · Briefings in Bioinformatics
  22. SPANN: annotating single-cell resolution spatial transcriptome data with scRNA-seq data
    Musu Yuan, Hui Song Wan, Zihao Wang, Qirui Guo, Minghua Deng · 2024 · Briefings in Bioinformatics
  23. hoodscanR: profiling single-cell neighborhoods in spatial transcriptomics data
    Ning Liu, Jarryd Martin, Dharmesh Dinesh Bhuva, Jinjin Chen, Mengbo Li, Sam Lee, Malvika Kharbanda, Jinming Cheng, Ahmed Mohamed, Arutha Kulasinghe et al. · 2026 · Bioinformatics
  24. Artificial intelligence in cell annotation for high-resolution RNA sequencing data
    Naiqiao Hou, Xinrui Lin, Li Lin, Xi Zeng, Zhixing Zhong, Xiaoyu Wang, Rui Cheng, Xin Lin, Chaoyong James Yang, Jia Tao Song · 2024 · TrAC Trends in Analytical Chemistry
  25. Spatial domains identification in spatial transcriptomics using modality-aware and subspace-enhanced graph contrastive learning
    Gui Yang, Chao Li, Yan Xu · 2024 · Computational and Structural Biotechnology Journal
  26. spatialGE Is a User-Friendly Web Application That Facilitates Spatial Transcriptomics Data Analysis
    Oscar E. Ospina, Roberto Manjarres-Betancur, Guillermo Gonzalez-Calderon, Alex C. Soupir, Inna Smalley, Kenneth Yee Tsai, Joseph Markowitz, Mariam L. Khaled, Ethan J. Vallebuona, Anders Berglund et al. · 2024 · Cancer Research
  27. SpatialCVGAE: Consensus Clustering Improves Spatial Domain Identification of Spatial Transcriptomics Using VGAE
    Jinyun Niu, Fangfang Zhu, Donghai Fang, Wenwen Min · 2024 · Interdisciplinary Sciences Computational Life Sciences
  28. STMiner: Gene-centric spatial transcriptomics for deciphering tumor tissues
    Peisen Sun, Stephen J. Bush, Songbo Wang, Peng Jia, Mingxuan Li, Tun Xu, Pengyu Zhang, Xiaofei Yang, Chengyao Wang, Linfeng Xu et al. · 2025 · Cell Genomics
  29. MuCST: restoring and integrating heterogeneous morphology images and spatial transcriptomics data with contrastive learning
    Yu Wang, Zaiyi Liu, Xiaoke Ma · 2025 · Genome Medicine
  30. Unveiling fine-scale spatial structures and amplifying gene expression signals in ultra-large ST slices with HERGAST
    Yuqiao Gong, Xin Yuan, Qiong Jiao, Zhangsheng Yu · 2025 · Nature Communications
  31. SMOPCA: spatially aware dimension reduction integrating multi-omics improves the efficiency of spatial domain detection
    Mo Chen, Ruihua Cheng, Jianuo He, Jun Chen, Jie Zhang · 2025 · Genome biology
  32. Artificial Intelligence–driven spatial transcriptomics in OSCC: Mapping the tumor microenvironment and personalizing therapy
    Soundharya Manogaran, Ramya Ramadoss, Suganya Panneer Selvam, Sandhya Sundar, Nitya Krishnasamy, Hema Shree K, Karunya Krishnakumar, Preethi Shankar · 2025 · Journal of Oral Biology and Craniofacial Research
  33. Enhancing RNA Capture Efficiency in Spatial Transcriptomics: A Review of Innovative Technologies and Strategies
    Qinyu Ge, Yuqi Sheng, Yuting Shan, Yuwei Yang, Haohan Jiang, Ruyue Wang · 2025 · International Journal of Molecular Sciences
  34. 3d-OT: a deep geometry-aware framework for heterogeneous slices alignment of spatial multi-omics
    Bingjie Dai, Litai Yi, Peizhuo Wang, Hanshuang Li, Pengwei Hu, Yancheng Song, Jixiang Xing, Zhenxing Feng, Zhiyuan Yuan, Yongchun Zuo · 2026 · Nature Methods
  35. Model-free prediction test with application to genomics data
    Zhanrui Cai, Jing Lei, Kathryn Roeder · 2022 · Proceedings of the National Academy of Sciences
  36. SMASH: Scalable Method for Analyzing Spatial Heterogeneity of genes in spatial transcriptomics data
    Souvik Seal, Benjamin Guy Bitler, Debashis Ghosh · 2023 · PLoS Genetics
  37. Deciphering spatial domains from spatially resolved transcriptomics with Siamese graph autoencoder
    Lei Cao, Chao Yang, Luni Hu, Wenjian Jiang, Yating Ren, Tianyi Xia, Mengyang Xu, Yishuai Ji, Mei Li, Xun Xu et al. · 2024 · GigaScience
  38. Integrative analysis methods for spatial transcriptomics
    Shaina Lu, Daniel Fürth, Jesse Gillis · 2021 · Nature Methods
  39. DenoiseST: A dual-channel unsupervised deep learning-based denoising method to identify spatial domains and functionally variable genes in spatial transcriptomics
    Yaxuan Cui, Ruheng Wang, Xin Zeng, Yang Cui, Zheyong Zhu, Kenta Nakai, Xiucai Ye, Tetsuya Sakurai, Leyi Wei · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  40. STGIC: A graph and image convolution-based method for spatial transcriptomic clustering
    Chen Zhang, Junhui Gao, Hongyu Chen, Lingxin Kong, Guangshuo Cao, Xiangyu Guo, Wei Liu, Bin Ren, Dong‐Qing Wei · 2024 · PLoS Computational Biology
  41. Pianno: a probabilistic framework automating semantic annotation for spatial transcriptomics
    Yuqiu Zhou, Wei He, Weizhen Hou, Ying Zhu · 2024 · Nature Communications
  42. ST-CellSeg: Cell segmentation for imaging-based spatial transcriptomics using multi-scale manifold learning
    Youcheng Li, Leann Lac, Qian Liu, Pingzhao Hu · 2024 · PLoS Computational Biology
  43. Unraveling spatial domain characterization in spatially resolved transcriptomics with robust graph contrastive clustering
    Yingxi Zhang, Zhuohan Yu, Ka‐Chun Wong, Xiangtao Li · 2024 · Bioinformatics
  44. Genome analysis through image processing with deep learning models
    Yaozhong Zhang, Seiya Imoto · 2024 · Journal of Human Genetics
  45. SpotGF: Denoising spatially resolved transcriptomics data using an optimal transport-based gene filtering algorithm
    Lin Du, Jingmin Kang, Yong Xia Hou, Hai‐Xi Sun, Bohan Zhang · 2024 · Cell Systems
  46. Spatial pattern and differential expression analysis with spatial transcriptomic data
    Fei Qin, Xizhi Luo, Qing Richard Lu, Bo Cai, Feifei Xiao, Guoshuai Cai · 2024 · Nucleic Acids Research
  47. NicheTrans: spatial-aware cross-omics translation
    Zhikang Wang, Qi Zou, Senlin Lin, Sijie Li, Yan Cui, Daoliang Zhang, Chuangyi Han, Yida Li, Jianmin Li, Yi Chen Zhao et al. · 2026 · Nature Methods
  48. Dissection of tumoral niches using spatial transcriptomics and deep learning
    Karla Paniagua, Yu-Fang Jin, Yidong Chen, Shou‐Jiang Gao, Yufei Huang, Mario A. Flores · 2025 · iScience
  49. Exploring the Latent Information in Spatial Transcriptomics Data via Multi‐View Graph Convolutional Network Based on Implicit Contrastive Learning
    Sheng Ren, Xingyu Liao, Farong Liu, Jie Li, Xin Gao, Bin Yu · 2025 · Advanced Science
  50. ONTraC characterizes spatially continuous variations of tissue microenvironment through niche trajectory analysis
    Wen Wang, Shiwei Zheng, Sujung Crystal Shin, Joselyn Chávez, Guo‐Cheng Yuan · 2025 · Genome biology
  51. SpaSEG: unsupervised deep learning for multi-task analysis of spatially resolved transcriptomics
    Yong Bai, Xiangyu Guo, Keyin Liu, Bingjie Zheng, Yilin Wei, Yingyue Wang, W H Zhang, Qiuhong Luo, Jianhua Yin, Liang Li Wu et al. · 2025 · Genome biology
  52. A comprehensive benchmarking for spatially resolved transcriptomics clustering methods across variable technologies, organs, and replicates
    Renjie Chen, Yue Yao, Jingyang Qian, Xin Xiang Peng, Xin Shao, Xiaohui Fan · 2025 · iMeta
  53. Engineering tumor spatial heterogeneity in vitro
    Changchong Chen, Zixuan Zhao, Dong Hua Seah, Kenny Zhuoran Wu, Senthilkumar Mohanaselvi, Eliza Li Shan Fong · 2025 · Advanced Drug Delivery Reviews
  54. Inferring spatial single-cell-level interactions through interpreting cell state and niche correlations learned by self-supervised graph transformer
    Xiao Xiao, Le Yuan Zhang, Hongyu Zhao, Zuoheng Wang · 2025 · Nature Machine Intelligence
  55. Mapping biology in space: from spatial transcriptomics platforms to analytical tools and databases
    Zizhen Guo, Renyan Wu, Weixiang Li, Keyu Yang, Xuexiang Ying, Hamid Alinejad-Rokny, Youqiong Ye · 2026 · 中国科学通报:英文版
  56. Spatially Resolved Transcriptomics Data Clustering With Modality Conflict Modulation
    Yuang Xiao, Zhenglai Li, Xiao Zheng, Chang Tang, Kun Sun, Xinwang Liu · 2026 · IEEE Transactions on Emerging Topics in Computational Intelligence
  57. CCPLS reveals cell-type-specific spatial dependence of transcriptomes in single cells
    Takaho Tsuchiya, Hiroki Hori, Haruka Ozaki · 2022 · Bioinformatics
  58. Spatial RNA sequencing methods show high resolution of single cell in cancer metastasis and the formation of tumor microenvironment
    Yue Zheng, Xiaofeng Yang · 2022 · Bioscience Reports
  59. An information theoretic approach to detecting spatially varying genes
    Daniel C. Jones, Patrick J. Danaher, Young‐Mi Kim, Joseph Beechem, Raphaël Gottardo, Evan William Newell · 2023 · Cell Reports Methods
  60. Bioinformatics in urology — molecular characterization of pathophysiology and response to treatment
    Ali Hashemi Gheinani, Jina Kim, Sungyong You, Rosalyn M. Adam · 2023 · Nature Reviews Urology
  61. SGCAST: symmetric graph convolutional auto-encoder for scalable and accurate study of spatial transcriptomics
    Jinzhao Li, Jiong Wang, Zhixiang Lin · 2023 · Briefings in Bioinformatics
  62. A comprehensive study on the longissius dorsi muscle of Ashdan yaks under different feeding regimes based on transcriptomic and metabolomic analyses
    Tong Wang, Xiaoming Ma, Qingbo Zheng, Chaofan Ma, Zhilong Zhang, Heping Pan, Xian Guo, Xiaoyun Wu, Min Chu, Chunnian Liang et al. · 2024 · Animal Biotechnology
  63. Bayesian Integrative Region Segmentation in Spatially Resolved Transcriptomic Studies
    Yinqiao Yan, Xiangyu Luo · 2024 · Journal of the American Statistical Association
  64. A review of recent advances in spatially resolved transcriptomics data analysis
    Yue Gao, Ying-Lian Gao, Jing Jing, Feng Li, Chun-Hou Zheng, Jin‐Xing Liu · 2024 · Neurocomputing
  65. Next‐generation spatial transcriptomics: unleashing the power to gear up translational oncology
    Nan Wang, Weifeng Hong, Yixing Wu, Zhe‐Sheng Chen, Minghua Bai, Weixin Wang, Ji Ye Zhu · 2024 · MedComm
  66. Spatial resolved transcriptomics: Computational insights into gene transcription across tissue and organ architecture in diverse applications
    Zhen Miao, Tian Tian, Wei Chen, Qianwen Wang, Liang Ma, Dan Zhang, Min Xie, Zijin Yu, Xiya Guo, Genxiang Bai et al. · 2024 · The Innovation Life
  67. BayeSMART: Bayesian clustering of multi-sample spatially resolved transcriptomics data
    Yanghong Guo, Bencong Zhu, Chen Tang, Ruichen Rong, Ying Ma, Guanghua Xiao, Lin Xu, Qiwei Li · 2024 · Briefings in Bioinformatics
  68. RETRACTED ARTICLE: Lung cell cancer identification mechanism using deep learning approach
    Shalini Vaibhav Wankhade, S. Vigneshwari · 2023 · Soft Computing · Retracted
  69. Monkeybread: A Python toolkit for the analysis of cellular niches in single-cell resolution spatial transcriptomics data
    Matthew N. Bernstein, Dillon Scott, Cynthia C. Hession, Tim O. Nieuwenhuis, Jacqueline S. Gerritsen, Siamak Tabrizi, Vandana Nandivada, Matthew A. Huggins, Meixue Duan, Shruti Malu et al. · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  70. A contrastive learning approach to integrate spatial transcriptomics and histological images
    Yu Lin, Yanchun Liang, Duolin Wang, Yuzhou Chang, Qin Ma, Yan Wang, Fei He, Dong He Xu · 2024 · Computational and Structural Biotechnology Journal
  71. HyperGCN: an effective deep representation learning framework for the integrative analysis of spatial transcriptomics data
    Yuanyuan Ma, Lifang Liu, Yongbiao Zhao, Bo Hang, Yanduo Zhang · 2024 · BMC Genomics
  72. Deep clustering representation of spatially resolved transcriptomics data using multi-view variational graph auto-encoders with consensus clustering
    Jinyun Niu, Fangfang Zhu, Taosheng Xu, Shunfang Wang, Wenwen Min · 2024 · Computational and Structural Biotechnology Journal
  73. Single-cell spatial (scs) omics: Recent developments in data analysis
    José Camacho, Michael Armstrong, Luz García, Caridad Díaz, Carolina Gómez‐Llorente · 2024 · TrAC Trends in Analytical Chemistry
  74. SpaFusion: A multi-level fusion model for clustering spatial multi-omics data
    Fuqun Chen, Guangchang Cai, Ying Li, Le Ou-Yang · 2025 · Information Fusion
  75. spCLUE: a contrastive learning approach to unified spatial transcriptomics analysis across single-slice and multi-slice data
    Xiang Wang, Wei Vivian Li, Hongwei Li · 2025 · Genome biology
  76. Across the space: applications of spatial transcriptomic technology in healthy and diseased muscle
    Laura Virtanen, Chiara D’Ercole, Lorenzo Giordani · 2025 · Frontiers in Cell and Developmental Biology
  77. Spatial transcriptomics: integrating platforms and computational approaches for clinical insights
    Wei Song, Duo Wang, Jinming Li, Rui Zhang · 2025 · Biotechnology Advances
  78. The interpretable multimodal dimension reduction framework SpaHDmap enhances resolution in spatial transcriptomics
    Junjie Tang, Zihao Chen, Kun Qian, Siyuan Huang, Yang He, Shenyi Yin, Xinyu He, Buqing Ye, YAN ZHUANG, Hongxue Meng et al. · 2026 · Nature Cell Biology
  79. Optimization-based decoding of Imaging Spatial Transcriptomics data
    John P Bryan, Loïc Binan, Cai McCann, Yonina C. Eldar, Samouil L. Farhi, Brian Cleary · 2023 · Bioinformatics
  80. Systematic evaluation with practical guidelines for single-cell and spatially resolved transcriptomics data simulation under multiple scenarios
    Hongrui Duo, Yinghong Li, Lan Yang, Jingxin Tao, Qingxia Yang, Yingxue Xiao, Jing Sun, Lei Li, Xiner Nie, Xiaoxi Zhang et al. · 2024 · Genome biology
  81. Recovering single-cell expression profiles from spatial transcriptomics with scResolve
    Hao Chen, Young Je Lee, José Antonio Ovando-Ricárdez, Lorena Rosas, Mauricio Rojas, Ana Lucia Mora, Ziv Bar‐Joseph, Jose Lugo-Martinez · 2024 · Cell Reports Methods
  82. Chrysalis: decoding tissue compartments in spatial transcriptomics with archetypal analysis
    Demeter Túrós, Jelica Vasiljević, Kerstin Hahn, Sven Rottenberg, Alberto Valdeolivas · 2024 · Communications Biology
  83. Precise gene expression deconvolution in spatial transcriptomics with STged
    Jia-Juan Tu, Hong Yan, Xiao-Fei Zhang, Zhixiang Lin · 2025 · Nucleic Acids Research
  84. A Study on the Construction of Translation Curriculum System for English Majors from the Perspective of Human-Computer Interaction
    Li Qi · 2022 · Advances in Multimedia
  85. Characterization of spatial homogeneous regions in tissues with concordex
    Kayla C. Jackson, A. Sina Booeshaghi, Ángel Gálvez-Merchán, Lambda Moses, Tara Chari, Alexandra Kim, Orhan Hosten-Mittermaier, Lior S. Pachter · 2026 · BMC Methods
  86. Hexagonal Convolutional Neural Network for Spatial Transcriptomics Classification
    Jing Gao, Fa Zhang, Kai Hu, Xuefeng Cui · 2022 · IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
  87. Towards a universal spatial molecular atlas of the mouse brain
    Yichun He, Hao Sheng, Hailing Shi, Wendy Xueyi Wang, Zefang Tang, Jia Liu B, Xiao Wang · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  88. Dimensionality Reduction and Denoising of Spatial Transcriptomics Data Using Dual-Channel Masked Graph Autoencoder
    Wenwen Min, Donghai Fang, Jinyu Chen, Shihua Zhang · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  89. Enhancing spatial domain detection in spatial transcriptomics with EnSDD
    Hui-Sheng Li, Yuting Tan, Xiao-Fei Zhang · 2024 · Communications Biology
  90. Machine learning approaches for spatial omics data analysis in digital pathology: tools and applications in genitourinary oncology
    Hojung Kim, Jina Kim, Su Yeon Yeon, Sungyong You · 2024 · Frontiers in Oncology
  91. Spatial Transcriptomics to Study Virus-Host Interactions
    Chase Holdener, Shaowen Jiang, Danica M. Sutherland, Kira A. Griswold, Terence S. Dermody, John S. L. Parker, Iwijn De Vlaminck · 2025 · Annual Review of Virology
  92. GASTON-Mix: a unified model of spatial gradients and domains using spatial mixture-of-experts
    Uthsav Chitra, Shu Dan, Fenna M. Krienen, Benjamin J. Raphael · 2025 · Bioinformatics
  93. DisConST: Distribution-aware Contrastive Learning for Spatial Domain Identification
    Peimeng Zhen, Xiaofeng Wang, Han Shu, Jialu Hu, Yongtian Wang, Jiajie Peng, Xuequn Shang, Jing Chen, Tao Wang · 2025 · Genomics Proteomics & Bioinformatics
  94. scBSP: a fast and accurate tool for identifying spatially variable features from high-resolution spatial omics data
    Jinpu Li, Mauminah Raina, Yiqing Wang, Chunhui Xu, Li Su, Qi Guo, Ricardo Melo Ferreira, Michael T. Eadon, Qin Ma, Juexin Wang et al. · 2025 · Bioinformatics
  95. Spatially resolving cancer: from cell states to therapy
    Guangsheng Pei, Yang Liu, Linghua Wang · 2025 · Trends in cancer
  96. Spatial transcriptomics and artificial intelligence: a scoping review of emerging applications in head and neck pathology
    Najwa Yousef, Wenshan Wu, Shahd A. Alajaji, Akshya Mahadevan, Ahmed S. Sultan, Erin K. Molloy, Joe T. Nguyen · 2026 · Head and Neck Pathology
  97. Multi-omics biomarkers in female fertility: from oocyte quality to endometrial receptivity and clinical translation
    Xue Liu, Chengli Bin, Qifeng Gao, Maoya Li, Lu Xue, Zehui Zhou, Min Liu, Xiaoli Ji, Shaobin Wei · 2026 · Biomarker Research
  98. SMART: spatial multi-omic aggregation using graph neural networks and metric learning
    Zhihua Du, Qiyi Chen, Weiliang Huang, Jinmiao Chen, Xubin Zheng · 2026 · Nature Communications
  99. SmartGate is a spatial metabolomics tool for resolving tissue structures
    Kaixuan Xiao, Yu Wang, Kangning Dong, Shihua Zhang · 2023 · Briefings in Bioinformatics
  100. Spatial and single-nucleus transcriptomics decoding the molecular landscape and cellular organization of avian optic tectum
    Kuo Liao, Ya Xiang, Fubaoqian Huang, Maolin Huang, Wenbo Xu, Youning Lin, Pingfang Liao, Zishi Wang, Lin Yang, Xinmao Tian et al. · 2024 · iScience