SpatialDE: identification of spatially variable genes

Svensson, Valentine, Teichmann, Sarah A, Stegle, Oliver·2018·Nature Methods

Cited by (710)

Items 401–500 of 710

  1. Sprod for De-noising Spatial Transcriptomics Data Based on Position and Image Information
    Yunguan Wang, Bing Song, Shidan Wang, Mingyi Chen, Yang Xie, Guanghua Xiao, Li Wang, Tao Wang · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
  2. SpatialCorr: Identifying Gene Sets with Spatially Varying Correlation Structure
    Matthew N. Bernstein, Zijian Ni, A. Krishna Prasad, Jared Brown, Chitrasen Mohanty, Ron M. Stewart, Michael A. Newton, Christina M. Kendziorski · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  3. Reconstruction of the cell pseudo-space from single-cell RNA sequencing data with scSpace
    Jie Liao, Jingyang Qian, Ziqi Liu, Ying Chi, Yanrong Zheng, Xin Shao, Junyun Cheng, Yongjin Cui, Wenbo Guo, Penghui Yang et al. · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  4. Spatial omics representation and functional tissue module inference using graph Fourier transform
    Yuzhou Chang, Jixin Liu, Anjun Ma, Sizun Jiang, Jordan Edward Krull, Yao Yu Yeo, Yang Liu, Scott J. Rodig, Dan H. Barouch, Rong Fan et al. · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  5. Integrating Image and Molecular Profiles for Spatial Transcriptomics Analysis
    Xi Jiang, Shidan Wang, Lei Guo, Zhuoyu Wen, Liwei Jia, Lin Xu, Guanghua Xiao, Qiwei Li · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  6. SIMVI reveals intrinsic and spatial-induced states in spatial omics data
    Mingze Dong, David G. Su, Harriet M. Kluger, Rong Fan, Yuval Kluger · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  7. Identifying spatially variable genes by projecting to morphologically relevant curves
    Phillip B. Nicol, Rong Ma, Rosalind J. Xu, Jeffrey R. Moffitt, Rafael A. Irizarry · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  8. MOSAIC: Intra-tumoral heterogeneity characterization through large-scale spatial and cell-resolved multi-omics profiling
    Caroline Hoffmann · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  9. Mapping spatial gradients in spatial transcriptomics data with score matching
    Ao Wang, Donald Geman, Uthsav Chitra, Laurent Younes B · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  10. Discrete Representation Learning for Modeling Imaging-based Spatial Transcriptomics Data
    Dig Vijay Kumar Yarlagadda, Joan Massagué, Christina S. Leslie · 2023 · IEEE International Conference on Computer Vision Workshops
  11. Artificial Intelligence-Powered Insights into Polyclonality and Tumor Evolution
    Hong Zhao, Trey E. Ideker, Stephen T. C. Wong · 2025 · Research
  12. Spatial multi-omics technologies and applications in cancer
    Lulin Ji · 2025 · Biosystems
  13. SEPAR enables spatial metagene discovery and associated molecular pattern characterization in spatial transcriptomics and multi-omics datasets
    Lei Zhang, Ying Zhu, Shuqin Zhang · 2025 · Communications Biology
  14. Differential expression analysis for spatially correlated data using smiDE
    Ana Gabriela Vasconcelos, Daniel McGuire, Noah Simon, Patrick J. Danaher, Ali Shojaie · 2026 · Genome biology
  15. Decoding immunotherapy response through computational modeling
    Bingrui Li, Ruihan Luo, Kexin Huang, Jiajia Liu, Weiling Zhao, Xiaobo Zhou · 2026 · Nature Communications
  16. Integrative spatial multi-omics reveals the tumor ecosystem: From mechanistic insights to therapeutic strategies
    Wenqiao Chang, Wen Zhang, Kening Li, Ping Huang · 2026 · iScience
  17. Joint Bayesian estimation of cell dependence and gene associations in spatially resolved transcriptomic data
    Arhit Chakrabarti, Yang Ni, Bani K. Mallick · 2024 · Scientific Reports
  18. Mapping the gene space at single-cell resolution with gene signal pattern analysis
    Aarthi Venkat, Sam Leone, Scott E. Youlten, Eric Fagerberg, John Attanasio, Nikhil S. Joshi, Michael Perlmutter, Smita Krishnaswamy · 2024 · Nature Computational Science
  19. Relation equivariant graph neural networks to explore the mosaic-like tissue architecture of kidney diseases on spatially resolved transcriptomics
    Mauminah Raina, Hao Cheng, Ricardo Melo Ferreira, Treyden Stansfield, Chandrima Modak, Ying‐Hua Cheng, Hari Naga Sai Kiran Suryadevara, Dong He Xu, Michael T. Eadon, Qin Ma et al. · 2025 · Bioinformatics
  20. ST-deconv: an accurate deconvolution approach for spatial transcriptome data utilizing self-encoding and contrastive learning
    Shurui Dai, Jiawei Li, Zhiliang Xia, Jingfeng Ou, Yan Ping Guo, Limin Jiang, Jijun Tang · 2025 · NAR Genomics and Bioinformatics
  21. PreTSA: computationally efficient modeling of temporal and spatial gene expression patterns
    Haotian Zhuang, Zhicheng Ji · 2026 · Genome biology
  22. Sampling and ranking spatial transcriptomics data embeddings to identify tissue architecture
    Yu Lin, Yan Wang, Yanchun Liang, Yang Yu, Jingyi Li, Qin Ma, Fei He, Dong He Xu · 2022 · Frontiers in Genetics
  23. An improved rhythmicity analysis method using Gaussian Processes detects cell-density dependent circadian oscillations in stem cells
    Shabnam Sahay, Shishir Adhikari, Sahand Hormoz, Shaon Chakrabarti · 2023 · Bioinformatics
  24. Decoding spatial transcriptomics: Current trends and future prospects in data analysis methodologies
    Runze Li, Xu Chen, Xuerui Yang · 2024 · Chinese Science Bulletin (Chinese Version)
  25. STAREG: Statistical replicability analysis of high throughput experiments with applications to spatial transcriptomic studies
    Yan Li, Xiang Zhou, Rui Chen, Xianyang Zhang, Hongyuan Cao · 2024 · PLoS Genetics
  26. A robust statistical approach for finding informative spatially associated pathways
    Leqi Tian, Jiashun Xiao, Tianwei Yu · 2024 · Briefings in Bioinformatics
  27. An Overview of Spatial Transcriptomics Methodologies in Traversing the Biological System
    Akhansha John, Saranya Nallusamy, N. Senthil, Bharathi Nathan, Anandhi Venugopal, Hema Bharathi Chinnaswamy · 2025 · Current Bioinformatics
  28. An accessible, interactive GenePattern Notebook for analysis and exploration of single-cell transcriptomic data
    Clarence K. Mah, Alexander T. Wenzel, Edwin F. Juarez, Thorin T. Tabor, Michael M. Reich, Jill P. Mesirov · 2019 · F1000Research
  29. Moore's Law in Single Cell Transcriptomics
    Valentine Svensson, Roser Vento‐Tormo, Sarah Amalia Teichmann · 2017 · arXiv (Cornell University)
  30. Position-informed contrastive learning for spatially resolved omics deciphers hierarchical tissue structure at both cellular and niche levels
    Meng Yang, Yue Wang, Xingmin Liu, Haiping Huang, Linqi Lan, Ming An Ni, Yuchen Han, Huanming Yang, Feng Mu · 2022 · Research Square
  31. Spatial Transcriptomics Arena (STAr): an Integrated Platform for Spatial Transcriptomics Methodology Research
    Xi Jiang, Danni Luo, Esteban Fernández, Jie Yang, Huimin Li, Kevin W. Jin, Yuanchun Zhan, Bo Yao, Suhana Bedi, Guanghua Xiao et al. · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  32. Dimension-agnostic and granularity-based spatially variable gene identification
    Juexin Wang, Jinpu Li, Skyler T. Kramer, Li Su, Yuzhou Chang, Chunhui Xu, Qin Ma, Dong He Xu · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  33. Automated Integration of Multi-Slice Spatial Transcriptomics Data in 2D and 3D
    Denis Bienroth, Natalie Charitakis, Dillon Wong, Sabrina Jaeger-Honz, Dimitar Garkov, Kevin I. Watt, Julian S. Stolper, Hazel Chambers-Smith, Duncan P MacGregor, Bronwyn Christiansen et al. · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  34. STAREG: an empirical Bayesian approach to detect replicable spatially variable genes in spatial transcriptomic studies
    Yan Li, Xiang Zhou, Rui Chen, Xianyang Zhang, Hongyuan Cao · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  35. Spatial IMIX: A Mixture Model Approach to Spatially Correlated Multi-Omics Data Integration
    Ziqiao Wang, Bogdan A. Czerniak, Peng Wei · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  36. Identification of perturbation-responsive regions and genes in comparative spatial transcriptomics atlases
    Alan Yue Yang Teo, Matthieu Gautier, Laurent Pierre Brock, Jennifer Tsai, Alexandra de Coucy, Achilleas Laskaratos, Nicola Regazzi, Quentin Barraud, Michael V. Sofroniew, Mark A. Anderson et al. · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  37. Accounting for Spatial Correlation in Graphical Analysis of Spatial Transcriptomics Data
    Ana Gabriela Vasconcelos, Patrick J. Danaher, Daniel McGuire, Jon Wakefield, Ali Shojaie · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  38. A comparative study of statistical methods for identifying differentially expressed genes in spatial transcriptomics
    Wang, Yishan, Zang, Chenxuan, Li, Ziyi, Guo, Charles C., Lai, Dejian, Wei, Peng · 2026 · PLOS Computational Biology
  39. SMORE: spatial motifs reveal patterns in cellular architecture of complex tissues
    Zainalabedin Samadi, Kai Hao, Amjad Askary · 2025 · Genome biology
  40. Spatial transcriptomics iterative hierarchical clustering (stIHC): A novel method for identifying spatial gene co‐expression modules
    Catherine Higgins, Jingyi Jessica Li, Michelle Carey · 2025 · Quantitative Biology
  41. SPaSE: Spatially resolved pathology scores using optimal transport on spatial transcriptomics data
    Mohammad Nuwaisir Rahman, Mohammed Abid Abrar, Vikram R. Shaw, James F. Martin, M. Saifur Rahman, Md. Abul Hassan Samee · 2025 · Cell Systems
  42. Immuno-laser capture microdissection of perfusion-fixed mouse brain tissue coupled to RNA-seq
    Shujun Ge, Wenqi Gan, Keaton S. Karlinsey, Beiyan Zhou, Joel S. Pachter · 2025 · Journal of Neuroscience Methods
  43. MuST: multiple-modality structure transformation for single-cell spatial transcriptomics
    Zelin Zang, Liangyu Li, Yongjie Xu, Chenrui Duan, Yue Shen, Yi Sun, Zhen Lei, Stan Ziqing Li · 2025 · Briefings in Bioinformatics
  44. Accurately Predicting Cell Type Abundance from Spatial Histology Image Through HPCell
    Yongkang Zhao, Youyang Li, Weijiang Yu, Hongyu Zhang, Zheng Wang, Yuedong Yang, Yuansong Zeng · 2025 · Interdisciplinary Sciences Computational Life Sciences
  45. SpNeigh: spatial neighborhood and differential expression analysis for high-resolution spatial transcriptomics
    Jinming Cheng, Pierce K. H. Chow, Nan Liu · 2026 · NAR Genomics and Bioinformatics
  46. STcompare: comparative spatial transcriptomics data analysis of structurally matched tissues to characterize differentially spatially patterned genes
    Kalen Clifton, Vivien Jiang, Rafael dos Santos Peixoto, Srujan Singh, Ryo Matsuura, Hamid Rabb, Jean Fan · 2026 · Bioinformatics
  47. The Evolution of Spatial Omics Technologies Introduces A Novel Avenue for Lung Cancer Research
    Yue He (何越), Zifan Li, Wenxiang Wang (王文香), Xu Liu, Shanshan Lu, Jing Bai (白晶), Lin Weng, Qingna Zhang, Jun Wang, Kezhong Chen · 2026 · Genomics Proteomics & Bioinformatics
  48. The applications of single-cell and spatial transcriptomics in neuroscience and brain disorders
    Qingzhong Wang, Yogesh Dwivedi · 2026 · Neuroscience & Biobehavioral Reviews
  49. MLN2SVG: domain-aware spatially variable gene detection using contrastive variational autoencoder and multi-level neighbor search
    Shabir Hussain, Muhammad Ayoub, Fei Ye, Xiao Liu · 2026 · Briefings in Bioinformatics
  50. 3D multi-omics tumour atlases: from technology to biology and clinical translation
    Miao Liu, Jorge I. Villazon, André Forjaz, Xiaolong Tian, Rong Fan, Siyuan Wang, Lingyan Shi, Denis Wirtz, Ashley L. Kiemen · 2026 · Nature reviews. Cancer
  51. GRIDGENE: Guided Region Identification based on Density of GENEs—a transcript density-based approach to characterize tissues by spatial transcriptomics
    Ana Marta Sequeira, Marieke E. Ijsselsteijn, M Rocha, Jessica P Roelands, Noel F.C.C. de Miranda · 2026 · Bioinformatics Advances
  52. Spatial isoform sequencing at single-cell resolution reveals cell-type-specific spatial isoform variability in multiple brain cell types
    Lieke Michielsen, Andrey D. Prjibelski, Careen Foord, Yelizaveta Spiegelman, Taewoo Kim, Wen Hu, Julien Jarroux, Justine Hsu, Rebecca Pfeil, Xinyi Zhang et al. · 2026 · Nature Methods
  53. Decoding cell–cell communication in spatial transcriptomics: mechanistic insights, modeling constraints, and analytical caveats
    Yuesong Wu, Haohao Su, Yuehua Cui · 2026 · Briefings in Bioinformatics
  54. Advances in single-cell epigenomics of the immune system
    Jonas Schulte-Schrepping, Humberto J. Ferreira, Adem Saglam, Emily R. Hinkley, Joachim Ludwig Schultze · 2020 · Elsevier eBooks
  55. Bayesian hidden mark interaction model for detecting spatially variable genes in imaging-based spatially resolved transcriptomics data
    Jie Yang, Xi Jiang, Kevin W. Jin, Sunyoung Shin, Qiwei Li · 2024 · Frontiers in Genetics
  56. Detecting significant expression patterns in single-cell and spatial transcriptomics with a flexible computational approach
    Hadas Biran, Tamar Hashimshony, Tamar Lahav, Or Efrat, Yael Mandel‐Gutfreund, Zohar Yakhini B · 2024 · Scientific Reports
  57. MVCLST: A spatial transcriptome data analysis pipeline for cell type classification based on multi-view comparative learning
    Wei Peng, Zhihao Zhang, Wei Dai, Zhihao Ping, Xiaodong Fu, Li Liu, Lijun Liu, Ning Yu · 2024 · Methods
  58. GAADE: identification spatially variable genes based on adaptive graph attention network
    Tianjiao Zhang, Hao Sun, Zhenao Wu, Zhongqian Zhao, Xingjie Zhao, Hongfei Zhang, Bo Gao, Guohua Wang · 2024 · Briefings in Bioinformatics
  59. Fast and reliable confidence intervals for a variance component
    Yiqiao Zhang, Karl Oskar Ekvall, Aaron J. Molstad · 2025 · Biometrika
  60. CeiTEA: Adaptive Hierarchy of Single Cells with Topological Entropy
    Bowen Tan, Shiying Li, Mengbo Wang, Shuai Cheng Li · 2025 · Advanced Science
  61. Bayesian nonparametric clustering with feature selection for spatially resolved transcriptomics data
    Bencong Zhu, Guanyu Hu, Lin Xu, Xiaodan Fan, Qiwei Li · 2025 · The Annals of Applied Statistics
  62. SC2Spa: a deep learning based approach to map transcriptome to spatial origins at cellular resolution
    Linbu Liao, Esha Madan, António M. Palma, Hyobin Kim, Amit Kumar, Praveen Bhoopathi, Robert A. Winn, Jose Trevino, Paul B. Fisher, Cord Brakebusch et al. · 2025 · BMC Bioinformatics
  63. Anomaly detection in spatial transcriptomics via spatially localized density comparison
    Gary Hu, Julian Gold, Uthsav Chitra, Sunay Joshi, Benjamin J. Raphael · 2025 · Bioinformatics
  64. SPACE: Spatially variable gene clustering adjusting for cell type effect for improved spatial domain detection
    Sikta Das Adhikari, Nina G. Steele, Brian K. Theisen, Jianrong Wang, Yuehua Cui · 2025 · Nucleic Acids Research
  65. Single‐Cell Mitochondrial Lineage Tracing Decodes Fate Decision and Spatial Clonal Architecture in Human Hematopoietic Organoids
    Yan Xue, Junhao Su, Yiming Chao, Lu Liu, Xinyi Lin, Yang Xiang, Mun Kay Ho, Zezhuo Su, Junyi Chen, Zhuojuan Luo et al. · 2026 · Advanced Science
  66. Finding structure in gene expression
    Darren J. Burgess · 2018 · Nature Reviews Genetics
  67. Bioinformatics approach to spatially resolved transcriptomics
    Ivan Krešimir Lukić · 2021 · Emerging Topics in Life Sciences
  68. Automatic estimation of spatial spectra via smoothing splines
    Shibin Zhang · 2021 · Computational Statistics
  69. Defining the microenvironment landscape of bladder cancer using highly multiplexed spatial genomic and proteomic analysis
    Jason Reeves, Zhaojie Zhang, Zachary K. Norgaard, Denise M Zhou, Jingjing Gong, Yan Liang, Subhasree Das, Sarah E. Warren, Manav Korpal, Margaret L. Hoang et al. · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
  70. SpaCeNet: Spatial Cellular Networks from omics data
    Stefan Schrod, Niklas Lück, Robert Lohmayer, Stefan Solbrig, Dennis Voelkl, Tina Wipfler, Katherine Hoff Shutta, Marouen Ben Guebila, Andreas Schäfer, Tim Beißbarth et al. · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  71. Methodology for inference of intercellular gene interactions
    Saurabh Modi, Ryan Zurakowski, Jason P. Gleghorn · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  72. Spatial Patterning Analysis of Cellular Ensembles (SPACE) discovers complex spatial organization at the cell and tissue levels
    Edward C. Schrom, Erin McCaffrey, Vivek Sreejithkumar, Andrea J. Radtke, Hiroshi Ichise, Armando Arroyo-Mejías, Emily E. Speranza, Leanne Arakkal, Nishant Thakur, Spencer M. Grant et al. · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  73. EnrichMap: Spatially informed enrichment analysis for functional interpretation of spatial transcriptomics
    Cenk Celik, Maria Secrier · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  74. From features to slice: parameter-cloud modeling of spatial transcriptomics for simulation and 3D interpolatory augmentation
    Yiru Chen, Manfei Xie, Yunfei Hu, Weiman Yuan, Hirak Sarkar, Bingshan Li, Lu Zhang, Xin Zhou · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  75. ChatSpatial: Schema-Enforced Agentic Orchestration for Reproducible and Cross-Platform Spatial Transcriptomics
    Chen Yang, Xianyang Zhang, Jun Chen · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  76. Statistical analysis of spatially resolved transcriptomic data by incorporating multiomics auxiliary information
    Yan Li, Xiang Zhou, Hongyuan Cao · 2022 · Genetics
  77. High-definition CODEX for 3D multiplex spatial cell phenotyping
    Thomas Hu, Nicholas Y. Zhang, Mythreye Venkatesan, Christian M. Schürch, Garry P. Nolan, Ahmet F. Coskun · 2024 · Elsevier eBooks
  78. Current computational methods for spatial transcriptomics in cancer biology
    Jaewoo Mo, J. Bae, Jahanzeb Saqib, Dohyun Hwang, Yunjung Jin, B. J. Park, Jeongbin Park, Junil Kim · 2024 · Advances in cancer research
  79. Homebuilt Imaging-Based Spatial Transcriptomics: Tertiary Lymphoid Structures as a Case Example
    Thomas Defard, Auxence Desrentes, Charles Fouillade, Florian Mueller · 2024 · Methods in molecular biology
  80. SciGeneX: enhancing transcriptional analysis through gene module detection in single-cell and spatial transcriptomics data
    Julie Bavais, Jessica Chevallier, Lionel Spinelli, Serge A. van de Pavert, Denis Puthier · 2025 · NAR Genomics and Bioinformatics
  81. DESpace2: detection of differential spatial patterns in spatial omics data
    Peiying Cai, Mark D. Robinson, Simone Tiberi · 2026 · Bioinformatics
  82. Cluster-independent multiscale marker identification in single-cell RNA-seq data using localized marker detector (LMD)
    Ruiqi Li, Rihao Qu, Fabio Parisi, Francesco Strino, Hainan Lam, Jay S. Stanley, Xiuyuan Cheng, Peggy S. Myung, Yuval Kluger · 2025 · Communications Biology
  83. Spatialsmooth: a spatially-aware convolutional autoencoder framework for enhanced deconvolution of spatial transcriptomics data
    Xiao Jing Yang, Jinjin Xiang, Yanbin Feng, Yanfang Zhao, Huamei Li, Xiaozhou Chen · 2025 · BMC Genomics
  84. jsPCA: fast, scalable, and interpretable identification of spatial domains and variable genes across multi-slice and multi-sample spatial transcriptomics data
    Ines Assali, Paul Escande, Franck Picard, Paul Villoutreix · 2026 · Bioinformatics Advances
  85. Advances in artificial intelligence for spatial transcriptomics in cancer: Special focus on Yin Yang 1 (YY1) and Raf kinase inhibitor protein (RKIP)
    Lekhya Dommalapati, Rachael E. Guenter, Yuvasri Golivi, Swapna Priya Ganji, Tatekalva Sandhya, Ganji Purnachandra Nagaraju, Madhu Sudhana Saddala · 2025 · Biochimica et Biophysica Acta (BBA) - Reviews on Cancer
  86. Integrating spatial omics with routine haematoxylin and eosin in formalin-fixed paraffin-embedded: a step-by-step clinical workflow
    Nasar Alwahaibi · 2025 · F1000Research
  87. Distance-Preserving Representations for Genomic Spatial Reconstruction
    Wenbin Zhou, Jin‐Hong Du · 2025 · IEEE Transactions on Computational Biology and Bioinformatics
  88. Lessons from 3D Reconstruction of Cancer
    Ashley L. Kiemen, Laura DeLong Wood · 2025 · Annual Review of Cancer Biology
  89. Spatial transcriptomic modeling of vascular remodeling in aortic aneurysm using integrated single-cell RNA sequencing analysis
    Shaodong Xiong, Ludong Liang, Tao Liu · 2025 · SLAS TECHNOLOGY
  90. Probabilistic-graph-based spatial context-aware framework for interpretable spatial omics denoising and augmentation
    Xuyang Qin, Chang Liu, Fei Gu, Xun Lan · 2025 · Briefings in Bioinformatics
  91. VST-DAVis: an R Shiny application and web-browser for spatial transcriptomics data analysis and visualization
    Jagadesan Sankarasubramanian, Chittibabu Guda · 2026 · Bioinformatics Advances
  92. A multimodal framework to identify molecular mechanisms driving patient group-associated morphology through the integration of spatial transcriptomics and whole slide imaging
    Reva Kulkarni, Avery Maddox, Sara Bailey, Arvind Rao · 2026 · npj Artificial Intelligence
  93. Integrating spatial omics with routine haematoxylin and eosin in formalin-fixed paraffin-embedded: a step-by-step clinical workflow
    Nasar Alwahaibi · 2026 · F1000Research
  94. Cellular-Resolution Reconstruction of Spatial Transcriptomics from Histology Images via Foundation Models and KANs
    R. Stephanie Huang, Leiming Fang, WenBing Li, Yuansong Zeng, Yuedong Yang · 2025 · IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
  95. A p63-dependent molecular switch directs epithelial fate to form a specialized seal at the tooth-gingiva interface
    Yu Liang, Jie Gao, Litian Han, Yao Zhou, Qianqian Li, Fei Pei, Zhi Chen, Fei Peng, Yufeng Zhang, Huan Liu · 2026 · Cell Reports
  96. In Silico Reconstruction of Primary and Metastatic Tumor Architecture Using Geographic Information System–Augmented Spatial Transcriptomics
    Jin Young Yoo, Sabrina Akter, Qianying Zuo, Matthew Rilloraza, Amir Kazemi, Wenjun Wu, Mahima Goel, Audrey Lam, Debapriya Dutta, Betsy Barnick et al. · 2026 · Cancer Research
  97. Castl: robust identification of spatially variable genes in spatial transcriptomics via an ensemble-based framework
    Yiyi Yu, Jiyuan Yang, PING-AN HE, Xiaoqi Zheng · 2026 · Briefings in Bioinformatics
  98. BEASTsim—a benchmarking and analysis platform for spatial transcriptomics simulations
    Tomás Bordoy García-Carpintero, Lucas Dyssel, Kristóf Péter, Nikolaj F. H. Hansen, Lena J. Straßer, Chit Tong Lio, Merle Stahl, Markus List, Richard Röttger · 2026 · Briefings in Bioinformatics
  99. Mapping safety in space: the emerging role of spatial transcriptomics in safe drug development
    Athena E. Golfinos, Terry Van Vleet, Rebecca A. Kohnken, Prathap Kumar S. Mahalingaiah, Stacey Fossey, Wayne Buck, Wei Liang, Shuaib Ali Khan Mayana, Anik Tuladhar, Panuwat Trairatphisan et al. · 2026 · Frontiers in Toxicology
  100. Computational analysis in spatial transcriptomics: methods and perspectives
    Qin Zhou, Yi Jiang, Peifeng Ruan, Guanghua Xiao, Yang Xie · 2026 · Briefings in Bioinformatics