BANKSY unifies cell typing and tissue domain segmentation for scalable spatial omics data analysis

Cited by (284)

Items 101–200 of 284

1. SpatialFusion: A lightweight multimodal foundation model for pathway-informed spatial niche mapping
   Josephine Yates, Mitra Shavakhi, Toni K. Choueiri, Eliezer M. Van Allen, Caroline Uhler · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
2. Deciphering progressive lesion areas in breast cancer spatial transcriptomics via TGR-NMF
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3. CXCR4 and CXCR6 dually limit T cell entry into the polyomavirus-infected brain
   Kalynn M Alexander, Elia Afanasiev, Arrienne B. Butic, Ge Jin, Mofida Abdelmageed, Anirban Paul, Jo Anne Stratton, Aron E. Lukacher, Samantha A. Spencer · 2025 · Journal of Neuroinflammation
4. GraphCellNet: A deep learning method for integrated single-cell and spatial transcriptomic analysis with applications in development and disease
   Ruoyan Dai, Zhenghui Wang, Zhiwei Zhang, Lixin Lei, Mengqiu Wang, Kaitai Han, Zijun Wang, Zhenxing Li, Jirui Zhang, Qianjin Guo · 2025 · Journal of Molecular Medicine
5. Spatial2GWAS: a database for linking spatial transcriptomic regions with GWAS traits
   Xi Hu, Aoqi Wang, Huan Yu, Pora Kim, Xiaobo Zhou · 2025 · Nucleic Acids Research
6. A surgical window of opportunity trial evaluating the effect of the PCSK9 inhibitor evolocumab on tumoral MHC-I expression and CD8+ infiltration in glioma
   Kirit Singh, Matthew W. Foster, Marlene J. Violette, Anna M. Corcoran, Kelly M. Hotchkiss, Chelsea O. Railton, Emily E. Blandford, Kathryn E. Blethen, Elizabeth Louise Thomas, William C. McIntosh et al. · 2025 · Scientific Reports
7. SCALE: unsupervised multiscale domain identification in spatial omics data
   Behnam Yousefi, Darius P. Schaub, Robin Khatri, Nico Kaiser, Malte B. Kuehl, Cedric Ly, Victor G. Puelles, Tobias B Huber, Immo Prinz, Christian F. Krebs et al. · 2026 · Nucleic Acids Research
8. Robust characterization and interpretation of rare pathogenic cell populations from spatial omics using GARDEN
   Xinming Zhang, Zhuohan Yu, Gaoyang Hao, Qi Yao, Yanmei Hu, Fuzhou Wang, Xingjian Chen, Linjing Liu, Ka‐Chun Wong, Xiangtao Li · 2026 · Nature Communications
9. SpatialOne: end-to-end analysis of visium data at scale
   Mena Kamel, Amrut Sarangi, Pavel Senin, Sergio M. Villordo, Mathew Sunaal, Het Barot, Seqian Wang, Ana Solbas, Luis Cano, Marion Classe et al. · 2024 · Bioinformatics
10. SpaceBF: spatial coexpression analysis using Bayesian fused approaches in spatial omics datasets
    Souvik Seal, Brian Neelon · 2026 · GigaScience
11. Interpretable, flexible and spatially aware integration of multiple spatial transcriptomics datasets from diverse sources
    Jia Zhao, Xiangyu Zhang, Gefei Wang, Yingxin Lin, Tianyu Liu, Rui B. Chang, Hongyu Zhao · 2026 · Nature Genetics
12. Scalable Condition-relevant Cell Niche Analysis of Spatial Omics Data with Taichi
    Yan Cui, Zhiyuan Yuan · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
13. spacedeconv: deconvolution of tissue architecture from spatial transcriptomics
    Constantin Zackl, Maria Zopoglou, Reto Stauffer, Markus Außerhofer, Marieke E. Ijsselsteijn, Gregor Sturm, Noel F.C.C. de Miranda, Francesca Finotello · 2024 · Research Square
14. Mapping the spatial architecture of glioblastoma from core to edge delineates niche-specific tumor cell states and intercellular interactions
    Saad M. Khan, Anthony Z. Wang, Rupen R. Desai, Gyeong Dae Kim, Colin McCornack, Rui Sun, Sonika M Dahiya, Jennifer Ann Foltz, Ngima D. Sherpa, Katherine Xu et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
15. Characterizing spatial functional microniches with SpaceTravLR
    Koushul Ramjattun, Alyson Wang, Hannah J. Lee, Shilpi Giri, Yijia Chen, William A. MacDonald, Nathan D. Lord, Amanda C. Poholek, Youjin Lee, Jishnu Das · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
16. 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)
17. Kontextual reframes analysis of spatial omics data and reveals consistent cell relationships across images
    Farhan Ameen, Nick Robertson, David Ming Lin, Shila Ghazanfar, Ellis Patrick · 2025 · Cell Reports Methods
18. Scalable analysis of whole slide spatial proteomics with Harpy
    Benjamin Rombaut, Arne Defauw, Frank Vernaillen, Julien Mortier, Evelien Van Hamme, Sofie Van Gassen, Ruth Seurinck, Yvan Saeys · 2022 · Bioinformatics
19. Spatial transcriptomics in Alzheimer's disease: technologies, challenges and discoveries
    Christina Huan Shi, Juan Piña-Crespo, Kevin Y. Yip, Timothy Y. Huang · 2026 · Molecular Neurodegeneration Advances
20. Epiblast diversification and blood formation in a human pregastrula
    Zhenyu Xiao, Yandong Gong, Xiaomin Yang, Nannan He, Xinyuan Wang, Guoju You, Hanlin Zhu, Yingping Liang, Xinwei Xie, Baoqi Fang et al. · 2026 · Nature
21. Single-cell multiomics and chromatin structure reveal gene-regulatory dynamics in heart failure
    Yang Xie, Luca Tucciarone, Elie N. Farah, Lei Chang, Qian Yang, Thirupura Sundari Shankar, Weston S. Elison, Shaina Tran, Jovina Djulamsah, Anita Lie et al. · 2026 · Science
22. Spatial atlas of the human brain vasculature reveals specialized cell ensembles
    Jerry C. Wang, Damian Sanchez, Santhosh Arul, Belda Gülsuyu, Adnan Gopinadhan, Tanzila Mukhtar, Joseph Kim, John P. Andrews, Marcus A. C. Williams, Yewon Jung et al. · 2026 · Cell
23. STHD: probabilistic cell typing of single spots in whole transcriptome spatial data with high definition
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24. Spatially aware adjusted Rand index for evaluating spatial transcriptomics clustering
    Yinqiao Yan, Xiangnan Feng, Xiangyu Luo · 2025 · Biometrics
25. metsDB: a knowledgebase of cancer metastasis at bulk, single-cell and spatial levels
    Sijia Wu, Jiajin Zhang, Yanfei Wang, Xinyu Qin, Zhaocan Zhang, Zhennan Lu, Pora Kim, Xiaobo Zhou, Liyu Huang · 2024 · Nucleic Acids Research
26. SpaDCN: Deciphering Spatial Functional Landscape from Spatially Resolved Transcriptomics by Aligning Cell–Cell Communications
    Xuefeng Bai, Xinyu Bao, Chuanchao Zhang, Qianqian Shi, Luonan Chen · 2025 · Small Methods
27. Spatial mutual nearest neighbors for spatial transcriptomics data
    Haowen Zhou, Pratibha Panwar, Boyi Guo, Caleb Hallinan, Shila Ghazanfar, Stephanie C. Hicks · 2025 · Bioinformatics
28. Decoding Spatial Tissue Architecture: A Scalable Bayesian Topic Model for Multiplexed Imaging Analysis
    Xiyu Peng, James William Smithy, Mohammad Yosofvand, Caroline E. Kostrzewa, MaryLena Bleile, Fiona D. Ehrich, Jasme Lee, Michael Andrew Postow, Margaret K. Callahan, Katherine S. Panageas et al. · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
29. Oncogenic drivers shape the tumor microenvironment in human gliomas
    Bo Zhao, Chae Yun Cho, Lingqun Ye, Tula Keal, Thomas Mitchell, Inés Martín-Barrio, Christina Abi Faraj, M. Unal, Jessica Alsing, Nora M. Lawson et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
30. A Multimodal Spatial and Epigenomic Atlas of Human Adult Lung Topography
    Thu Elizabeth Duong, Dinh H. Diep, Kimberly Y. Conklin, Indy Bui, Jeffrey M. Purkerson, Eric Boone, Jacqueline Olness, Sahil Patel, Beverly F Peng, Colin Kern et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
31. Mapping spatially organized molecular and genetic signatures of schizophrenia across multiple scales in human prefrontal cortex
    Sang Ho Kwon, Boyi Guo, Cindy Fang, Madhavi Tippani, Svitlana V. Bach, Geo M. Pertea, Ryan A. Miller, Sarah E. Maguire, Artemis Iatrou, Nicholas J. Eagles et al. · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
32. Denoising spatially resolved transcriptomics with consistency of heterogeneous spatial coordinates, transcription, and morphology
    Haiyue Wang, Peng Gao, Shaoqing Feng, Xiaoke Ma · 2025 · Briefings in Bioinformatics
33. Cross-expression meta-analysis of mouse brain slices reveals coordinated gene expression across spatially adjacent cells
    Ameer Sarwar, Mara C.P. Rue, Leon French, Helen Cross, SARAH E. CHOI, Xiaoyin Chen, Jesse Gillis · 2025 · Genome biology
34. Vector-guided graph learning for spatial multi-slice multi-omics alignment
    Yikai Lou, Xuan Li, Qixing Yang, Hao Dai, Kaiyue Ma, Chunman Zuo · 2025 · Cell Reports Methods
35. Hypergraph-driven spatial multimodal fusion for precise domain delineation and tumor microenvironment decoding
    Chengyang Zhang, X. Li, Bo Li, Chenxun Deng, Mengran Li, Shiqi Zhang, Weijiang Yu, Hongyu Zhang, Zhengtao Wang, Yuedong Yang et al. · 2025 · Communications Biology
36. Multiscale domain identification for spatial transcriptomics via persistent homology
    Perry Beamer, Zixuan Cang · 2026 · Cell Reports Methods
37. Spatially resolved single-cell analyses of human meningioma identify novel cell states influencing tumor microenvironment and progression
    Alexander Landry, Leeor S. Yefet, Justin Z. Wang, Andrew A. Ajisebutu, Chloe Gui, Yosef Ellenbogen, Jeff Liu, Vikas Patil, Colleen Q. Ding, Qingxia Wei et al. · 2026 · Nature Genetics
38. Spatio-DARLIN enables robust and efficient in situ lineage tracing in mice at single-cell resolution
    Jianing Gao, Zhanhao Zhang, Daolong Chen, Sijie Diao, Simin Liu, Shou‐Wen Wang, Li Li · 2026 · Nature Methods
39. Decoding cell–cell communication in spatial transcriptomics: mechanistic insights, modeling constraints, and analytical caveats
    Yuesong Wu, Haohao Su, Yuehua Cui · 2026 · Briefings in Bioinformatics
40. BACT: nonparametric Bayesian cell typing for single-cell spatial transcriptomics data
    Yinqiao Yan, Xiangyu Luo · 2024 · Briefings in Bioinformatics
41. SPARROW reveals microenvironment-zone-specific cell states in healthy and diseased tissues
    Peiyao A Zhao, Ruoxin Li, Temi Adewunmi, Jessica Garber, Claire E. Gustafson, June Kim, Jocelin Malone, Adam K. Savage, Peter J. Skene, Xiaojun Li · 2025 · Cell Systems
42. Anomaly detection in spatial transcriptomics via spatially localized density comparison
    Gary Hu, Julian Gold, Uthsav Chitra, Sunay Joshi, Benjamin J. Raphael · 2025 · Bioinformatics
43. Dual probe ligation in situ hybridization with rolling-circle amplification for high-plex spatial transcriptomics
    Sarah E. Maguire, Joel J. Credle, Elizabeth Bertelson, Sunny Lee, Boyoung Cha, Dan Xie, Gregory Dale Kirk, Debjit Ray, Logan George, Aditya Suru et al. · 2025 · Biochemistry and Biophysics Reports
44. Co-fluctuations of genes in single cells predict transcriptome-wide outcomes to perturbations
    Benjamin Kuznets-Speck, Nitu Kumari, Irish Senthilkumar, Jaekwon Jung, Hector Manuel Lopez Rios, Leon Schwartz, Hanxiao Sun, Vidyesh Rao Anisetti, Changhu Wang, Qingyang Wang et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
45. GatorST: A Versatile Contrastive Meta-Learning Framework for Spatial Transcriptomic Data Analysis
    Song Wang, Yuxi Liu, Zhenhao Zhang, Qin Ma, Qianqian Song, Jiang Bian · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
46. Fibroblasts sense spatial proximity via an EGFR–CREB5 axis to restore quiescent synovial lining in remission rheumatoid arthritis
    Sonia Presti, Ksenia S. Anufrieva, Ce Gao, Sean A Prell, Kartik Bhamidipati, Vikram Khedgikar, PHILIP E. BLAZAR, Jeffrey K. Lange, Morgan H Jones, Michael B. Brenner et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
47. spaTransfer: transfer learning for single-cell and spatial transcriptomics data using non-negative matrix factorization
    Cindy Fang, Kelsey D. Montgomery, Sarah E. Maguire, Anthony D. Ramnauth, Boyi Guo, Ryan Miller, Joel E. Kleinman, Thomas M. Hyde, Keri Martinowich, Kristen R. Maynard et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
48. Single cell and spatial characterization of the human pancreas reveals drivers of beta cell dysfunction in cystic fibrosis
    Hannah M Mummey, Sierra Corban, Jacinta D. Lucero, Rebecca L. Melton, Madeleine Pittigher, Victoria C. Johnston, Gail H. Deutsch, Agnieszka D’Antonio‐Chronowska, Allen S. Wang, Rebecca L. Hull-Meichle et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
49. A lightweight, ultrafast and general embedding framework for large-scale spatial omics data
    Bingjie Dai, Yuchao Liang, Litai Yi, Pengwei Hu, Yancheng Song, Binzhi Qian, Miaoxia He, Linhui Wang, Zhiyuan Yuan, Yongchun Zuo · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
50. High-resolution spatial transcriptomics of adult and pediatric human liver with Visium HD
    Faizan Hasan, Rachel D. Edgar, Jawairia Atif, Diana Nakib, Cornelia E. Thoeni, Amanda Ricciuto, Blayne Amir Sayed, Ian D. McGilvray, Gary D. Bader, Sonya A. MacParland · 2026 · Scientific Data
51. Three dimensional reconstruction of the human nucleus accumbens reveals topographic organization and molecular heterogeneity of D1-islands across the anterior posterior axis
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52. A Robust Kernel‐Based Workflow for Niche Trajectory Analysis
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53. DESpace2: detection of differential spatial patterns in spatial omics data
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54. Kandinsky: Enabling neighbourhood analysis of spatial omics data for functional insights on cell ecosystems
    Pietro Andrei, Mariachiara Grieco, Amelia Acha‐Sagredo, Tommaso Becchi, Pawan Dhami, Kathy Fung, Manuel Rodriguez‐Justo, Matteo Cereda, Francesca D. Ciccarelli · 2026
55. ST-Community Detection Methods for Spatial Transcriptomics Data Analysis
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56. M‐STGCN: A Position‐Aware Multimodal Graph Convolutional Framework for Joint Spatial Domain Identification and Gene Expression Denoising
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57. scACAN: An Adaptive Learning Framework Aggregating Local Graph Structure Context for Rare Cell Type Identification
    Shijia Yan, Junliang Shang, Shoujia Jiang, Xiaohan Zhang, Fanyu Zhang, Yan Sun, Jinxing Liu · 2026 · Journal of Chemical Information and Modeling
58. HRCHY-CytoCommunity identifies hierarchical tissue organization in cell-type spatial maps
    Runzhi Xie, Zekun Wang, Jianrui Liu, Han Xu, Yafei Xu, Jiadong Lin, Yuxuan Hu, Lin Gao · 2026 · Nature Communications
59. AI-driven deciphering of cell niches with single-cell and spatial omics: a new perspective for traditional Chinese medicine research
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60. MSAGCN: Multi-Scale Adaptive Graph Convolutional Network for Integrative Analysis of Single-Cell Spatial Multi-Omics Data
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61. Single-cell spatial analysis stratifies lung adenocarcinoma with rare actionable mutations and reveals immune-modulatory cellular crosstalk
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62. Multimodal sequencing identifies synergistic mechanisms driving resistance to neoadjuvant nivolumab treatment in hepatocellular carcinoma
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63. Tissueformer: extending single-cell foundation models to predict population-level phenotypes
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64. Cerebrovascular vulnerability and fibrosis in human brain aneurysms
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65. Spatial architecture of autism pathogenesis reveals mosaic structural disarray during early development
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66. Gene expression profiling enables refined parcellation of cortical layers in the heterogeneous human cerebral cortex
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67. Cadmium Exposure and Osteoporosis: A Spatially Contextualized Adverse Outcome Pathway Integrating Epidemiology, Toxicogenomics and Transcriptomics
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68. Human and mouse adrenal glands are characterized by species-specific steroidogenic states and tissue turnover
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69. The spatial and single-cell landscape of skin: Charting the multiscale regulation of skin immune function
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70. A Meta-Review of Spatial Transcriptomics Analysis Software
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71. Spatial pattern enhanced cellular and tissue recognition for spatial transcriptomics
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72. SPARROW reveals cell states and functions influenced by microenvironment zones in complex tissues
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73. Single-cell and spatial atlas of steatotic liver disease-related hepatocellular carcinoma
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74. Spatially informed phenotyping by cyclic-in-situ-hybridization identifies novel fibroblast populations and their pathogenic niches in systemic sclerosis
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75. Guidestar: a spike-in approach to improve RNA detection accuracy in imaging-based spatial transcriptomics
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76. Spatial metabolomics reveals persistent localized niche-specific metabolic failure in kidneys following ischemia-reperfusion injury
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77. SimSpace: a comprehensive in-silico spatial omics data simulation and modeling framework
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78. Spatial Dependence and Heterogeneity in Molecular Imaging: Moran Quadrant Maps Enable Advanced Spatial-Statistical Analysis
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79. 4D multimodal wound healing atlas reveals organ-level controls of repair phase transitions
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80. SpatialBench : Comparative cross-platform benchmarking of high-resolution spatial transcriptomics using matched mouse lymphoid tissue
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81. A multimodal interrogation of Broca’s area in the pediatric and adult human brain
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82. A conserved population of genetically defined striatal neurons gates opioid reward
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83. Clustering laminar cytoarchitecture: in vivo parcellation based on cortical granularity
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84. VIB Hackathon on spatial omics tools and methods
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85. Evaluation of the microenvironment formed by interferon-β
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86. Energy-Regularized Graph Learning for Multiscale Spatial Representation
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87. Development of an Integrated Single-Cell and Spatial Transcriptomics Atlas of Healthy Human Skin Focusing on the Pilosebaceous Unit
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88. Preserving tissue structure through density-based spatial analysis with scider
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89. How to get the most out of your cancer spatial transcriptomics data
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90. CONCLAVE: CONsensus CLustering with Annotation-Validation Extrapolation for cyclic multiplexed immunofluorescence data
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91. Colorectal cancer relies on an immunosuppressive cellular topography and genomic adaptations for establishing brain metastases
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92. Tissue architecture and immune niches govern ctDNA release in colorectal cancer
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93. ClustSIGNAL identifies cell types and subtypes using an adaptive smoothing approach for scalable spatial omics clustering
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94. Biophysical simulation enables segmentation and nervous system atlas mapping for image first spatial omics
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95. DOMINO: graph diffusion learning identifies spatial domain structures with enhanced accuracy and scalability
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96. Additional file 1 of StaVia: spatially and temporally aware cartography with higher-order random walks for cell atlases
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97. Additional file 3 of Benchmarking clustering, alignment, and integration methods for spatial transcriptomics
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98. Additional file 2 of Benchmarking clustering, alignment, and integration methods for spatial transcriptomics
    Yunfei Hu, Manfei Xie, Li, Yikang, Mingxing Rao, Wenjun Shen, Can Luo, Haoran Qin, Jihoon Baek, Zhou, Xin Maizie · 2024 · Figshare
99. Additional file 2 of Multi-slice spatial transcriptome domain analysis with SpaDo
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100. Additional file 1 of Multi-slice spatial transcriptome domain analysis with SpaDo
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