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
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- Neurogenesis drives hippocampal formation-wide spatial transcription alterations in health and Alzheimer's diseaseZachery D. Morrissey, Pavan Kumar, Trongha Phan, Mark Maienschein‐Cline, Alex Leow, Orly Lazarov · 2025 · Frontiers in Dementia
- Bayesian nonparametric clustering with feature selection for spatially resolved transcriptomics dataBencong Zhu, Guanyu Hu, Lin Xu, Xiaodan Fan, Qiwei Li · 2025 · The Annals of Applied Statistics
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- Data enhancement in the age of spatial biologyLinbu Liao, Patrick C. N. Martin, Hyobin Kim, Sanaz Panahandeh, Kyoung‐Jae Won · 2024 · Advances in cancer research
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- AFSC: A self-supervised augmentation-free spatial clustering method based on contrastive learning for identifying spatial domainsRui Han, Xu Wang, Xuan Wang, Yadong Wang, Junyi Li · 2024 · Computational and Structural Biotechnology Journal
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- Protocol to boost the robustness and accuracy of spatial transcriptomics algorithms using ensemble techniquesJiazhang Cai, Shushan Wu, Huimin Cheng, Wenxuan Zhong, Guo‐Cheng Yuan, Ping Ma · 2025 · STAR Protocols
- Improved Spatial Transcriptomics Clustering with Nested Graph Neural NetworksAtishay Jain, David H. Laidlaw, Ying Ma, Ritambhara Singh · 2025 · ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB)
- A deep generative framework with embedded vector arithmetic and classifier for sample generation, label transfer, and clustering of single-cell dataLifei Wang, Rui Nie, Zhang Zhang, Weiwei Gu, Shuo Wang, Anqi Wang, Jiang Zhang, Jun Cai · 2023 · Cell Reports Methods
- Hexagonal image segmentation on spatially resolved transcriptomicsJing Gao, Kai Hu, Fa Zhang, Xuefeng Cui · 2023 · Methods
- Well-ST-seq: Cost-Effective and Near-Cellular Spatial Transcriptomics Using Deterministic Barcoded Bead ArraysNianzuo Yu, Zhengyang Jin, Shoujun Zhu, Zhiying Hu, Xiaoduo Tang, Chongyang Liang, Junhu Zhang, Bai Yang · 2026 · Analytical Chemistry
- Spatial Transcriptomics Arena (STAr): an Integrated Platform for Spatial Transcriptomics Methodology ResearchXi 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)
- DANCE 2.0: Transforming single-cell analysis from black box to transparent workflowJiayuan Ding, Zhijin XING, Yixin Wang, Renming Liu, Sheng Liu, Zhi Huang, Wenzhuo Tang, Yuying Xie, James Zou, Xiaojie Qiu et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
- Hypergraph Neural Networks Reveal Spatial Domains from Single-cell Transcriptomics DataMehrad Soltani, Luis Rueda · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
- Inferring spatial gene expression from tissue images using large-scale histology foundation model with SpaFoundationNing Zhang, Yahui Long, Sibo Xia, Pengzhen Jia, Yujie Jin, Siqi Chen, Jinmiao Chen, Min Li · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
- OmniCell: Unified Foundation Modelling of Single-Cell and Spatial Transcriptomics for Cellular and Molecular InsightsJiangshuan Pang, Ping Sun Qiu, Youzhe He, Yiting Deng, Wangyang Tang, Zhi Huang, Jing Yan, Baolong Li, Adi Lin, Lei Cao et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
- A lightweight, ultrafast and general embedding framework for large-scale spatial omics dataBingjie 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)
- Artificial Intelligence, Bioinformatics, and PathologyJoshua Levy, Yunrui Lu, Marietta K. Saldias Montivero, Ojas A. Ramwala, Jason R. McFadden, Carly Miles, Adam Gilbert Diamond, Ramya Reddy, Ram Reddy, Taylor R. Hudson et al. · 2022 · Advances in Molecular Pathology
- Cell Segmentation of in situ Transcriptomics Data Using Signed Graph PartitioningAxel Andersson, Andrea Beháňová, Carolina Wählby, Filip Malmberg · 2023 · Lecture notes in computer science
- STADS: Spatial Transcriptomics to Aid Drug-reposition RecommendationAbdullah Karaaslanli, Yijun Guo, Haodong Liang, Ziyin N. Huang, Lana Xia Garmire · 2023 · IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
- Current computational methods for spatial transcriptomics in cancer biologyJaewoo Mo, J. Bae, Jahanzeb Saqib, Dohyun Hwang, Yunjung Jin, B. J. Park, Jeongbin Park, Junil Kim · 2024 · Advances in cancer research
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- A Robust Kernel‐Based Workflow for Niche Trajectory AnalysisWen Wang, Sujung Crystal Shin, Joselyn Chávez, Guo‐Cheng Yuan · 2024 · Small Methods
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- DCMatch - Identify Matching Architectures in Deep Clustering Through Meta-learningMamdouh Aljoud, Gabriel Marques Tavares, Collin Leiber, Thomas Seidl · 2025 · Lecture notes in computer science
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- SURF: A Self‐Supervised Deep Learning Method for Reference‐Free Deconvolution in Spatial TranscriptomicsShuyu Liang, Zixia Zhou, Peng Huang, Junhu Fu, Jing Jiao, Yunxia Huang, Shichong Zhou, Guanlin Wang, Yuanyuan Wang, Yi Guo · 2025 · Advanced Science
- stImage: a versatile framework for optimizing spatial transcriptomic analysis through customizable deep histology and location informed integrationYu Wang, Haichun Yang, Ruining Deng, Yuankai Huo, Qi Liu, Yu Shyr, Shilin Zhao · 2025 · Briefings in Bioinformatics
- STADiffuser: high-fidelity simulation and full-view 3D modeling of spatial transcriptomicsChihao Zhang, Shihua Zhang · 2026 · Nature Communications
- jsPCA: fast, scalable, and interpretable identification of spatial domains and variable genes across multi-slice and multi-sample spatial transcriptomics dataInes Assali, Paul Escande, Franck Picard, Paul Villoutreix · 2026 · Bioinformatics Advances
- MoST-IG: Morphology-Guided Spatial Transcriptomics Integration via Visual-Genomic Graph Optimal TransportLiting Yu, Tao Ma, Weiqin Zhao, Zhuo Liang, Lequan Yu · 2025 · Lecture notes in computer science
- A comprehensive comparison on clustering methods for multi-slice spatially resolved transcriptomics data analysisCaiwei Xiong, Shuai Huang, Muqing Zhou, Yiyan Zhang, Wenrong Wu, Xihao Li, Huaxiu Yao, Jiawen Chen, Yun Li · 2025 · Briefings in Bioinformatics
- CoCo-ST detects global and local biological structures in spatial transcriptomics datasetsMuhammad Aminu, Bo Zhu, Natalie I. Vokes, Hong Chen, Lingzhi Hong, Jianrong Li, Junya Fujimoto, Mehdi Chaib, Yuqiu Yang, Bo Wang et al. · 2025 · Nature Cell Biology
- DiffuScope: A diffusion-regularized autoencoder for spatial transcriptomic clusteringHua Wang Shi, Ding Yi, Yang Cui, Ruheng Wang, Yan Li, Chunyan Ao, Ruihua Guo, Weihang Zhang, Tao Peng, Le Yuan et al. · 2025 · Computational Biology and Chemistry
- scDIFF: automatic cell type annotation using scATAC-seq data by incorporating bulk-level genomic and epigenomic information in a deep diffusive transformerHaoyu Wang, Hao Dong, Pu-Feng Du · 2025 · Briefings in Bioinformatics
- Diffusion-based representation integration for foundation models improves spatial transcriptomics analysisAtishay Jain, Tuan Minh Pham, David H. Laidlaw, Ying Ma, Ritambhara Singh · 2026 · Bioinformatics
- VARGG: a deep learning framework advancing precise spatial domain identification and cellular heterogeneity analysis in spatial transcriptomicsMengqiu Wang, Zhiwei Zhang, Lixin Lei, Kaitai Han, Zhenghui Wang, Ruoyan Dai, Zijun Wang, Chaojing Shi, Xudong Zhao, Qianjin Guo · 2025 · Briefings in Functional Genomics
- Transformer and graph variational autoencoder to identify microenvironments: A deep learning protocol for spatial transcriptomicsKarla Paniagua, Yufei Huang, Shou‐Jiang Gao, Yidong Chen, Yu-Fang Jin, Mario A. Flores · 2025 · STAR Protocols
- Novel Tensor Decomposition-Based Approach for Cell-Type Deconvolution in Visium Datasets with Reference scRNA-Seq Data Containing Multiple Minor Cell TypesY.-H. Taguchi, Turki Turki · 2025 · Mathematics
- Probabilistic-graph-based spatial context-aware framework for interpretable spatial omics denoising and augmentationXuyang Qin, Chang Liu, Fei Gu, Xun Lan · 2025 · Briefings in Bioinformatics
- ST-Community Detection Methods for Spatial Transcriptomics Data AnalysisCharles Zhao, Jian-Jian Ren · 2026 · Stats
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- stRGAT: identifying spatial domains in spatial transcriptomics via a relational graph attention networkZhengqian Zhang, Jialiang Wang, Junjun Ren, Yiduo Zhao, Yang Xu, Jingyi Bai, Shuang Liu, Yongzhuang Liu · 2026 · Journal of Translational Medicine
- Imaging-anchored multiomics in cardiovascular disease: integrating cardiac imaging, bulk, single-cell, and spatial transcriptomicsLe Huu Nhat Minh, Thanh-Huy Nguyen, Tao Li, Tao Li, Han H. Huynh, Monika Raj, Carl Yang, Min Xu, Tuan Vinh, Nguyen Quoc Khanh Le · 2026 · Briefings in Bioinformatics
- Combining spatial and single-cell transcriptome data to analyze tertiary lymphoid structures in clear cell renal cell carcinoma reveals prognostic biomarkersXuechao Li, Pu Liu, Man Li, Yongzhu Zhou, Tianwei Li, Tao Yang, JinKai Dong, Chengwei Fu, Yunping Zhu, L. Chen et al. · 2026 · Journal of Translational Medicine
- A multimodal framework to identify molecular mechanisms driving patient group-associated morphology through the integration of spatial transcriptomics and whole slide imagingReva Kulkarni, Avery Maddox, Sara Bailey, Arvind Rao · 2026 · npj Artificial Intelligence
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- M‐STGCN: A Position‐Aware Multimodal Graph Convolutional Framework for Joint Spatial Domain Identification and Gene Expression DenoisingXin Chen, Chaowen Li, Qirui Zhou, Ning Cui, Yun Huang, Chao Jie Chen, Junyi Lan, Songqing Gu, Hongtao Liu, Chao Yang et al. · 2026 · Small Methods
- SpaConTDS: A multimodal contrastive learning framework for identifying spatial domains by applying tuple disturbing strategyRuiwen Xu, Xiaoqing Cheng, Wai‐Ki Ching, Siyao Wu, Yuanben Zhang, Yidan Zhang · 2026 · PLoS Computational Biology
- Zero-Shot Grounding of Histological Images Using Single-Cell Transcriptomic ProfilesChaochen Wu, Meiyun Zuo, Lei Xie · 2025 · IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
- Cellular-Resolution Reconstruction of Spatial Transcriptomics from Histology Images via Foundation Models and KANsR. Stephanie Huang, Leiming Fang, WenBing Li, Yuansong Zeng, Yuedong Yang · 2025 · IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
- An End-to-End Dual-View Architecture for Spatial Clustering of Spatial Transcriptomics Data by Integrating Histology ImagesXinru Xu, Shengjun Li, Juan Wang · 2025 · IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
- Bayesian Hyperspherical Graph Mixture-of-Experts Deciphers Cell–Cell Interaction in Spatial TranscriptomicsWenchuan Zhang, Yujian Lee, Ricky Yuen-Tan Hou, Weifeng Su, Hong Yan, Wentao Fan · 2026 · IEEE Transactions on Computational Biology and Bioinformatics
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- CEMUSA: a graph-based integrative metric for evaluating clusters in spatial transcriptomicsJie Hu, Yihang Du, Suyang Hou, Yueyang Ding, Jinyan Li, Hao Wu, Xiaobo Sun · 2026 · Bioinformatics
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- stDyer-image improves clustering analysis of spatially resolved transcriptomics and proteomics with morphological imagesKe Xu, Xin Zhou, Lu Zhang · 2026 · Bioinformatics
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