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

DOI 10.1038/s41592-021-01255-8

Cited by (1,117)

Items 201–300 of 1,117

NeST: nested hierarchical structure identification in spatial transcriptomic data
Benjamin L. Walker, Qing Hua Nie · 2023 · Nature Communications
Unravelling tumour spatiotemporal heterogeneity using spatial multimodal data
Chunman Zuo, Junchao Zhu, Jiawei Zou, Luonan Chen · 2025 · Clinical and Translational Medicine
Artificial intelligence–enabled multi-omics biomarkers for immune checkpoint blockade: mechanisms, predictive modeling, and clinical translation
Xiaodong Wang, Di Xiong, Songli Cui, Bingchen Duan, Gouping Ding, Yiping Huang, Qianqian Wang · 2026 · Frontiers in Immunology
Cell composition inference and identification of layer-specific spatial transcriptional profiles with POLARIS
Jiawen Chen, Tianyou Luo, Min-Zhi Jiang, Jiandong Liu, Gaorav P. Gupta, Yun Li · 2023 · Science Advances
Graph deep learning enabled spatial domains identification for spatial transcriptomics
Teng Liu, Zhaoyu Fang, Xin Li, Lining Zhang, Dongsheng Cao, Mingzhu Yin · 2023 · Briefings in Bioinformatics
Charting the tumor microenvironment with spatial profiling technologies
Mattia Toninelli, Grazisa Rossetti, Massimiliano Pagani · 2023 · Trends in cancer
Disparities in spatially variable gene calling highlight the need for benchmarking spatial transcriptomics methods
Natalie Charitakis, Agus Salim, Adam T. Piers, Kevin I. Watt, Enzo R. Porrello, David A. Elliott, Mirana Ramialison · 2023 · Genome biology
spVC for the detection and interpretation of spatial gene expression variation
Shan Yu, Wei Vivian Li · 2024 · Genome biology
scSemiProfiler: Advancing large-scale single-cell studies through semi-profiling with deep generative models and active learning
Jingtao Wang, Gregory J. Fonseca, Jun Ding · 2024 · Nature Communications
Simulating multiple variability in spatially resolved transcriptomics with scCube
Jingyang Qian, Hudong Bao, Xin Shao, Fang Yin, Jie Liao, Zhuo Chen, Chengyu Li, Wenbo Guo, Yining Hu, Anyao Li et al. · 2024 · Nature Communications
Deep cell phenotyping and spatial analysis of multiplexed imaging with TRACERx-PHLEX
Alastair J. Magness, Emma Colliver, Katey S.S. Enfield, Claudia Lee, Masako Shimato, Emer Daly, David Allan Moore, Monica Sivakumar, Karishma Valand, Dina Levi et al. · 2024 · Nature Communications
Deep Learning of radiology-genomics integration for computational oncology: A mini review
Feng‐ao Wang, Y Li, Tao Zeng · 2024 · Computational and Structural Biotechnology Journal
SpatialLeiden: spatially aware Leiden clustering
Niklas Müller‐Bötticher, Shashwat Sahay, Roland Eils, Naveed Ishaque · 2025 · Genome biology
scPlantLLM: A Foundation Model for Exploring Single-cell Expression Atlases in Plants
Guangshuo Cao, Haoyu Chao, Wenqi Zheng, Yangming Lan, Kaiyan Lu, Yueyi Wang, Ming Chen, He Zhang, Dijun Chen · 2025 · Genomics Proteomics & Bioinformatics
SpaNorm: spatially-aware normalization for spatial transcriptomics data
Agus Salim, Dharmesh Dinesh Bhuva, Carissa Chen, Chin Wee Tan, Pengyi Yang, Melissa J. Davis, Jean Yee Hwa Yang · 2025 · Genome biology
Leveraging multi-modal foundation models for analysing spatial multi-omic and histopathology data
Tianyu Liu, Tinglin Huang, Tong Ding, Hao Wu, Peter Humphrey, Sudhir Perincheri, Kurt Schalper, Rex Ying, Hua Xu, James Zou et al. · 2026 · Nature Biomedical Engineering
ADEPT: Autoencoder with differentially expressed genes and imputation for robust spatial transcriptomics clustering
Yunfei Hu, Yuying Zhao, Curtis T. Schunk, Yingxiang Ma, Tyler Derr, Xin Zhou · 2023 · iScience
Atrial Fibrillation Detection Algorithm Based on Graph Convolution Network
Hua Ma, Lingnan Xia · 2023 · IEEE Access
Tissue module discovery in single-cell-resolution spatial transcriptomics data via cell-cell interaction-aware cell embedding
Yuzhe Li, Jinsong Zhang, Xin Gao, Qiangfeng Cliff Zhang · 2024 · Cell Systems
A composite scaling network of EfficientNet for improving spatial domain identification performance
Yanan Zhao, Chunshen Long, Wenjing Shang, Zhihao Si, Zhigang Liu, Zhenxing Feng, Yongchun Zuo · 2024 · Communications Biology
A point cloud segmentation framework for image-based spatial transcriptomics
Thomas Defard, Hugo Laporte, Mallick Ayan, Juliette Soulier, Sandra Curras-Alonso, Christian Weber, Florian Massip, Arturo Londoño‐Vallejo, Charles Fouillade, Florian Mueller et al. · 2024 · Communications Biology
Benchmarking algorithms for spatially variable gene identification in spatial transcriptomics
Xuanwei Chen, Qinghua Ran, Junjie Tang, Zihao Chen, Siyuan Huang, Xingjie Shi, Ruibin Xi · 2025 · Bioinformatics
spaLLM: enhancing spatial domain analysis in multi-omics data through large language model integration
Longyu Li, Liyan Dong, Hao Zhang, Dong He Xu, Yongli Li · 2025 · Briefings in Bioinformatics
MultiGATE: integrative analysis and regulatory inference in spatial multi-omics data via graph representation learning
Jishuai Miao, Jinzhao Li, Jingxue Xin, Jia-Juan Tu, Muyang Ge, Ji Qi, Xiaocheng Zhou, Ying Zhu, Can Yang, Zhixiang Lin · 2025 · Nature Communications
Streamlining spatial omics data analysis with Pysodb
Senlin Lin, Fangyuan Zhao, Zihan Wu, Jianhua Yao, Yi Chen Zhao, Zhiyuan Yuan · 2023 · Nature Protocols
Integrating spatial transcriptomics and bulk RNA-seq: predicting gene expression with enhanced resolution through graph attention networks
Sudipto Baul, Khandakar Tanvir Ahmed, Qibing Jiang, Guangyu Wang, Qian Li, Jeongsik Yong, Wei Zhang · 2024 · Briefings in Bioinformatics
Detecting anomalous anatomic regions in spatial transcriptomics with STANDS
Kaichen Xu, Yan Lu, Suyang Hou, Kainan Liu, Yihang Du, Mengqian Huang, Hao Feng, Hao Wu, Xiaobo Sun · 2024 · Nature Communications
MAEST: accurately spatial domain detection in spatial transcriptomics with graph masked autoencoder
Pengfei Zhu, Han Shu, Yongtian Wang, Xiaofeng Wang, Yuan Zhao, Jialu Hu, Jiajie Peng, Xuequn Shang, Zhen Tian, Jing Chen et al. · 2025 · Briefings in Bioinformatics
AAV‐delivered diacylglycerol kinase DGKk achieves long‐term rescue of fragile X syndrome mouse model
Karima Habbas, Oktay Cakil, Boglárka Zámbó, Ricardos Tabet, Fabrice Riet, Doulaye Dembélé, Jean‐Louis Mandel, Michaël Hocquemiller, Ralph Laufer, Françoise Piguet et al. · 2022 · EMBO Molecular Medicine
Single‐cell RNA‐sequencing and spatial transcriptomic analysis reveal a distinct population of APOE− cells yielding pathological lymph node metastasis in papillary thyroid cancer
Guohui Xiao, Rongli Xie, Jianhua Gu, Yishu Huang, Min Ding, Dongjie Shen, Jiqi Yan, Jianming Yuan, Qiong Yang, Wen He et al. · 2025 · Clinical and Translational Medicine
Roles of Cellular Neighborhoods in Hepatocellular Carcinoma Pathogenesis
Lichun Ma, C Li, Xin Wei Wang · 2025 · Annual Review of Pathology Mechanisms of Disease
stClinic dissects clinically relevant niches by integrating spatial multi-slice multi-omics data in dynamic graphs
Chunman Zuo, Junjie Xia, Yupeng Xu, Ying Xu, Pingting Gao, Jing Zhang, Yan Wang, Luonan Chen · 2025 · Nature Communications
Cancer therapy resistance from a spatial‐omics perspective
Yinghao Zhang, Cheng Yang, Xi Chen, Liang Li Wu, Zhiyuan Yuan, Fan Zhang, Bin‐Zhi Qian · 2025 · Clinical and Translational Medicine
SpaICL: image-guided curriculum strategy-based graph contrastive learning for spatial transcriptomics clustering
Jingcheng Zhao, Wenwen Min · 2025 · Briefings in Bioinformatics
Vesalius: high‐resolution in silico anatomization of spatial transcriptomic data using image analysis
Patrick C. N. Martin, Hyobin Kim, Cecilia Lövkvist, Byung‐Woo Hong, Kyoung‐Jae Won · 2022 · Molecular Systems Biology
Integrating multi-modal information to detect spatial domains of spatial transcriptomics by graph attention network
Yuying Huo, Yilang Guo, Jiakang Wang, Huijie Xue, Yujuan Feng, Weizheng Chen, Xiangyu Li · 2023 · Journal of genetics and genomics/Journal of Genetics and Genomics
An integrated study to decipher immunosuppressive cellular communication in the PDAC environment
Gülben Avşar, Pınar Pir · 2023 · npj Systems Biology and Applications
Attention-guided variational graph autoencoders reveal heterogeneity in spatial transcriptomics
Lixin Lei, Kaitai Han, Zijun Wang, Chaojing Shi, Zhenghui Wang, Ruoyan Dai, Zhiwei Zhang, Mengqiu Wang, Qianjin Guo · 2024 · Briefings in Bioinformatics
SPADE: spatial deconvolution for domain specific cell-type estimation
Yingying Lu, Qin M. Chen, Lingling An · 2024 · Communications Biology
A novel multislice framework for precision 3D spatial domain reconstruction and disease pathology analysis
Dai-Jun Zhang, Ren Qi, Xun Lan, Bin Liu · 2025 · Genome Research
Large language model agents for biological intelligence across genomics, proteomics, spatial biology, and biomedicine
Sajib Acharjee Dip, Ditipriya Mallick, Uddip Acharjee Shuvo, Shovito Barua Soumma, Fazle Rafsani, Bikash Kumar Paul, Nazifa Ahmed Moumi, Shafayat Ahmed, Liqing Zhang · 2026 · Briefings in Bioinformatics
Recent advances in differential expression analysis for single-cell RNA-seq and spatially resolved transcriptomic studies
Xiya Guo, Jin Ning, Yuanze Chen, Guoliang Liu, Liyan Zhao, Yue Fan, Shiquan Sun · 2023 · Briefings in Functional Genomics
DESpace : spatially variable gene detection via differential expression testing of spatial clusters
Peiying Cai, Mark D. Robinson, Simone Tiberi · 2024 · Bioinformatics
Spatially Resolved Multiomics: Data Analysis from Monoomics to Multiomics
Changxiang Huan, Jinze Li, Yingxue Li, Shasha Zhao, Qi Yang, Zhiqi Zhang, Chuanyu Li, Shuli Li, Zhenzhong Guo, Jia Yao et al. · 2024 · BME Frontiers
Emerging AI approaches for cancer spatial omics
Javad Noorbakhsh, Ali Foroughi pour, Jeffrey H. Chuang · 2025 · GigaScience
Bridging single cells to organs: Mesoscale modules as fundamental units of tissue function
Yun Chen, Ronald N. Germain, Ginger L. Hunter, Rajan P. Kulkarni, Arthur D. Lander, Pedro Ricardo Lowenstein, Jeremy E. Purvis, Harikesh S. Wong · 2025 · Cell
Identification and Classification of Small Sample Desert Grassland Vegetation Communities Based on Dynamic Graph Convolution and UAV Hyperspectral Imagery
Tao Zhang, Yuge Bi, Xiangbing Zhu, Xinchao Gao · 2023 · Sensors
Spatial omics: An innovative frontier in aging research
Ying Chen, Shuhao Yang, Kaixu Yu, Jinjin Zhang, Meng Wu, Yongqiang Zheng, Yun Zhu, Jun Dai, Chunyan Wang, Xiaoran Zhu et al. · 2023 · Ageing Research Reviews
stAA: adversarial graph autoencoder for spatial clustering task of spatially resolved transcriptomics
Zhaoyu Fang, Teng Liu, Ruiqing Zheng, Jin A, Mingzhu Yin, Min Li · 2023 · Briefings in Bioinformatics
SpatialPrompt: spatially aware scalable and accurate tool for spot deconvolution and domain identification in spatial transcriptomics
Asish Kumar Swain, Vrushali Pandit, Jyoti Sharma, Pankaj Yadav · 2024 · Communications Biology
aKNNO: single-cell and spatial transcriptomics clustering with an optimized adaptive k-nearest neighbor graph
Jia Li, Yu Shyr, Qi Liu · 2024 · Genome biology
SpaGIC: graph-informed clustering in spatial transcriptomics via self-supervised contrastive learning
Wei Liu, Bo Wang, Yuting Bai, Xiao Liang, Li Xue, Jiawei Luo · 2024 · Briefings in Bioinformatics
Advanced Carriers for Precise Delivery and Therapeutic Mechanisms of Traditional Chinese Medicines: Integrating Spatial Multi‐Omics and Delivery Visualization
Yusheng Zhang, Zhiguo Lü, Jing Guo, Qīng Wáng, Xin Zhang, Hongjun Yang, Xianyu Li · 2025 · Advanced Healthcare Materials
Stardust : improving spatial transcriptomics data analysis through space-aware modularity optimization-based clustering
Simone Avesani, Eva Viesi, Luca Alessandrì, Giovanni Motterle, Vincenzo Bonnici, Marco Beccuti, Raffaele Calogero, Rosalba Giugno · 2022 · GigaScience
Deciphering cell to cell spatial relationship for pathology images using SpatialQPFs
Li Xiao · 2024 · Scientific Reports
CellLENS enables cross-domain information fusion for enhanced cell population delineation in single-cell spatial omics data
Bokai Zhu, Sheng Gao, Shuxiao Chen, Yuchen Wang, Jason Yeung, Yunhao Bai, Amy Y. Huang, Yao Yu Yeo, Guanrui Liao, Shulin Mao et al. · 2025 · Nature Immunology
SIDISH integrates single-cell and bulk transcriptomics to identify high-risk cells and guide precision therapeutics through in silico perturbation
Yasmin Jolasun, Kailu Song, Yumin Zheng, Jingtao Wang, Gregory J. Fonseca, David H. Eidelman, Jun Ding · 2025 · Nature Communications
Single‐Cell and Spatial Multiomics: Applications for Diseases
Wentao Li, Chao Chen, Xin Zhu, Chenping Zhang · 2025 · MedComm
Cellular neighborhoods in cancer
Lichun Ma, Barbara Xiong, M. Liu, Kai Tan · 2026 · Nature Cancer
Revealing Tissue Heterogeneity and Spatial Dark Genes from Spatially Resolved Transcriptomics by Multiview Graph Networks
Ying Li, Yuejing Lu, Kang Chen, Peiluan Li, Luonan Chen · 2023 · Research
MVST: Identifying spatial domains of spatial transcriptomes from multiple views using multi-view graph convolutional networks
Hao Duan, Qingchen Zhang, Feifei Cui, Quan Zou, Zilong Zhang · 2024 · PLoS Computational Biology
Deciphering tissue heterogeneity from spatially resolved transcriptomics by the autoencoder-assisted graph convolutional neural network
Xinxing Li, Wendong Huang, Xuan Xu, Hongyu Zhang, Qianqian Shi · 2023 · Frontiers in Genetics
Defining transcriptomic niches in human fibrotic lung with multi-sample spatial transcriptomics analysis using the MAPLE algorithm
Hyeongseon Jeon, Carter Allen, N.D.P. Vanegas, Juan Xie, Ahmed H. Ghobashi, Jhonny Rodriguez-Lopez, Lorena Rosas, Cankun Wang, Hao Cheng, Yuzhou Chang et al. · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
stHGC: a self-supervised graph representation learning for spatial domain recognition with hybrid graph and spatial regularization
Rongxian Wang, Qiguo Dai, Xiaodong Duan, Quan Zou · 2024 · Briefings in Bioinformatics
Spatial Patterning Analysis of Cellular Ensembles (SPACE) finds 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. · 2025 · Proceedings of the National Academy of Sciences
DeepGFT: identifying spatial domains in spatial transcriptomics of complex and 3D tissue using deep learning and graph Fourier transform
Shuli Sun, Jixin Liu, Guojun Li, Bingqiang Liu · 2025 · Genome biology
Advancing Cardiovascular Research With Single-Cell and Spatial Transcriptomics
Kai Li, Samaneh Samiei, Daryna Pikulska, Sebastian Foecking, Christoph Kuppe · 2026 · Circulation Research
Deep Learning-Enabled Multi-Omics Integration: A New Frontier in Precise Drug Target Discovery
Yufei Ren, Haotian Bai, Jihan Wang, Yanning Yang, Yangyang Wang · 2026 · Biology
Modulating autophagy to treat diseases: A revisited review on in silico methods
Lifeng Wu, Wenke Jin, Haiyang Yu, Bo Liu · 2023 · Journal of Advanced Research
Navigating the landscapes of spatial transcriptomics: How computational methods guide the way
Runze Li, Xu Chen, Xuerui Yang · 2024 · Wiley Interdisciplinary Reviews - RNA
Complete spatially resolved gene expression is not necessary for identifying spatial domains
Senlin Lin, Yan Cui, Fangyuan Zhao, Zhidong Yang, Jiangning Song, Jianhua Yao, Yu Shan Zhao, Bin‐Zhi Qian, Yi Chen Zhao, Zhiyuan Yuan · 2024 · Cell Genomics
GraphPCA: a fast and interpretable dimension reduction algorithm for spatial transcriptomics data
Jiyuan Yang, Lu Wang, Lin L. Liu, Xiaoqi Zheng · 2024 · Genome biology
Characterizing cell-type spatial relationships across length scales in spatially resolved omics data
Rafael dos Santos Peixoto, Brendan F. Miller, Maigan Brusko, Gohta Aihara, Lyla Atta, Manjari M-G Anant, Mark A. Atkinson, Todd M. Brusko, Clive Henry Wasserfall, Jean Fan · 2025 · Nature Communications
StereoMM: a graph fusion model for integrating spatial transcriptomic data and pathological images
Bingying Luo, Fei Teng, Guo Tang, Weixuan Cen, Xing Liu, Jinmiao Chen, Chi Qu, Xuanzhu Liu, Xin Liu, Wenyan Jiang et al. · 2025 · Briefings in Bioinformatics
spaMGCN: a graph convolutional network with autoencoder for spatial domain identification using multi-scale adaptation
Tianjiao Zhang, Hongfei Zhang, Zhongqian Zhao, Saihong Shao, Yucai Jiang, Xiang Zhang, Guohua Wang · 2025 · Genome biology
stGRL: spatial domain identification, denoising, and imputation algorithm for spatial transcriptome data based on multi-task graph contrastive representation learning
Xin Lu, Murong Zhou, Bo Gao, Fang Wang, Shuilin Jin, Qiaoming Liu, Guohua Wang · 2025 · BMC Biology
Advances in plant spatial multi-omics data analysis
Jie Yao, Alexandre P. Marand, Yinqi Bai, Robert J. Schmitz, Longjiang Fan · 2025 · Trends in Plant Science
The spatiotemporal dynamics of spatially variable genes in developing mouse brain revealed by a novel computational scheme
Yingzhou Hong, Kai Song, Zongbo Zhang, Yuxia Deng, Xue Zhang, Jinqian Zhao, Jun Jiang, Qing Zhang, Chunming Guo, Cheng Peng · 2023 · Cell Death Discovery
scBOL: a universal cell type identification framework for single-cell and spatial transcriptomics data
Yuyao Zhai, Liang Chen, Minghua Deng · 2024 · Briefings in Bioinformatics
Points2Regions : Fast, interactive clustering of imaging‐based spatial transcriptomics data
Axel Andersson, Andrea Beháňová, Christophe Avenel, Jonas Windhager, Filip Malmberg, Carolina Wählby · 2024 · Cytometry Part A
PCA-based spatial domain identification with state-of-the-art performance
Darius P. Schaub, Behnam Yousefi, Nico Kaiser, Robin Khatri, Victor G. Puelles, Christian F. Krebs, Ulf Panzer, Stefan Bonn · 2024 · Bioinformatics
LETSmix: a spatially informed and learning-based domain adaptation method for cell-type deconvolution in spatial transcriptomics
Yangen Zhan, Yongbing Zhang, Zheqi Hu, Yifeng Wang, Zirui Zhu, Sijing Du, Xiangming Yan, Xiu Li · 2025 · Genome Medicine
Perspective on recent developments and challenges in regulatory and systems genomics
Julia Zeitlinger, Sushmita Roy, Ferhat Ay, Anthony Mathelier, Alejandra Medina-Rivera, Shaun Mahony, Saurabh Kumar Sinha, Jason Ernst · 2024 · Bioinformatics Advances
DANCE: a deep learning library and benchmark platform for single-cell analysis
Jiayuan Ding, Renming Liu, Hongzhi Wen, Wenzhuo Tang, Zhaoheng Li, Julian Venegas, Runze Su, Dylan Molho, Wei Jin, Yixin Wang et al. · 2024 · Genome biology
Data-driven fine-grained region discovery in the mouse brain with transformers
Alex J. Lee, Alma Dubuc, Michael Kunst, Shenqin Yao, Nicholas A. Lusk, Lydia Ng, Hongkui Zeng, Bosiljka Tasic, Reza Abbasi-Asl · 2025 · Nature Communications
Single‐Cell and Spatial Omics: Methods and Applications
Xiaoping Cen, Xiaolan Huang, Erle Deng, Xue Gong, Na Tan, J. T. Ye, Yin Wang, Roland Eils, Qun Luo, Yixue Li et al. · 2026 · MedComm
Dissecting Spatiotemporal Structures in Spatial Transcriptomics via Diffusion-Based Adversarial Learning
Haiyun Wang, Jianping Zhao, Qing Hua Nie, Chun-Hou Zheng, Xiaoqiang Sun · 2024 · Research
Discovery and generalization of tissue structures from spatial omics data
Zhenqin Wu, Ayano Kondo, Monee McGrady, Ethan A. G. Baker, Benjamin Chidester, Eric Wu, Maha K. Rahim, Nathan A. Bracey, Vivek Charu, Raymond Jaihyun Cho et al. · 2024 · Cell Reports Methods
STIE: Single-cell level deconvolution, convolution, and clustering in in situ capturing-based spatial transcriptomics
Shijia Zhu, Naoto Kubota, Shidan Wang, Tao Wang, Guanghua Xiao, Yujin Hoshida · 2024 · Nature Communications
A comprehensive review of approaches for spatial domain recognition of spatial transcriptomes
Ziyi Wang, Aoyun Geng, Hao Duan, Feifei Cui, Quan Zou, Zilong Zhang · 2024 · Briefings in Functional Genomics
High-resolution mapping of single cells in spatial context
Jincan Ke, Jian Xu, Jia Liu B, Yumeng Yang, Chenkai Guo, Bingbing Xie, Guizhong Cui, Guangdun Peng, Shengbao Suo · 2025 · Nature Communications
Deep learning applications advance plant genomics research
Wenyuan Fan, Zhongwei Guo, Xiang Wang, Lingkui Zhang, Yuanhang Liu, Chengcheng Cai, Kang Zhang, Feng Cheng · 2025 · Horticultural Plant Journal
Single-cell sequencing: expansion, integration and translation
Xiaofeng Dai, Linhan Cai, Fule He · 2022 · Briefings in Functional Genomics
Spatially aware self-representation learning for tissue structure characterization and spatial functional genes identification
Chuanchao Zhang, Xinxing Li, Wendong Huang, Lequn Wang, Qianqian Shi · 2023 · Briefings in Bioinformatics
ConSpaS: a contrastive learning framework for identifying spatial domains by integrating local and global similarities
Siyao Wu, Yushan Qiu, Xiaoqing Cheng · 2023 · Briefings in Bioinformatics
A model-based constrained deep learning clustering approach for spatially resolved single-cell data
Xiang Lin, Le Gao, Nathan P. Whitener, Asraa Ahmed, Zhi Wei · 2022 · Genome Research
Artificial Intelligence Revolution in Transcriptomics: From Single Cells to Spatial Atlases
Shixin Li, Tianxiang Xiao, Yuanyuan Lan, Chao Wu, Zhouying Li, Rong Liu, Qing Fang, Chao Zhang · 2025 · Advanced Science
Predicting total organic carbon from well logs based on deep spatial-sequential graph convolutional network
Xiaocai Shan, Zhangxin Chen, Bo-Ye Fu, Wang Zhang, Jing Li, Keliu Wu · 2023 · Geophysics
Cross-modality representation and multi-sample integration of spatially resolved omics data
Zhen Li, Xuejian Cui, Xiaoyang Chen, Zijing Gao, Yuyao Liu, Yan Pan, Shengquan Chen, Hairong Lv, Lei Zhai, Rui Jiang · 2026 · Briefings in Bioinformatics
Efficient and scalable prediction of stochastic reaction–diffusion processes using graph neural networks
Zhixing Cao, Rui Chen, Libin Xu, Xinyi Zhou, Xiaoming Fu, Weimin Zhong, Ramon Grima · 2024 · Mathematical Biosciences