Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays
Chen, Ao, Liao, Sha, Cheng, Mengnan, Ma, Kailong, Wu, Liang, Lai, Yiwei, Qiu, Xiaojie, Yang, Jin, Xu, Jiangshan, Hao, Shijie, Wang, Xin, Lu, Huifang, Chen, Xi, Liu, Xing, Huang, Xin, Li, Zhao, Hong, Yan, Jiang, Yujia, Peng, Jian, Liu, Shuai, Shen, Mengzhe, Liu, Chuanyu, Li, Quanshui, Yuan, Yue, Wei, Xiaoyu, Zheng, Huiwen, Feng, Weimin, Wang, Zhifeng, Liu, Yang, Wang, Zhaohui, Yang, Yunzhi, Xiang, Haitao, Han, Lei, Qin, Baoming, Guo, Pengcheng, Lai, Guangyao, Muñoz-Cánoves, Pura, Maxwell, Patrick H., Thiery, Jean Paul, Wu, Qing-Feng, Zhao, Fuxiang, Chen, Bichao, Li, Mei, Dai, Xi, Wang, Shuai, Kuang, Haoyan, Hui, Junhou, Wang, Liqun, Fei, Ji-Feng, Wang, Ou, Wei, Xiaofeng, Lu, Haorong, Wang, Bo, Liu, Shiping, Gu, Ying, Ni, Ming, Zhang, Wenwei, Mu, Feng, Yin, Ye, Yang, Huanming, Lisby, Michael, Cornall, Richard J., Mulder, Jan, Uhlén, Mathias, Esteban, Miguel A., Li, Yuxiang, Liu, Longqi, Xu, Xun, Wang, Jian·2022·Cell
Cited by (1,000)
Items 201–300 of 1,000
- STdGCN: spatial transcriptomic cell-type deconvolution using graph convolutional networksYawei Li, Yuan Luo · 2024 · Genome biology
- Custom microfluidic chip design enables cost-effective three-dimensional spatiotemporal transcriptomics with a wide field of viewJunjie Zhu, Kun Pang, Beiyu Hu, Ruiqiao He, Ning Wang, Zewen Jiang, Peifeng Ji, Fangqing Zhao · 2024 · Nature Genetics
- SpaMask: Dual masking graph autoencoder with contrastive learning for spatial transcriptomicsWenwen Min, Donghai Fang, Jinyu Chen, Shihua Zhang · 2025 · PLoS Computational Biology
- Library size confounds biology in spatial transcriptomics dataDharmesh Dinesh Bhuva, Chin Wee Tan, Agus Salim, Claire Marceaux, Marie A. Pickering, Jinjin Chen, Malvika Kharbanda, Xinyi Jin, Ning Liu, Kristen Feher et al. · 2024 · Genome biology
- FICTURE: scalable segmentation-free analysis of submicron-resolution spatial transcriptomicsYichen Si, ChangHee Lee, Yongha Hwang, Jeong Hyun Yun, Weiqiu Cheng, Chun‐Seok Cho, Miguel Quirós, Asma Nusrat, Weizhou Zhang, Goo Jun et al. · 2024 · Nature Methods
- Stereo-seq of the prefrontal cortex in aging and Alzheimer’s diseaseYun Gong, Mohammad Haeri, Xiao Zhang, Yisu Li, Anqi Liu, Di Wu, Qi‐Lei Zhang, S. Michal Jazwinski, Xiang Zhou, Xiaoying Wang et al. · 2025 · Nature Communications
- Advances in spatial transcriptomics and its application in the musculoskeletal systemHaoyu Wang, Peng Cheng, Juan Wang, Hongzhi Lv, Jie Han, Zhiyong Hou, Ren Xu, Wei Chen · 2025 · Bone Research
- Sequencing-free whole-genome spatial transcriptomics at single-molecule resolutionYubao Cheng, Shengyuan Dang, Yuan Zhang, Yanbo Chen, Ruihuan Yu, Liu Miao, Shengyan Jin, Ailin Han, Samuel G. Katz, Siyuan Wang · 2025 · Cell
- Challenges and Opportunities for the Clinical Translation of Spatial Transcriptomics TechnologiesKelly D. Smith, David K. Prince, James W. MacDonald, Theo K. Bammler, Shreeram Akilesh · 2024 · Glomerular Diseases
- Spatial transcriptomics using multiplexed deterministic barcoding in tissueJohannes Wirth, Nina Huber, Kelvin Yin, Sophie Brood, Simon Chang, Celia Pilar Martinez‐Jimenez, Matthias Meier · 2023 · Nature Communications
- Fibrosis in Pathology of Heart and Kidney: From Deep RNA-Sequencing to Novel Molecular TargetsFelix Schreibing, Teresa M Anslinger, Rafael Kramann · 2023 · Circulation Research
- Spotless, a reproducible pipeline for benchmarking cell type deconvolution in spatial transcriptomicsChananchida Sang-aram, Robin Browaeys, Ruth Seurinck, Yvan Saeys · 2023 · eLife
- SONAR enables cell type deconvolution with spatially weighted Poisson-Gamma model for spatial transcriptomicsZhiyuan Liu, Dafei Wu, Weiwei Zhai, Liang Ma · 2023 · Nature Communications
- Dissecting tumor microenvironment from spatially resolved transcriptomics data by heterogeneous graph learningChunman Zuo, Junjie Xia, Luonan Chen · 2024 · Nature Communications
- Deciphering functional tumor-immune crosstalk through highly multiplexed imaging and deep visual proteomicsXiang Zheng, Andreas Mund, Matthias Mann · 2025 · Molecular Cell
- Spatiotemporal transcriptomic maps of mouse intracerebral hemorrhage at single-cell resolutionRong Xiang, Junmin Wang, Zhan Chen, Jin Zhong Tao, Qinfeng Peng, Ruoqi Ding, Tao Zhou, Zhencheng Tu, Tao Yang, Tao Yang et al. · 2025 · Neuron
- Categorization of 34 computational methods to detect spatially variable genes from spatially resolved transcriptomics dataGuanao Yan, Shuo Harper Hua, Jingyi Jessica Li · 2025 · Nature Communications
- Spatial transcriptomic characterization of a Carnegie stage 7 human embryoLina Cui, Sirui Lin, Xiaolong Yang, Xinwei Xie, Xiaoyan Wang, Nannan He, H. J. Yang, Xin Zhang, Xiaojian Lu, Xiaodi Yan et al. · 2025 · Nature Cell Biology
- STAIG: Spatial transcriptomics analysis via image-aided graph contrastive learning for domain exploration and alignment-free integrationYitao Yang, Yang Cui, Xin Zeng, Yubo Zhang, Martin Loza, Sung‐Joon Park, Kenta Nakai · 2025 · Nature Communications
- Spatially resolved gene regulatory and disease-related vulnerability map of the adult Macaque cortexYing Lei, Mengnan Cheng, Zihao Li, Zhenkun Zhuang, Liang Li Wu, Yunong Sun, Lei Han, Zhi‐Hao Huang, Yuzhou Wang, Zifei Wang et al. · 2022 · Nature Communications
- High resolution spatial profiling of kidney injury and repair using RNA hybridization-based in situ sequencingHao Wu, Eryn E. Dixon, Qiao Xuanyuan, Juanru Guo, Yasuhiro Yoshimura, Debashish Chitnis, Anezka Niesnerova, Hao Ying Xu, M. Rouault, Benjamin D. Humphreys · 2024 · Nature Communications
- Advances and challenges in cell–cell communication inference: a comprehensive review of tools, resources, and future directionsGiulia Cesaro, James Shiniti Nagai, Gnoato Nicolò, Alice Chiodi, Gaia Tussardi, Vanessa Klöker, Carmelo Vittorio Musumarra, Ettore Mosca, Ivan G. Costa, Barbara Di Camillo et al. · 2025 · Briefings in Bioinformatics
- Cellular heterogeneity and stem cells of vascular endothelial cells in blood vessel formation and homeostasis: Insights from single-cell RNA sequencingTaku Wakabayashi, Hisamichi Naito · 2023 · Frontiers in Cell and Developmental Biology
- Adrenomedullin has a pivotal role in trophoblast differentiation: A promising nanotechnology-based therapeutic target for early-onset preeclampsiaQingqing Zhang, Cheuk‐Lun Lee, Tingyu Yang, Jianlin Li, Qunxiong Zeng, Xiaofeng Liu, Zhongzhen Liu, Degong Ruan, Zhuoxuan Li, Anita Sik Yau Kan et al. · 2023 · Science Advances
- Seq-Scope: Repurposing Illumina sequencing flow cells for high-resolution spatial transcriptomicsKim, Yongsung, Cheng, Weiqiu, Cho, Chun-Seok, Hwang, Yongha, Si, Yichen, Park, Anna, Schrank, Mitchell, Hsu, Jer-En, Anacleto, Angelo, Xi, Jingyue et al. · 2025 · Nature Protocols
- Microtechnologies for single-cell and spatial multi-omicsYanxiang Deng, Zhiliang Bai, Rong Fan · 2023 · Nature Reviews Bioengineering
- Transformer with convolution and graph-node co-embedding: An accurate and interpretable vision backbone for predicting gene expressions from local histopathological imageXiao Xiao, Yan Kong, Rong-Han Li, Zuoheng Wang, Hui Juan Lu · 2023 · Medical Image Analysis
- Molecular, Metabolic, and Subcellular Mapping of the Tumor Immune Microenvironment via 3D Targeted and Non-Targeted Multiplex Multi-Omics AnalysesSammy Ferri Borgogno, Jared K. Burks, Erin H. Seeley, Trevor D. McKee, Danielle L. Stolley, Akshay Basi, Javier A. Gomez, Basant T. Gamal, Shamini Ayyadhury, Barrett Craig Lawson et al. · 2024 · Cancers
- Unlocking the power of spatial omics with AIKyle Coleman, Amelia R. Schroeder, Mingyao Li · 2024 · Nature Methods
- Spatial omics advances for in situ RNA biologyJingyi Ren, Shuchen Luo, Hailing Shi, Xiao Wang · 2024 · Molecular Cell
- Challenges and Opportunities in the Clinical Translation of High-Resolution Spatial TranscriptomicsTancredi Massimo Pentimalli, Nikos Karaiskos, Nikolaus Rajewsky · 2024 · Annual Review of Pathology Mechanisms of Disease
- Enhancer-driven cell type comparison reveals similarities between the mammalian and bird palliumNikolai Hecker, Niklas Kempynck, David Mauduit, Darina Abaffyová, Roel Vandepoel, Sam Dieltiens, Lars E. Borm, Ioannis Sarropoulos, Carmen Bravo González‐Blas, Julie De Man et al. · 2025 · Science
- The spatial transcriptomic landscape of human gingiva in health and periodontitisZongshan Shen, Ran Zhang, Yunjia Huang, Jiayao Chen, Mengjun Yu, Chunhua Li, Yong Zhang, Lingling Chen, Xin Huang, Jichen Yang et al. · 2023 · Science China Life Sciences
- Innovative super-resolution in spatial transcriptomics: a transformer model exploiting histology images and spatial gene expressionChongyue Zhao, Zhongli Xu, Xinjun Wang, Shiyue Tao, William A MacDonald, Kun He, Amanda C. Poholek, Kong Chen, Heng Huang, Wei Chen · 2024 · Briefings in Bioinformatics
- A single-cell and spatial wheat root atlas with cross-species annotations delineates conserved tissue-specific marker genes and regulatorsYuji Ke, Vincent Pujol, Jasper Staut, Lotte Pollaris, Ruth Seurinck, Thomas Eekhout, Carolin Seyfferth, Maite Saura-Sánchez, Michiel Van Bel, Marnik Vuylsteke et al. · 2025 · Cell Reports
- High-resolution spatial mapping of cell state and lineage dynamics in vivo with PEtracerLuke W. Koblan, Kathryn E. Yost, Pu Zheng, William N. Colgan, Matthew G. Jones, Dian Yang, Arhan Kumar, Jaspreet Sandhu, Alexandra Schnell, Dawei Sun et al. · 2025 · Science
- Stereo-cell: Spatial enhanced-resolution single-cell sequencing with high-density DNA nanoball-patterned arraysSha Liao, Xiaoxi Zhou, Chuanyu Liu, Chang Liu, Shijie Hao, Hongyu Luo, Huan Hou, Qian Liu, Zhe Zhang, Liyun Xiao et al. · 2025 · Science
- Aquila: a spatial omics database and analysis platformYimin Zheng, Yitian Chen, Xianting Ding, Koon Ho Wong, Edwin Chong Wing Cheung · 2022 · Nucleic Acids Research
- Interpretable and context-free deconvolution of multi-scale whole transcriptomic data with UniCell deconvolveDaniel Charytonowicz, Rachel Brody, Robert Sebra · 2023 · Nature Communications
- RNA trafficking and subcellular localization—a review of mechanisms, experimental and predictive methodologiesJun Wang, Marc Horlacher, Lixin Cheng, Ole Winther · 2023 · Briefings in Bioinformatics
- Identifying spatial domains of spatially resolved transcriptomics via multi-view graph convolutional networksXuejing Shi, Juntong Zhu, Yahui Long, Cheng Liang · 2023 · Briefings in Bioinformatics
- PROST: quantitative identification of spatially variable genes and domain detection in spatial transcriptomicsYuchen Liang, Guowei Shi, Runlin Cai, Yuchen Yuan, Ziying Xie, Long Yu, Yingjian Huang, Qian Shi, Lizhe Wang, Jun Li et al. · 2024 · Nature Communications
- Region-specific transcriptomic responses to obesity and diabetes in macaque hypothalamusYing Lei, Xian Liang, Yunong Sun, Ting Shan Yao, Hongyu Gong, Zhenhua Chen, Yuanqing Gao, Hui Wang, Ru Wang, Yunqi Huang et al. · 2024 · Cell Metabolism
- Lost in space: what single-cell RNA sequencing cannot tell youKelvin Adema, Michael A. Schon, Michael D. Nodine, Wouter Kohlen · 2024 · Trends in Plant Science
- A large-scale integrated transcriptomic atlas for soybean organ developmentJingwei Fan, Yanting Shen, Chuan Chen, Xi Xian Chen, Xiaoyue Yang, Haixia Liu, Ruiying Chen, Shu‐Lin Liu, Bohan Zhang, Min Zhang et al. · 2025 · Molecular Plant
- Spatially resolved genome-wide joint profiling of epigenome and transcriptome with spatial-ATAC-RNA-seq and spatial-CUT&Tag-RNA-seqHaikuo Li, Shuozhen Bao, Negin Farzad, Xiaoyu Qin, Anthony A. Fung, Di Zhang, Zhiliang Bai, Bo Tao, Rong Fan · 2025 · Nature Protocols
- Spatial multiomics decipher fibroblast–macrophage dynamics in systemic sclerosisZhijian Li, Aleix Rius Rigau, Wenjie Xie, Linlin Huang, Wenjing Ye, Yinan Li, Alexandru‐Emil Matei, Christina Bergmann, Xian Shao, Hejian Zou et al. · 2025 · Annals of the Rheumatic Diseases
- Systematic benchmarking of computational methods to identify spatially variable genesZhijian Li, Zain M.Patel, Dongyuan Song, Sai Nirmayi Yasa, Robrecht Cannoodt, Guanao Yan, Jingyi Jessica Li, Luca Pinello · 2025 · Genome biology
- Single-cell and spatial transcriptomics integration: new frontiers in tumor microenvironment and cellular communicationWenxin Shi, Zhiqiang Zhang, Xiaotong Xu, Yanpeng Tian, Li Feng, Xianghua Huang, Yanfang Du, Zhongkang Li · 2025 · Frontiers in Immunology
- Precision medicine in rheumatoid arthritisKartik Bhamidipati, Kevin S. Wei · 2022 · Best Practice & Research Clinical Rheumatology
- Microglial contribution to the pathology of neurodevelopmental disorders in humansRugilė Matulevičiūtė, Elizabeth Toyin Akinluyi, Tim A.O. Muntslag, Jennifer M. Dewing, Katherine R. Long, Anthony Christopher Vernon, Marie‐Ève Tremblay, David A. Menassa · 2023 · Acta Neuropathologica
- A comprehensive overview of graph neural network-based approaches to clustering for spatial transcriptomicsTeng Liu, Zhaoyu Fang, Zongbo Zhang, Yongxiang Yu, Min Li, Mingzhu Yin · 2023 · Computational and Structural Biotechnology Journal
- The Advancement and Application of the Single-Cell Transcriptome in Biological and Medical ResearchKongwei Huang, Yixue Xu, Tong Feng, Hong Lan, Fei Ling, Hai Xiang, Qingyou Liu · 2024 · Biology
- Spatiotemporal transcriptomics elucidates the pathogenesis of fulminant viral myocarditisLi, Huihui, Chen, Xueting, Wang, James Jiqi, Shen, Juan, Abuduwufuer, Kudusi, Zhang, Zhao, Dong, Zhensheng, Wen, Zheng, He, Jingwei, Chen, Silian et al. · 2025 · Signal Transduction and Targeted Therapy
- Massively Parallel CRISPR‐Based Genetic Perturbation Screening at Single‐Cell ResolutionJunyun Cheng, Gaole Lin, Tianhao Wang, Yunzhu Wang, Wenbo Guo, Jie Liao, Penghui Yang, Jie Chen, Xin Shao, Xiaoyan Lu et al. · 2022 · Advanced Science
- Opportunities and Challenges in Advancing Plant Research with Single-cell OmicsMohammad Saidur Rhaman, Muhammad Ali, Wenxiu Ye, Bosheng Li · 2024 · Genomics Proteomics & Bioinformatics
- A multi-view graph contrastive learning framework for deciphering spatially resolved transcriptomics dataLei Zhang, Shu Liang, Lin Wan · 2024 · Briefings in Bioinformatics
- Towards generative digital twins in biomedical researchJiqing Wu, Viktor Hendrik Koelzer · 2024 · Computational and Structural Biotechnology Journal
- Spatial transcriptomics in breast cancer: providing insight into tumor heterogeneity and promoting individualized therapyJunsha An, Yajie Lu, Yuxi Chen, Yuling Chen, Zhaokai Zhou, Jianping Chen, Cheng Yun Peng, Ruizhen Huang, Fu Peng · 2024 · Frontiers in Immunology
- From morphology to single-cell molecules: high-resolution 3D histology in biomedicineXintian Xu, Jimeng Su, Rongyi Zhu, Kailong Li, Xiaolu Zhao, Jibiao Fan, Fengbiao Mao · 2025 · Molecular Cancer
- Spatially resolved atlas of breast cancer uncovers intercellular machinery of venular niche governing lymphocyte extravasationXin Wang, Zhanyu Wang, Qijun Liao, Pei Yuan, Junpu Mei, Yin Zhang, Chao Wu, Xiyu Kang, Sufei Zheng, Chenxuan Yang et al. · 2025 · Nature Communications
- Single‐cell multiome reveals root hair‐specific responses to salt stressQing Liu, Jingmin Kang, Lin Du, Zhaokun Liu, Hao Liang, Kailai Wang, Haijiao He, Xiaonan Zhang, Qifan Wang, Yiguo Hong et al. · 2025 · New Phytologist
- Single-cell spatial transcriptomics of tertiary lymphoid organ-like structures in human atherosclerotic plaquesZhichao Lai, Deqiang Kong, Q L Li, Yue Wang, Kang V. Li, Xiaohan Duan, Jiang Shao, Yiyun Xie, Junye Chen, Tianjing Zhang et al. · 2025 · Nature Cardiovascular Research
- Spatial epitope barcoding reveals clonal tumor patch behaviorsXavier Rovira‐Clavé, Alexandros P. Drainas, Sizun Jiang, Yunhao Bai, Maya Baron, Bokai Zhu, Alec E. Dallas, Myung Chang Lee, Theresa P. Chu, Alessandra M. E. Holzem et al. · 2022 · Cancer Cell
- Spatial transcriptome analysis on peanut tissues shed light on cell heterogeneity of the pegYiyang Liu, Chunhua Li, Yan Han, Rongchong Li, Feng Cui, He Zhang, Xiaoshan Su, Xiawei Liu, Guoxin Xu, Shubo Wan et al. · 2022 · Plant Biotechnology Journal
- Deconvolution algorithms for inference of the cell-type composition of the spatial transcriptomeYingkun Zhang, Xinrui Lin, Zhixian Yao, Di Sun, Xin Lin, Xiaoyu Wang, Chaoyong James Yang, Jia Tao Song · 2022 · Computational and Structural Biotechnology Journal
- scBridge embraces cell heterogeneity in single-cell RNA-seq and ATAC-seq data integrationYunfan Li, Dan Zhang, Mouxing Yang, Dezhong Peng, Jun Yu, Yu Liu, Jiancheng Lv, Lu Chen, Xi Peng · 2023 · Nature Communications
- Opportunities and challenges of single-cell and spatially resolved genomics methods for neuroscience discoveryBoyan Bonev, Gonçalo Castelo‐Branco, Fei Chen, Simone Codeluppi, M. Ryan Corces, Jean Fan, Myriam Heiman, Kenneth Harris, Fumitaka Inoue, M Kellis et al. · 2024 · Nature Neuroscience
- Spotiphy enables single-cell spatial whole transcriptomics across an entire sectionJiyuan Yang, Ziqian Zheng, Yun Jiao, Kaiwen Yu, Sheetal Bhatara, Xu Yang, Sivaraman Natarajan, Jiahui Zhang, Qingfei Pan, John B. Easton et al. · 2025 · Nature Methods
- SpotSweeper: spatially aware quality control for spatial transcriptomicsMichael S. Totty, Stephanie C. Hicks, Boyi Guo · 2025 · Nature Methods
- Integration of imaging-based and sequencing-based spatial omics mapping on the same tissue section via DBiTplusArchibald Enninful, Zhaojun Zhang, Dmytro Klymyshyn, Matthew H. Ingalls, Mingyu Yang, Hailing Zong, Zhiliang Bai, Negin Farzad, Graham Su, Alev Baysoy et al. · 2026 · Nature Methods
- Sequential sequencing by synthesis and the next-generation sequencing revolutionMathias Uhlén, Stephen R. Quake · 2023 · Trends in biotechnology
- Mapping human tissues with highly multiplexed RNA in situ hybridizationKian Kalhor, Chien-Ju Chen, Ho Suk Lee, Matthew Cai, Mahsa Nafisi, Richard A. Que, Carter R. Palmer, Yixu Yuan, Yida Zhang, Xuwen Li et al. · 2024 · Nature Communications
- Latent feature extraction with a prior-based self-attention framework for spatial transcriptomicsZhen Li, Xiaoyang Chen, Xuegong Zhang, Rui Jiang, Shengquan Chen · 2023 · Genome Research
- Mapping the molecular landscape of Lotus japonicus nodule organogenesis through spatiotemporal transcriptomicsKeyi Ye, Fengjiao Bu, Liyuan Zhong, Zhaonian Dong, Zhaoxu Ma, Zhanpeng Tang, Yu Zhang, Xue Yong Yang, Xun Xu, Ertao Wang et al. · 2024 · Nature Communications
- Nova-ST: Nano-patterned ultra-dense platform for spatial transcriptomicsSuresh Kumar Poovathingal, Kristofer Davie, Lars E. Borm, Roel Vandepoel, Nicolas Poulvellarie, Annelien Verfaillie, Nikky Corthout, Stein Aerts · 2024 · Cell Reports Methods
- Inferring pattern-driving intercellular flows from single-cell and spatial transcriptomicsAxel A. Almet, Yuan‐Chen Tsai, Momoko Watanabe, Qing Hua Nie · 2024 · Nature Methods
- SpaDiT: diffusion transformer for spatial gene expression prediction using scRNA-seqXiaoyu Li, Fangfang Zhu, Wenwen Min · 2024 · Briefings in Bioinformatics
- Current state and future prospects of spatial biology in colorectal cancerFrancisco Carranza, Fernando C. Diaz, Maria Ninova, Enrique I. Velazquez-Villarreal · 2024 · Frontiers in Oncology
- Whole-embryo spatial transcriptomics at subcellular resolution from gastrulation to organogenesisYinan Wan, Jakob El Kholtei, Ignatius Jenie, Mariona Colomer-Rosell, Jialin Liu, Qinghua Zhang, Joaquín Navajas Acedo, Lucia Y. Du, Mireia Codina-Tobias, Mengfan Wang et al. · 2026 · Science
- Spateo: multidimensional spatiotemporal modeling of single-cell spatial transcriptomicsXiaojie Qiu, Daniel Y. Zhu, Jiajun Yao, Zehua Jing, Lulu Zuo, Mingyue Wang, Kyung Hoi Min, Hailin Pan, Shuai Wang, Sha Liao et al. · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
- Dissecting the brain with spatially resolved multi-omicsYijia Fangma, Mengting Liu, Jie Liao, Zhong Chen, Yanrong Zheng · 2023 · Journal of Pharmaceutical Analysis
- An immunohistochemical atlas of necroptotic pathway expressionShene Chiou, Aysha Al‐Ani, Yi Pan, Komal M. Patel, Isabella Y. Kong, Lachlan W. Whitehead, Amanda Light, Samuel N. Young, Marilou H. Barrios, Callum J. Sargeant et al. · 2024 · EMBO Molecular Medicine
- SANTO: a coarse-to-fine alignment and stitching method for spatial omicsHaoyang Li, Yingxin Lin, Wenjia He, Wenkai Han, Xiaopeng Xu, Chencheng Xu, Elva Gao, Hongyu Zhao, Xin Gao · 2024 · Nature Communications
- Multi-omics integration for both single-cell and spatially resolved data based on dual-path graph attention auto-encoderTongxuan Lv, Yong Zhang, Junlin Liu, Qiang Kang, Lin Liu · 2024 · Briefings in Bioinformatics
- Superstable lipid vacuoles endow cartilage with its shape and biomechanicsRaúl Ramos, Kim T. Pham, Richard C. Prince, Leith B. Leiser‐Miller, Maneeshi S. Prasad, Xiaojie Wang, Rachel C. Nordberg, Benjamin J. Bielajew, Jerry C. Y. Hu, Kosuke Yamaga et al. · 2025 · Science
- Benchmarking spatial transcriptomics technologies with the multi-sample SpatialBenchVisium datasetMei R. M. Du, Changqing Wang, Charity W. Law, Daniela Amann‐Zalcenstein, Casey J. A. Anttila, Ling Ling, Peter F. Hickey, Callum J. Sargeant, Yunshun Chen, Lisa J. Ioannidis et al. · 2025 · Genome biology
- An organ-wide spatiotemporal transcriptomic and cellular atlas of the regenerating zebrafish heartLei Li, Meina Lu, Lidong Guo, Xuejiao Zhang, Qun Liu, Meiling Zhang, Junying Gao, Mengyang Xu, Yijian Lu, Fang Zhang et al. · 2025 · Nature Communications
- Spatially Resolved Transcriptomics Technology Facilitates Cancer ResearchQian Wang, Yuan Zhi, Moxin Zi, Yongzhen Mo, Yumin Wang, Qianjin Liao, Shanshan Zhang, Zhaojian Gong, Fuyan Wang, Zhaoyang Zeng et al. · 2023 · Advanced Science
- Comparison of spatial transcriptomics technologies using tumor cryosectionsAnne Rademacher, Alik Huseynov, Michele Bortolomeazzi, Sina Jasmin Wille, Sabrina Schumacher, Pooja Sant, Denise Keitel, Konstantin Okonechnikov, David R. Ghasemi, Kristian W. Pajtler et al. · 2025 · Genome biology
- Spatially resolved transcriptomics: advances and applicationsHonglin Duan, Tao Cheng, Hui Cheng · 2022 · Blood Science
- Accurately deciphering spatial domains for spatially resolved transcriptomics with stClusterTao Wang, Han Shu, Jialu Hu, Yongtian Wang, Jing Wen Chen, Jiajie Peng, Xuequn Shang · 2024 · Briefings in Bioinformatics
- Inferring cell trajectories of spatial transcriptomics via optimal transport analysisXunan Shen, Lulu Zuo, Zhongfei Ye, Zhongyang Yuan, Ke Huang, Zeyu Li, Qichao Yu, Xuanxuan Zou, Xiaoyu Wei, Ping Xu et al. · 2025 · Cell Systems
- Molecular pathways and diagnosis in spatially resolved Alzheimer’s hippocampal atlasPan Wang, Lei Han, Lifang Wang, Quyuan Tao, Zhen Guo, Ting Luo, Youzhe He, Zhi Ping Xu, Jiayi Yu, Yuyang Liu et al. · 2025 · Neuron
- Time-aligned hourglass gastrulation models in rabbit and mouseYoav Mayshar, Ofir Raz, Saifeng Cheng, Raz Ben-Yair, Ron Hadas, Netta Reines, Markus Mittnenzweig, Oren Ben-Kiki, Aviezer Lifshitz, Amos Tanay et al. · 2023 · Cell
- Multi-slice spatial transcriptome domain analysis with SpaDoBin Duan, Shaoqi Chen, Xiaojie Cheng, Qi Liu · 2024 · Genome biology
- A practical guide to spatial transcriptomicsLukáš Valihrach, Daniel Žucha, Pavel Abaffy, Mikael Kubista · 2024 · Molecular Aspects of Medicine
- Unraveling aging from transcriptomicsYuanfang Huang, Shouxuan Zhu, Shuai Yao, Haotian Zhai, Chenyang Liu, Jing‐Dong J. Han · 2024 · Trends in Genetics
- Psychedelic control of neuroimmune interactions governing fearElizabeth N Chung, Jinsu Lee, Carolina Manganeli Polonio, Joshua Choi, Camilo Faust Akl, Michael Kilian, Wiebke M. Weiß, Georgia Gunner, Mingyu Ye, Tae Hyun Heo et al. · 2025 · Nature
- Tri-omic single-cell mapping of the 3D epigenome and transcriptome in whole mouse brains throughout the lifespanHaoxi Chai, Xingyu Huang, Guangzhou Xiong, Jiaxiang Huang, Katarzyna Karolina Pels, Lingyun Meng, Jin Han, Dongmei Tang, Guanjing Pan, Liang Deng et al. · 2025 · Nature Methods