Exploring tissue architecture using spatial transcriptomics

Citations

Cited by:

1. Johannes Wirth & Nina Huber & Kelvin Yin & Sophie Brood & Simon Chang & Celia P. Martinez-Jimenez & Matthias Meier, 2023. "Spatial transcriptomics using multiplexed deterministic barcoding in tissue," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
2. Zhiyuan Liu & Dafei Wu & Weiwei Zhai & Liang Ma, 2023. "SONAR enables cell type deconvolution with spatially weighted Poisson-Gamma model for spatial transcriptomics," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
3. Wenyi Yang & Pingping Wang & Shouping Xu & Tao Wang & Meng Luo & Yideng Cai & Chang Xu & Guangfu Xue & Jinhao Que & Qian Ding & Xiyun Jin & Yuexin Yang & Fenglan Pang & Boran Pang & Yi Lin & Huan Nie , 2024. "Deciphering cell–cell communication at single-cell resolution for spatial transcriptomics with subgraph-based graph attention network," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
4. Xinyu Hu & Bob van Sluijs & Óscar García-Blay & Yury Stepanov & Koen Rietrae & Wilhelm T. S. Huck & Maike M. K. Hansen, 2024. "ARTseq-FISH reveals position-dependent differences in gene expression of micropatterned mESCs," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
5. Juexin Wang & Jinpu Li & Skyler T. Kramer & Li Su & Yuzhou Chang & Chunhui Xu & Michael T. Eadon & Krzysztof Kiryluk & Qin Ma & Dong Xu, 2023. "Dimension-agnostic and granularity-based spatially variable gene identification using BSP," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
6. Zhiyuan Yuan, 2024. "MENDER: fast and scalable tissue structure identification in spatial omics data," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
7. Lulu Shang & Xiang Zhou, 2022. "Spatially aware dimension reduction for spatial transcriptomics," Nature Communications, Nature, vol. 13(1), pages 1-22, December.
8. Xinrui Zhou & Wan Yi Seow & Norbert Ha & Teh How Cheng & Lingfan Jiang & Jeeranan Boonruangkan & Jolene Jie Lin Goh & Shyam Prabhakar & Nigel Chou & Kok Hao Chen, 2024. "Highly sensitive spatial transcriptomics using FISHnCHIPs of multiple co-expressed genes," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
9. Honglei Ren & Benjamin L. Walker & Zixuan Cang & Qing Nie, 2022. "Identifying multicellular spatiotemporal organization of cells with SpaceFlow," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
10. Wei Liu & Xu Liao & Ziye Luo & Yi Yang & Mai Chan Lau & Yuling Jiao & Xingjie Shi & Weiwei Zhai & Hongkai Ji & Joe Yeong & Jin Liu, 2023. "Probabilistic embedding, clustering, and alignment for integrating spatial transcriptomics data with PRECAST," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
11. Linhua Wang & Mirjana Maletic-Savatic & Zhandong Liu, 2022. "Region-specific denoising identifies spatial co-expression patterns and intra-tissue heterogeneity in spatially resolved transcriptomics data," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
12. Zhenzhen Xun & Xinyu Ding & Yao Zhang & Benyan Zhang & Shujing Lai & Duowu Zou & Junke Zheng & Guoqiang Chen & Bing Su & Leng Han & Youqiong Ye, 2023. "Reconstruction of the tumor spatial microenvironment along the malignant-boundary-nonmalignant axis," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
13. Zhuoxuan Li & Tianjie Wang & Pentao Liu & Yuanhua Huang, 2023. "SpatialDM for rapid identification of spatially co-expressed ligand–receptor and revealing cell–cell communication patterns," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
14. Michaela Schwaiger-Haber & Ethan Stancliffe & Dhanalakshmi S. Anbukumar & Blake Sells & Jia Yi & Kevin Cho & Kayla Adkins-Travis & Milan G. Chheda & Leah P. Shriver & Gary J. Patti, 2023. "Using mass spectrometry imaging to map fluxes quantitatively in the tumor ecosystem," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
15. Anurendra Kumar & Alex W. Schrader & Bhavay Aggarwal & Ali Ebrahimpour Boroojeny & Marisa Asadian & JuYeon Lee & You Jin Song & Sihai Dave Zhao & Hee-Sun Han & Saurabh Sinha, 2024. "Intracellular spatial transcriptomic analysis toolkit (InSTAnT)," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
16. Yoshihiro Morishita & Sang-Woo Lee & Takayuki Suzuki & Hitoshi Yokoyama & Yasuhiro Kamei & Koji Tamura & Aiko Kawasumi-Kita, 2023. "An archetype and scaling of developmental tissue dynamics across species," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
17. Haoyang Li & Yingxin Lin & Wenjia He & Wenkai Han & Xiaopeng Xu & Chencheng Xu & Elva Gao & Hongyu Zhao & Xin Gao, 2024. "SANTO: a coarse-to-fine alignment and stitching method for spatial omics," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
18. Quentin Blampey & Kevin Mulder & Margaux Gardet & Stergios Christodoulidis & Charles-Antoine Dutertre & Fabrice André & Florent Ginhoux & Paul-Henry Cournède, 2024. "Sopa: a technology-invariant pipeline for analyses of image-based spatial omics," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
19. Arezou Rahimi & Luis A. Vale-Silva & Maria Fälth Savitski & Jovan Tanevski & Julio Saez-Rodriguez, 2024. "DOT: a flexible multi-objective optimization framework for transferring features across single-cell and spatial omics," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
20. Kian Kalhor & Chien-Ju Chen & Ho Suk Lee & Matthew Cai & Mahsa Nafisi & Richard Que & Carter R. Palmer & Yixu Yuan & Yida Zhang & Xuwen Li & Jinghui Song & Amanda Knoten & Blue B. Lake & Joseph P. Gau, 2024. "Mapping human tissues with highly multiplexed RNA in situ hybridization," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
21. Xiaomeng Wan & Jiashun Xiao & Sindy Sing Ting Tam & Mingxuan Cai & Ryohichi Sugimura & Yang Wang & Xiang Wan & Zhixiang Lin & Angela Ruohao Wu & Can Yang, 2023. "Integrating spatial and single-cell transcriptomics data using deep generative models with SpatialScope," Nature Communications, Nature, vol. 14(1), pages 1-22, December.
22. Peter Androvic & Martina Schifferer & Katrin Perez Anderson & Ludovico Cantuti-Castelvetri & Hanyi Jiang & Hao Ji & Lu Liu & Garyfallia Gouna & Stefan A. Berghoff & Simon Besson-Girard & Johanna Knofe, 2023. "Spatial Transcriptomics-correlated Electron Microscopy maps transcriptional and ultrastructural responses to brain injury," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
23. Raman Sethi & Kok Siong Ang & Mengwei Li & Yahui Long & Jingjing Ling & Jinmiao Chen, 2024. "ezSingleCell: an integrated one-stop single-cell and spatial omics analysis platform for bench scientists," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
24. Reza Mirzazadeh & Zaneta Andrusivova & Ludvig Larsson & Phillip T. Newton & Leire Alonso Galicia & Xesús M. Abalo & Mahtab Avijgan & Linda Kvastad & Alexandre Denadai-Souza & Nathalie Stakenborg & Ale, 2023. "Spatially resolved transcriptomic profiling of degraded and challenging fresh frozen samples," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
25. Rongbo Shen & Lin Liu & Zihan Wu & Ying Zhang & Zhiyuan Yuan & Junfu Guo & Fan Yang & Chao Zhang & Bichao Chen & Wanwan Feng & Chao Liu & Jing Guo & Guozhen Fan & Yong Zhang & Yuxiang Li & Xun Xu & Ji, 2022. "Spatial-ID: a cell typing method for spatially resolved transcriptomics via transfer learning and spatial embedding," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
26. Qingnan Liang & Yuefan Huang & Shan He & Ken Chen, 2023. "Pathway centric analysis for single-cell RNA-seq and spatial transcriptomics data with GSDensity," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
27. Xin Yuan & Yanran Ma & Ruitian Gao & Shuya Cui & Yifan Wang & Botao Fa & Shiyang Ma & Ting Wei & Shuangge Ma & Zhangsheng Yu, 2024. "HEARTSVG: a fast and accurate method for identifying spatially variable genes in large-scale spatial transcriptomics," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
28. Gabrielle A. Dotson & Can Chen & Stephen Lindsly & Anthony Cicalo & Sam Dilworth & Charles Ryan & Sivakumar Jeyarajan & Walter Meixner & Cooper Stansbury & Joshua Pickard & Nicholas Beckloff & Amit Su, 2022. "Deciphering multi-way interactions in the human genome," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
29. Hua Zhang & Yuan Liu & Lauren Fields & Xudong Shi & Penghsuan Huang & Haiyan Lu & Andrew J. Schneider & Xindi Tang & Luigi Puglielli & Nathan V. Welham & Lingjun Li, 2023. "Single-cell lipidomics enabled by dual-polarity ionization and ion mobility-mass spectrometry imaging," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
30. Yahui Long & Kok Siong Ang & Mengwei Li & Kian Long Kelvin Chong & Raman Sethi & Chengwei Zhong & Hang Xu & Zhiwei Ong & Karishma Sachaphibulkij & Ao Chen & Li Zeng & Huazhu Fu & Min Wu & Lina Hsiu Ki, 2023. "Spatially informed clustering, integration, and deconvolution of spatial transcriptomics with GraphST," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
31. Yuchen Liang & Guowei Shi & Runlin Cai & Yuchen Yuan & Ziying Xie & Long Yu & Yingjian Huang & Qian Shi & Lizhe Wang & Jun Li & Zhonghui Tang, 2024. "PROST: quantitative identification of spatially variable genes and domain detection in spatial transcriptomics," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
32. Tianyi Xia & Luni Hu & Lulu Zuo & Lei Cao & Yunjia Zhang & Mengyang Xu & Qin Lu & Lei Zhang & Taotao Pan & Bohan Zhang & Bowen Ma & Chuan Chen & Junfu Guo & Chang Shi & Mei Li & Chao Liu & Yuxiang Li , 2024. "ST-GEARS: Advancing 3D downstream research through accurate spatial information recovery," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
33. Wei Feng & Abha Bais & Haoting He & Cassandra Rios & Shan Jiang & Juan Xu & Cindy Chang & Dennis Kostka & Guang Li, 2022. "Single-cell transcriptomic analysis identifies murine heart molecular features at embryonic and neonatal stages," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
34. Zhixing Zhong & Junchen Hou & Zhixian Yao & Lei Dong & Feng Liu & Junqiu Yue & Tiantian Wu & Junhua Zheng & Gaoliang Ouyang & Chaoyong Yang & Jia Song, 2024. "Domain generalization enables general cancer cell annotation in single-cell and spatial transcriptomics," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
35. Manuel Sigle & Anne-Katrin Rohlfing & Martin Kenny & Sophia Scheuermann & Na Sun & Ulla Graeßner & Verena Haug & Jessica Sudmann & Christian M. Seitz & David Heinzmann & Katja Schenke-Layland & Patric, 2023. "Translating genomic tools to Raman spectroscopy analysis enables high-dimensional tissue characterization on molecular resolution," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
36. Jongsu Choi & Jin Li & Salma Ferdous & Qingnan Liang & Jeffrey R. Moffitt & Rui Chen, 2023. "Spatial organization of the mouse retina at single cell resolution by MERFISH," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
37. Hao Xu & Shuyan Wang & Minghao Fang & Songwen Luo & Chunpeng Chen & Siyuan Wan & Rirui Wang & Meifang Tang & Tian Xue & Bin Li & Jun Lin & Kun Qu, 2023. "SPACEL: deep learning-based characterization of spatial transcriptome architectures," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
38. Connor Stashko & Mary-Kate Hayward & Jason J. Northey & Neil Pearson & Alastair J. Ironside & Johnathon N. Lakins & Roger Oria & Marie-Anne Goyette & Lakyn Mayo & Hege G. Russnes & E. Shelley Hwang & , 2023. "A convolutional neural network STIFMap reveals associations between stromal stiffness and EMT in breast cancer," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
39. Simon Davis & Connor Scott & Janina Oetjen & Philip D. Charles & Benedikt M. Kessler & Olaf Ansorge & Roman Fischer, 2023. "Deep topographic proteomics of a human brain tumour," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
40. Meilin Xue & Youwei Zhu & Yongsheng Jiang & Lijie Han & Minmin Shi & Rui Su & Liwen Wang & Cheng Xiong & Chaofu Wang & Ting Wang & Shijie Deng & Dong Wu & Yizhi Cao & Lei Dong & Fan Bai & Shulin Zhao , 2023. "Schwann cells regulate tumor cells and cancer-associated fibroblasts in the pancreatic ductal adenocarcinoma microenvironment," Nature Communications, Nature, vol. 14(1), pages 1-18, December.