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Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+
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- Kosuke Tomimatsu & Takeru Fujii & Ryoma Bise & Kazufumi Hosoda & Yosuke Taniguchi & Hiroshi Ochiai & Hiroaki Ohishi & Kanta Ando & Ryoma Minami & Kaori Tanaka & Taro Tachibana & Seiichi Mori & Akihito, 2024. "Precise immunofluorescence canceling for highly multiplexed imaging to capture specific cell states," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
- Xinyi Zhang & Saradha Venkatachalapathy & Daniel Paysan & Paulina Schaerer & Claudio Tripodo & Caroline Uhler & G. V. Shivashankar, 2024. "Unsupervised representation learning of chromatin images identifies changes in cell state and tissue organization in DCIS," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
- Jingyang Qian & Hudong Bao & Xin Shao & Yin Fang & Jie Liao & Zhuo Chen & Chengyu Li & Wenbo Guo & Yining Hu & Anyao Li & Yue Yao & Xiaohui Fan & Yiyu Cheng, 2024. "Simulating multiple variability in spatially resolved transcriptomics with scCube," Nature Communications, Nature, vol. 15(1), pages 1-21, December.
- Yichun He & Xin Tang & Jiahao Huang & Jingyi Ren & Haowen Zhou & Kevin Chen & Albert Liu & Hailing Shi & Zuwan Lin & Qiang Li & Abhishek Aditham & Johain Ounadjela & Emanuelle I. Grody & Jian Shu & Ji, 2021. "ClusterMap for multi-scale clustering analysis of spatial gene expression," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
- Lulu Shang & Xiang Zhou, 2022. "Spatially aware dimension reduction for spatial transcriptomics," Nature Communications, Nature, vol. 13(1), pages 1-22, December.
- 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.
- Paul W Angel & Nadia Rajab & Yidi Deng & Chris M Pacheco & Tyrone Chen & Kim-Anh Lê Cao & Jarny Choi & Christine A Wells, 2020. "A simple, scalable approach to building a cross-platform transcriptome atlas," PLOS Computational Biology, Public Library of Science, vol. 16(9), pages 1-21, September.
- 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.
- S. Vickovic & B. Lötstedt & J. Klughammer & S. Mages & Å Segerstolpe & O. Rozenblatt-Rosen & A. Regev, 2022. "SM-Omics is an automated platform for high-throughput spatial multi-omics," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
- Brendan F. Miller & Feiyang Huang & Lyla Atta & Arpan Sahoo & Jean Fan, 2022. "Reference-free cell type deconvolution of multi-cellular pixel-resolution spatially resolved transcriptomics data," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
- Jingyang Qian & Jie Liao & Ziqi Liu & Ying Chi & Yin Fang & Yanrong Zheng & Xin Shao & Bingqi Liu & Yongjin Cui & Wenbo Guo & Yining Hu & Hudong Bao & Penghui Yang & Qian Chen & Mingxiao Li & Bing Zha, 2023. "Reconstruction of the cell pseudo-space from single-cell RNA sequencing data with scSpace," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
- Jie Liao & Jingyang Qian & Yin Fang & Zhuo Chen & Xiang Zhuang & Ningyu Zhang & Xin Shao & Yining Hu & Penghui Yang & Junyun Cheng & Yang Hu & Lingqi Yu & Haihong Yang & Jinlu Zhang & Xiaoyan Lu & Li , 2022. "De novo analysis of bulk RNA-seq data at spatially resolved single-cell resolution," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
- Zhaohui Cao & Wenlong Zuo & Lanxiang Wang & Junyu Chen & Zepeng Qu & Fan Jin & Lei Dai, 2023. "Spatial profiling of microbial communities by sequential FISH with error-robust encoding," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
- 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.
- 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.
- 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.
- 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.
- Misa Minegishi & Takahiro Kuchimaru & Kaori Nishikawa & Takayuki Isagawa & Satoshi Iwano & Kei Iida & Hiromasa Hara & Shizuka Miura & Marika Sato & Shigeaki Watanabe & Akifumi Shiomi & Yo Mabuchi & Hi, 2023. "Secretory GFP reconstitution labeling of neighboring cells interrogates cell–cell interactions in metastatic niches," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
- Ian Covert & Rohan Gala & Tim Wang & Karel Svoboda & Uygar Sümbül & Su-In Lee, 2023. "Predictive and robust gene selection for spatial transcriptomics," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
- Xin Shao & Chengyu Li & Haihong Yang & Xiaoyan Lu & Jie Liao & Jingyang Qian & Kai Wang & Junyun Cheng & Penghui Yang & Huajun Chen & Xiao Xu & Xiaohui Fan, 2022. "Knowledge-graph-based cell-cell communication inference for spatially resolved transcriptomic data with SpaTalk," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
- 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.
- Xinyi Zhang & Xiao Wang & G. V. Shivashankar & Caroline Uhler, 2022. "Graph-based autoencoder integrates spatial transcriptomics with chromatin images and identifies joint biomarkers for Alzheimer’s disease," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
- 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.
- 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.
- 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.
- Zhiyuan Yuan, 2024. "MENDER: fast and scalable tissue structure identification in spatial omics data," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
- Yingfeng Tao & Xiaoliu Zhou & Leqiang Sun & Da Lin & Huaiyuan Cai & Xi Chen & Wei Zhou & Bing Yang & Zhe Hu & Jing Yu & Jing Zhang & Xiaoqing Yang & Fang Yang & Bang Shen & Wenbao Qi & Zhenfang Fu & J, 2023. "Highly efficient and robust π-FISH rainbow for multiplexed in situ detection of diverse biomolecules," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
- Bohan Li & Feng Bao & Yimin Hou & Fengji Li & Hongjue Li & Yue Deng & Qionghai Dai, 2024. "Tissue characterization at an enhanced resolution across spatial omics platforms with deep generative model," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
- Zixiang Zhou & Yunshan Zhong & Zemin Zhang & Xianwen Ren, 2023. "Spatial transcriptomics deconvolution at single-cell resolution using Redeconve," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
- Chen-Rui Xia & Zhi-Jie Cao & Xin-Ming Tu & Ge Gao, 2023. "Spatial-linked alignment tool (SLAT) for aligning heterogenous slices," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
- Beibei Ru & Jinlin Huang & Yu Zhang & Kenneth Aldape & Peng Jiang, 2023. "Estimation of cell lineages in tumors from spatial transcriptomics data," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
- 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.
- David L. Hölscher & Nassim Bouteldja & Mehdi Joodaki & Maria L. Russo & Yu-Chia Lan & Alireza Vafaei Sadr & Mingbo Cheng & Vladimir Tesar & Saskia V. Stillfried & Barbara M. Klinkhammer & Jonathan Bar, 2023. "Next-Generation Morphometry for pathomics-data mining in histopathology," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
- Gennady Gorin & Mengyu Wang & Ido Golding & Heng Xu, 2020. "Stochastic simulation and statistical inference platform for visualization and estimation of transcriptional kinetics," PLOS ONE, Public Library of Science, vol. 15(3), pages 1-12, March.
- Benjamin L. Walker & Qing Nie, 2023. "NeST: nested hierarchical structure identification in spatial transcriptomic data," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
- Wei Zhao & Kevin G. Johnston & Honglei Ren & Xiangmin Xu & Qing Nie, 2023. "Inferring neuron-neuron communications from single-cell transcriptomics through NeuronChat," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
- Haoyang Li & Juexiao Zhou & Zhongxiao Li & Siyuan Chen & Xingyu Liao & Bin Zhang & Ruochi Zhang & Yu Wang & Shiwei Sun & Xin Gao, 2023. "A comprehensive benchmarking with practical guidelines for cellular deconvolution of spatial transcriptomics," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
- Arpiar Saunders & Kee Wui Huang & Cassandra Vondrak & Christina Hughes & Karina Smolyar & Harsha Sen & Adrienne C. Philson & James Nemesh & Alec Wysoker & Seva Kashin & Bernardo L. Sabatini & Steven A, 2022. "Ascertaining cells’ synaptic connections and RNA expression simultaneously with barcoded rabies virus libraries," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
- Michal Polonsky & Louisa M. S. Gerhardt & Jina Yun & Kari Koppitch & Katsuya Lex Colón & Henry Amrhein & Barbara Wold & Shiwei Zheng & Guo-Cheng Yuan & Matt Thomson & Long Cai & Andrew P. McMahon, 2024. "Spatial transcriptomics defines injury specific microenvironments and cellular interactions in kidney regeneration and disease," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
- Zhiyuan Yuan & Yisi Li & Minglei Shi & Fan Yang & Juntao Gao & Jianhua Yao & Michael Q. Zhang, 2022. "SOTIP is a versatile method for microenvironment modeling with spatial omics data," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
- Shijia Zhu & Naoto Kubota & Shidan Wang & Tao Wang & Guanghua Xiao & Yujin Hoshida, 2024. "STIE: Single-cell level deconvolution, convolution, and clustering in in situ capturing-based spatial transcriptomics," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
- Kristina Handler & Karsten Bach & Costanza Borrelli & Salvatore Piscuoglio & Xenia Ficht & Ilhan E. Acar & Andreas E. Moor, 2023. "Fragment-sequencing unveils local tissue microenvironments at single-cell resolution," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
- Lukas M. Weber & Arkajyoti Saha & Abhirup Datta & Kasper D. Hansen & Stephanie C. Hicks, 2023. "nnSVG for the scalable identification of spatially variable genes using nearest-neighbor Gaussian processes," Nature Communications, Nature, vol. 14(1), pages 1-12, December.