SPACEL: deep learning-based characterization of spatial transcriptome architectures
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DOI: 10.1038/s41467-023-43220-3
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- Andrew Erickson & Mengxiao He & Emelie Berglund & Maja Marklund & Reza Mirzazadeh & Niklas Schultz & Linda Kvastad & Alma Andersson & Ludvig Bergenstråhle & Joseph Bergenstråhle & Ludvig Larsson & Lei, 2022. "Spatially resolved clonal copy number alterations in benign and malignant tissue," Nature, Nature, vol. 608(7922), pages 360-367, August.
- 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.
- Kangning Dong & Shihua Zhang, 2022. "Deciphering spatial domains from spatially resolved transcriptomics with an adaptive graph attention auto-encoder," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
- Wei Liu & Xu Liao & Ziye Luo & Yi Yang & Mai Chan Lau & Yuling Jiao & Xingjie Shi & Weiwei Zhai & Hongkai Ji & Joe Yeong & Jin Liu, 2023. "Author Correction: Probabilistic embedding, clustering, and alignment for integrating spatial transcriptomics data with PRECAST," Nature Communications, Nature, vol. 14(1), pages 1-1, December.
- Rebecca D. Hodge & Trygve E. Bakken & Jeremy A. Miller & Kimberly A. Smith & Eliza R. Barkan & Lucas T. Graybuck & Jennie L. Close & Brian Long & Nelson Johansen & Osnat Penn & Zizhen Yao & Jeroen Egg, 2019. "Conserved cell types with divergent features in human versus mouse cortex," Nature, Nature, vol. 573(7772), pages 61-68, 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.
- Christoph Kuppe & Ricardo O. Ramirez Flores & Zhijian Li & Sikander Hayat & Rebecca T. Levinson & Xian Liao & Monica T. Hannani & Jovan Tanevski & Florian Wünnemann & James S. Nagai & Maurice Halder &, 2022. "Spatial multi-omic map of human myocardial infarction," Nature, Nature, vol. 608(7924), pages 766-777, August.
- Gioele La Manno & Kimberly Siletti & Alessandro Furlan & Daniel Gyllborg & Elin Vinsland & Alejandro Mossi Albiach & Christoffer Mattsson Langseth & Irina Khven & Alex R. Lederer & Lisa M. Dratva & An, 2021. "Molecular architecture of the developing mouse brain," Nature, Nature, vol. 596(7870), pages 92-96, August.
- Anjali Rao & Dalia Barkley & Gustavo S. França & Itai Yanai, 2021. "Exploring tissue architecture using spatial transcriptomics," Nature, Nature, vol. 596(7871), pages 211-220, August.
- Meng Zhang & Stephen W. Eichhorn & Brian Zingg & Zizhen Yao & Kaelan Cotter & Hongkui Zeng & Hongwei Dong & Xiaowei Zhuang, 2021. "Spatially resolved cell atlas of the mouse primary motor cortex by MERFISH," Nature, Nature, vol. 598(7879), pages 137-143, October.
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- 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.
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