Spatial reconstruction of single-cell gene expression data

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Items 701–800 of 1,061

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    Sagner, Andreas, Gaber, Zachary B., Delile, Julien, Kong, Jennifer H., Rousso, David L., Pearson, Caroline A., Weicksel, Steven E., Melchionda, Manuela, Mousavy Gharavy, S. Neda, Briscoe, James et al. · 2018 · PLoS Biology
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    Velasco, Silvia, Ibrahim, Mahmoud M., Kakumanu, Akshay, Garipler, Görkem, Aydin, Begüm, Al-Sayegh, Mohamed Ahmed, Hirsekorn, Antje, Abdul-Rahman, Farah, Satija, Rahul, Ohler, Uwe et al. · 2017 · Cell Stem Cell
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    Yanyong Cao, Juan Ma, Shengbo Han, Mengwei Hou, Xun Wei, Xingrui Zhang, Zhanyuan J. Zhang, Suli Sun, Lixia Ku, Jihua Tang et al. · 2023 · Plant Biotechnology Journal
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    Yu-Jui Ho, Naishitha Anaparthy, David C. Molik, Grinu Mathew, Toby P. Aicher, Ami K. Patel, James B Hicks, Molly Hammell · 2018 · Genome Research
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    Mengmeng Jiang, Yanyu Xiao, E Weigao, Lifeng Ma, Jingjing Wang, Haide Chen, Ce Gao, Yuan Liao, Qile Guo, Jinrong Peng et al. · 2021 · Frontiers in Cell and Developmental Biology
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    Heon‐Woo Lee, Yanying Xu, Xiaolong Zhu, Cholsoon Jang, Woosoung Choi, Hosung Bae, Weiwei Wang, Liqun He, Suk‐Won Jin, Zoltan Pierre Arany et al. · 2022 · The EMBO Journal
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    Lihong Peng, Feixiang Wang, Zhao Wang, Jingwei Tan, Huang Li, Xiongfei Tian, Guangyi Liu, Liqian Zhou · 2022 · Briefings in Bioinformatics
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