Spatial reconstruction of single-cell gene expression data

Cited by (1,061)

Items 101–200 of 1,061

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   Wagner, Allon, Regev, Aviv, Yosef, Nir · 2016 · Nature Biotechnology
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   Maximilian Strunz, Lukas Mikolaj Simon, Meshal Ansari, Jaymin J. Kathiriya, Ilias Angelidis, Christoph H. Mayr, George Tsidiridis, Marius Lange, Laura F. Mattner, Min Yee et al. · 2020 · Nature Communications
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   Shah, Sheel, Lubeck, Eric, Zhou, Wen, Cai, Long · 2016 · Neuron
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   Liwen Xu, Chunyu Deng, Bo Pang, Xinxin Zhang, Wei Liu, Gaoming Liao, Huating Yuan, Cheng Peng, Feng Li, Zhilin Long et al. · 2018 · Cancer Research
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   Svensson, Valentine, Teichmann, Sarah A, Stegle, Oliver · 2018 · Nature Methods
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    Asp, Michaela, Bergenstråhle, Joseph, Lundeberg, Joakim · 2020 · BioEssays
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    S. Steven Potter · 2018 · Nature Reviews Nephrology
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    Bushra Raj, Daniel E. Wagner, Aaron McKenna, Shristi Pandey, Allon Moshe Klein, Jay Shendure, James A. Gagnon, Alexander F. Schier · 2018 · Nature Biotechnology
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    Yang, Andrew C., Kern, Fabian, Losada, Patricia M., Agam, Maayan R., Maat, Christina A., Schmartz, Georges P., Fehlmann, Tobias, Stein, Julian A., Schaum, Nicholas, Lee, Davis P. et al. · 2021 · Nature
25. Spatiotemporal Developmental Trajectories in the Arabidopsis Root Revealed Using High-Throughput Single Cell RNA Sequencing
    Tom Denyer, Xiaoli Ma, Simon Klesen, Emanuele Scacchi, Kay Nieselt, Marja C.P. Timmermans · 2018 · Developmental Cell
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    Daniel E. Wagner, Allon Moshe Klein · 2020 · Nature Reviews Genetics
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    Dario Bressan, Giorgia Battistoni, Gregory J. Hannon · 2023 · Science
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    Pierson, Emma, Yau, Christopher · 2015 · Genome Biology
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    Habib, Naomi, Li, Yinqing, Heidenreich, Matthias, Swiech, Lukasz, Avraham-Davidi, Inbal, Trombetta, John J., Hession, Cynthia, Zhang, Feng, Regev, Aviv · 2016 · Science
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    2018
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    Hicks, Stephanie C, Townes, F William, Teng, Mingxiang, Irizarry, Rafael A · 2018 · Biostatistics
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    Si Wang, Yuxuan Zheng, Jingyi Li, Yang Yu, Weiqi Zhang, Moshi Song, Zunpeng Liu, Zheying Min, Huifang Hu, Ying Jing et al. · 2020 · Cell
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    Fujii, Masayuki, Matano, Mami, Toshimitsu, Kohta, Takano, Ai, Mikami, Yohei, Nishikori, Shingo, Sugimoto, Shinya, Sato, Toshiro · 2018 · Cell Stem Cell
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    Rafael José Argüello, Alexis J. Combes, Rémy Char, Julien Paul Gigan, Ania I. Baaziz, Evens Bousiquot, Voahirana Camosseto, Bushra Samad, Jessica L. Tsui, Peter Yan et al. · 2020 · Cell Metabolism
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    Chen, Yang, Kim, Jiha, Yang, Sujuan, Wang, Huamin, Wu, Chang-Jiun, Sugimoto, Hikaru, LeBleu, Valerie S., Kalluri, Raghu · 2021 · Cancer Cell
37. High-throughput single-cell gene-expression profiling with multiplexed error-robust fluorescence in situ hybridization
    Jeffrey R. Moffitt, Junjie Hao, Guiping Wang, Kok Hao Chen, Hazen P. Babcock, Xiaowei Zhuang · 2016 · Proceedings of the National Academy of Sciences
38. Single-cell transcriptomes of the human skin reveal age-related loss of fibroblast priming
    Solé-Boldo, Llorenç, Raddatz, Günter, Schütz, Sabrina, Mallm, Jan-Philipp, Rippe, Karsten, Lonsdorf, Anke S., Rodríguez-Paredes, Manuel, Lyko, Frank · 2020 · Communications Biology
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    Kevin R. King, Aaron D. Aguirre, Yuxiang Ye, Yuan Sun, Jason D. Roh, Richard P Ng, Rainer H. Köhler, Sean P. Arlauckas, Yoshiko Iwamoto, Andrej J. Savol et al. · 2017 · Nature Medicine
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    Orit Rozenblatt–Rosen, Aviv Regev, Philipp Oberdoerffer, Tal Nawy, Anna Hupalowska, Jennifer Rood, Orr Ashenberg, Ethan G Cerami, Robert J. Coffey, Emek Demir et al. · 2020 · Cell
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    Kotliar, Dylan, Veres, Adrian, Nagy, M Aurel, Tabrizi, Shervin, Hodis, Eran, Melton, Douglas A, Sabeti, Pardis C · 2019 · eLife
43. The dynamics of gene expression in vertebrate embryogenesis at single-cell resolution
    James Briggs, Caleb Weinreb, Daniel E. Wagner, Sean G. Megason, Leonid Peshkin, Marc W. Kirschner, Allon Moshe Klein · 2018 · Science
44. Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity
    Emelie Berglund, Jonas Maaskola, Niklas Schultz, Stefanie Friedrich, Maja Marklund, Joseph Bergenstråhle, Firas Tarish, Anna Tanoglidi, Sanja Vicković, Ludvig Larsson et al. · 2018 · Nature Communications
45. Single-Cell RNA-Seq Analysis Maps Development of Human Germline Cells and Gonadal Niche Interactions
    Li Li, Ji Dong, Liying Yan, Jun Yong, Xixi Liu, Yuqiong Hu, Xiaoying Fan, Xinglong Wu, Hongshan Guo, Xiaoye Wang et al. · 2017 · Cell stem cell
46. Transcriptional Reprogramming of Distinct Peripheral Sensory Neuron Subtypes after Axonal Injury
    William R. Renthal, Ivan Tochitsky, Lite Yang, Yung‐Chih Cheng, Emmy Li, Riki Kawaguchi, Daniel H. Geschwind, Clifford J. Woolf · 2020 · Neuron
47. Molecular architecture of the developing mouse brain
    La Manno, Gioele, Siletti, Kimberly, Furlan, Alessandro, Gyllborg, Daniel, Vinsland, Elin, Mossi Albiach, Alejandro, Mattsson Langseth, Christoffer, Khven, Irina, Lederer, Alex R., Dratva, Lisa M. et al. · 2021 · Nature
48. Single-Cell Transcriptomics of Regulatory T Cells Reveals Trajectories of Tissue Adaptation
    Miragaia, Ricardo J., Gomes, Tomás, Chomka, Agnieszka, Jardine, Laura, Riedel, Angela, Hegazy, Ahmed N., Whibley, Natasha, Tucci, Andrea, Chen, Xi, Lindeman, Ida et al. · 2019 · Immunity
49. Simultaneous lineage tracing and cell-type identification using CRISPR–Cas9-induced genetic scars
    Spanjaard, Bastiaan, Hu, Bo, Mitic, Nina, Olivares-Chauvet, Pedro, Janjuha, Sharan, Ninov, Nikolay, Junker, Jan Philipp · 2018 · Nature Biotechnology
50. Metabolic modeling of single Th17 cells reveals regulators of autoimmunity
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51. A Comprehensive Roadmap of Murine Spermatogenesis Defined by Single-Cell RNA-Seq
    Christopher Daniel Green, Qianyi Ma, Gabriel L. Manske, Adrienne Niederriter Shami, Xianing Zheng, Simone Marini, Lindsay Moritz, Caleb Sultan, Stephen J. Gurczynski, Bethany B. Moore et al. · 2018 · Developmental Cell
52. Single-cell analysis reveals fibroblast heterogeneity and myeloid-derived adipocyte progenitors in murine skin wounds
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53. Single-cell analysis reveals T cell infiltration in old neurogenic niches
    Dulken, Ben W., Buckley, Matthew T., Navarro Negredo, Paloma, Saligrama, Naresha, Cayrol, Romain, Leeman, Dena S., George, Benson M., Boutet, Stéphane C., Hebestreit, Katja, Pluvinage, John V. et al. · 2019 · Nature
54. Genetic identification of vagal sensory neurons that control feeding
    Bai, Ling, Mesgarzadeh, Sheyda, Ramesh, Karthik S., Huey, Erica L., Liu, Yin, Gray, Lindsay A., Aitken, Tara J., Chen, Yiming, Beutler, Lisa R., Ahn, Jamie S. et al. · 2019 · Cell
55. A Single-Cell RNA Sequencing Profiles the Developmental Landscape of Arabidopsis Root
    Tian‐Qi Zhang, Zhou-Geng Xu, Guan-Dong Shang, Jiawei Wang · 2019 · Molecular Plant
56. Benchmarking single-cell RNA-sequencing protocols for cell atlas projects
    Mereu, Elisabetta, Lafzi, Atefeh, Moutinho, Catia, Ziegenhain, Christoph, McCarthy, Davis J., Álvarez-Varela, Adrián, Batlle, Eduard, Sagar, Grün, Dominic, Lau, Julia K. et al. · 2020 · Nature Biotechnology
57. Evolution of pallium, hippocampus, and cortical cell types revealed by single-cell transcriptomics in reptiles
    Tosches, Maria Antonietta, Yamawaki, Tracy M., Naumann, Robert K., Jacobi, Ariel A., Tushev, Georgi, Laurent, Gilles · 2018 · Science
58. Supervised classification enables rapid annotation of cell atlases
    Pliner, Hannah A., Shendure, Jay, Trapnell, Cole · 2019
59. Zygotic Genome Activation in Vertebrates
    David Jukam, S. Ali Shariati, Jan Marcel Skotheim · 2017 · Developmental Cell
60. Single-cell analysis of experience-dependent transcriptomic states in the mouse visual cortex
    Hrvatin, Sinisa, Hochbaum, Daniel R., Nagy, M. Aurel, Cicconet, Marcelo, Robertson, Keiramarie, Cheadle, Lucas, Zilionis, Rapolas, Ratner, Alex, Borges-Monroy, Rebeca, Klein, Allon M. et al. · 2018 · Nature Neuroscience
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    Mathys, Hansruedi, Peng, Zhuyu, Boix, Carles A., Victor, Matheus B., Leary, Noelle, Babu, Sudhagar, Abdelhady, Ghada, Jiang, Xueqiao, Ng, Ayesha P., Ghafari, Kimia et al. · 2023 · Cell
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63. Spatial heterogeneity in the mammalian liver
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65. Single-Cell RNA Sequencing in Cancer: Lessons Learned and Emerging Challenges
    Mario L. Suvà, Itay Tirosh · 2019 · Molecular Cell
66. Single-Cell Transcriptome Analysis Maps the Developmental Track of the Human Heart
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    Huang, Youtong, Happonen, Kaisa E., Burrola, Patrick G., O’Connor, Carolyn, Hah, Nasun, Huang, Ling, Nimmerjahn, Axel, Lemke, Greg · 2021 · Nature Immunology
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    Olsson, Andre, Venkatasubramanian, Meenakshi, Chaudhri, Viren K., Aronow, Bruce J., Salomonis, Nathan, Singh, Harinder, Grimes, H. Leighton · 2016 · Nature
69. Single-Cell RNA Sequencing Analysis Reveals Sequential Cell Fate Transition during Human Spermatogenesis
    Mei Wang, Xixi Liu, Gang Chang, Yidong Chen, Geng An, Liying Yan, Shuai Gao, Yanwen Xu, Yueli Cui, Ji Dong et al. · 2018 · Cell stem cell
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    Fu, Tong, Dai, Lei-Jie, Wu, Song-Yang, Xiao, Yi, Ma, Ding, Jiang, Yi-Zhou, Shao, Zhi-Ming · 2021 · Journal of Hematology & Oncology
73. High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin
    Achim, Kaia, Pettit, Jean-Baptiste, Saraiva, Luis R, Gavriouchkina, Daria, Larsson, Tomas, Arendt, Detlev, Marioni, John C · 2015 · Nature Biotechnology
74. Niche-Specific Reprogramming of Epigenetic Landscapes Drives Myeloid Cell Diversity in Nonalcoholic Steatohepatitis
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79. Design and computational analysis of single-cell RNA-sequencing experiments
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84. The promise of spatial transcriptomics for neuroscience in the era of molecular cell typing
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85. Sensory neuron diversity in the inner ear is shaped by activity
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86. Mapping systemic lupus erythematosus heterogeneity at the single-cell level
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87. Spatially resolved multiomics of human cardiac niches
    Kanemaru, Kazumasa, Cranley, James, Muraro, Daniele, Miranda, Antonio M. A., Ho, Siew Yen, Wilbrey-Clark, Anna, Patrick Pett, Jan, Polanski, Krzysztof, Richardson, Laura, Litvinukova, Monika et al. · 2023 · Nature
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    Benjamin Kaminow, Dinar Yunusov, Alexander Dobin · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
89. Thirst-associated preoptic neurons encode an aversive motivational drive.
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90. Childhood cerebellar tumours mirror conserved fetal transcriptional programs
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91. Single-cell RNA-seq uncovers dynamic processes and critical regulators in mouse spermatogenesis
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93. Single-cell analysis uncovers convergence of cell identities during axolotl limb regeneration
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94. Emergence of a High-Plasticity Cell State during Lung Cancer Evolution
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96. Single-cell reconstruction of the adult human heart during heart failure and recovery reveals the cellular landscape underlying cardiac function
    Li Wang, Yu Peng, Bingying Zhou, Jiangping Song, Zheng Li, Mingzhi Zhang, Guangran Guo, Yin Wang, Xiao Chen, Leng Han et al. · 2020 · Nature Cell Biology
97. MetaCell: analysis of single-cell RNA-seq data using K-nn graph partitions
    Yael Baran, Akhiad Bercovich, Arnau Sebé-Pedrós, Yaniv Lubling, Amir Giladi, Elad Chomsky, Zohar Meir, Michael Hoichman, Aviezer Lifshitz, Amos Tanay · 2019 · Genome biology
98. Paired-cell sequencing enables spatial gene expression mapping of liver endothelial cells
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99. Tubular cell and keratinocyte single-cell transcriptomics applied to lupus nephritis reveal type I IFN and fibrosis relevant pathways
    the Accelerating Medicines Partnership Rheumatoid Arthritis and Systemic Lupus Erythematosus (AMP RA/SLE) Consortium, Der, Evan, Suryawanshi, Hemant, Morozov, Pavel, Kustagi, Manjunath, Goilav, Beatrice, Ranabothu, Saritha, Izmirly, Peter, Clancy, Robert, Belmont, H. Michael et al. · 2019 · Nature Immunology
100. Inferring spatial and signaling relationships between cells from single cell transcriptomic data
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