Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors

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    Anne Jacobi, Nicholas M. Tran, Wenjun Yan, Inbal Benhar, Feng Tian, Rebecca Schaffer, Zhigang He, Joshua R. Sanes · 2022 · Neuron
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    Yiming Liu, Jingyu Ge, Yufei Chen, Tong Liu, Lie Chen, Cui‐Cui Liu, Ding Ma, Yiyu Chen, Yuwen Cai, Yingying Xu et al. · 2023 · Advanced Science
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    Schonhoff, A. M., Figge, D. A., Williams, G. P., Jurkuvenaite, A., Gallups, N. J., Childers, G. M., Webster, J. M., Standaert, D. G., Goldman, J. E., Harms, A. S. · 2023 · Nature Communications
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    Mazène Hochane, Patrick R. van den Berg, Xueying Fan, Noémie M. L. P. Bérenger-Currias, Esmée Adegeest, Monika Bialecka, Maaike C. Nieveen, Maarten Menschaart, Susana M. Chuva de Sousa Lopes, Stefan Semrau · 2019 · PLoS Biology
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    Yue Cheng Deng, Feng Bao, Qionghai Dai, Lani F. Wu, Steven J. Altschuler · 2019 · Nature Methods
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    Maria Kuksin, Daphné Morel, Marine Aglave, François‐Xavier Danlos, Aurélien Marabelle, Andrei Y. Zinovyev, Daniel Gautheret, Loïc Verlingue · 2021 · European Journal of Cancer
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    Zheng Wang, Chengyan Chai, Rui Wang, Yimei Feng, Lei Huang, Yiming Zhang, Xia Xiao, Shijie Yang, Yunfang Zhang, Xi Zhang · 2021 · Clinical and Translational Medicine
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    Nan Yang, Javier Del Ser, Simon L. F. Walsh, Carola‐Bibiane Schönlieb, Michael T. Roberts, IAN A. SELBY, Kit Howard, John Owen, Jon Neville, Julien Guiot et al. · 2022 · Information Fusion
33. Searching large-scale scRNA-seq databases via unbiased cell embedding with Cell BLAST
    Zhi‐Jie Cao, Wei Lin, Lu Shen, De-Chang Yang, Ge Gao · 2020 · Nature Communications
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    Vera Thiel, Simon Renders, Jasper Panten, Nicolas Dross, Katharina Bauer, Daniel Domínguez Azorín, Vanessa Henriques, Vanessa Vogel, Corinna Klein, Aino‐Maija Leppä et al. · 2025 · Nature
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    Allison C. Warren, Yejia Chen, Andrew Jones, Tsukasa Shibue, William C. Hahn, Jesse S. Boehm, Francisca Vázquez, Aviad Tsherniak, James M. McFarland · 2021 · Nature Communications
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    Menglan Xiang, Rubén Adrián Grosso, Akira Takeda, Junliang Pan, Tove Bekkhus, Kevin Brulois, Denis Đermadi, Sofia Nordling, Michael Vanlandewijck, Sirpa Jalkanen et al. · 2020 · Frontiers in Cardiovascular Medicine
39. A mixture-of-experts deep generative model for integrated analysis of single-cell multiomics data
    Kodai Minoura, Ko Abe, Hyunha Nam, Hiroyoshi Nishikawa, Teppei Shimamura · 2021 · Cell Reports Methods
40. Evaluating measures of association for single-cell transcriptomics
    Skinnider, Michael A., Squair, Jordan W., Foster, Leonard J. · 2019 · Nature Methods
41. Single-Cell Transcriptomics of Parkinson’s Disease Human In Vitro Models Reveals Dopamine Neuron-Specific Stress Responses
    Hugo J. R. Fernandes, Nikolaos Patikas, Stefanie Foskolou, Sarah Frances Field, Jong-Eun Park, Meg L. Byrne, Andrew Roger Bassett, Emmanouil Metzakopian · 2020 · Cell Reports
42. Comparative analysis of cell–cell communication at single-cell resolution
    Aaron J. Wilk, Alex K. Shalek, Susan Holmes, Catherine A. Blish · 2023 · Nature Biotechnology
43. Schwann cells regulate tumor cells and cancer-associated fibroblasts in the pancreatic ductal adenocarcinoma microenvironment
    Meilin Xue, Youwei Zhu, Yongsheng Jiang, Lijie Han, Minmin Shi, Rui Jun Su, Liwen Wang, Cheng Xiong, Chaofu Wang, Ting Wang et al. · 2023 · Nature Communications
44. Deep learning applications in single-cell genomics and transcriptomics data analysis
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45. Single Cell RNA Sequencing in Atherosclerosis Research
    Jesse W. Williams, Holger Winkels, Christopher P. Durant, Konstantin Zaitsev, Yanal Ghosheh, Klaus F. Ley · 2020 · Circulation Research
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    Marina Sanaki-Matsumiya, Mitsuhiro Matsuda, Nicola Gritti, Fumio Nakaki, James A. Sharpe, Vikas Trivedi, Miki Ebisuya · 2022 · Nature Communications
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    Noriki Fujimoto, Yuliang He, Marco D’Addio, Carlotta Tacconi, Michael J. Detmar, Lothar C. Dieterich · 2020 · PLoS Biology
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    Tongxin Wang, Travis S. Johnson, Wei Shao, Zixiao Lu, Bryan R. Helm, Jie Zhang, Kun Huang · 2019 · Genome biology
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    James D. Hocker, Olivier Poirion, Fugui Zhu, Justin Buchanan, Kai Zhang, Joshua Chiou, Tsui‐Min Wang, Qingquan Zhang, Xiaomeng Hou, Yang Eric Li et al. · 2021 · Science Advances
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    Hongyu Guo, Jun Li · 2021 · Genome biology
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    Jiwoon Park, Junbum Kim, Tyler Lewy, Charles M. Rice, Olivier Elemento, André F. Rendeiro, Christopher E. Mason · 2022 · Genome biology
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76. Dissecting Cellular Heterogeneity Using Single-Cell RNA Sequencing.
    Yoon Ha Choi, Jong Kyoung Kim · 2019 · Europe PMC (PubMed Central)
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    Jennifer Rood, Tim Stuart, Shila Ghazanfar, Tommaso Biancalani, Eyal Fisher, Andrew Butler, Anna Hupalowska, Leslie Gaffney, William M. Mauck, Gökçen Eraslan et al. · 2019 · Cell
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    Wei Liu, Xu Liao, Ziye Luo, Yi Yang, Mai Chan Lau, Yuling Jiao, Xingjie Shi, Weiwei Zhai, Hongkai Ji, Joe Poh-Sheng Yeong et al. · 2023 · Nature Communications
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    Wenhao Tang, François Bertaux, Philipp Thomas, Claire Stefanelli, Malika Saint, Samuel Marguerat, Vahid Shahrezaei · 2019 · Bioinformatics
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    Zhibo Ma, Nikki K. Lytle, Bob Chen, Nidhi Jyotsana, Sammy Weiser Novak, Charles J. Cho, Leah R. Caplan, Olivia Ben‐Levy, Abigail C. Neininger, Dylan T. Burnette et al. · 2021 · Gastroenterology
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    Lu Wen, Guoqiang Li, Tao Huang, Wei Geng, Hao Pei, Jialiang Yang, Miao Zhu, Pengfei Zhang, Rui Hou, Geng Tian et al. · 2022 · The Innovation
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    Kenneth D. Birnbaum · 2018 · Annual Review of Genetics
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    Masato Ogishi, Rui Yang, Caner Aytekin, David Langlais, Mathieu Bourgey, Taushif Khan, Fatima Al Ali, Mahbuba Rahman, Ottavia M. Delmonte, Maya Chrabieh et al. · 2021 · Nature Medicine
89. Review of single-cell RNA-seq data clustering for cell-type identification and characterization
    Shixiong Zhang, Xiangtao Li, Jiecong Lin, Qiuzhen Lin, Ka‐Chun Wong · 2023 · RNA
90. Single-Cell RNA-Seq of the Pancreatic Islets––a Promise Not yet Fulfilled?
    Yue Julia Wang, Klaus H. Kaestner · 2018 · Cell Metabolism
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    Lin Guo, Lihui Lin, Xiaoshan Wang, Mingwei Gao, Shangtao Cao, Yuanbang Mai, Fang Wu, Junqi Kuang, He Liu, Jiaqi Yang et al. · 2018 · Molecular Cell
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    Zhencong Chen, Mengnan Zhao, Jiaqi Liang, Zhengyang Hu, Yiwei Huang, Ming Li, Yanrui Pang, Tao Lu, Qihai Sui, Cheng Zhan et al. · 2021 · EBioMedicine
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    Chen, Wanqiu, Zhao, Yongmei, Chen, Xin, Yang, Zhaowei, Xu, Xiaojiang, Bi, Yingtao, Chen, Vicky, Li, Jing, Choi, Hannah, Ernest, Ben et al. · 2021 · Nature Biotechnology
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    Chen, Xi, Teichmann, Sarah A., Meyer, Kerstin B. · 2018 · Annual Review of Biomedical Data Science
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    Tessa Dignum, Barbara Varnum‐Finney, Sanjay R Srivatsan, Stacey Dozono, Olivia G. Waltner, Adam M. Heck, Takashi Ishida, Cynthia Nourigat-Mckay, Dana L. Jackson, Shahin Rafii et al. · 2021 · Cell Reports
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    Anna Julie Peired, Giulia Antonelli, Maria Lucia Angelotti, Marco Allinovi, Francesco Guzzi, Alessandro Sisti, Roberto Semeraro, Carolina Conte, Benedetta Mazzinghi, Sara Nardi et al. · 2020 · Science Translational Medicine
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