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

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Items 101–200 of 1,012

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    Christina Ernst, Nils Eling, Celia Pilar Martinez‐Jimenez, John C. Marioni, Duncan T. Odom · 2019 · Nature Communications
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    Lawrence Peter Andrews, Samuel C. Butler, Jian Cui, Anthony Richard Cillo, Carly Cardello, Chang Liu, Erin A. Brunazzi, Andrew Baessler, Bingxian Xie, Sheryl R. Kunning et al. · 2024 · Cell
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    Akshayalakshmi Sridhar, Akina Hoshino, Connor Finkbeiner, Alex Chitsazan, Li Dai, Alexandra K. Haugan, Kayla M. Eschenbacher, Dana L. Jackson, Cole Trapnell, Olivia Bermingham‐McDonogh et al. · 2020 · Cell Reports
23. scVAE: variational auto-encoders for single-cell gene expression data
    Christopher Heje Grønbech, Maximillian Fornitz Vording, Pascal N. Timshel, Casper Kaae Sønderby, Tune H. Pers, Ole Winther · 2020 · Bioinformatics
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    Xu, Heping, Ding, Jiarui, Porter, Caroline B.M., Wallrapp, Antonia, Tabaka, Marcin, Ma, Sai, Fu, Shujie, Guo, Xuanxuan, Riesenfeld, Samantha J., Su, Chienwen et al. · 2019 · Immunity
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    Lukas M. Weber, Małgorzata Nowicka, Charlotte Soneson, Mark D. Robinson · 2019 · Communications Biology
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    Sanjay R Srivatsan, Mary C. Regier, Eliza R. Barkan, Jennifer M. Franks, Jonathan S. Packer, Parker Grosjean, Madeleine Duran, Sarah H. Saxton, Jon J. Ladd, Malte Spielmann et al. · 2021 · Science
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    Skinnider, Michael A., Squair, Jordan W., Kathe, Claudia, Anderson, Mark A., Gautier, Matthieu, Matson, Kaya J. E., Milano, Marco, Hutson, Thomas H., Barraud, Quentin, Phillips, Aaron A. et al. · 2021 · Nature Biotechnology
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    Weilin Pu, Xiao Shi, Pengcheng Yu, Meiying Zhang, Zhiyan Liu, Licheng Tan, Peizhen Han, Yu Wang, Dongmei Ji, Hualei Gan et al. · 2021 · Nature Communications
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    DeTomaso, David, Yosef, Nir · 2021 · Cell Systems
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    Steuernagel, Lukas, Lam, Brian Y. H., Klemm, Paul, Dowsett, Georgina K. C., Bauder, Corinna A., Tadross, John A., Hitschfeld, Tamara Sotelo, del Rio Martin, Almudena, Chen, Weiyi, de Solis, Alain J. et al. · 2022 · Nature Metabolism
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    Pepe-Mooney, Brian J., Dill, Michael T., Alemany, Anna, Ordovas-Montanes, Jose, Matsushita, Yuki, Rao, Anuradha, Sen, Anushna, Miyazaki, Makoto, Anakk, Sayeepriyadarshini, Dawson, Paul A. et al. · 2019 · Cell Stem Cell
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    Jinling Liao, Zhenyuan Yu, Chen Yang, Mengying Bao, Chunlin Zou, Haiying Zhang, Deyun Liu, Tianyu Li, Qingyun Zhang, Jiaping Li et al. · 2020 · Scientific Data
35. Single-Cell Sequencing of Brain Cell Transcriptomes and Epigenomes
    Armand, Ethan J., Li, Junhao, Xie, Fangming, Luo, Chongyuan, Mukamel, Eran A. · 2021 · Neuron
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    Ryan M. Samuel, Homa Majd, Mikayla N Richter, Zaniar Ghazizadeh, Seyedeh Maryam Zekavat, Albertas Navickas, Jonathan T. Ramirez, Hosseinali Asgharian, Camille R. Simoneau, Luke R. Bonser et al. · 2020 · Cell stem cell
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    Shaojie Ma, Mario Škarica, Qian Li, Chuan Xu, Ryan D. Risgaard, Andrew T.N. Tebbenkamp, Xoel Mato-Blanco, Rothem Kovner, Željka Krsnik, Xabier de Martin et al. · 2022 · Science
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    Bo Li, Joshua Gould, Yiming Yang, Siranush Sarkizova, Marcin Tabaka, Orr Ashenberg, Yanay Rosen, Michal Slyper, Monika S. Kowalczyk, Alexandra–Chloé Villani et al. · 2020 · Nature Methods
39. SCDC: bulk gene expression deconvolution by multiple single-cell RNA sequencing references
    Meichen Dong, Aatish Thennavan, Eugene Urrutia, Yun Li, Charles M. Perou, Fei Zou, Yuchao Jiang · 2019 · Briefings in Bioinformatics
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    Ilya Korsunsky, Kevin Wei, Mathilde Pohin, Edy Yong Kim, Francesca Barone, Triin Major, Emily Taylor, Rahul Prashanth Ravindran, Samuel Kemble, Gerald F.M. Watts et al. · 2022 · Med
41. ACTINN: automated identification of cell types in single cell RNA sequencing
    Ma, Feiyang, Pellegrini, Matteo · 2020 · Bioinformatics
42. IFN-γ and TNF-α drive a CXCL10+ CCL2+ macrophage phenotype expanded in severe COVID-19 lungs and inflammatory diseases with tissue inflammation
    Fan Zhang, Joseph Mears, Lorien Shakib, Jessica I. Beynor, Sara Shanaj, Ilya Korsunsky, Aparna Nathan, Laura T. Donlin, Soumya Raychaudhuri · 2021 · Genome Medicine
43. Characterizing cis-regulatory elements using single-cell epigenomics
    Preissl, Sebastian, Gaulton, Kyle J., Ren, Bing · 2023 · Nature Reviews Genetics
44. An MRI radiomics approach to predict survival and tumour-infiltrating macrophages in gliomas
    Guan-Zhang Li, Lin Li, Yi-Ming Li, Zeng-Hui Qian, Fan Wu, Yu-Fei He, Hao-Yu Jiang, Ren-Peng Li, Die Wang, Y. Zhai et al. · 2022 · Brain : a journal of neurology
45. Multi-omics integration in the age of million single-cell data
    Zhen Miao, Benjamin D. Humphreys, Andrew P. McMahon, Junhyong Kim · 2021 · Nature Reviews Nephrology
46. Fully defined human pluripotent stem cell-derived microglia and tri-culture system model C3 production in Alzheimer’s disease
    Sudha R. Guttikonda, Lisa Sikkema, Jason H. Tchieu, Nathalie G. Saurat, Ryan M. Walsh, Oliver Harschnitz, Gabriele Ciceri, Marjolein A. M. Sneeboer, Linas Mažutis, Manu N. Setty et al. · 2021 · Nature Neuroscience
47. Harmonized cross-species cell atlases of trigeminal and dorsal root ganglia
    Shamsuddin A. Bhuiyan, Mengyi Xu, Lite Yang, Evangelia Semizoglou, Parth Bhatia, Katerina I. Pantaleo, Ivan Tochitsky, Aakanksha Jain, Burcu Erdoğan, Steven J. Blair et al. · 2024 · Science Advances
48. Advances in spatial transcriptomic data analysis
    Ruben Dries, Jiaji George Chen, Natalie Del Rossi, Mohammed Muzamil Khan, Adriana Sistig, Guo‐Cheng Yuan · 2021 · Genome Research
49. Concepts and limitations for learning developmental trajectories from single cell genomics
    Sophie Tritschler, Maren Büttner, David S. Fischer, Marius Lange, Volker Bergen, Heiko Lickert, Fabian Joachim Theis · 2019 · Development
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    Yu Wang, Qing Huan, Xiao Chu, Ke Li, Wenfeng Qian · 2021 · Journal of genetics and genomics/Journal of Genetics and Genomics
51. Improved reconstruction of single-cell developmental potential with CytoTRACE 2
    Minji Kang, José Juan Almagro Armenteros, Gunsagar Singh Gulati, Rachel Gleyzer, Susanna Avagyan, Erin L. Brown, Wubing Zhang, Abul Usmani, Noah J. Earland, Zhenqin Wu et al. · 2025 · Nature Methods
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    Young, Adam M. H., Kumasaka, Natsuhiko, Calvert, Fiona, Hammond, Timothy R., Knights, Andrew, Panousis, Nikolaos, Park, Jun Sung, Schwartzentruber, Jeremy, Liu, Jimmy, Kundu, Kousik et al. · 2021 · Nature Genetics
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    Shuai He, Lin-He Wang, Yang Liu, Yiqi Li, Hai-Tian Chen, Jing-hong Xu, Wan Peng, Guo-Wang Lin, Pan-Pan Wei, Bo Li et al. · 2020 · Genome biology
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    Poller, Wolfram C., Downey, Jeffrey, Mooslechner, Agnes A., Khan, Nargis, Li, Long, Chan, Christopher T., McAlpine, Cameron S., Xu, Chunliang, Kahles, Florian, He, Shun et al. · 2022 · Nature
55. Efficient and precise single-cell reference atlas mapping with Symphony
    Joyce B. Kang, Aparna Nathan, Kathryn Weinand, Fan Zhang, Nghia Millard, Laurie Rumker, David Branch Moody, Ilya Korsunsky, Soumya Raychaudhuri · 2021 · Nature Communications
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    Changde Cheng, Wenan Chen, Hongjian Jin, Xiang 'Anthony' Chen · 2023 · Cells
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    Lisa Willemsen, Menno P.J. de Winther · 2020 · The Journal of Pathology
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    Bernardo Oldak, Emilie Wildschutz, Vladyslav Bondarenko, Mehmet-Yunus Comar, Cheng Zhao, Alejandro Aguilera-Castrejon, Shadi Tarazi, Sergey V. Viukov, Thi Xuan Ai Pham, Shahd Ashouokhi et al. · 2023 · Nature
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    Qianqian Song, Jing Su · 2020 · Briefings in Bioinformatics
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    Xiaoying Fan, Ji Dong, Suijuan Zhong, Yuan Wei, Qian Wu, Liying Yan, Jun Yong, Le Sun, Xiaoye Wang, Yangyu Zhao et al. · 2018 · Cell Research
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    Burkhardt, Daniel B., Stanley, Jay S., Tong, Alexander, Perdigoto, Ana Luisa, Gigante, Scott A., Herold, Kevan C., Wolf, Guy, Giraldez, Antonio J., van Dijk, David, Krishnaswamy, Smita · 2021 · Nature Biotechnology
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    Guangshuai Jia, J. Preussner, Xi Chen, S. Guenther, Xue-Jun Yuan, Michail Yekelchyk, C. Kuenne, M. Looso, Yonggang Zhou, S. Teichmann et al. · 2018 · Nature Communications
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    Matthew Carr, Jeremy S. Toma, Adam P. W. Johnston, Patrick E. Steadman, Scott A. Yuzwa, Neemat Mahmud, Paul W. Frankland, David R. Kaplan, Freda D. Miller · 2018 · Cell stem cell
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    Lafzi, Atefeh, Moutinho, Catia, Picelli, Simone, Heyn, Holger · 2018 · Nature Protocols
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    Eloïse M. Grasset, Matthew Dunworth, Gaurav Sharma, Melanie Loth, Joseph A. Tandurella, Ashley Cimino‐Mathews, Melissa Gentz, Sydney A. Bracht, Meagan Haynes, Elana Judith Fertig et al. · 2022 · Science Translational Medicine
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    Yingchao Shi, Mengdi Wang, Da Mi, Tian Lu, Bosong Wang, Hao Dong, Suijuan Zhong, Youqiao Chen, Le Sun, Xin Zhou et al. · 2021 · Science
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    Olli Dufva, Petri Pölönen, Oscar E. Brück, Mikko A. I. Keränen, Jay Klievink, Juha Mehtonen, Jani Huuhtanen, Ashwini Kumar, Disha Malani, Sanna M. Siitonen et al. · 2020 · Cancer Cell
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    Jean Fan, Kamil Slowikowski, Fan Zhang · 2020 · Experimental & Molecular Medicine
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    Blagoje Soskic, Eddie Cano-Gamez, Deborah J. Smyth, Kirsty Ambridge, Ziying Ke, Julie C. Matte, Lara Bossini‐Castillo, Joanna Kaplanis, Lucia Ramirez-Navarro, Anna Lorenc et al. · 2022 · Nature Genetics
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    Peter See, Josephine Lum, Jinmiao Chen, Florent Ginhoux · 2018 · Frontiers in Immunology
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    Joshua Chiou, Chun Zeng, Cheng Zhang, Jee Yun Han, Michael Schlichting, Michael Miller, Robert Mendez, Serina Huang, Jinzhao Wang, Yinghui Sui et al. · 2021 · Nature Genetics
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    Chenfei Wang, Dongqing Sun, Xin Huang, Changxin Wan, Ziyi Li, Ya Han, Qian Qin, Jing‐Yu Fan, Xintao Qiu, Yingtian Xie et al. · 2020 · Genome biology
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    Nguyen, Quy H., Pervolarakis, Nicholas, Nee, Kevin, Kessenbrock, Kai · 2018 · Frontiers in Cell and Developmental Biology
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    Gaël Castel, Dimitri Meistermann, Betty Bretin, Julie Firmin, Justine Blin, Sophie Loubersac, Alexandre Bruneau, Simon Chevolleau, Stéphanie Kilens, Caroline Chariau et al. · 2020 · Cell Reports
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    Zhongshan Shi, Pei Yu, Wei‐Jye Lin, Sitai Chen, Xia Hu, Siqi Chen, Jinping Cheng, Qiang Liu, Yuhua Yang, Shaojian Li et al. · 2023 · Neuron
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