Bulk tissue cell type deconvolution with multi-subject single-cell expression reference
Wang, Xuran, Park, Jihwan, Susztak, Katalin, Zhang, Nancy R., Li, Mingyao
Published in Nature communications (22.01.2019)
Published in Nature communications (22.01.2019)
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SpaGCN: Integrating gene expression, spatial location and histology to identify spatial domains and spatially variable genes by graph convolutional network
Hu, Jian, Li, Xiangjie, Coleman, Kyle, Schroeder, Amelia, Ma, Nan, Irwin, David J., Lee, Edward B., Shinohara, Russell T., Li, Mingyao
Published in Nature methods (01.11.2021)
Published in Nature methods (01.11.2021)
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Single-cell transcriptomics of the mouse kidney reveals potential cellular targets of kidney disease
Park, Jihwan, Shrestha, Rojesh, Qiu, Chengxiang, Kondo, Ayano, Huang, Shizheng, Werth, Max, Li, Mingyao, Barasch, Jonathan, Suszták, Katalin
Published in Science (American Association for the Advancement of Science) (18.05.2018)
Published in Science (American Association for the Advancement of Science) (18.05.2018)
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Deep learning enables accurate clustering with batch effect removal in single-cell RNA-seq analysis
Li, Xiangjie, Wang, Kui, Lyu, Yafei, Pan, Huize, Zhang, Jingxiao, Stambolian, Dwight, Susztak, Katalin, Reilly, Muredach P., Hu, Gang, Li, Mingyao
Published in Nature communications (11.05.2020)
Published in Nature communications (11.05.2020)
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Single-Cell Genomics Reveals a Novel Cell State During Smooth Muscle Cell Phenotypic Switching and Potential Therapeutic Targets for Atherosclerosis in Mouse and Human
Pan, Huize, Xue, Chenyi, Auerbach, Benjamin J., Fan, Jiaxin, Bashore, Alexander C., Cui, Jian, Yang, Dina Y., Trignano, Sarah B., Liu, Wen, Shi, Jianting, Ihuegbu, Chinyere O., Bush, Erin C., Worley, Jeremy, Vlahos, Lukas, Laise, Pasquale, Solomon, Robert A., Connolly, Edward S., Califano, Andrea, Sims, Peter A., Zhang, Hanrui, Li, Mingyao, Reilly, Muredach P.
Published in Circulation (New York, N.Y.) (24.11.2020)
Published in Circulation (New York, N.Y.) (24.11.2020)
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MicroRNA-mediated inhibition of transgene expression reduces dorsal root ganglion toxicity by AAV vectors in primates
Hordeaux, Juliette, Buza, Elizabeth L, Jeffrey, Brianne, Song, Chunjuan, Jahan, Tahsin, Yuan, Yuan, Zhu, Yanqing, Bell, Peter, Li, Mingyao, Chichester, Jessica A, Calcedo, Roberto, Wilson, James M
Published in Science translational medicine (11.11.2020)
Published in Science translational medicine (11.11.2020)
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LIQA: long-read isoform quantification and analysis
Hu, Yu, Fang, Li, Chen, Xuelian, Zhong, Jiang F, Li, Mingyao, Wang, Kai
Published in Genome Biology (17.06.2021)
Published in Genome Biology (17.06.2021)
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Adeno-Associated Virus-Induced Dorsal Root Ganglion Pathology
Hordeaux, Juliette, Buza, Elizabeth L, Dyer, Cecilia, Goode, Tamara, Mitchell, Thomas W, Richman, Laura, Denton, Nathan, Hinderer, Christian, Katz, Nathan, Schmid, Ralf, Miller, Rod, Choudhury, Gourav R, Horiuchi, Makoto, Nambiar, Kalyani, Yan, Hanying, Li, Mingyao, Wilson, James M
Published in Human gene therapy (01.08.2020)
Published in Human gene therapy (01.08.2020)
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Single cell regulatory landscape of the mouse kidney highlights cellular differentiation programs and disease targets
Miao, Zhen, Balzer, Michael S., Ma, Ziyuan, Liu, Hongbo, Wu, Junnan, Shrestha, Rojesh, Aranyi, Tamas, Kwan, Amy, Kondo, Ayano, Pontoglio, Marco, Kim, Junhyong, Li, Mingyao, Kaestner, Klaus H., Susztak, Katalin
Published in Nature communications (15.04.2021)
Published in Nature communications (15.04.2021)
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Image harmonization: A review of statistical and deep learning methods for removing batch effects and evaluation metrics for effective harmonization
Hu, Fengling, Chen, Andrew A., Horng, Hannah, Bashyam, Vishnu, Davatzikos, Christos, Alexander-Bloch, Aaron, Li, Mingyao, Shou, Haochang, Satterthwaite, Theodore D., Yu, Meichen, Shinohara, Russell T.
Published in NeuroImage (Orlando, Fla.) (01.07.2023)
Published in NeuroImage (Orlando, Fla.) (01.07.2023)
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CDK1 serves as a potential prognostic biomarker and target for lung cancer
Li, Mingyao, He, Fenyi, Zhang, Zhanchun, Xiang, Zhenfei, Hu, Danfei
Published in Journal of international medical research (01.02.2020)
Published in Journal of international medical research (01.02.2020)
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Single cell transcriptomics identifies a unique adipose lineage cell population that regulates bone marrow environment
Zhong, Leilei, Yao, Lutian, Tower, Robert J, Wei, Yulong, Miao, Zhen, Park, Jihwan, Shrestha, Rojesh, Wang, Luqiang, Yu, Wei, Holdreith, Nicholas, Huang, Xiaobin, Zhang, Yejia, Tong, Wei, Gong, Yanqing, Ahn, Jaimo, Susztak, Katalin, Dyment, Nathanial, Li, Mingyao, Long, Fanxin, Chen, Chider, Seale, Patrick, Qin, Ling
Published in eLife (14.04.2020)
Published in eLife (14.04.2020)
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The Nuclear Receptor ESRRA Protects from Kidney Disease by Coupling Metabolism and Differentiation
Dhillon, Poonam, Park, Jihwan, Hurtado del Pozo, Carmen, Li, Lingzhi, Doke, Tomohito, Huang, Shizheng, Zhao, Juanjuan, Kang, Hyun Mi, Shrestra, Rojesh, Balzer, Michael S., Chatterjee, Shatakshee, Prado, Patricia, Han, Seung Yub, Liu, Hongbo, Sheng, Xin, Dierickx, Pieterjan, Batmanov, Kirill, Romero, Juan P., Prósper, Felipe, Li, Mingyao, Pei, Liming, Kim, Junhyong, Montserrat, Nuria, Susztak, Katalin
Published in Cell metabolism (02.02.2021)
Published in Cell metabolism (02.02.2021)
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Mapping the genetic architecture of human traits to cell types in the kidney identifies mechanisms of disease and potential treatments
Sheng, Xin, Guan, Yuting, Ma, Ziyuan, Wu, Junnan, Liu, Hongbo, Qiu, Chengxiang, Vitale, Steven, Miao, Zhen, Seasock, Matthew J., Palmer, Matthew, Shin, Myung K., Duffin, Kevin L., Pullen, Steven S., Edwards, Todd L., Hellwege, Jacklyn N., Hung, Adriana M., Li, Mingyao, Voight, Benjamin F., Coffman, Thomas M., Brown, Christopher D., Susztak, Katalin
Published in Nature genetics (01.09.2021)
Published in Nature genetics (01.09.2021)
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