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ArticlesPeer ReviewedFull Text
Impact of similarity metrics on single-cell RNA-seq data clustering
Author / Creator:Kim, Taiyun ; Chen, Irene Rui ; Lin, Yingxin ; Wang, Andy Yi-Yang ; Yang, Jean Yee Hwa ; Yang, Pengyi
Publisher:England: Oxford University Press
Journal title:Briefings in bioinformatics, 2019-11, Vol.20 (6), p.2316-2326
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scClassify: sample size estimation and multiscale classification of cells using single and multiple reference
Author / Creator:Lin, Yingxin ; Cao, Yue ; Kim, Hani Jieun ; Salim, Agus ; Speed, Terence P ; Lin, David M ; Yang, Pengyi ; Yang, Jean Yee Hwa
Publisher:London: Nature Publishing Group UK
Journal title:Molecular systems biology, 2020-06, Vol.16 (6), p.e9389-n/a
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scMerge leverages factor analysis, stable expression, and pseudoreplication to merge multiple single-cell RNA-seq datasets
Author / Creator:Lin, Yingxin ; Ghazanfar, Shila ; Wang, Kevin Y. X. ; Gagnon-Bartsch, Johann A. ; Lo, Kitty K. ; Su, Xianbin ; Han, Ze-Guang ; Ormerod, John T. ; Speed, Terence P. ; Yang, Pengyi ; Yang, Jean Yee Hwa
Publisher:United States: National Academy of Sciences
Journal title:Proceedings of the National Academy of Sciences - PNAS, 2019-05, Vol.116 (20), p.9775-9784
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Genetically defined causal effects of natural killer cells related traits in risk of infection: a Mendelian randomization study
Author / Creator:Lin, Yingxin ; Zhang, Sheng ; Wang, Xueqing ; Wang, Junshi ; Huang, Lei
Publisher:England: BioMed Central Ltd
Journal title:BMC infectious diseases, 2024-09, Vol.24 (1), p.986-12, Article 986
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Atlas-scale single-cell multi-sample multi-condition data integration using scMerge2
Author / Creator:Lin, Yingxin ; Cao, Yue ; Willie, Elijah ; Patrick, Ellis ; Yang, Jean Y. H.
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2023-07, Vol.14 (1), p.4272-4272, Article 4272
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BIDCell: Biologically-informed self-supervised learning for segmentation of subcellular spatial transcriptomics data
Author / Creator:Fu, Xiaohang ; Lin, Yingxin ; Lin, David M. ; Mechtersheimer, Daniel ; Wang, Chuhan ; Ameen, Farhan ; Ghazanfar, Shila ; Patrick, Ellis ; Kim, Jinman ; Yang, Jean Y. H.
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2024-01, Vol.15 (1), p.509-509, Article 509
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SANTO: a coarse-to-fine alignment and stitching method for spatial omics
Author / Creator:Li, Haoyang ; Lin, Yingxin ; He, Wenjia ; Han, Wenkai ; Xu, Xiaopeng ; Xu, Chencheng ; Gao, Elva ; Zhao, Hongyu ; Gao, Xin
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2024-07, Vol.15 (1), p.6048-12, Article 6048
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Scalable workflow for characterization of cell-cell communication in COVID-19 patients
Author / Creator:Lin, Yingxin ; Loo, Lipin ; Tran, Andy ; Lin, David M. ; Moreno, Cesar ; Hesselson, Daniel ; Neely, G. Gregory ; Yang, Jean Y. H.
Publisher:United States: Public Library of Science
Journal title:PLoS computational biology, 2022-10, Vol.18 (10), p.e1010495
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scDC: single cell differential composition analysis
Author / Creator:Cao, Yue ; Lin, Yingxin ; Ormerod, John T. ; Yang, Pengyi ; Yang, Jean Y.H. ; Lo, Kitty K.
Publisher:England: BioMed Central Ltd
Journal title:BMC bioinformatics, 2019-12, Vol.20 (S19), p.721-721, Article 721
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A CD26+ tendon stem progenitor cell population contributes to tendon repair and heterotopic ossification
Author / Creator:Chen, Siwen ; Lin, Yingxin ; Yang, Hao ; Li, Zihao ; Li, Sifang ; Chen, Dongying ; Hao, Wenjun ; Zhang, Shuai ; Chao, Hua ; Zhang, Jingyu ; Wang, Jianru ; Li, Zemin ; Li, Xiang ; Zhan, Zhongping ; Liu, Hui
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2025-01, Vol.16 (1), p.749-18, Article 749
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Toward High-Performance Electrochromic Conjugated Polymers: Influence of Local Chemical Environment and Side-Chain Engineering
Author / Creator:Lin, Kaiwen ; Wu, Changjun ; Zhang, Guangyao ; Wu, Zhixin ; Tang, Shiting ; Lin, Yingxin ; Li, Xinye ; Jiang, Yuying ; Lin, Hengjia ; Wang, Yuehui ; Ming, Shouli ; Lu, Baoyang
Publisher:Switzerland: MDPI AG
Journal title:Molecules (Basel, Switzerland), 2022-12, Vol.27 (23), p.8424
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simKAP: simulation framework for the kidney allocation process with decision making model
Author / Creator:Zhang, Yunwei ; Hu, Anne ; Lin, Yingxin ; Cao, Yue ; Muller, Samuel ; Wong, Germaine ; Yang, Jean Yee Hwa
Publisher:London: Nature Publishing Group UK
Journal title:Scientific reports, 2023-09, Vol.13 (1), p.16367-16367, Article 16367
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Stress hyperglycemia ratio as a predictor of acute kidney injury and its outcomes in critically ill patients
Author / Creator:Lin, Yingxin ; Zhang, Sheng ; Chen, Zeling ; Lin, Xuwei ; Wang, Xueqing ; Shen, Xiaojun ; Huang, Lei ; Deng, Yiyu ; Chen, Chunbo
Publisher:England: Taylor & Francis
Journal title:Renal failure, 2025-12, Vol.47 (1), p.2499228
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Case report of Salmonella derby septicemia complicated with co-occurrence of disseminated intravascular coagulation and thrombotic microangiopathy
Author / Creator:Lin, Yingxin ; Huang, Lei ; Tu, Yunliang ; Huang, Bin ; Zhang, Sheng ; Chen, Yingqun ; Li, Weijia
Publisher:England: BioMed Central Ltd
Journal title:BMC infectious diseases, 2022-12, Vol.22 (1), p.914-914, Article 914
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Gene regulatory network reconstruction: harnessing the power of single-cell multi-omic data
Author / Creator:Kim, Daniel ; Tran, Andy ; Kim, Hani Jieun ; Lin, Yingxin ; Yang, Jean Yee Hwa ; Yang, Pengyi
Publisher:London: Nature Publishing Group UK
Journal title:NPJ systems biology and applications, 2023-10, Vol.9 (1), p.51-13, Article 51
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Clonal evolution in liver cancer at single-cell and single-variant resolution
Author / Creator:Su, Xianbin ; Zhao, Linan ; Shi, Yi ; Zhang, Rui ; Long, Qi ; Bai, Shihao ; Luo, Qing ; Lin, Yingxin ; Zou, Xin ; Ghazanfar, Shila ; Tao, Kun ; Yang, Guoliang ; Wang, Lan ; He, Kun-Yan ; Cui, Xiaofang ; He, Jian ; Wu, Jiao-Xiang ; Han, Bo ; Yan, Bin ; Deng, Biao ; Wang, Na ; Li, Xiaolin ; Yang, Pengyi ; Hou, Shangwei ; Sun, Jielin ; Yang, Jean Y. H. ; Chen, Jinhong ; Han, Ze-Guang
Publisher:England: BioMed Central Ltd
Journal title:Journal of hematology and oncology, 2021-02, Vol.14 (1), p.22-22, Article 22
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Leveraging single‐cell RNA‐seq for uncovering naïve B cells associated with better prognosis of hepatocellular carcinoma
Author / Creator:Sun, Qingjia ; Gao, Rui ; Lin, Yingxin ; Zhou, Xianchao ; Wang, Tao ; He, Jian
Publisher:China: John Wiley & Sons, Inc
Journal title:MedComm (2020), 2024-09, Vol.5 (9), p.e563-n/a
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How did we protect ourselves during intubation for a COVID-19 patient in the context of PPE shortage?
Author / Creator:Zhang, Sheng ; Lin, Yingxin ; Li, Yanyan ; Zhang, Weixing ; Feng, Qing ; Luo, Hua
Publisher:Italy: Journal of Infection in Developing Countries
Journal title:Journal of infection in developing countries, 2021-12, Vol.15 (12), p.1808-1812
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Dynamic Changes in Vitamin E Biosynthesis during Germination in Brown Rice (Oryza sativa L.)
Author / Creator:Kong, Leilei ; Lin, Yingxin ; Liang, Jiayan ; Hu, Xiaodan ; Ashraf, Umair ; Guo, Xinbo ; Bai, Song
Publisher:Switzerland: MDPI AG
Journal title:Foods, 2022-10, Vol.11 (20), p.3200
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Thinking process templates for constructing data stories with SCDNEY [version 1; peer review: 1 approved, 1 approved with reservations]
Author / Creator:Cao, Yue ; Tran, Andy ; Kim, Hani ; Robertson, Nick ; Lin, Yingxin ; Torkel, Marni ; Yang, Pengyi ; Patrick, Ellis ; Ghazanfar, Shila ; Yang, Jean
Publisher:England: F1000 Research Ltd
Journal title:F1000 research, 2023, Vol.12, p.261
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Showing 1 to 20 of 52 results

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Impact of similarity metrics on single-cell RNA-seq data clustering

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scClassify: sample size estimation and multiscale classification of cells using single and multiple reference

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scMerge leverages factor analysis, stable expression, and pseudoreplication to merge multiple single-cell RNA-seq datasets

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Genetically defined causal effects of natural killer cells related traits in risk of infection: a Mendelian randomization study

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Atlas-scale single-cell multi-sample multi-condition data integration using scMerge2

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BIDCell: Biologically-informed self-supervised learning for segmentation of subcellular spatial transcriptomics data

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SANTO: a coarse-to-fine alignment and stitching method for spatial omics

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Scalable workflow for characterization of cell-cell communication in COVID-19 patients

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scDC: single cell differential composition analysis

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A CD26+ tendon stem progenitor cell population contributes to tendon repair and heterotopic ossification

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Toward High-Performance Electrochromic Conjugated Polymers: Influence of Local Chemical Environment and Side-Chain Engineering

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simKAP: simulation framework for the kidney allocation process with decision making model

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Stress hyperglycemia ratio as a predictor of acute kidney injury and its outcomes in critically ill patients

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Case report of Salmonella derby septicemia complicated with co-occurrence of disseminated intravascular coagulation and thrombotic microangiopathy

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Gene regulatory network reconstruction: harnessing the power of single-cell multi-omic data

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Clonal evolution in liver cancer at single-cell and single-variant resolution

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Leveraging single‐cell RNA‐seq for uncovering naïve B cells associated with better prognosis of hepatocellular carcinoma

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How did we protect ourselves during intubation for a COVID-19 patient in the context of PPE shortage?

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Dynamic Changes in Vitamin E Biosynthesis during Germination in Brown Rice (Oryza sativa L.)

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Thinking process templates for constructing data stories with SCDNEY [version 1; peer review: 1 approved, 1 approved with reservations]

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