Xue Liu (Xun Xu)

Scopus Author ID ORCID

Publication Activity (10 Years)

Years Active: 2018-2024
Publications (10 Years): 131

Top Venues

Nature communications

Nature genetics

GigaScience

Nature

BGI-Shenzhen

This page only lists publications with an associated author ORCID identifier.

Affiliation History

BGI-Shenzhen Sep 01 2007

China

President, Professor :: Research

Publications

Lei Cao, Chao Yang, Luni Hu, Wenjian Jiang, Yating Ren, Tianyi Xia, Mengyang Xu, Yishuai Ji, Mei Li, Xue Liu, Yuxiang Li, Yong Zhang, Shuangsang Fang
Deciphering spatial domains from spatially resolved transcriptomics with Siamese graph autoencoder. GigaScience 13 (1) (2024)
Jiangshan Xu, Pengcheng Guo, Shijie Hao, Shuncheng Shangguan, Quan Shi, Giacomo Volpe, Keke Huang, Jing Zuo, Juan An, Yue Yuan, Mengnan Cheng, Qiuting Deng, Xiao Zhang, Guangyao Lai, Haitao Nan, Baihua Wu, Xinyi Shentu, Liang Wu, Xiaoyu Wei, Yujia Jiang, Xin Huang, Fengyu Pan, Yumo Song, Ronghai Li, Zhifeng Wang, Chuanyu Liu, Shi-Ping Liu, Yuxiang Li, Tao Yang, Zhicheng Xu, Wensi Du, Ling Li, Tanveer Ahmed, Kai You, Zhen Dai, Li Li, Baoming Qin, Yin-Xiong Li, Liangxue Lai, Dajiang Qin, Junling Chen, Rong Fan, Yongyin Li, Jin-Lin Hou, Michael Ott, Amar Deep Sharma, Tobias Cantz, Axel Schambach, Karsten Kristiansen, Andrew P Hutchins, Berthold Göttgens, Patrick H Maxwell, Lijian Hui, Xue Liu, Longqi Liu, Ao Chen, Yiwei Lai, Miguel Angel Esteban
A spatiotemporal atlas of mouse liver homeostasis and regeneration. Nature genetics 56 (5) (2024)
An Jiang, Kai Han, Jiankai Wei, Xiaoshan Su, Rui Wang, Wei Zhang, Xiawei Liu, Jinghan Qiao, Penghui Liu, Qun Liu, Jin Zhang, Nannan Zhang, Yonghang Ge, Yuan Zhuang, Haiyan Yu, Shi Wang, Kai Chen, Wange Lu, Xue Liu, Huanming Yang, Guang-Yi Fan, Bo Dong
Spatially resolved single-cell atlas of ascidian endostyle provides insight into the origin of vertebrate pharyngeal organs. Science advances 10 (13) (2024)
Xiaomin Liu, Xin Tong, Leying Zou, Yanmei Ju, Mingliang Liu, Mo Han, Haorong Lu, Huanming Yang, Jian Wang, Yang Zong, Weibin Liu, Xue Liu, Xin Jin, Liang Xiao, Huijue Jia, Ruijin Guo, Tao Zhang
A genome-wide association study reveals the relationship between human genetic variation and the nasal microbiome. Communications biology 7 (1) (2024)
Bohan Zhang, Mei Li, Qiang Kang, Zhonghan Deng, Hua Qin, Kui Su, Xiuwen Feng, Lichuan Chen, Huanlin Liu, Shuangsang Fang, Yong Zhang, Yuxiang Li, Susanne B Pedersen, Xue Liu
Generating single-cell gene expression profiles for high-resolution spatial transcriptomics based on cell boundary images. GigaByte (Hong Kong, China) 2024 (2024)
Keyi Ye, Fengjiao Bu, Li-Yuan Zhong, Zhaonian Dong, Zhaoxu Ma, Zhanpeng Tang, Yu Zhang, Xueyong Yang, Xue Liu, Ertao Wang, William J Lucas, Sanwen Huang, Huan Liu, Jianshu Zheng
Mapping the molecular landscape of Lotus japonicus nodule organogenesis through spatiotemporal transcriptomics. Nature communications 15 (1) (2024)
Tiange Wang, Zhun Shi, Huahui Ren, Yanan Hou, Jieli Lu, Fangming Yang, Chaojie Ye, Kui Wu, Ming-Ling Chen, Xue Liu, Dong Liu, Lijie Kong, Ruizhi Zheng, Jie Zheng, Mian Li, Yu Xu, Zhiyun Zhao, Yuhong Chen, Huanming Yang, Jian Wang, Guang Ning, Junhua Li, Huanzi Zhong, Yu-Fang Bi, Wei-Qing Wang
Divergent age-associated and metabolism-associated gut microbiome signatures modulate cardiovascular disease risk. Nature medicine 30 (6) (2024)
Jian-Wei Chen, Yangyang Jia, Ying Sun, Kun Liu, Changhao Zhou, Chuan Liu, Denghui Li, Guilin Liu, Chengsong Zhang, Tao Yang, Lei Huang, Yunyun Zhuang, Dazhi Wang, Dayou Xu, Qiaoling Zhong, Yang Guo, Anduo Li, Inge Seim, Ling Jiang, Lushan Wang, Simon Ming Yuen Lee, Yujing Liu, Dantong Wang, Guoqiang Zhang, Shanshan Liu, Xiaofeng Wei, Zhen Yue, Shanmin Zheng, Xuechun Shen, Sen Wang, Chen Qi, Jing Chen, Chen Ye, Fang Zhao, Jun Wang, Jie Fan, Baitao Li, Jiahui Sun, Xiaodong Jia, Zhangyong Xia, He Zhang, Junnian Liu, Yue Zheng, Xin Liu, Jian Wang, Huanming Yang, Karsten Kristiansen, Xue Liu, Thomas Mock, Shengying Li, Wenwei Zhang, Guang-Yi Fan
Global marine microbial diversity and its potential in bioprospecting. Nature (2024)
Shengpeng Wang, Lizhi Leng, Quanlei Wang, Yi-Fan Gu, Jinlu Li, Yanru An, Qiuting Deng, Pingyuan Xie, Can Cheng, Xueqin Chen, Qinwei Zhou, Jia Lu, Fang Chen, Longqi Liu, Huanming Yang, Jian Wang, Xue Liu, Yong Hou, Fei Gong, Liang Hu, Guangxiu Lu, Zhouchun Shang, Ge Lin
A single-cell transcriptome atlas of human euploid and aneuploid blastocysts. Nature genetics 56 (7) (2024)
Yahui Long, Kok Siong Ang, Raman Sethi, Sha Liao, Yang Heng, Lynn van Olst, Shuchen Ye, Chengwei Zhong, Jinmiao Chen, Di Zhang, Immanuel Kwok, Nazihah Husna, Min Jian, Lai Guan Ng, Ao Chen, Nicholas R J Gascoigne, David Gate, Rong Fan, Xue Liu, Jinmiao Chen
Deciphering spatial domains from spatial multi-omics with SpatialGlue. Nature methods (2024)
Yuebin Wang, Yun Luo, Xing Guo, Yunfu Li, Jiali Yan, Wenwen Shao, Wenjie Wei, Xiaofeng Wei, Tao Yang, Jing Chen, Lihua Chen, Qian Ding, Minji Bai, Lin Zhuo, Li Li, David P Jackson, Zhuxin Zhang, Xue Liu, Jianbing Yan, Huan Liu, Lei Liu, Ning Yang
A spatial transcriptome map of the developing maize ear. Nature plants 10 (5) (2024)
Shengpeng Wang, Lizhi Leng, Quanlei Wang, Yi-Fan Gu, Jinlu Li, Yanru An, Qiuting Deng, Pingyuan Xie, Can Cheng, Xueqin Chen, Qinwei Zhou, Jia Lu, Fang Chen, Longqi Liu, Huanming Yang, Jian Wang, Xue Liu, Yong Hou, Fei Gong, Liang Hu, Guangxiu Lu, Zhouchun Shang, Ge Lin
A single-cell transcriptome atlas of human euploid and aneuploid blastocysts. Nature genetics 56 (7) (2024)
Vanika Garg, Abhishek Bohra, Martin Mascher, Manuel Spannagl, Xue Liu, Michael W Bevan, Jeffrey L Bennetzen, Rajeev Kumar Varshney
Unlocking plant genetics with telomere-to-telomere genome assemblies. Nature genetics (2024)
Yuebin Wang, Yun Luo, Xing Guo, Yunfu Li, Jiali Yan, Wenwen Shao, Wenjie Wei, Xiaofeng Wei, Tao Yang, Jing Chen, Lihua Chen, Qian Ding, Minji Bai, Lin Zhuo, Li Li, David P Jackson, Zhuxin Zhang, Xue Liu, Jianbing Yan, Huan Liu, Lei Liu, Ning Yang
A spatial transcriptome map of the developing maize ear. Nature plants 10 (5) (2024)
Tongxuan Lv, Ying Zhang, Mei Li, Qiang Kang, Shuangsang Fang, Yong Zhang, Susanne B Pedersen, Xue Liu
EAGS: efficient and adaptive Gaussian smoothing applied to high-resolved spatial transcriptomics. GigaScience 13 (1) (2024)
Weibin Liu, Yan Li, George P Patrinos, Shuhua Xu, Meow-Keong Thong, Zhengming Chen, Francis P Crawley, Liming Li, Perihan Elif Ekmekci, Radoje Drmanac, Weiyang Cheong, Robert Benamouzig, Quan Nguyen, Pavel Volchkov, Juergen K V Reichardt, Piero Carnici, Partha Majumder, Xin Jin, George M Church, Jian Wang, Xue Liu
The 1% gift to humanity: The Human Genome Project II. Cell research (2024)
Tiange Wang, Zhun Shi, Huahui Ren, Yanan Hou, Jieli Lu, Fangming Yang, Chaojie Ye, Kui Wu, Ming-Ling Chen, Xue Liu, Dong Liu, Lijie Kong, Ruizhi Zheng, Jie Zheng, Mian Li, Yu Xu, Zhiyun Zhao, Yuhong Chen, Huanming Yang, Jian Wang, Guang Ning, Junhua Li, Huanzi Zhong, Yu-Fang Bi, Wei-Qing Wang
Divergent age-associated and metabolism-associated gut microbiome signatures modulate cardiovascular disease risk. Nature medicine 30 (6) (2024)
Fu-Sheng Yang, Min Liu, Xing Guo, Chao Xu, Juan Jiang, Weixue Mu, Dongming Fang, Yong-Chao Xu, Fu-Min Zhang, Ying-Hui Wang, Ting Yang, Hongyun Chen, Sunil Kumar Sahu, Ruirui Li, Guanlong Wang, Qiang Wang, Xue Liu, Song Ge, Huan Liu, Ya-Long Guo
Signatures of Adaptation and Purifying Selection in Highland Populations of Dasiphora fruticosa. Molecular biology and evolution 41 (6) (2024)
Chao Zhang, Lin Liu, Ying Zhang, Mei Li, Shuangsang Fang, Qiang Kang, Ao Chen, Xue Liu, Yong Zhang, Yuxiang Li
spatiAlign: an unsupervised contrastive learning model for data integration of spatially resolved transcriptomics. GigaScience 13 (2024)
An Jiang, Kai Han, Jiankai Wei, Xiaoshan Su, Rui Wang, Wei Zhang, Xiawei Liu, Jinghan Qiao, Penghui Liu, Qun Liu, Jin Zhang, Nannan Zhang, Yonghang Ge, Yuan Zhuang, Haiyan Yu, Shi Wang, Kai Chen, Wange Lu, Xue Liu, Huanming Yang, Guang-Yi Fan, Bo Dong
Spatially resolved single-cell atlas of ascidian endostyle provides insight into the origin of vertebrate pharyngeal organs. Science advances 10 (13) (2024)
Tiange Wang, Zhun Shi, Huahui Ren, Yanan Hou, Jieli Lu, Fangming Yang, Chaojie Ye, Kui Wu, Ming-Ling Chen, Xue Liu, Dong Liu, Lijie Kong, Ruizhi Zheng, Jie Zheng, Mian Li, Yu Xu, Zhiyun Zhao, Yuhong Chen, Huanming Yang, Jian Wang, Guang Ning, Junhua Li, Huanzi Zhong, Yu-Fang Bi, Wei-Qing Wang
Divergent age-associated and metabolism-associated gut microbiome signatures modulate cardiovascular disease risk. Nature medicine (2024)
Chao Zhang, Qiang Kang, Mei Li, Hongqing Xie, Shuangsang Fang, Xue Liu
BatchEval Pipeline: batch effect evaluation workflow for multiple datasets joint analysis. GigaByte (Hong Kong, China) 2024 (2024)
Yuebin Wang, Yun Luo, Xing Guo, Yunfu Li, Jiali Yan, Wenwen Shao, Wenjie Wei, Xiaofeng Wei, Tao Yang, Jing Chen, Lihua Chen, Qian Ding, Minji Bai, Lin Zhuo, Li Li, David P Jackson, Zhuxin Zhang, Xue Liu, Jianbing Yan, Huan Liu, Lei Liu, Ning Yang
A spatial transcriptome map of the developing maize ear. Nature plants (2024)
Yahui Long, Kok Siong Ang, Raman Sethi, Sha Liao, Yang Heng, Lynn van Olst, Shuchen Ye, Chengwei Zhong, Jinmiao Chen, Di Zhang, Immanuel Kwok, Nazihah Husna, Min Jian, Lai Guan Ng, Ao Chen, Nicholas R J Gascoigne, David Gate, Rong Fan, Xue Liu, Jinmiao Chen
Deciphering spatial domains from spatial multi-omics with SpatialGlue. Nature methods (2024)
Jiangshan Xu, Pengcheng Guo, Shijie Hao, Shuncheng Shangguan, Quan Shi, Giacomo Volpe, Keke Huang, Jing Zuo, Juan An, Yue Yuan, Mengnan Cheng, Qiuting Deng, Xiao Zhang, Guangyao Lai, Haitao Nan, Baihua Wu, Xinyi Shentu, Liang Wu, Xiaoyu Wei, Yujia Jiang, Xin Huang, Fengyu Pan, Yumo Song, Ronghai Li, Zhifeng Wang, Chuanyu Liu, Shi-Ping Liu, Yuxiang Li, Tao Yang, Zhicheng Xu, Wensi Du, Ling Li, Tanveer Ahmed, Kai You, Zhen Dai, Li Li, Baoming Qin, Yin-Xiong Li, Liangxue Lai, Dajiang Qin, Junling Chen, Rong Fan, Yongyin Li, Jin-Lin Hou, Michael Ott, Amar Deep Sharma, Tobias Cantz, Axel Schambach, Karsten Kristiansen, Andrew P Hutchins, Berthold Göttgens, Patrick H Maxwell, Lijian Hui, Xue Liu, Longqi Liu, Ao Chen, Yiwei Lai, Miguel Angel Esteban
A spatiotemporal atlas of mouse liver homeostasis and regeneration. Nature genetics (2024)
Yiwei Lai, Ignacio Ramírez-Pardo, Joan Isern, Juan An, Eusebio Perdiguero, Antonio L Serrano, Jinxiu Li, Esther Garcia-Dominguez, Jessica Segalés, Pengcheng Guo, Vera Lukesova, Eva Andrés, Jing Zuo, Yue Yuan, Chuanyu Liu, José Viña, Julio Domenech-Fernandez, Marie-Carmen Gomez-Cabrera, Yancheng Song, Longqi Liu, Xue Liu, Pura Muñoz-Cánoves, Miguel Angel Esteban
Multimodal cell atlas of the ageing human skeletal muscle. Nature 629 (8010) (2024)
Xiaomin Liu, Xin Tong, Leying Zou, Yanmei Ju, Mingliang Liu, Mo Han, Haorong Lu, Huanming Yang, Jian Wang, Yang Zong, Weibin Liu, Xue Liu, Xin Jin, Liang Xiao, Huijue Jia, Ruijin Guo, Tao Zhang
A genome-wide association study reveals the relationship between human genetic variation and the nasal microbiome. Communications biology 7 (1) (2024)
Yiwei Lai, Ignacio Ramírez-Pardo, Joan Isern, Juan An, Eusebio Perdiguero, Antonio L Serrano, Jinxiu Li, Esther Garcia-Dominguez, Jessica Segalés, Pengcheng Guo, Vera Lukesova, Eva Andrés, Jing Zuo, Yue Yuan, Chuanyu Liu, José Viña, Julio Domenech-Fernandez, Marie-Carmen Gomez-Cabrera, Yancheng Song, Longqi Liu, Xue Liu, Pura Muñoz-Cánoves, Miguel Angel Esteban
Multimodal cell atlas of the ageing human skeletal muscle. Nature (2024)
Youwen Qin, Xin Tong, Wei-Jian Mei, Yanshuang Cheng, Yuanqiang Zou, Kai Han, Jiehai Yu, Zhuye Jie, Tao Zhang, Shida Zhu, Xin Jin, Jian Wang, Huanming Yang, Xue Liu, Huanzi Zhong, Liang Xiao, Pei-Rong Ding
Consistent signatures in the human gut microbiome of old- and young-onset colorectal cancer. Nature communications 15 (1) (2024)
Chao Zhang, Lin Liu, Ying Zhang, Mei Li, Shuangsang Fang, Qiang Kang, Ao Chen, Xue Liu, Yong Zhang, Yuxiang Li
spatiAlign: an unsupervised contrastive learning model for data integration of spatially resolved transcriptomics. GigaScience 13 (2024)
Fu-Sheng Yang, Min Liu, Xing Guo, Chao Xu, Juan Jiang, Weixue Mu, Dongming Fang, Yong-Chao Xu, Fu-Min Zhang, Ying-Hui Wang, Ting Yang, Hongyun Chen, Sunil Kumar Sahu, Ruirui Li, Guanlong Wang, Qiang Wang, Xue Liu, Song Ge, Huan Liu, Ya-Long Guo
Signatures of adaptation and purifying selection in highland populations of Dasiphora fruticosa. Molecular biology and evolution (2024)
Tongxuan Lv, Ying Zhang, Mei Li, Qiang Kang, Shuangsang Fang, Yong Zhang, Susanne B Pedersen, Xue Liu
EAGS: efficient and adaptive Gaussian smoothing applied to high-resolved spatial transcriptomics. GigaScience 13 (1) (2024)
Luís Nunes, Fuqiang Li, Meizhen Wu, Tian Luo, Klara Hammarström, Emma Torell, Ingrid Ljuslinder, Artur Mezheyeuski, Per-Henrik D Edqvist, Anna Löfgren-Burström, Carl Zingmark, Sofia Edin, Chatarina Larsson, Lucy Mathot, Erik Osterman, Emerik Osterlund, Viktor Ljungström, Inês Neves, Nicole Yacoub, Unnur Guðnadóttir, Helgi Birgisson, Malin Enblad, Frederik Pontén, Richard Palmqvist, Xue Liu, Mathias Uhlen, Kui Wu, Bengt Glimelius, Cong Lin, Tobias Sjöblom
Prognostic genome and transcriptome signatures in colorectal cancers. Nature (2024)
Chun Gong, Shengkang Li, Leying Wang, Fuxiang Zhao, Shuangsang Fang, Dong Yuan, Zijian Zhao, Qiqi He, Mei Li, Weiqing Liu, Zhaoxun Li, Hongqing Xie, Sha Liao, Ao Chen, Yong Zhang, Yuxiang Li, Xue Liu
SAW: an efficient and accurate data analysis workflow for Stereo-seq spatial transcriptomics. GigaByte (Hong Kong, China) 2024 (2024)
Lei Cao, Chao Yang, Luni Hu, Wenjian Jiang, Yating Ren, Tianyi Xia, Mengyang Xu, Yishuai Ji, Mei Li, Xue Liu, Yuxiang Li, Yong Zhang, Shuangsang Fang
Deciphering spatial domains from spatially resolved transcriptomics with Siamese graph autoencoder. GigaScience 13 (1) (2024)
Fu-Sheng Yang, Min Liu, Xing Guo, Chao Xu, Juan Jiang, Weixue Mu, Dongming Fang, Yong-Chao Xu, Fu-Min Zhang, Ying-Hui Wang, Ting Yang, Hongyun Chen, Sunil Kumar Sahu, Ruirui Li, Guanlong Wang, Qiang Wang, Xue Liu, Song Ge, Huan Liu, Ya-Long Guo
Signatures of Adaptation and Purifying Selection in Highland Populations of Dasiphora fruticosa. Molecular biology and evolution 41 (6) (2024)
Keyi Ye, Fengjiao Bu, Li-Yuan Zhong, Zhaonian Dong, Zhaoxu Ma, Zhanpeng Tang, Yu Zhang, Xueyong Yang, Xue Liu, Ertao Wang, William J Lucas, Sanwen Huang, Huan Liu, Jianshu Zheng
Mapping the molecular landscape of Lotus japonicus nodule organogenesis through spatiotemporal transcriptomics. Nature communications 15 (1) (2024)
Chao Zhang, Lin Liu, Ying Zhang, Mei Li, Shuangsang Fang, Qiang Kang, Ao Chen, Xue Liu, Yong Zhang, Yuxiang Li
spatiAlign: an unsupervised contrastive learning model for data integration of spatially resolved transcriptomics. GigaScience 13 (2024)
Yiwei Lai, Ignacio Ramírez-Pardo, Joan Isern, Juan An, Eusebio Perdiguero, Antonio L Serrano, Jinxiu Li, Esther Garcia-Dominguez, Jessica Segalés, Pengcheng Guo, Vera Lukesova, Eva Andrés, Jing Zuo, Yue Yuan, Chuanyu Liu, José Viña, Julio Domenech-Fernandez, Marie-Carmen Gomez-Cabrera, Yancheng Song, Longqi Liu, Xue Liu, Pura Muñoz-Cánoves, Miguel Angel Esteban
Multimodal cell atlas of the ageing human skeletal muscle. Nature 629 (8010) (2024)
Yiwei Lai, Ignacio Ramírez-Pardo, Joan Isern, Juan An, Eusebio Perdiguero, Antonio L Serrano, Jinxiu Li, Esther Garcia-Dominguez, Jessica Segalés, Pengcheng Guo, Vera Lukesova, Eva Andrés, Jing Zuo, Yue Yuan, Chuanyu Liu, José Viña, Julio Domenech-Fernandez, Marie-Carmen Gomez-Cabrera, Yancheng Song, Longqi Liu, Xue Liu, Pura Muñoz-Cánoves, Miguel Angel Esteban
Multimodal cell atlas of the ageing human skeletal muscle. Nature 629 (8010) (2024)
Youwen Qin, Xin Tong, Wei-Jian Mei, Yanshuang Cheng, Yuanqiang Zou, Kai Han, Jiehai Yu, Zhuye Jie, Tao Zhang, Shida Zhu, Xin Jin, Jian Wang, Huanming Yang, Xue Liu, Huanzi Zhong, Liang Xiao, Pei-Rong Ding
Consistent signatures in the human gut microbiome of old- and young-onset colorectal cancer. Nature communications 15 (1) (2024)
Na Chen, Lilan Hao, Zhe Zhang, Chenglu Qin, Zhuye Jie, Hongxin Pan, Jiali Duan, Xincheng Huang, Yunhong Zhang, Hongqin Gao, Ruike Lu, Tianshu Sun, Hua Yang, Jinqiu Shi, Maolian Liang, Jianbin Guo, Qianqian Gao, Xiaoyue Zhao, Zhiyuan Dou, Liang Xiao, Shaoqiao Zhang, Xin Jin, Xue Liu, Huanming Yang, Jian Wang, Huijue Jia, Tao Zhang, Karsten Kristiansen, Chen Chen, Lan Zhu
Insights into the assembly of the neovaginal microbiota in Mayer-Rokitansky-Küster-Hauser (MRKH) syndrome patients. Nature communications 15 (1) (2024)
Jiangshan Xu, Pengcheng Guo, Shijie Hao, Shuncheng Shangguan, Quan Shi, Giacomo Volpe, Keke Huang, Jing Zuo, Juan An, Yue Yuan, Mengnan Cheng, Qiuting Deng, Xiao Zhang, Guangyao Lai, Haitao Nan, Baihua Wu, Xinyi Shentu, Liang Wu, Xiaoyu Wei, Yujia Jiang, Xin Huang, Fengyu Pan, Yumo Song, Ronghai Li, Zhifeng Wang, Chuanyu Liu, Shi-Ping Liu, Yuxiang Li, Tao Yang, Zhicheng Xu, Wensi Du, Ling Li, Tanveer Ahmed, Kai You, Zhen Dai, Li Li, Baoming Qin, Yin-Xiong Li, Liangxue Lai, Dajiang Qin, Junling Chen, Rong Fan, Yongyin Li, Jin-Lin Hou, Michael Ott, Amar Deep Sharma, Tobias Cantz, Axel Schambach, Karsten Kristiansen, Andrew P Hutchins, Berthold Göttgens, Patrick H Maxwell, Lijian Hui, Xue Liu, Longqi Liu, Ao Chen, Yiwei Lai, Miguel Angel Esteban
A spatiotemporal atlas of mouse liver homeostasis and regeneration. Nature genetics 56 (5) (2024)
Shengpeng Wang, Lizhi Leng, Quanlei Wang, Yi-Fan Gu, Jinlu Li, Yanru An, Qiuting Deng, Pingyuan Xie, Can Cheng, Xueqin Chen, Qinwei Zhou, Jia Lu, Fang Chen, Longqi Liu, Huanming Yang, Jian Wang, Xue Liu, Yong Hou, Fei Gong, Liang Hu, Guangxiu Lu, Zhouchun Shang, Ge Lin
A single-cell transcriptome atlas of human euploid and aneuploid blastocysts. Nature genetics (2024)
Youwen Qin, Xin Tong, Wei-Jian Mei, Yanshuang Cheng, Yuanqiang Zou, Kai Han, Jiehai Yu, Zhuye Jie, Tao Zhang, Shida Zhu, Xin Jin, Jian Wang, Huanming Yang, Xue Liu, Huanzi Zhong, Liang Xiao, Pei-Rong Ding
Consistent signatures in the human gut microbiome of old- and young-onset colorectal cancer. Nature communications 15 (1) (2024)
Jiangshan Xu, Pengcheng Guo, Shijie Hao, Shuncheng Shangguan, Quan Shi, Giacomo Volpe, Keke Huang, Jing Zuo, Juan An, Yue Yuan, Mengnan Cheng, Qiuting Deng, Xiao Zhang, Guangyao Lai, Haitao Nan, Baihua Wu, Xinyi Shentu, Liang Wu, Xiaoyu Wei, Yujia Jiang, Xin Huang, Fengyu Pan, Yumo Song, Ronghai Li, Zhifeng Wang, Chuanyu Liu, Shi-Ping Liu, Yuxiang Li, Tao Yang, Zhicheng Xu, Wensi Du, Ling Li, Tanveer Ahmed, Kai You, Zhen Dai, Li Li, Baoming Qin, Yin-Xiong Li, Liangxue Lai, Dajiang Qin, Junling Chen, Rong Fan, Yongyin Li, Jin-Lin Hou, Michael Ott, Amar Deep Sharma, Tobias Cantz, Axel Schambach, Karsten Kristiansen, Andrew P Hutchins, Berthold Göttgens, Patrick H Maxwell, Lijian Hui, Xue Liu, Longqi Liu, Ao Chen, Yiwei Lai, Miguel Angel Esteban
A spatiotemporal atlas of mouse liver homeostasis and regeneration. Nature genetics (2024)
Youwen Qin, Xin Tong, Wei-Jian Mei, Yanshuang Cheng, Yuanqiang Zou, Kai Han, Jiehai Yu, Zhuye Jie, Tao Zhang, Shida Zhu, Xin Jin, Jian Wang, Huanming Yang, Xue Liu, Huanzi Zhong, Liang Xiao, Pei-Rong Ding
Consistent signatures in the human gut microbiome of old- and young-onset colorectal cancer. Nature communications 15 (1) (2024)
Keyi Ye, Fengjiao Bu, Li-Yuan Zhong, Zhaonian Dong, Zhaoxu Ma, Zhanpeng Tang, Yu Zhang, Xueyong Yang, Xue Liu, Ertao Wang, William J Lucas, Sanwen Huang, Huan Liu, Jianshu Zheng
Mapping the molecular landscape of Lotus japonicus nodule organogenesis through spatiotemporal transcriptomics. Nature communications 15 (1) (2024)
Luís Nunes, Fuqiang Li, Meizhen Wu, Tian Luo, Klara Hammarström, Emma Torell, Ingrid Ljuslinder, Artur Mezheyeuski, Per-Henrik D Edqvist, Anna Löfgren-Burström, Carl Zingmark, Sofia Edin, Chatarina Larsson, Lucy Mathot, Erik Osterman, Emerik Osterlund, Viktor Ljungström, Inês Neves, Nicole Yacoub, Unnur Guðnadóttir, Helgi Birgisson, Malin Enblad, Frederik Pontén, Richard Palmqvist, Xue Liu, Mathias Uhlen, Kui Wu, Bengt Glimelius, Cong Lin, Tobias Sjöblom
Prognostic genome and transcriptome signatures in colorectal cancers. Nature (2024)
Fu-Sheng Yang, Min Liu, Xing Guo, Chao Xu, Juan Jiang, Weixue Mu, Dongming Fang, Yong-Chao Xu, Fu-Min Zhang, Ying-Hui Wang, Ting Yang, Hongyun Chen, Sunil Kumar Sahu, Ruirui Li, Guanlong Wang, Qiang Wang, Xue Liu, Song Ge, Huan Liu, Ya-Long Guo
Signatures of Adaptation and Purifying Selection in Highland Populations of Dasiphora fruticosa. Molecular biology and evolution 41 (6) (2024)
Tongxuan Lv, Ying Zhang, Mei Li, Qiang Kang, Shuangsang Fang, Yong Zhang, Susanne B Pedersen, Xue Liu
EAGS: efficient and adaptive Gaussian smoothing applied to high-resolved spatial transcriptomics. GigaScience 13 (1) (2024)
Chun Gong, Shengkang Li, Leying Wang, Fuxiang Zhao, Shuangsang Fang, Dong Yuan, Zijian Zhao, Qiqi He, Mei Li, Weiqing Liu, Zhaoxun Li, Hongqing Xie, Sha Liao, Ao Chen, Yong Zhang, Yuxiang Li, Xue Liu
SAW: an efficient and accurate data analysis workflow for Stereo-seq spatial transcriptomics. GigaByte (Hong Kong, China) 2024 (2024)
Youwen Qin, Xin Tong, Wei-Jian Mei, Yanshuang Cheng, Yuanqiang Zou, Kai Han, Jiehai Yu, Zhuye Jie, Tao Zhang, Shida Zhu, Xin Jin, Jian Wang, Huanming Yang, Xue Liu, Huanzi Zhong, Liang Xiao, Pei-Rong Ding
Consistent signatures in the human gut microbiome of old- and young-onset colorectal cancer. Nature communications 15 (1) (2024)
An Jiang, Kai Han, Jiankai Wei, Xiaoshan Su, Rui Wang, Wei Zhang, Xiawei Liu, Jinghan Qiao, Penghui Liu, Qun Liu, Jin Zhang, Nannan Zhang, Yonghang Ge, Yuan Zhuang, Haiyan Yu, Shi Wang, Kai Chen, Wange Lu, Xue Liu, Huanming Yang, Guang-Yi Fan, Bo Dong
Spatially resolved single-cell atlas of ascidian endostyle provides insight into the origin of vertebrate pharyngeal organs. Science advances 10 (13) (2024)
Tongxuan Lv, Ying Zhang, Mei Li, Qiang Kang, Shuangsang Fang, Yong Zhang, Susanne B Pedersen, Xue Liu
EAGS: efficient and adaptive Gaussian smoothing applied to high-resolved spatial transcriptomics. GigaScience 13 (1) (2024)
Xiaomin Liu, Xin Tong, Leying Zou, Yanmei Ju, Mingliang Liu, Mo Han, Haorong Lu, Huanming Yang, Jian Wang, Yang Zong, Weibin Liu, Xue Liu, Xin Jin, Liang Xiao, Huijue Jia, Ruijin Guo, Tao Zhang
A genome-wide association study reveals the relationship between human genetic variation and the nasal microbiome. Communications biology 7 (1) (2024)
Fu-Sheng Yang, Min Liu, Xing Guo, Chao Xu, Juan Jiang, Weixue Mu, Dongming Fang, Yong-Chao Xu, Fu-Min Zhang, Ying-Hui Wang, Ting Yang, Hongyun Chen, Sunil Kumar Sahu, Ruirui Li, Guanlong Wang, Qiang Wang, Xue Liu, Song Ge, Huan Liu, Ya-Long Guo
Signatures of Adaptation and Purifying Selection in Highland Populations of Dasiphora fruticosa. Molecular biology and evolution 41 (6) (2024)
Lei Cao, Chao Yang, Luni Hu, Wenjian Jiang, Yating Ren, Tianyi Xia, Mengyang Xu, Yishuai Ji, Mei Li, Xue Liu, Yuxiang Li, Yong Zhang, Shuangsang Fang
Deciphering spatial domains from spatially resolved transcriptomics with Siamese graph autoencoder. GigaScience 13 (1) (2024)
Tiange Wang, Zhun Shi, Huahui Ren, Yanan Hou, Jieli Lu, Fangming Yang, Chaojie Ye, Kui Wu, Ming-Ling Chen, Xue Liu, Dong Liu, Lijie Kong, Ruizhi Zheng, Jie Zheng, Mian Li, Yu Xu, Zhiyun Zhao, Yuhong Chen, Huanming Yang, Jian Wang, Guang Ning, Junhua Li, Huanzi Zhong, Yu-Fang Bi, Wei-Qing Wang
Divergent age-associated and metabolism-associated gut microbiome signatures modulate cardiovascular disease risk. Nature medicine (2024)
Bohan Zhang, Mei Li, Qiang Kang, Zhonghan Deng, Hua Qin, Kui Su, Xiuwen Feng, Lichuan Chen, Huanlin Liu, Shuangsang Fang, Yong Zhang, Yuxiang Li, Susanne B Pedersen, Xue Liu
Generating single-cell gene expression profiles for high-resolution spatial transcriptomics based on cell boundary images. GigaByte (Hong Kong, China) 2024 (2024)
An Jiang, Kai Han, Jiankai Wei, Xiaoshan Su, Rui Wang, Wei Zhang, Xiawei Liu, Jinghan Qiao, Penghui Liu, Qun Liu, Jin Zhang, Nannan Zhang, Yonghang Ge, Yuan Zhuang, Haiyan Yu, Shi Wang, Kai Chen, Wange Lu, Xue Liu, Huanming Yang, Guang-Yi Fan, Bo Dong
Spatially resolved single-cell atlas of ascidian endostyle provides insight into the origin of vertebrate pharyngeal organs. Science advances 10 (13) (2024)
Lei Cao, Chao Yang, Luni Hu, Wenjian Jiang, Yating Ren, Tianyi Xia, Mengyang Xu, Yishuai Ji, Mei Li, Xue Liu, Yuxiang Li, Yong Zhang, Shuangsang Fang
Deciphering spatial domains from spatially resolved transcriptomics with Siamese graph autoencoder. GigaScience 13 (1) (2024)
Chao Zhang, Qiang Kang, Mei Li, Hongqing Xie, Shuangsang Fang, Xue Liu
BatchEval Pipeline: batch effect evaluation workflow for multiple datasets joint analysis. GigaByte (Hong Kong, China) 2024 (2024)
Sunil Kumar Sahu, Min Liu, Yewen Chen, Jinshan Gui, Dongming Fang, Xiaoli Chen, Ting Yang, Chengzhong He, Le Cheng, Jinlong Yang, Durgesh Nandini Sahu, Linzhou Li, Hongli Wang, Weixue Mu, Jinpu Wei, Jie Liu, Yuxian Zhao, Shouzhou Zhang, Michael Lisby, Xin Liu, Xue Liu, Laigeng Li, Sibo Wang, Huan Liu
Chromosome-scale genomes of commercial timber trees (Ochroma pyramidale, Mesua ferrea, and Tectona grandis). Scientific data 10 (1) (2023)
Qionghua Zhu, Xin Zhao, Yuanhang Zhang, Yanping Li, Shang Liu, Jingxuan Han, Zhiyuan Sun, Chunqing Wang, Daqi Deng, Shanshan Wang, Yisen Tang, Yaling Huang, Siyuan Jiang, Chi Tian, Xi Chen, Yue Yuan, Zeyu Li, Tao Yang, Tingting Lai, Yiqun Liu, Wenzhen Yang, Xuanxuan Zou, Mingyuan Zhang, Huanhuan Cui, Chuanyu Liu, Xin Jin, Yuhui Hu, Ao Chen, Xue Liu, Guipeng Li, Yong Hou, Longqi Liu, Shi-Ping Liu, Liang Fang, Wei Chen, Liang Wu
Single cell multi-omics reveal intra-cell-line heterogeneity across human cancer cell lines. Nature communications 14 (1) (2023)
Xiaoqian Lin, Tongyuan Hu, Jian-Wei Chen, Hewei Liang, Jianwei Zhou, Zhinan Wu, Chen Ye, Xin Jin, Xue Liu, Wenwei Zhang, Xiaohuan Jing, Tao Yang, Jian Wang, Huanming Yang, Karsten Kristiansen, Liang Xiao, Yuanqiang Zou
The genomic landscape of reference genomes of cultivated human gut bacteria. Nature communications 14 (1) (2023)
Chentao Yang, Yang Zhou, Yanni Song, Dongya Wu, Yan Zeng, Lei Nie, Panhong Liu, Shilong Zhang, Guangii Chen, Jinjin Xu, Hongling Zhou, Long Zhou, Xiaobo Qian, Chenlu Liu, Shangjin Tan, Chengran Zhou, Wei Dai, Mengyang Xu, Yanwei Qi, Xiaobo Wang, Lidong Guo, Guangyi Fan, Aijun Wang, Yuan Deng, Yong Zhang, Jiazheng Jin, Yunqiu He, Chunxue Guo, Guoji Guo, Qing Zhou, Xue Liu, Huanming Yang, Jian Wang, Shuhua Xu, Yafei Mao, Xin Jin, Jue Ruan, Guo-Jie Zhang
The complete and fully-phased diploid genome of a male Han Chinese. Cell research (2023)
Tiantian Chang, Weichao Ding, Shirui Yan, Yun Wang, Haoling Zhang, Yu Zhang, Zhi Ping, Huiming Zhang, Yijian Huang, Jiahui Zhang, Dan Wang, Wenwei Zhang, Xue Liu, Yue Shen, Xian Fu
A robust yeast biocontainment system with two-layered regulation switch dependent on unnatural amino acid. Nature communications 14 (1) (2023)
Xiaoqian Lin, Tongyuan Hu, Jian-Wei Chen, Hewei Liang, Jianwei Zhou, Zhinan Wu, Chen Ye, Xin Jin, Xue Liu, Wenwei Zhang, Xiaohuan Jing, Tao Yang, Jian Wang, Huanming Yang, Karsten Kristiansen, Liang Xiao, Yuanqiang Zou
The genomic landscape of reference genomes of cultivated human gut bacteria. Nature communications 14 (1) (2023)
Ruihua Zhang, Qun Liu, Shanshan Pan, Yingying Zhang, Yating Qin, Xiao Du, Zengbao Yuan, Yongrui Lu, Yue Song, Mengqi Zhang, Nannan Zhang, Jie Ma, Zhe Zhang, Xiaodong Jia, Kun Wang, Shunping He, Shanshan Liu, Ming Ni, Xin Liu, Xue Liu, Huanming Yang, Jian Wang, Inge Seim, Guang-Yi Fan
A single-cell atlas of West African lungfish respiratory system reveals evolutionary adaptations to terrestrialization. Nature communications 14 (1) (2023)
Sunil Kumar Sahu, Min Liu, Guanlong Wang, Yewen Chen, Ruirui Li, Dongming Fang, Durgesh Nandini Sahu, Weixue Mu, Jinpu Wei, Jie Liu, Yuxian Zhao, Shouzhou Zhang, Michael Lisby, Xin Liu, Xue Liu, Lai-Geng Li, Sibo Wang, Huan Liu, Chengzhong He
Chromosome-scale genomes of commercially important mahoganies, Swietenia macrophylla and Khaya senegalensis. Scientific data 10 (1) (2023)
Fei Hao, Xue Liu, Bo-Tong Zhou, Zunzhe Tian, Lina Zhou, Hang Zong, Jiyan Qi, Juan He, Yongting Zhang, Peng Zeng, Qiong Li, Kai Wang, Keke Xia, Xing Guo, Li Li, Wenwen Shao, Bohan Zhang, Shengkang Li, Haifeng Yang, Linchong Hui, Wei Chen, Lixin Peng, Feipeng Liu, Zi-Qiang Rong, Yingmei Peng, Wenbo Zhu, John A McCallum, Zhen Li, Xun Xu, Hui Yang, Richard C Macknight, Wen Wang, Jing Cai
Chromosome-level genomes of three key Allium crops and their trait evolution. Nature genetics (2023)
Marty Kardos, Yaolei Zhang, Kim M Parsons, Yunga A, Hui Kang, Xue Liu, Xin Liu, Craig O Matkin, Peijun Zhang, Eric J Ward, M Bradley Hanson, Candice K Emmons, Michael J Ford, Guang-Yi Fan, Songhai Li
Inbreeding depression explains killer whale population dynamics. Nature ecology & evolution (2023)
Xiaoqian Lin, Tongyuan Hu, Jian-Wei Chen, Hewei Liang, Jianwei Zhou, Zhinan Wu, Chen Ye, Xin Jin, Xue Liu, Wenwei Zhang, Xiaohuan Jing, Tao Yang, Jian Wang, Huanming Yang, Karsten Kristiansen, Liang Xiao, Yuanqiang Zou
The genomic landscape of reference genomes of cultivated human gut bacteria. Nature communications 14 (1) (2023)
Wenxi Li, Hewei Liang, Xiaoqian Lin, Tongyuan Hu, Zhinan Wu, Wenxin He, Mengmeng Wang, Jiahao Zhang, Zhuye Jie, Xin Jin, Xue Liu, Jian Wang, Huanming Yang, Wenwei Zhang, Karsten Kristiansen, Liang Xiao, Yuanqiang Zou
A catalog of bacterial reference genomes from cultivated human oral bacteria. NPJ biofilms and microbiomes 9 (1) (2023)
Canqing Yu, Xianmei Lan, Ye Tao, Yu Guo, Dianjianyi Sun, Puyi Qian, Yuwen Zhou, Robin G Walters, Linxuan Li, Yunqing Zhu, Jingyu Zeng, Iona Y Millwood, Ruidong Guo, Pei Pei, Tao Yang, Huaidong Du, Fan Yang, Ling Yang, Fangyi Ren, Yiping Chen, Fengzhen Chen, Xiaosen Jiang, Zhiqiang Ye, Lanlan Dai, Xiaofeng Wei, Xue Liu, Huanming Yang, Jian Wang, Zhengming Chen, Huanhuan Zhu, Jun Lv, Xin Jin, Liming Li
A high-resolution haplotype-resolved Reference panel constructed from the China Kadoorie Biobank Study. Nucleic acids research (2023)
Ruilian Yin, Keke Xia, Xue Liu
Spatial transcriptomics drives a new era in plant research. The Plant journal : for cell and molecular biology (2023)
Fei Hao, Xue Liu, Bo-Tong Zhou, Zunzhe Tian, Lina Zhou, Hang Zong, Jiyan Qi, Juan He, Yongting Zhang, Peng Zeng, Qiong Li, Kai Wang, Keke Xia, Xing Guo, Li Li, Wenwen Shao, Bohan Zhang, Shengkang Li, Haifeng Yang, Linchong Hui, Wei Chen, Lixin Peng, Feipeng Liu, Zi-Qiang Rong, Yingmei Peng, Wenbo Zhu, John A McCallum, Zhen Li, Xun Xu, Hui Yang, Richard C Macknight, Wen Wang, Jing Cai
Author Correction: Chromosome-level genomes of three key Allium crops and their trait evolution. Nature genetics (2023)
Xiaoli Chen, Dongming Fang, Yuxing Xu, Kunyu Duan, Satoko Yoshida, Shuai Yang, Sunil Kumar Sahu, Hui Fu, Xuanmin Guang, Min Liu, Chenyu Wu, Yang Liu, Weixue Mu, Yewen Chen, Yannan Fan, Fang Wang, Shufeng Peng, Dishen Shi, Yayu Wang, Runxian Yu, Wen Zhang, Yuqing Bai, Zhong-Jian Liu, Qiaoshun Yan, Xin Liu, Xue Liu, Huanming Yang, Jianqiang Wu, Sean W Graham, Huan Liu
Balanophora genomes display massively convergent evolution with other extreme holoparasites and provide novel insights into parasite-host interactions. Nature plants (2023)
Liang Wu, Jiayan Yan, Yinqi Bai, Feiyu Chen, Xuanxuan Zou, Jiangshan Xu, Ao Huang, Liangzhen Hou, Yu Zhong, Zehua Jing, Qichao Yu, Xiaorui Zhou, Zhifeng Jiang, Chunqing Wang, Mengnan Cheng, Yuan Ji, Yingyong Hou, Rongkui Luo, Qinqin Li, Liang Wu, Jianwen Cheng, Pengxiang Wang, Dezhen Guo, Waidong Huang, Junjie Lei, Shang Liu, Yizhen Yan, Yiling Chen, Sha Liao, Yuxiang Li, Haixiang Sun, Na Yao, Xiangyu Zhang, Shiyu Zhang, Xi Chen, Yang Yu, Yao Li, Fengming Liu, Zheng Wang, Shaolai Zhou, Huanming Yang, Shuang Yang, Xue Liu, Longqi Liu, Qiang Gao, Zhaoyou Tang, Xiangdong Wang, Jian Wang, Jia Fan, Shi-Ping Liu, Xin-Rong Yang, Ao Chen, Jian Zhou
An invasive zone in human liver cancer identified by Stereo-seq promotes hepatocyte-tumor cell crosstalk, local immunosuppression and tumor progression. Cell research (2023)
Zhicheng Xu, Weiwen Wang, Tao Yang, Ling Li, Xizheng Ma, Jing Chen, Jieyu Wang, Yan Huang, Joshua Gould, Huifang Lu, Wensi Du, Sunil Kumar Sahu, Fan Yang, Zhiyong Li, Qingjiang Hu, Cong Hua, Shoujie Hu, Yiqun Liu, Jia Cai, Lijin You, Yong Zhang, YuXiang Li, Wenjun Zeng, Ao Chen, Bo Wang, Longqi Liu, Fengzhen Chen, Kailong Ma, Xue Liu, Xiaofeng Wei
STOmicsDB: a comprehensive database for spatial transcriptomics data sharing, analysis and visualization. Nucleic acids research (2023)
Si Cheng, Zhe Xu, Shengzhe Bian, Xi Chen, Yanfeng Shi, Yanran Li, Yunyun Duan, Yang Liu, Jinxi Lin, Yong Jiang, Jing Jing, Zixiao Li, Yilong Wang, Xia Meng, Yaou Liu, Mingyan Fang, Xin Jin, Xue Liu, Jian Wang, Chaolong Wang, Hao Li, Siyang Liu, Yongjun Wang
The STROMICS genome study: deep whole-genome sequencing and analysis of 10K Chinese patients with ischemic stroke reveal complex genetic and phenotypic interplay. Cell discovery 9 (1) (2023)
Zhi Ping, Shihong Chen, Guangyu Zhou, Xiaoluo Huang, Sha Joe Zhu, Haoling Zhang, Henry H Lee, Zhaojun Lan, Jie Cui, Tai Chen, Wenwei Zhang, Huanming Yang, Xue Liu, George M Church, Yue Shen
Towards practical and robust DNA-based data archiving using the yin-yang codec system. Nature computational science 2 (4) (2022)
Yang Liu, Sibo Wang, Linzhou Li, Ting Yang, Shanshan Dong, Tong Wei, Sheng-Dan Wu, Yongbo Liu, Yiqing Gong, Xiuyan Feng, Jianchao Ma, Guanxiao Chang, Jinling Huang, Yong Yang, Hongli Wang, Min Liu, Yan Xu, Hongping Liang, Jin Yu, Yuqing Cai, Zhaowu Zhang, Yannan Fan, Weixue Mu, Sunil Kumar Sahu, Shuchun Liu, Xiaoan Lang, Leilei Yang, Na Li, Sadaf Habib, Yongqiong Yang, Anders Jan Lindström, Pei Liang, Bernard Goffinet, Sumaira Zaman, Jill L Wegrzyn, Dexiang Li, Jian Liu, Jie Cui, Eva Christina Sonnenschein, Xiao-Bo Wang, Jue Ruan, Jia-Yu Xue, Zhu-Qing Shao, Chi Song, Guangyi Fan, Zhen Li, Liangsheng Zhang, Jian-Quan Liu, Zhong-Jian Liu, Yuan-Nian Jiao, Xiao-Quan Wang, Hong Wu, Ertao Wang, Michael Lisby, Huanming Yang, Jian Wang, Xin Liu, Xue Liu, Nan Li, Pamela S Soltis, Yves Van de Peer, Douglas Edward Soltis, Xun Gong, Huan Liu, Shou-Zhou Zhang
The Cycas genome and the early evolution of seed plants. Nature plants 8 (4) (2022)
Xiaoyu Wei, Sulei Fu, Hanbo Li, Yang Liu, Shuai Wang, Weimin Feng, Yunzhi Yang, Xiawei Liu, Yan-Yun Zeng, Mengnan Cheng, Yiwei Lai, Xiaojie Qiu, Liang Wu, Nannan Zhang, Yujia Jiang, Jiangshan Xu, Xiaoshan Su, Cheng Peng, Lei Han, Wilson Pak-Kin Lou, Chuanyu Liu, Yue Yuan, Kailong Ma, Tao Yang, Xiangyu Pan, Shang Gao, Ao Chen, Miguel Angel Esteban, Huanming Yang, Jian Wang, Guangyi Fan, Longqi Liu, Liang Chen, Xue Liu, Ji-Feng Fei, Ying Gu
Single-cell Stereo-seq reveals induced progenitor cells involved in axolotl brain regeneration. Science (New York, N.Y.) 377 (6610) (2022)
Qiye Li, Mingyue Wang, Pei Zhang, Yang Liu, Qunfei Guo, Yuanzhen Zhu, Tinggang Wen, Xueqin Dai, Xiafang Zhang, Manuel Nagel, Bjarke Hamberg Dethlefsen, Nianxia Xie, Jie Zhao, Wei Jiang, Lei Han, Liang Wu, Wenjiang Zhong, Zhifeng Wang, Xiaoyu Wei, Wei Dai, Longqi Liu, Xue Liu, Haorong Lu, Huanming Yang, Jian Wang, Jacobus Jan Boomsma, Chuanyu Liu, Guo-Jie Zhang, Weiwei Liu
A single-cell transcriptomic atlas tracking the neural basis of division of labour in an ant superorganism. Nature ecology & evolution 6 (8) (2022)
Rongbo Shen, Lin Liu, Zihan Wu, Ying Zhang, Zhiyuan Yuan, Junfu Guo, Fan Yang, Chao Zhang, Bichao Chen, Wanwan Feng, Chao Liu, Jing Guo, Guozhen Fan, Yong Zhang, Yuxiang Li, Xue Liu, Jianhua Yao
Spatial-ID: a cell typing method for spatially resolved transcriptomics via transfer learning and spatial embedding. Nature communications 13 (1) (2022)
Zhi Ping, Shihong Chen, Guangyu Zhou, Xiaoluo Huang, Sha Joe Zhu, Haoling Zhang, Henry H Lee, Zhaojun Lan, Jie Cui, Tai Chen, Wenwei Zhang, Huanming Yang, Xue Liu, George M Church, Yue Shen
Towards practical and robust DNA-based data archiving using the yin-yang codec system. Nature computational science 2 (4) (2022)
Md Abdul Mazid, Carl Ward, Zhiwei Luo, Chuanyu Liu, Yunpan Li, Yiwei Lai, Liang Wu, Jinxiu Li, Wenqi Jia, Yu Jiang, Hao Liu, Lixin Fu, Yueli Yang, David P Ibañez, Junjian Lai, Xiaoyu Wei, Juan An, Pengcheng Guo, Yue Yuan, Qiuting Deng, Yang Wang, Ying Liu, Fei Gao, Junwen Wang, Shahriar Zaman, Baoming Qin, Guangming Wu, Patrick H Maxwell, Xue Liu, Longqi Liu, Wenjuan Li, Miguel Angel Esteban
Rolling back human pluripotent stem cells to an eight-cell embryo-like stage. Nature 605 (7909) (2022)
Rongbo Shen, Lin Liu, Zihan Wu, Ying Zhang, Zhiyuan Yuan, Junfu Guo, Fan Yang, Chao Zhang, Bichao Chen, Wanwan Feng, Chao Liu, Jing Guo, Guozhen Fan, Yong Zhang, Yuxiang Li, Xue Liu, Jianhua Yao
Spatial-ID: a cell typing method for spatially resolved transcriptomics via transfer learning and spatial embedding. Nature communications 13 (1) (2022)
Yayu Wang, Xiaolin Wang, Shuai Sun, Canzhi Jin, Jianmu Su, Jinpu Wei, Xinyue Luo, Jiawen Wen, Tong Wei, Sunil Kumar Sahu, Hongfeng Zou, Hongyun Chen, Zhixin Mu, Gengyun Zhang, Xin Liu, Xue Liu, Lone Gram, Huanming Yang, Ertao Wang, Huan Liu
GWAS, MWAS and mGWAS provide insights into precision agriculture based on genotype-dependent microbial effects in foxtail millet. Nature communications 13 (1) (2022)
Zhi Ping, Shihong Chen, Guangyu Zhou, Xiaoluo Huang, Sha Joe Zhu, Haoling Zhang, Henry H Lee, Zhaojun Lan, Jie Cui, Tai Chen, Wenwei Zhang, Huanming Yang, Xue Liu, George M Church, Yue Shen
Towards practical and robust DNA-based data archiving using the yin-yang codec system. Nature computational science 2 (4) (2022)
Haolin Zhang, Xuemei Gong, Qianqian Zhao, Takahito Mukai, Oscar Vargas-Rodriguez, Huiming Zhang, Yuxing Zhang, Paul Wassel, Kazuaki Amikura, Julie A Maupin-Furlow, Yan Ren, Xue Liu, Yuri I Wolf, Kira S Makarova, Eugene V Koonin, Yue Shen, Dieter Söll, Xian Fu
The tRNA discriminator base defines the mutual orthogonality of two distinct pyrrolysyl-tRNA synthetase/tRNAPyl pairs in the same organism. Nucleic acids research 50 (8) (2022)
Xiaoguang Pan, Kunli Qu, Hao Yuan, Xi Xiang, Christian Anthon, Liubov Pashkova, Xue Liang, Peng Han, Giulia I Corsi, Fengping Xu, Ping Liu, Jiayan Zhong, Yan Zhou, Tao Ma, Hui Jiang, Junnian Liu, Jian Wang, Niels Jessen, Lars Bolund, Huanming Yang, Xue Liu, George M Church, Jan Gorodkin, Lin Lin, Yonglun Luo
Massively targeted evaluation of therapeutic CRISPR off-targets in cells. Nature communications 13 (1) (2022)
Rongbo Shen, Lin Liu, Zihan Wu, Ying Zhang, Zhiyuan Yuan, Junfu Guo, Fan Yang, Chao Zhang, Bichao Chen, Wanwan Feng, Chao Liu, Jing Guo, Guozhen Fan, Yong Zhang, Yuxiang Li, Xue Liu, Jianhua Yao
Spatial-ID: a cell typing method for spatially resolved transcriptomics via transfer learning and spatial embedding. Nature communications 13 (1) (2022)
Ying Lei, Mengnan Cheng, Zihao Li, Zhenkun Zhuang, Liang Wu, Yunong Sun, Lei Han, Zhihao Huang, Yuzhou Wang, Zifei Wang, Liqin Xu, Yue Yuan, Shang Liu, Taotao Pan, Jiarui Xie, Chuanyu Liu, Giacomo Volpe, Carl Ward, Yiwei Lai, Jiangshan Xu, Mingyue Wang, Hao Yu, Haixi Sun, Qichao Yu, Liang Wu, Chunqing Wang, Chi Wai Wong, Wei Liu, Liangzhi Xu, Jingkuan Wei, Dandan Chen, Zhouchun Shang, Gui-Bo Li, Kun Ma, Le Cheng, Fei Ling, Tao Tan, Kai Chen, Bosiljka Tasic, Michael Dean, Weizhi Ji, Huanming Yang, Ying Gu, Miguel Angel Esteban, Yuxiang Li, Ao Chen, Yuyu Niu, Hongkui Zeng, Yong Hou, Longqi Liu, Shi-Ping Liu, Xue Liu
Spatially resolved gene regulatory and disease-related vulnerability map of the adult Macaque cortex. Nature communications 13 (1) (2022)
Xiaomin Liu, Xin Tong, Yuanqiang Zou, Xiaoqian Lin, Hui Zhao, Liu Tian, Zhuye Jie, Qi Wang, Zhe Zhang, Haorong Lu, Liang Xiao, Xuemei Qiu, Jin Zi, Rong Wang, Xue Liu, Huanming Yang, Jian Wang, Yang Zong, Weibin Liu, Yong Hou, Shida Zhu, Huijue Jia, Tao Zhang
Mendelian randomization analyses support causal relationships between blood metabolites and the gut microbiome. Nature genetics 54 (1) (2022)
Fei Wang, Peiwen Ding, Xue Liang, Xiangning Ding, Camilla Blunk Brandt, Evelina Sjöstedt, Jiacheng Zhu, Saga Bolund, Lijing Zhang, Laura P M H de Rooij, Lihua Luo, Yanan Wei, Wandong Zhao, Zhiyuan Lv, János Haskó, Runchu Li, Qiuyu Qin, Yi Jia, Wendi Wu, Yuting Yuan, Mingyi Pu, Haoyu Wang, Aiping Wu, Lin Xie, Ping Liu, Fang Chen, Jacqueline Herold, Joanna M Kalucka, Max J Karlsson, Xiuqing Zhang, Rikke Bek Helmig, Linn Fagerberg, Cecilia Lindskog, Frederik Pontén, Mathias Uhlen, Lars Bolund, Niels Jessen, Hui Jiang, Xue Liu, Huanming Yang, Peter Carmeliet, Jan Mulder, Dongsheng Chen, Lin Lin, Yonglun Luo
Endothelial cell heterogeneity and microglia regulons revealed by a pig cell landscape at single-cell level. Nature communications 13 (1) (2022)
Fei Wang, Peiwen Ding, Xue Liang, Xiangning Ding, Camilla Blunk Brandt, Evelina Sjöstedt, Jiacheng Zhu, Saga Bolund, Lijing Zhang, Laura P M H de Rooij, Lihua Luo, Yanan Wei, Wandong Zhao, Zhiyuan Lv, János Haskó, Runchu Li, Qiuyu Qin, Yi Jia, Wendi Wu, Yuting Yuan, Mingyi Pu, Haoyu Wang, Aiping Wu, Lin Xie, Ping Liu, Fang Chen, Jacqueline Herold, Joanna M Kalucka, Max J Karlsson, Xiuqing Zhang, Rikke Bek Helmig, Linn Fagerberg, Cecilia Lindskog, Frederik Pontén, Mathias Uhlen, Lars Bolund, Niels Jessen, Hui Jiang, Xue Liu, Huanming Yang, Peter Carmeliet, Jan Mulder, Dongsheng Chen, Lin Lin, Yonglun Luo
Author Correction: Endothelial cell heterogeneity and microglia regulons revealed by a pig cell landscape at single-cell level. Nature communications 13 (1) (2022)
Rongbo Shen, Lin Liu, Zihan Wu, Ying Zhang, Zhiyuan Yuan, Junfu Guo, Fan Yang, Chao Zhang, Bichao Chen, Wanwan Feng, Chao Liu, Jing Guo, Guozhen Fan, Yong Zhang, Yuxiang Li, Xue Liu, Jianhua Yao
Spatial-ID: a cell typing method for spatially resolved transcriptomics via transfer learning and spatial embedding. Nature communications 13 (1) (2022)

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Xue Liu (Xun Xu)