百晓学者学者目录

廖莎

副教授、教授、硕士生导师、讲师，西北大学

精选作品

期刊论文

2026

牡丹文化基因的数字转译

廖莎

《文化产业》

2026

非遗数字化教育转化的理论构建与实践探索——基于人工智能动作捕捉的白马藏族幼儿舞蹈创编研究

廖莎，李青窈，邹雨豪

《尚舞》

2026

数字舞蹈艺术赋能川西北儿童传统文化认知提升的路径研究

张婷，廖莎，王浩

《明周刊》

2026

Spatial transcriptomics uncovers vasculature-centered cellular interactions driving Japanese encephalitis progression in a mouse model

Zhi-Hua Ou, Zhao-Yang Wang, Qi Chen, Peidi Ren, Xiuju He, Yan Liang, Ying'an Liang, Jia-Xuan Wang, Sha Liao, Dexin Wang, Jie Zhao, Ou-Jia Zhang, Zhen-Yu Peng, Jian-Guo Su, Wangsheng Li, Guohai Hu, Ao Chen, Zi-Qing Deng, Xin Jin, Xun Xu, Jun-Hua Li, Gong Cheng

Nature Communications

DOI

2026

HESTIA: scalable multimodal integration of histology and high-resolution spatial Transcriptomics for robust spatial domain identification

Zheng Zhong, Xiao-Yu Zhu, Jing Guo, Sha Liao, Ao Chen

bioRxiv

DOI

2026

The potential of wheat spatial omics

Xiao-Yuan Tao, Cong Tan, Yifan Liu, Yuan-Yuan Wang, A. Raza, Jing He, Lu-Lu Wang, Keke Xia, Yanpeng Yan, Sha Liao, Wei Jiang, Yue Qu, Bo Xu, Yi Zhou, Xiu-Juan Yang, S. Roy, MD Denton, Matthew Tucker, Jay D. Able, M. Gilliham, Peter Langridge, Hang-Wei Hu, Ji-Zheng He, Chen-Chen Zhao, Mei-Xue Zhou, R. R. Mir, A. Chitikineni, Chengdao Li, Peng Zhang, R. Trethowan, Yi Ding, Jianping Zhang, Peter Franks, Qiu-Hong Wu, Ling-Jie Ye, Yi-Zhou Wang, Feibo Wu, Guo-Ping Zhang, S. Cai, Qiu-Fang Shen, Hang-Yu Jiang, Guang Chen, Yun Zhou, Chun-Peng Song, Yu-Mei Zhang, Wu-Jun Ma, Xi-Mei Li, Wei-Wei Guo, Jian-Bin Zeng, Xiaoyan He, Wen-Xing Liu, Xue Feng, Rongzhi Zhang, Gen-Ying Li, Xin-You Cao, Shu-Bing Liu, Qier Liu, Jian-Sheng Chen, Xueyong Zhang, Lu Liu, F. Zeng, Feng-Lin Deng, Yuan Qin, Xiangqian Zhu, Sergey Shabala, E. Tee, Thorsten Schnurbusch, M. Mascher, Hong-Hong Wu, M. Spannagl, Ming Xin, Jinying Gou, G. Brar, Dawei Xue, Wei Wang, Matthew P. Reynolds, Yu-Sheng Zhao, Zhiyong Liu, T. Krugman, Y. Sakata, Suyan Yee, K. Chan, Barry J. Pogson, Yi-Jing Zhang, D. Marchant, K. Siddique, Xiaodong Fang, Ao Chen, R. Henry, Scott A. Boden, R. Varshney, Sheng Xu, Xun Xu, Zhong-Hua Chen

Nature Genetics

DOI

2026

Evolutionary conservation and divergence of phagocytic and coagulation programs across bilaterian circulating immune cells

Yanan Li, Xiang Liu, Hongxi Chen, Qi Yang, Qun Liu, Hongyan Wang, Shuo Li, Xianghui Zhang, Yida Huang, Jianyang Chen, L. Doretto, I. F. Rosa, Shenglei Han, Chen Li, Inge Seim, Yi-Fan Lu, Kai Liu, Junqiang Xu, Ying-Ying Zhang, Shijie Hao, Sha Liao, Shan-Shan Pan, Junjie Shi, Ya-Dong Chen, Chenghua Li, Qian Wang, Shanshan Liu, Guang-Yi Fan, Chang-Wei Shao

Molecular biology and evolution

DOI

2026

Full-length single-cell spatial transcriptomics reveals spatial and cell-type-specific transcript isoforms in the primate brain

Hengxin Liu, Yanhong Hong, Y. Zhang, Liyuan Xi, Huiying Yan, Yuxuan Liu, Qianqian Yang, Xing Sun, Shou-Liang Guan, Zan Chen, Yu Feng, Tao Zeng, Juan Meng, Sha Liao, Nini Yuan, Z. Liu, Chao Li, Zhi-Yong Liu, Lei Han, Zhi-Jian Shen, Ao Chen, Yi-Di Sun, Yu-Liang Dong, Longqi Liu, Cheng-Yu T. Li, Wu Wei

Nature Methods

DOI

2025

Spatial transcriptomics elucidates the central role of cerebral vasculatures in the progression of Japanese encephalitis

Zhi-Hua Ou, Zhao-Yang Wang, Qi Chen, Peidi Ren, Xiuju He, Yan Liang, Ying'an Liang, Jiaxuan Wang, Sha Liao, Dexin Wang, Jie Zhao, Ou-Jia Zhang, Zhen-Yu Peng, J. Su, Wangsheng Li, Guohai Hu, Ao Chen, Zi-Qing Deng, Xin Jin, Xun Xu, Jun-Hua Li, Gong Cheng

bioRxiv

DOI

2025

StereoMM: a graph fusion model for integrating spatial transcriptomic data and pathological images

Bingying Luo, Fei Teng, Guo Tang, Weixuan Cen, Xing Liu, Jin-Miao Chen, Chi Qu, Xuan-Zhu Liu, Xin Liu, Wenyan Jiang, Huaqiang Huang, Yu Feng, Xue Zhang, Min Jian, Mei Li, Feng Xi, Guibo Li, Sha Liao, Ao Chen, Weimiao Yu, Xun Xu, Jiajun Zhang

Briefings Bioinform.

DOI

2025

Single-cell spatial transcriptomic atlas of the whole mouse brain.

Lei Han, Zhen Liu, Zehua Jing, Yuxuan Liu, Yujie Peng, Huizhong Chang, Junjie Lei, Kexin Wang, Yuanfang Xu, Wei Liu, Zihan Wu, Qian Li, Xiaoxue Shi, Mingyuan Zheng, He Wang, Juan Deng, Yan Zhong, Hailin Pan, Jun-Kai Lin, Rui-Yi Zhang, Yu Chen, Jin-Hua Wu, Mingrui Xu, Bi-Yu Ren, Mengnan Cheng, Qian Yu, Xinxiang Song, Yanbing Lu, Yuan-Chun Tang, Nini Yuan, Suhong Sun, Yingjie An, Wenqun Ding, Xing Sun, Yan-Rong Wei, Shuzhen Zhang, Yannong Dou, Yun Zhao, Luyao Han, Qianhua Zhu, Junfeng Xu, Shi-Wen Wang, Dan Wang, Yinqi Bai, Yikai Liang, Yuan Liu, Meng-Meng Chen, Chun Xie, Bin-Shi Bo, Mei Li, Xinyan Zhang, Wang Ting, Zhenhua Chen, Jiao Fang, Shu-Ting Li, Yujia Jiang, Xingjun Tan, Guo-Long Zuo, Yue Xie, Huan-Huan Li, Qu-Yuan Tao, Yan Li, Jian-Feng Liu, Yuyang Liu, Mingkun Hao, Jingjing Wang, Huiying Wen, Jia-Bing Liu, Yi-Zhen Yan, Hui Zhang, Yifan Sheng, Shuiping Yu, Xiaoyan Liao, Xu-Xu Jiang, Guangling Wang, Huanlin Liu, Congcong Wang, Ning Feng, Xin Liu, Kailong Ma, Xiangjie Xu, T. Han, Huateng Cao, Huiwen Zheng, Ya-Dong Chen, Hao-Rong Lu, Zixian Yu, Jinsong Zhang, Bo Wang, Zhifeng Wang, Qing Xie, Shan-Shan Pan, Chuan-Yu Liu, Chan Xu, Luman Cui, Yu-Xiang Li, Shi-Ping Liu, Sha Liao, Ao Chen, Qing-Feng Wu, Jian Wang, Zhiyong Liu, Yi-Di Sun, Jan Mulder, Huanming Yang, Xiao-Fei Wang, Chao Li, Jianhua Yao, Xun Xu, Longqi Liu, Zhi-Jian Shen, Wu Wei, Yan-Gang Sun

Neuron

DOI

2025

Abstract 5302: Mapping the tumor microenvironment at single-cell resolution with Stereo-seq v1.3

Jiajun Zhang, Xing Liu, Ze-Xian Zeng, Rui Zhang, Tibby Tianbi Duan, Jing Guo, Liang Wu, Sha Liao, Ao Chen

Cancer Research

DOI

2025

ST-FFPE-mIF: integrating spatial transcriptomics and multiplex immunofluorescence in formalin-fixed paraffin-embedded tissues using Stereo-seq

Xue Zhang, Meng Zhang, Yuan Xu, Yang-Yang Song, Xing-Feng Yang, Ya-Nan Wu, Xuelin Zhao, Dong-Sheng Ran, Xin Liu, Huaqiang Huang, Wen-Xiao Lei, Hongyan Li, Yongfeng Zhang, Feng Xi, Guibo Li, Xing Liu, Luohao Xu, Ao Chen, Sha Liao, Jiajun Zhang

bioRxiv

DOI

2025

CellBinDB: a large-scale multimodal annotated dataset for cell segmentation with benchmarking of universal models

Can Shi, Jinghong Fan, Zhonghan Deng, Huanlin Liu, Qiang Kang, Yu-Mei Li, Jing Guo, Jingwen Wang, Jinjiang Gong, Sha Liao, Ao Chen, Ying Zhang, Mei Li

GigaScience

DOI

2025

Spatiotemporal Transcriptomic Profiling Reveals the Dynamic Immunological Landscape of Alveolar Echinococcosis (Adv. Sci. 18/2025)

Zhi-Hua Ou, Li Li, Peidi Ren, Ting‐Ting Zhou, Fan He, Jialing Chen, Huimin Cai, Xiu-Min Han, Yao-Dong Wu, Jian-Dong Li, Xiu-Rong Li, Qiming Tan, Wenhui Li, Qi Chen, Nian-Zhang Zhang, Xiuju He, Wei-Gang Chen, Yan-Ping Zhao, Jiwen Sun, Qian Zhang, Yan-Tao Wu, Ying'an Liang, Jie You, Guohai Hu, Xue-Qi Tian, Sha Liao, Bao-Quan Fu, Ao Chen, Xue-Peng Cai, Huanming Yang, Jian Wang, Xin Jin, Xun Xu, W. Jia, Jun-Hua Li, Hong-Bin Yan

Advancement of science

DOI

2025

CSRefiner: a lightweight framework for fine-tuning cell segmentation models with small datasets

Can Shi, Yu-Mei Li, Jing Guo, Qiuling Chen, Tingting Cao, Sha Liao, Ao Chen, Mei Li, Ying Zhang

bioRxiv

DOI

2025

Stereo-cell: Spatial enhanced-resolution single-cell sequencing with high-density DNA nanoball-patterned arrays.

Sha Liao, Xiao-Xi Zhou, Chuan Liu, Chang Liu, Shijie Hao, Hong-Yu Luo, Huan Hou, Qian Liu, Zhe Zhang, Ling Xiao, Yuan Xu, Yaling Huang, Si-Ning Zhou, Xue-Rong Li, Yang Wang, Lulin Xie, Zhi-Chun Zhou, Shichen Dong, Yi-Ru Wang, Xiao-Jing Xu, Peng-Cheng Guo, Xiu-Mei Lin, Jiajie Lei, Qiaoling Wang, Yu-Xin Gong, Jiaming Cheng, Zi-Xin Yuan, Yong-Qing Yang, Zhi Huang, Shenglong Li, Yu-Hui Zheng, Shichen Yang, Xin Huang, Weiqing Liu, Mei Li, Zhonghan Deng, Xinyu Yang, Jian-Hua Yin, Yingjie Luo, Yi-Wei Lai, Yue Yuan, Mengnan Cheng, Bo Wang, Jian-Song Ji, Miguel A. Esteban, Yuxiang Li, Ying Gu, Yijun Ruan, Liang Chen, Xiangdong Wang, Jun Xie, Jian Wang, Longqi Liu, Ao Chen, Xun Xu

Science

DOI

2025

CellBin:a generalist framework to process spatial omics data to cell level

Ying Zhang, Huanlin Liu, Haoxiu Wang, Zi-Rong Li, Yu-Mei Li, Ji-Dong Chen, Jinghong Fan, Ji Yi, Can Shi, Xinyu Ren, Qiang Kang, Yinqi Bai, Shuang-Sang Fang, Jing Guo, Yang Heng, Dongmei Jia, Sha Liao, Ao Chen, H.-S. Shao, Mei Li

bioRxiv

DOI

2025

Stereo-seq V2: Spatial mapping of total RNA on FFPE sections with high resolution.

Yu Zhao, Young Li, Ying He, Jun-Qi Wu, Yi Liu, Xinxing Li, Zhaoxun Li, Qiaomei Yuan, Jia-Lu Li, Xinyan Zhang, Xiaole Hu, Guifang Wu, Ying Qiu, Jie Yuan, Xin Huang, Meng Xu, Mei Yang, Jing Guo, Tingting Cao, Qiuling Chen, Dandan Li, Jiajun Zhang, Xiao-Xi Zhou, Xia Jiang, Fan Zhu, Xuan Dong, Rong Xiang, Hailin Pan, Lei Han, Zi-Qing Deng, Hao-Hao Deng, Yan Zhang, Maoyuan Liu, Qin Wu, Gaoyang Wang, J. Zhai, Wei-Hong Tan, Xia-Wei Liu, Ze-Hao Wang, Shanshan Li, Tianbi Duan, Longqi Liu, Ao Chen, Hai-Ying Liu, Chang Chen, Sha Liao, Xun Xu

Cell

DOI

2024

舞蹈生态因子对白马藏族“跳曹盖”风格特征的影响

廖莎

《艺术家》

2024

Spatiotemporal modeling of molecular holograms.

Xiao-Jie Qiu, Daniel Y. Zhu, Yi-Fan Lu, Jia-Jun Yao, Zehua Jing, Kyung Hoi Min, Mengnan Cheng, Hailin Pan, Lulu Zuo, Samuel King, Qi Fang, Huiwen Zheng, Mingyue Wang, Shuai Wang, Qingquan Zhang, Sichao Yu, Sha Liao, Chao Liu, Xin-Chao Wu, Yi-Wei Lai, Shijie Hao, Zhewei Zhang, Liang Wu, Yong Zhang, Mei Li, Zhencheng Tu, Jinpei Lin, Zhuoxuan Yang, Yu-Xiang Li, Ying Gu, David Ellison, Ao Chen, Long-Qi Liu, Jonathan S. Weissman, Jiayi Ma, Xun Xu, Shi-Ping Liu, Yinqi Bai

Cell

DOI

2024

CellBin: a highly accurate single-cell gene expression processing pipeline for high-resolution spatial transcriptomics

Mei Li, Huanlin Liu, Qiang Kang, Shuangsang Fang, Min Li, Jiajun Zhang, Fei Teng, Danzhi Wang, Weixuan Cen, Zepeng Li, Ning Feng, Jing Guo, Qi-Qi He, Leying Wang, T. Zheng, Sheng-Kang Li, Yin-Qi Bai, Min Xie, Yong Bai, Sha Liao, Ao Chen, Yong Zhang, S. Brix, Xun Xu, Yu-Xiang Li

bioRxiv

DOI

2024

SCIITensor: A tensor decomposition based algorithm to construct actionable TME modules with spatially resolved intercellular communications

Huaqiang Huang, Chuandong Liu, Xin Liu, Jingyi Tian, Feng Xi, Mei Li, Guibo Li, Ao Chen, Xun Xu, Sha Liao, Jiajun Zhang, Xing Liu

bioRxiv

DOI

2024

Lamination-based organoid spatially resolved transcriptomics technique for primary lung and liver organoid characterization

Shaohua Ma, Wanlong Wang, Jiaqi Zhou, Shang-Feng Liao, Hai Cheng, Yi-Bo Hou, Zhi-Chun Zhou, Zi-Tian Wang, Yingshi Su, Yu Zhu, Xiaoyong Dai, Yuan Zhao, Sha Liao, Yongde Cai, Xun Xu

Proceedings of the National Academy of Sciences of the United States of America

DOI

2024

Deciphering spatial domains from spatial multi-omics with SpatialGlue

Ya-Hui Long, Kok Siong Ang, Raman Sethi, Sha Liao, Yang Heng, L. van Olst, Shucheng Ye, Chengwei Zhong, Hang Xu, Di Zhang, Immanuel Kwok, Nazihah Husna, Min Jian, Lai-Guan Ng, Ao Chen, Nicholas R. J. Gascoigne, David M. Gate, Rong Fan, Xun Xu, Jin-Miao Chen

Nature Methods

DOI

2023

Clonal dynamics and Stereo-seq resolve origin and phenotypic plasticity of adenosquamous carcinoma

Rui-Ying Zhao, Yun-hua Xu, Yedan Chen, Jiajun Zhang, Fei Teng, Sha Liao, Sheng-Nan Chen, Qian Wu, C. Xiang, J. Pang, Z. Shang, Ji-Kai Zhao, Hairong Bao, Hua Bao, Yang Shao, Shun Lu, Yuchen Han

npj Precision Oncology

DOI

2023

Single-cell spatial transcriptome reveals cell-type organization in the macaque cortex.

Ao Chen, Yi-Di Sun, Ying Lei, C. Li, Sha Liao, Juan Meng, Yiqin Bai, Zhen Liu, Zhifeng Liang, Zhiyong Zhu, Nini Yuan, Hao Yang, Zihan Wu, Feng Lin, Kexin Wang, Mei Li, Shuzhen Zhang, Meisong Yang, Tian-Yi Fei, Zhen-Kun Zhuang, Yiming Huang, Yong Zhang, Yuanfang Xu, Luman Cui, Ruiyi Zhang, Lei Han, Xing Sun, Bichao Chen, Wenjiao Li, Baoqian Huangfu, Kailong Ma, Jianyun Ma, Zhao Li, Yikun Lin, Henan Wang, Yan Zhong, Huifang Zhang, Qian Yu, Yaqian Wang, Xing Liu, Jian Peng, Chuan-Yu Liu, W. Chen, Wentao Pan, Yingjie An, Shihui Xia, Yanbing Lu, Mingli Wang, Xin-Xiang Song, Shuai Liu, Zhi-Feng Wang, Chun Gong, Xin Huang, Yue Yuan, Yun Zhao, Qinwen Chai, Xingjun Tan, Jian-Feng Liu, M. Zheng, Sheng-Kang Li, Yaling Huang, Y. Hong, Zirui Huang, Min Li, Meng-Meng Jin, Yan Li, Hui Zhang, Suhong Sun, Li Gao, Yinqi Bai, Mengnan Cheng, Guohai Hu, Shi-Ping Liu, Bo Wang, Bin Xiang, Shu-Ting Li, Huanhuan Li, Meng-Meng Chen, Shiwen Wang, Ming-Long Li, Wei-Bin Liu, Xin Liu, Qian Zhao, Michael Lisby, Jing Wang, Jiao Fang, Yun Lin, Qing Xie, Jie He, Huatai Xu, Wei Huang, J. Mulder, H. Yang, Yangang Sun, Mathias Uhlén, Mu-chou Poo, Jian Wang, Jianhua Yao, Wu Wei, Yu-Xiang Li, Zhi-ming Shen, Long-Qi Liu, Zhi-Yong Liu, Xun Xu, Cheng-Yu T. Li

Cell

DOI

2023

Spatially resolved molecular and cellular atlas of the mouse brain

Lei Han, Zhen Liu, Zehua Jing, Yuxuan Liu, Huizhong Chang, Junjie Lei, Yujie Peng, Kexin Wang, Yuanfang Xu, Wei Liu, Zihan Wu, Qian Li, Xiaoxue Shi, Mingyuan Zheng, He Wang, Juan Deng, Yan Zhong, Hailin Pan, Jun-Kai Lin, Rui-Yi Zhang, Yu Chen, Jin-Hua Wu, Mingrui Xu, Bi-Yu Ren, Mengnan Cheng, Qian Yu, Xinxiang Song, Yanbing Lu, Yuan-Chun Tang, Nini Yuan, Suhong Sun, Yingjie An, Wenqun Ding, Xing Sun, Yan-Rong Wei, Shuzhen Zhang, Yannong Dou, Yun Zhao, Luyao Han, Qianhua Zhu, Junfeng Xu, Shiwen Wang, Hanbo Chen, Dan Wang, Yinqi Bai, Yikai Liang, Yuan Liu, Meng-Meng Chen, Chun Xie, Bin-Shi Bo, Mei Li, Xinyan Zhang, Wang Ting, Zhenhua Chen, Jiao Fang, Shu-Ting Li, Yu-Jia Jiang, Xingjun Tan, Guo-Long Zuo, Yue Xie, Huan-Huan Li, Qu-Yuan Tao, Yan Li, Jian-Feng Liu, Yu-Yang Liu, Mingkun Hao, Jingjing Wang, Huiying Wen, Jia-Bing Liu, Yi-Zhen Yan, Hui Zhang, Yifan Sheng, Min Han, Shui Yu, Xiaoyan Liao, Xu-Xu Jiang, Guangling Wang, Huanlin Liu, Congcong Wang, Ning Feng, Xin Liu, Kailong Ma, Xiangjie Xu, T. Han, Hua-Teng Cao, Hui-chao Zheng, Ya-Dong Chen, Hao-Rong Lu, Zixian Yu, Jinsong Zhang, Bo Wang, Zhi-Feng Wang, Qing Xie, Shan-Shan Pan, Chuan-Yu Liu, Chan Xu, Luman Cui, Yu-Xiang Li, Shi-Ping Liu, Sha Liao, Ao Chen, Qing-Feng Wu, Jian Wang, Zhi-Yong Liu, Yi-Di Sun, Jan Mulder, Huanming Yang, Xiao-Fei Wang, Chao Li, Jian-Hua Yao, Xun Xu, Long-Qi Liu, Zhi-Jian Shen, Wu Wei, Yangang Sun

bioRxiv

DOI

2023

Integrated Spatial Transcriptomic and Proteomic Analysis of Fresh Frozen Tissue Based on Stereo-seq

Sha Liao, Yang Heng, Weiqing Liu, J. Xiang, Yong Ma, Ligen Chen, Xiuwen Feng, Dongmei Jia, Diyan Liang, Caili Huang, Jiajun Zhang, Min Jian, Kui Su, Mei Li, Joey Loh, Ao Chen, Xun Xu

bioRxiv

DOI

2023

An invasive zone in human liver cancer identified by Stereo-seq promotes hepatocyte–tumor cell crosstalk, local immunosuppression and tumor progression

Liang Wu, Jiayan Yan, Yinqi Bai, Fei-Yu Chen, Xuan-Xuan Zou, Jiangshan Xu, Ao Huang, Liang-Zhen Hou, Yu Zhong, Zehua Jing, Qi-Chao Yu, Xiao-Rui Zhou, Zhi-Feng Jiang, Chunqing Wang, Mengnan Cheng, Yuan Ji, Yingyong Hou, Rong-Kui Luo, Qinqin Li, Jianwen Cheng, Pengxiang Wang, De-Zhen Guo, Waidong Huang, Jun-Jie Lei, Shang Liu, Yizhen Yan, Yiling Chen, Sha Liao, Yu-Xiang Li, Hai-Xiang Sun, N. Yao, Xiang-Yu Zhang, Shiyu Zhang, Xi Chen, Yang Yu, Yao Li, Feng-Ming Liu, Zheng Wang, Shao-Lai Zhou, Huan-Ming Yang, Shuang Yang, Xun Xu, Long-Qi Liu, Qiang Gao, Zhao-You Tang, Xiangdong Wang, Jian Wang, Jia Fan, Shi-Ping Liu, Xin-Rong Yang, Ao Chen, Jian Zhou

Cell Research

DOI

2023

StereoSiTE: a framework to spatially and quantitatively profile the cellular neighborhood organized iTME

Xing Liu, C. Qu, Chuandong Liu, Na Zhu, Huaqiang Huang, Fei Teng, Caili Huang, Bingying Luo, Xuanzhu Liu, Min Xie, Feng Xi, Mei Li, Liang Wu, Yu-Xiang Li, Ao Chen, Xun Xu, Sha Liao, Jiajun Zhang

bioRxiv

DOI

2023

SAW: an efficient and accurate data analysis workflow for Stereo-seq spatial transcriptomics

Chun Gong, Sheng-Kang Li, Leying Wang, Fuxiang Zhao, Shuangsang Fang, Dong Yuan, Zijian Zhao, Qi-Qi He, Mei Li, Weiqing Liu, Zhaoxun Li, Hongqing Xie, Sha Liao, Ao Chen, Yong Zhang, Yu-Xiang Li, Xun Xu

bioRxiv

DOI

2023

Integrated analysis of spatial multi-omics with SpatialGlue

Yahui Long, Kok Siong Ang, Sha Liao, R. Sethi, Heng Yang, Chengwei Zhong, Hang Xu, Nazihah Husna, Min Jian, L. Ng, Ao Chen, N. Gascoigne, Xun Xu, Jin-Miao Chen

bioRxiv

DOI

2022

Global Spatial Transcriptome of Macaque Brain at Single-Cell Resolution

Ao Chen, Yi-Di Sun, Ying Lei, Chao Li, Sha Liao, Zhifeng Liang, Feng Lin, Nini Yuan, Mei Li, Kexin Wang, Meisong Yang, Shuzhen Zhang, Zhen-Kun Zhuang, Juan Meng, Qiong Song, Yong Zhang, Yuanfang Xu, Luman Cui, Lei Han, Hao Yang, Xing Sun, Tian-Yi Fei, Bichao Chen, Wenjiao Li, Baoqian Huangfu, Kailong Ma, Zhao Li, Yikun Lin, Zhen Liu, Henan Wang, Yan Zhong, Huifang Zhang, Qian Yu, Yaqian Wang, Zhi-Gang Zhu, Xing Liu, Jianjun Peng, Chuan-Yu Liu, W. Chen, Yingjie An, Shihui Xia, Yanbing Lu, Mingli Wang, Xin Song, Shuai Liu, Zhi-Feng Wang, Chun Gong, Xin Huang, Yue Yuan, Yun Zhao, Zhen-Hui Luo, Xingjun Tan, Jianfeng Liu, Min-qiao Zheng, Sheng-Kang Li, Yaling Huang, Yan-hua Hong, Zirui Huang, Min Li, Rui-Yi Zhang, Meng-Meng Jin, Yan Li, Hui Zhang, Suhong Sun, Yinqi Bai, Mengnan Cheng, Guohai Hu, Shi-Ping Liu, Bo Wang, Bin Xiang, Shu-Ting Li, Huan-Huan Li, Meng-Meng Chen, Shiwen Wang, Qi Zhang, Wei-Bin Liu, Xin Liu, Qian Zhao, Michael Lisby, Jing Wang, Jiao Fang, Zhiyue Lu, Yun Lin, Qingbin Xie, Jie-bing He, Huatai Xu, Wei Huang, Wu Wei, Huan-Ming Yang, Yangang Sun, Mu-chou Poo, Jian Wang, Yu-Xiang Li, Zhi-ming Shen, Long-Qi Liu, Zhi-Yong Liu, Xun Xu, Cheng-Yu T. Li

bioRxiv

DOI

2022

A Cellular Resolution Spatial Transcriptomic Landscape of the Medial Structures in Postnatal Mouse Brain

Mengnan Cheng, Liang Wu, Lei Han, Xin Huang, Yiwei Lai, Jiangshan Xu, Shuai Wang, Mei Li, Hui-chao Zheng, Weimin Feng, Zirui Huang, Yu-Jia Jiang, Shijie Hao, Zhao Li, Xi Chen, Jian Peng, Pengcheng Guo, Xiao Zhang, Guang-Shun Lai, Q. Deng, Yue Yuan, Fangming Yang, Xiaoyu Wei, Sha Liao, Ao Chen, G. Volpe, M. Esteban, Yong Hou, Chuan-Yu Liu, Long-Qi Liu

Frontiers in Cell and Developmental Biology

DOI

2022

Spateo: multidimensional spatiotemporal modeling of single-cell spatial transcriptomics

Xiaojie Qiu, Daniel Y. Zhu, Jiajun Yao, Zehua Jing, Lulu Zuo, Mingyue Wang, Kyung Hoi (Joseph) Min, Hai-Lin Pan, Shuai Wang, Sha Liao, Yiwei Lai, Shijie Hao, Yuancheng Ryan Lu, M. Hill, Jorge D. Martin-Rufino, Chen Weng, Anna Maria Riera-Escandell, Mengnan Chen, Liang Wu, Yong Zhang, Xiaoyu Wei, Mei Li, Xin Huang, Rong Xiang, Zhuoxuan Yang, Chao Liu, Tian-Yi Xia, Ying-Xin Liang, Junqiang Xu, Qinan Hu, Yuhui Hu, Hongmei Zhu, Yu-Xiang Li, Ao Chen, M. Esteban, Ying Gu, D. Lauffenburger, Xun Xu, Long-Qi Liu, J. Weissman, Shi-Ping Liu, Yinqi Bai

bioRxiv

DOI

2022

Spatial Transcriptome Uncovers the Mouse Lung Architectures and Functions

Yu-Jia Jiang, Shijie Hao, Xi Chen, Mengnan Cheng, Jiangshan Xu, Chenghao Li, Hui-Wen Zheng, G. Volpe, Ao Chen, Sha Liao, Chuan-Yu Liu, Long-Qi Liu, Xun Xu

Frontiers in Genetics

DOI

2021

Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball patterned arrays

Ao Chen, Sha Liao, Mengnan Cheng, Kailong Ma, Liang Wu, Yiwei Lai, Xiaojie Qiu, Jin Yang, Jiangshan Xu, Shijie Hao, Xin Wang, Hui-Fang Lu, Xi Chen, Xing Liu, Xin Huang, Zhao-Peng Li, Yanping Hong, Yu-Jia Jiang, Jian Peng, Shuai Liu, Mengzhe Shen, Chuan-Yu Liu, Quan-Zhen Li, Yue Yuan, Xiaoyu Wei, Hui-chao Zheng, Weimin Feng, Zhi-Feng Wang, Yang Liu, Zhao-Hui Wang, Yunzhi Yang, Haitao Xiang, Lei Han, Bao-Ming Qin, Pengcheng Guo, Guang-Yao Lai, P. Muñoz-Cánoves, P. Maxwell, J. Thiery, Qing-Feng Wu, Fuxiang Zhao, Bichao Chen, Mei Li, Xi Dai, Shuai Wang, Haoyan Kuang, Jun-Hou Hui, Liqun Wang, Jianjun Fei, Ou Wang, Xiao-Feng Wei, Hao-Rong Lu, Bo Wang, Shi-Ping Liu, Ying Gu, Ming Ni, Wen-Wei Zhang, Feng Mu, Ye Yin, Huan-Ming Yang, Michael Lisby, R. Cornall, J. Mulder, M. Uhlén, M. Esteban, Yu-Xiang Li, Long-Qi Liu, Xun Xu, Jian Wang

bioRxiv

DOI

2021

Spatially-resolved transcriptomics analyses of invasive fronts in solid tumors

Liang Wu, Jia Yan, Yinqi Bai, Fei-Yu Chen, Jiangshan Xu, Xuan-Xuan Zou, Ao Huang, Liang-Zhen Hou, Yu Zhong, Zehua Jing, Xiao-Rui Zhou, Hai-Xiang Sun, Mengnan Cheng, Yuan Ji, Rong-Kui Luo, Qinqin Li, Liang Wu, Pengxiang Wang, De-Liang Guo, Waidong Huang, Jun-Jie Lei, Sha Liao, Yu-Xiang Li, Zhi-Feng Jiang, N. Yao, Yang Yu, Yao Li, Feng-Ming Liu, Ming-Yuan Zhang, Huan-Ming Yang, Shuang Yang, Xun Xu, Long-Zi Liu, Xiang-Dong Wang, Jian Wang, Jia Fan, Shi-Ping Liu, Xin-Rong Yang, Ao Chen, Jian Zhou

bioRxiv

DOI

2020

Efficient COI barcoding using high throughput single-end 400 bp sequencing

Chentao Yang, Yuxuan Zheng, Shang-Jin Tan, Guan-Liang Meng, Wei Rao, Cai-Qing Yang, D. Bourne, P. A. O'Brien, Junqiang Xu, Sha Liao, Ao Chen, Xiaowei Chen, Xinrui Jia, Ai-Bing Zhang, Shanlin Liu

BMC Genomics

DOI

2020

BGISEQ-500 （DNBSEQ-G50） Sequencing v1

Jie Huang, Xinming Liang, Yuan-Kai Xuan, C. Geng, Yu-Xiang Li, Hao-Rong Lu, Shoufang Qu, Xiang-Lin Mei, Hong-Bo Chen, Ting Yu, Nan Sun, Junhua Rao, Jiahao Wang, Wen-Wei Zhang, Ying Chen, Sha Liao, Hui Jiang, Xin Liu, Zhao-Peng Yang, Feng Mu, Shang-Xian Gao

protocols.io

DOI

2020

BGISEQ-500 （DNBSEQ-G50）WGS library construction v1

Jie Huang, Xinming Liang, Yuan-Kai Xuan, C. Geng, Yu-Xiang Li, Hao-Rong Lu, Shoufang Qu, Xiang-Lin Mei, Hong-Bo Chen, Ting Yu, Nan Sun, Junhua Rao, Jiahao Wang, Wen-Wei Zhang, Ying Chen, Sha Liao, Hui Jiang, Xin Liu, Zhao-Peng Yang, Feng Mu, Shang-Xian Gao

protocols.io

DOI

2020

CoolMPS™: Advanced massively parallel sequencing using antibodies specific to each natural nucleobase

S. Drmanac, M. Callow, Linsu Chen, P. Zhou, L. Eckhardt, Chongjun Xu, Meihua Gong, Scott Gablenz, J. Rajagopal, Q. Yang, Christian Villarosa, Anthony K. Au, Kyle Davis, Alexander Jorjorian, Jingjing Wang, Ao Chen, Xian Zhang, Adam Borcherding, Xiaofang Wei, Mingxuan Zhang, Yonghui Xie, Nina Barua, Jay Shafto, Yu-Liang Dong, Yuehua Zheng, Lin Wang, Li Zhai, Jiguang Li, Sha Liao, Wen-Wei Zhang, Jian Liu, Hui Jiang, Jian Wang, Han-qiu Li, Xun Xu, R. Drmanac

bioRxiv

DOI

2018

Erratum to: A reference human genome dataset of the BGISEQ-500 sequencer

Jie Huang, Xinming Liang, Yuan-Kai Xuan, C. Geng, Yu-Xiang Li, Hao-Rong Lu, Shoufang Qu, Xiang-Lin Mei, Hong-Bo Chen, Ting Yu, Nan Sun, Junhua Rao, Jiahao Wang, Wen-Wei Zhang, Ying Chen, Sha Liao, Hui Jiang, Xin Liu, Zhao-Peng Yang, Feng Mu, Shang-Xian Gao

GigaScience

DOI

2017

A reference human genome dataset of the BGISEQ-500 sequencer

Jie Huang, Xinming Liang, Yuan-Kai Xuan, C. Geng, Yu-Xiang Li, Hao-Rong Lu, Shoufang Qu, Xiang-Lin Mei, Hong-Bo Chen, Ting Yu, Nan Sun, Junhua Rao, Jiahao Wang, Wen-Wei Zhang, Ying Chen, Sha Liao, Hui Jiang, Xin Liu, Zhao-Peng Yang, Feng Mu, Shang-Xian Gao

GigaScience

DOI

2010

利用DGGE—cloning技术分析农肥和化肥施用对黑土细菌多样性的影响

廖莎，廖莎 王宏燕 赵伟

《农业现代化研究》，Vol. 31, No. 3

下载原文

Title : Large field of view-spatially resolved transcriptomics at nanoscale resolution Short title : DNA nanoball stereo-sequencing

Ao Chen, Sha Liao, Mengnan Cheng, Kailong Ma, Liang Wu, Yiwei, Lai, Jin Yang, Wenjia Li, Jiangshan Xu, Shijie Hao, Hui-Fang Lu, Xi Chen, Xing Liu, Xin Huang, Feng Lin, Xiao-Chun Tang, Z. Li, Ya-Zhen Hong, Defeng, Fu, Yu-Jia Jiang, Jian Peng, Shuaishuai Liu, Meng-Jia Shen, Chuan-Yu Liu, Quanshui, Li, Zhi-Feng Wang, Zhao-Hui Wang, Yue Yuan, G. Volpe, C. Ward, P. Muñoz-Cánoves, J. Thiery, Fuxiang Zhao, Mei Li, Haoyan Kuang, Ou Wang, Hao-Rong Lu, Bo Wang, Ming Ni, Wen-Wei Zhang, Feng Mu, Ye Yin, Huan-Ming Yang, Michael Lisby, R. Cornall, M. Uhlén, M. Esteban, Yu-Xiang Li, Long-Qi Liu, Xun, Xu, Jian Wang

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