Xuegong Zhang

Publication Activity (10 Years)

Years Active: 2016-2024
Publications (10 Years): 38

Top Topics

Helicobacter Pylori

Top Venues

Communications biology

Nature immunology

Genomics, proteomics & bioinformatics

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

Publications

Xue Bai, Sijie Chen, Xinxin Chi, Bowen Xie, Xinyi Guo, Han Feng, Peng Wei, Di Zhang, Shan Xie, Tian Xie, Yongzhen Chen, Mengting Gou, Qin Qiao, Xinwei Liu, Wei Jin, Wei Xu, Zixuan Zhao, Qi Xing, Xiaohu Wang, Xuegong Zhang, Chen Dong
Reciprocal regulation of T follicular helper cells and dendritic cells drives colitis development. Nature immunology 25 (8) (2024)
Ziming Jiang, Yanhong Wu, Yuxin Miao, Kaige Deng, Fan Yang, Shuhuan Xu, Yupeng Wang, Renke You, Lei Zhang, Yuhan Fan, Wenbo Guo, Qiuyu Lian, Lei Chen, Xuegong Zhang, Yong-Chang Zheng, Jin Gu
HCCDB v2.0: Decompose Expression Variations by Single-cell RNA-seq and Spatial Transcriptomics in HCC. Genomics, proteomics & bioinformatics 22 (1) (2024)
Minsheng Hao, Erpai Luo, Yixin Chen, Yanhong Wu, Chen Li, Sijie Chen, Haoxiang Gao, Haiyang Bian, Jin Gu, Lei Wei, Xuegong Zhang
STEM enables mapping of single-cell and spatial transcriptomics data with transfer learning. Communications biology 7 (1) (2024)
Haoxiang Gao, Kui Hua, Xinze Wu, Lei Wei, Sijie Chen, Qijin Yin, Rui Jiang, Xuegong Zhang
Building a learnable universal coordinate system for single-cell atlas with a joint-VAE model. Communications biology 7 (1) (2024)
Minsheng Hao, Erpai Luo, Yixin Chen, Yanhong Wu, Chen Li, Sijie Chen, Haoxiang Gao, Haiyang Bian, Jin Gu, Lei Wei, Xuegong Zhang
STEM enables mapping of single-cell and spatial transcriptomics data with transfer learning. Communications biology 7 (1) (2024)
Haoxiang Gao, Kui Hua, Xinze Wu, Lei Wei, Sijie Chen, Qijin Yin, Rui Jiang, Xuegong Zhang
Building a learnable universal coordinate system for single-cell atlas with a joint-VAE model. Communications biology 7 (1) (2024)
Minsheng Hao, Jing Gong, Xin Zeng, Chiming Liu, Yucheng Guo, Xingyi Cheng, Taifeng Wang, Jianzhu Ma, Xuegong Zhang, Le Song
Large-scale foundation model on single-cell transcriptomics. Nature methods 21 (8) (2024)
Ziming Jiang, Yanhong Wu, Yuxin Miao, Kaige Deng, Fan Yang, Shuhuan Xu, Yupeng Wang, Renke You, Lei Zhang, Yuhan Fan, Wenbo Guo, Qiuyu Lian, Lei Chen, Xuegong Zhang, Yong-Chang Zheng, Jin Gu
HCCDB v2.0: Decompose Expression Variations by Single-cell RNA-seq and Spatial Transcriptomics in HCC. Genomics, proteomics & bioinformatics 22 (1) (2024)
Haoxiang Gao, Kui Hua, Xinze Wu, Lei Wei, Sijie Chen, Qijin Yin, Rui Jiang, Xuegong Zhang
Building a learnable universal coordinate system for single-cell atlas with a joint-VAE model. Communications biology 7 (1) (2024)
Najeebullah Shah, Qiuchen Meng, Ziheng Zou, Xuegong Zhang
Systematic analysis on the horse-shoe-like effect in PCA plots of scRNA-seq data. Bioinformatics advances 4 (1) (2024)
Xinyue Chen, Yin Huang, Liangfeng Huang, Ziliang Huang, Zhao-Zhe Hao, Lahong Xu, Nana Xu, Zhi Li, Yong-Gao Mou, Mingli Ye, Renke You, Xuegong Zhang, Sheng Liu, Zhichiao Miao
A brain cell atlas integrating single-cell transcriptomes across human brain regions. Nature medicine (2024)
Minsheng Hao, Jing Gong, Xin Zeng, Chiming Liu, Yucheng Guo, Xingyi Cheng, Taifeng Wang, Jianzhu Ma, Xuegong Zhang, Le Song
Large-scale foundation model on single-cell transcriptomics. Nature methods 21 (8) (2024)
Erpai Luo, Minsheng Hao, Lei Wei, Xuegong Zhang
scDiffusion: conditional generation of high-quality single-cell data using diffusion model. Bioinformatics (Oxford, England) 40 (9) (2024)
Najeebullah Shah, Qiuchen Meng, Ziheng Zou, Xuegong Zhang
Systematic analysis on the horse-shoe-like effect in PCA plots of scRNA-seq data. Bioinformatics advances 4 (1) (2024)
Minsheng Hao, Erpai Luo, Yixin Chen, Yanhong Wu, Chen Li, Sijie Chen, Haoxiang Gao, Haiyang Bian, Jin Gu, Lei Wei, Xuegong Zhang
STEM enables mapping of single-cell and spatial transcriptomics data with transfer learning. Communications biology 7 (1) (2024)
Ziming Jiang, Yanhong Wu, Yuxin Miao, Kaige Deng, Fan Yang, Shuhuan Xu, Yupeng Wang, Renke You, Lei Zhang, Yuhan Fan, Wenbo Guo, Qiuyu Lian, Lei Chen, Xuegong Zhang, Yong-Chang Zheng, Jin Gu
HCCDB v2.0: Decompose Expression Variations by Single-cell RNA-seq and Spatial Transcriptomics in HCC. Genomics, proteomics & bioinformatics 22 (1) (2024)
Xue Bai, Sijie Chen, Xinxin Chi, Bowen Xie, Xinyi Guo, Han Feng, Peng Wei, Di Zhang, Shan Xie, Tian Xie, Yongzhen Chen, Mengting Gou, Qin Qiao, Xinwei Liu, Wei Jin, Wei Xu, Zixuan Zhao, Qi Xing, Xiaohu Wang, Xuegong Zhang, Chen Dong
Reciprocal regulation of T follicular helper cells and dendritic cells drives colitis development. Nature immunology (2024)
Xue Bai, Sijie Chen, Xinxin Chi, Bowen Xie, Xinyi Guo, Han Feng, Peng Wei, Di Zhang, Shan Xie, Tian Xie, Yongzhen Chen, Mengting Gou, Qin Qiao, Xinwei Liu, Wei Jin, Wei Xu, Zixuan Zhao, Qi Xing, Xiaohu Wang, Xuegong Zhang, Chen Dong
Reciprocal regulation of T follicular helper cells and dendritic cells drives colitis development. Nature immunology 25 (8) (2024)
Minsheng Hao, Erpai Luo, Yixin Chen, Yanhong Wu, Chen Li, Sijie Chen, Haoxiang Gao, Haiyang Bian, Jin Gu, Lei Wei, Xuegong Zhang
STEM enables mapping of single-cell and spatial transcriptomics data with transfer learning. Communications biology 7 (1) (2024)
Minsheng Hao, Erpai Luo, Yixin Chen, Yanhong Wu, Chen Li, Sijie Chen, Haoxiang Gao, Haiyang Bian, Jin Gu, Lei Wei, Xuegong Zhang
STEM enables mapping of single-cell and spatial transcriptomics data with transfer learning. Communications biology 7 (1) (2024)
Minsheng Hao, Jing Gong, Xin Zeng, Chiming Liu, Yucheng Guo, Xingyi Cheng, Taifeng Wang, Jianzhu Ma, Xuegong Zhang, Le Song
Large-scale foundation model on single-cell transcriptomics. Nature methods (2024)
Zhen Li, Xiaoyang Chen, Xuegong Zhang, Rui Jiang, Shengquan Chen
Latent feature extraction with a prior-based self-attention framework for spatial transcriptomics. Genome research (2023)
Jiaqi Li, Zhenbin Qiu, Chao Zhang, Sijie Chen, Mengmin Wang, Qiuchen Meng, Haiming Lu, Lei Wei, Hairong Lv, Wenzhao Zhong, Xuegong Zhang
ITHscore: comprehensive quantification of intra-tumor heterogeneity in NSCLC by multi-scale radiomic features. European radiology (2022)
Tianxing Ma, Qiao Liu, Haochen Li, Mu Zhou, Rui Jiang, Xuegong Zhang
DualGCN: a dual graph convolutional network model to predict cancer drug response. BMC bioinformatics 23 (Suppl 4) (2022)
Yifan Zhou, Yusra B Medik, Bhakti Patel, Daniel B Zamler, Sijie Chen, Thomas Chapman, Sarah M Schneider, Elizabeth M Park, Rachel L Babcock, Taylor T Chrisikos, Laura M Kahn, Allison M Dyevoich, Josué E Pineda, Matthew C Wong, Aditya K Mishra, Samuel H Cass, Alexandria P Cogdill, Daniel H Johnson, Sarah B Johnson, Khalida M Wani, Debora A Ledesma, Courtney W Hudgens, Jingjing Wang, Md Abdul Wadud Khan, Christine B Peterson, Aron Y Joon, Weiyi Peng, Haiyan S Li, Reetakshi Arora, Ximing Tang, Maria Gabriela Raso, Xuegong Zhang, Wai Chin Foo, Michael T Tetzlaff, Gretchen E Diehl, Karen Clise-Dwyer, Elizabeth M Whitley, Matthew M Gubin, James P Allison, Patrick Hwu, Nadim J Ajami, Adi Diab, Jennifer A Wargo, Stephanie S Watowich
Intestinal toxicity to CTLA-4 blockade driven by IL-6 and myeloid infiltration. The Journal of experimental medicine 220 (2) (2022)
Liang Chen, Kui Hua, Ningning Zhang, Jingyu Wang, Jian Meng, Zhenliang Hu, Haoxiang Gao, Fanhong Li, Yang Chen, Jie Ren, Liyang Liu, Qiming Zhou, Jin Gu, Jiang-Ping Song, Xuegong Zhang, Shengshou Hu
Multifaceted Spatial and Functional Zonation of Cardiac Cells in Adult Human Heart. Circulation 145 (4) (2022)
Qijin Yin, Qiao Liu, Zhuoran Fu, Wanwen Zeng, Boheng Zhang, Xuegong Zhang, Rui Jiang, Hairong Lv
scGraph: a graph neural network-based approach to automatically identify cell types. Bioinformatics (Oxford, England) 38 (11) (2022)
Sijie Chen, Yanting Luo, Haoxiang Gao, Fanhong Li, Jiaqi Li, Yixin Chen, Renke You, Hairong Lv, Kui Hua, Rui Jiang, Xuegong Zhang
Toward a unified information framework for cell atlas assembly. National science review 9 (3) (2021)
Shengquan Chen, Qiao Liu, Xuejian Cui, Zhanying Feng, Chun-Quan Li, Xiaowo Wang, Xuegong Zhang, Yong Wang, Rui Jiang
OpenAnnotate: a web server to annotate the chromatin accessibility of genomic regions. Nucleic acids research 49 (W1) (2021)
Yixin Chen, Sijie Chen, Xuegong Zhang
Using DenseFly algorithm for cell searching on massive scRNA-seq datasets. BMC genomics 21 (Suppl 5) (2020)
Yue Hu, Xi Xi, Qian Yang, Xuegong Zhang
SCeQTL: an R package for identifying eQTL from single-cell parallel sequencing data. BMC bioinformatics 21 (1) (2020)
Sebastien M Weyn-Vanhentenryck, Huijuan Feng, Dmytro Ustianenko, Rachel Duffié, Qinghong Yan, Martin Jacko, Jose C Martinez, Marianne Goodwin, Xuegong Zhang, Ulrich Hengst, Stavros Lomvardas, Maurice S Swanson, Chaolin Zhang
Precise temporal regulation of alternative splicing during neural development. Nature communications 9 (1) (2018)
Lihong He, Dongyang Luo, Fan Yang, Chunhao Li, Xuegong Zhang, Haiteng Deng, Jing-Ren Zhang
Multiple domains of bacterial and human Lon proteases define substrate selectivity. Emerging microbes & infections 7 (1) (2018)
Aziz Khan, Anthony Mathelier, Xuegong Zhang
Super-enhancers are transcriptionally more active and cell type-specific than stretch enhancers. Epigenetics 13 (9) (2018)
Aziz Khan, Xuegong Zhang
Making genome browsers portable and personal. Genome biology 19 (1) (2018)
Jiaxing Cui, Hongfei Cui, Mingran Yang, Shiyu Du, Junfeng Li, Yingxue Li, Liyang Liu, Xuegong Zhang, Shao Li
Tongue coating microbiome as a potential biomarker for gastritis including precancerous cascade. Protein & cell 10 (7) (2018)
Zhiyi Qin, Xuegong Zhang
The identification of switch-like alternative splicing exons among multiple samples with RNA-Seq data. PloS one 12 (5) (2017)
Jing Li, Jing-Wen Li, Zhixing Feng, Juanjuan Wang, Haoran An, Yanni Liu, Yang Wang, Kailing Wang, Xuegong Zhang, Zhun Miao, Wenbo Liang, Robert Sebra, Guilin Wang, Wen-Ching Wang, Jing-Ren Zhang
Epigenetic Switch Driven by DNA Inversions Dictates Phase Variation in Streptococcus pneumoniae. PLoS pathogens 12 (7) (2016)