Publications
Note: # These authors contributed equally to this work, * Corresponding author
最新研究成成果
- Zixiang Zhou(#), Yunshan Zhong(#), Zemin Zhang, Xianwen Ren(*) Spatial transcriptomics deconvolution at single-cell resolution by Redeconve, bioRxiv preprint, 2022 Nov, doi: https://doi.org/10.1101/2022.12.22.521551.
代表性成果
- Yedan Liu(#), Qiming Zhang(#), Baocai Xing, Nan Luo, Ranran Gao, Kezhuo Yu, Xueda Hu, Zhaode Bu, Jirun Peng(*), Xianwen Ren(*), Zemin Zhang Immune phenotypic linkage between colorectal cancer and liver metastasis, Cancer Cell. 2022 Mar 10;S1535-6108(22)00065-4. doi: 10.1016/j.ccell.2022.02.013.
- Ren Xianwen(*#), Zhong Guojie(#), Zhang Qiming, Zhang Lei, Sun Yujie, Zhang Zemin(*), Reconstruction of cell spatial organization from single-cell RNA sequencing data based on ligand-receptor mediated self-assembly, Cell Research, 2020.06.15, 30: 763–778
- Ren Xianwen(#), Wen Wen(#), Fan Xiaoying(#), Hou Wenhong(#), Su Bin(#), Cai Pengfei(#), Li Jiesheng(#), Liu Yang(#), Tang Fei(#), Zhang Fan(#), Yang Yu(#), He Jiangping(#), Ma Wenji(#), He Jingjing(#), Wang Pingping(#), Cao Qiqi, Chen Fangjin, Chen Yuqing, Cheng Xuelian, Deng Guohong, Deng Xilong, Ding Wenyu, Feng Yingmei, Gan Rui, Guo Chuang, Guo Weiqiang, He Shuai, Jiang Chen, Liang Juanran, Li Yi-min, Lin Jun, Ling Yun, Liu Haofei, Liu Jianwei, Liu Nianping, Liu Shu-Qiang, Luo Meng, Ma Qiang, Song Qibing, Sun Wujianan, Wang GaoXiang, Wang Feng, Wang Ying, Wen Xiaofeng, Wu Qian, Xu Gang, Xie Xiaowei, Xiong Xinxin, Xing Xudong, Xu Hao, Yin Chonghai, Yu Dongdong, Yu Kezhuo, Yuan Jin, Zhang Biao, Zhang Peipei(#), Zhang Tong, Zhao Jincun, Zhao Peidong, Zhou Jianfeng, Zhou Wei, Zhong Sujuan, Zhong Xiaosong, Zhang Shuye, Zhu Lin, Zhu Ping, Zou Bin, Zou Jiahua, Zuo Zengtao, Bai Fan, Huang Xi, Zhou Penghui(*), Jiang Qinghua(*), Huang Zhiwei(*), Bei Jin-Xin(*), Wei Lai(*), Bian Xiu-Wu(*), Liu Xindong(*), Cheng Tao(*), Li Xiangpan(*), Zhao Pingsen(*), Wang Fu-Sheng(*), Wang Hongyang(*), Su Bing(*), Zhang Zheng(*), Qu Kun(*), Wang Xiaoqun(*), Chen Jiekai(*), Jin Ronghua(*), Zhang Zemin(*), COVID-19 immune features revealed by a large-scale single cell transcriptome atlas, Cell, 2021, online https://doi.org/10.1016/j.cell.2021.01.053
- Zhang Qiming(#), He Yao(#), Luo Nan(#), Patel Shashank J, Han Yanjie, Gao Ranran, Modak Madhura, Carotta Sebastian, Haslinger Christian, Kind David, Peet Gregory W, Zhong Guojie, Lu Shuangjia, Zhu Weihua, Mao Yilei, Xiao Mengmeng, Bergmann Michael, Hu Xueda, Kerkar Sid P, Vogt Anne B, Pflanz Stefan, Liu Kang(*), Peng Jirun(*), Ren Xianwen(*), Zhang Zemin(*), Landscape and Dynamics of Single Immune Cells in Hepatocellular Carcinoma, Cell, 2019.10.31, 179(4):829-845.e29
- Li Chenwei (#), Liu Baolin (#), Kang Boxi, Liu Zedao, Liu Yedan, Chen Changya, Ren Xianwen(*), Zhang Zemin(*), SciBet as a portable and fast single cell type identifier, Nature Communications 2020.04.14, 11: 1818
- Ren Xianwen(#)(*), Zheng Liangtao(#), Zhang Zemin(*), SSCC: A Novel Computational Framework for Rapid and Accurate Clustering Large-scale Single Cell RNA-seq Data, Genomics, Proteomics & Bioinformatics,2019.4, 17(2):201-210
其他第一作者或通讯作者论文(含共同)
- Ren Xianwen(#), Zhang Lei(#), Zhang Yuanyuan, Ziyi Li, Siemers Nathan, Zhang Zemin(*), Insights Gained from Single-Cell Analysis of Immune Cells in the Tumor Microenvironment, Annual Review of Immunology, 2021, online https://doi.org/10.1146/annurev-immunol-110519-071134
- Yang Rui (#), Cheng Sijin (#), Luo Nan (#), Gao Ranran, Yu Kezhuo, Kang Boxi, Wang Li, Zhang Qiming, Fang Qiao, Zhang Lei, Li Chen, He Aibin, Hu Xueda, Peng Jirun (*), Ren Xianwen (*), Zhang Zemin (*), Distinct epigenetic features of tumor-reactive CD8+ T cells in colorectal cancer patients revealed by genome-wide DNA methylation analysis, Genome Biology, 2019, 21:2
- Li Jiesheng, Hannah Y.Comeau, Zhang Zemin(*), Ren Xianwen(*), Landscape of transcript isoforms in single T cells infiltrating in non-small-cell lung cancer, Journal of Genetics and Genomics, 2020.07.20, 47(7): 373-388
- Liu Juntao, Liu Xiangyu, Ren Xianwen(*), Li Guojun(*), scRNAss: a single-cell RNA-seq assembler via imputing dropouts and combing junctions, Bioinformatics, 2019.11.01, 35(21):4264-4271
- Ren Xianwen(#)(*); Kang Boxi; Zhang Zemin(*), Understanding tumor ecosystems by single-cell sequencing: promises and limitations, Genome Biology, 2018.12.03, 9(211)
- Ren Xianwen(#)(*);Zhang Zemin, Understanding tumor-infiltrating lymphocytes by single cell RNA sequencing, Advances in immunology,2019, 144:217-245
- Zhou Siyu(#); Ren Xianwen(*); Yang Jian(*); Jin Qi(*), Evaluating the Value of Defensins for Diagnosing Secondary Bacterial Infections in Influenza-Infected Patients, Frontiers in Microbiology, 2018.11.20, 9(2762)
- Ren Xianwen(#); Wang Yong(#); Chen Luonan(*); Zhang Xiang-Sun(*); Jin Qi(*), ellipsoidFN: a tool for identifying a heterogeneous set of cancer biomarkers based on gene expressions, Nucleic Acids Res, 2013, 41(4)
- Ren Xianwen(#); Wang Yong(#); Zhang Xiang-Sun(*); Jin Qi(*), iPcc: a novel feature extraction method for accurate disease class discovery and prediction, Nucleic Acids Research, 2013.6, 41(14)
- Ren Xianwen(#); Yang Fan(#); Hu Yongfeng(#); Zhang Ting(#); Liu Liguo(#); Dong, Jie; Sun Lilian; Zhu Yafang; Xiao Yan; Li Li; Yang Jian; Wang Jianwei; Jin Qi(*), Full Genome of Influenza A (H7N9) Virus Derived by Direct Sequencing without Culture, Emerging Infectious Diseases, 2013.11, 19(11): 1881~1884
- Ren Xianwen(#)(*); Fu Hua(#); Jin Qi(*), Integrating heterogeneous genomic data to accurately identify disease subtypes, BMC Medical Genomics, 2015.11.20, 8(78)
- Ren Xianwen(#); Jin Qi(*), Safe sequencing depth to estimate the intra-host heterogeneity of viruses, Briefings in Functional Genomics, 2015.10.1, 15(4): 275~277
- Ren Xianwen(#); Hu Yongfeng(#); Yang Fan(#); Xiao Yan; Li Li; Dong Jie; Sun Lilian; Zhu Yafang; Jin Qi(*), Clinical utility comparison of two benchtop deep sequencing instruments for rapid diagnosis of newly emergent influenza infections, Clin Microbiol Infect, 2014.10.29, 21(3)
- Ren Xianwen(#); Liu Tao(#); Dong Jie; Sun Lilian; Yang Jian; Zhu Yafang; Jin Qi(*), Evaluating de Bruijn Graph Assemblers on 454 Transcriptomic Data, PLos One, 2012.12.7, 7(12): 0~e51188
- Ren Xianwen(#)(*), Toward a more systematic understanding of bacterial virulence factors and establishing Koch postulates in silico, Virulence, 2013.8.22, 4(6): 0~437
- Ren Xianwen(#); Wang Yong(*); Wang Jiguang; Zhang Xiang-Sun(*), A unified computational model for revealing and predicting subtle subtypes of cancers, BMC Bioinformatics, 2012.5.1, 13: 0~70
- Ren Xianwen(#); Wang Yongcui(#); Wang Yong; Zhang Xiangsun(*); Deng Naiyang(*), Improving accuracy of protein-protein interaction prediction by considering the converse problem for sequence representation, BMC Bioinformatics, 2011.10.24, 12: 0~409
- Ren Xianwen(#); Zhou Xiaobo(*); Chang Chung-Che, The network properties of myelodysplastic syndromes pathogenesis revealed by an integrative systems biological method, Mol Biosyst, 2011.4.19, 7(6): 2048~54
- Ren Xianwen(#)(*); Zhang Xiang-Sun, A linear programming model based on network flow for pathway inference, Journal of Systems Science and Complexity, 2010.10, 23(5): 971~977
- Ren Xianwen(#); Zhou Xiaobo; Wu Ling-Yun; Zhang Xiang-Sun(*), An information-flow-based model with dissipation, saturation and direction for active pathway inference, BMC Systems Biology, 2010.5.27, 4: 0~72
- Ren Xianwen(#)(*); Wang Yong; Wang Jiguang; Zhang Xiang-Sun, An Optimization Model for Fuzzy Binary Clustering, 9th International Symposium on Operations Research and Its Applications, 2010
- Wu Zhiqiang(#); Ren Xianwen(#); Yang Li(#); Hu Yongfeng(#); Yang Jian; He Guimei; Zhang Junpeng; Dong Jie; Sun Lilian; Du Jiang; Liu Liguo; Xue Ying; Wang Jianmin; Yang Fan; Zhang Shuyi(*); Jin Qi(*), Virome Analysis for Identification of Novel Mammalian Viruses in Bat Species from Chinese Provinces, Journal of Virology, 2012.10, 86(20): 10999~11012
- Wang Yongcui(#); Ren Xianwen(#); Zhang Chunhua; Deng Naiyang(*); Zhang Xiangsun(*), Interrogating noise in protein sequences from the perspective of protein-protein interactions prediction, J Theor Biol, 2012.9.18, 315: 64~70
- Yang Li(#); Wu Zhiqiang(#); Ren Xianwen(#); Yang Fan(#); He Guimei; Zhang Junpeng; Dong Jie; Sun Lilian; Zhu Yafang; Du Jiang; Zhang Shuyi; Jin Qi(*), Novel SARS-like Betacoronaviruses in Bats, China, 2011, Emerging Infectious Diseases, 2013.6, 19(6): 989~991
- Yang Li(#); Wu Zhiqiang(#); Ren Xianwen(#); Yang Fan(#); Zhang Junpeng; He Guimei; Dong Jie; Sun Lilian; Zhu Yafang; Zhang Shuyi; Jin Qi(*), MERS-Related Betacoronavirus in Vespertilio superans Bats, China, Emerging Infectious Diseases, 2014.7, 20(7): 1260~1262
- Wu Zhiqiang(#); Yang Li(#); Yang Fan(#); Ren Xianwen(#); Jiang Jinyong; Dong Jie; Sun Lilian; Zhu Yafang; Zhou Hongning; Jin Qi(*), Novel Henipa-like Virus, Mojiang Paramyxovirus, in Rats, China, 2012, Emerging Infectious Diseases, 2014.6, 20(6): 1064~1066
- Liu Tao(#); Ren Xianwen(#); Xiao Tengfei(#); Yang Jian; Xu Xingye; Dong Jie; Sun Lilian; Chen Runsheng(*); Jin Qi(*),Identification and Characterisation of Non-coding Small RNAs in the Pathogenic Filamentous Fungus Trichophyton rubrum, BMC Genomics, 2013.12.30, 14: 0~931
- Wu Zhiqiang(#); Yang Li(#); Ren Xianwen(#); He Guimei(#); Zhang Junpeng; Yang Jian; Qian Zhaohui; Dong Jie; Sun Lilian; Zhu Yafang; Du Jiang; Yang Fan; Zhang Shuyi(*); Jin Qi(*), Deciphering the bat virome catalog to better understand the ecological diversity of bat viruses and the bat origin of emerging infectious diseases, The ISME Journal, 2015.08.11,10(3): 609~620
- Xu Xingye(#); Liu Tao(#); Ren Xianwen(#); Liu Bo; Yang Jian; Chen Lihong; Wei Candong; Zheng Jianhua; Dong Jie; Sun Lilian; Zhu Yafang; Jin Qi(*), Proteogenomic Analysis of Trichophyton rubrum Aided by RNA Sequencing, Journal of Proteome Research, 2015.4.14, 14(5): 2207~2218
- Hu Yongfeng(#); Ren Xianwen(#); Liu Yingmei(#); Yang Fan; Liu Haiying; Cao Bin(*); Jin Qi(*), Serial high-resolution analysis of blood virome and host cytokines expression profile of a patient with fatal H7N9 infection by massively parallel RNA sequencing, Clinical Microbiology and Infection, 2015.4.13, 21(7)
- Wu Zhiqiang(#); Yang Li(#); Ren Xianwen(#); Zhang Junpeng; Yang Fan; Zhang Shuyi(*); Jin Qi(*), ORF8-Related Genetic Evidence for Chinese Horseshoe Bats as the Source of Human Severe Acute Respiratory Syndrome Coronavirus, Journal of Infectious Diseases, 2016.2.15, 213(4): 579~583
- Chen, Zhe(#); Ren Xianwen(#); Yang, Jian; Dong, Jie; Xue, Ying; Sun, Lilian; Zhu, Yafang; Jin, Qi(*), An elaborate landscape of the human antibody repertoire against enterovirus 71 infection is revealed by phage display screening and deep sequencing, mAbs, 2017, 9(2): 342~349
- Hu Yongfeng(#); Ren Xianwen(#); Li Li; Xiao Yan; Dong Jie; Sun Lilian; Zhu Yafang; Yang Fan(*); Zhang Xi(*); Jin Qi(*), Rapid genome sequencing and characterization of novel avian-origin influenza A H7N9 virus directly from clinical sample by semiconductor sequencing, Journal of Clinical Virology, 2015.10.30, 73: 84-88
- Ren Lili(#); Yang Donghong(#); Ren Xianwen(#); Li Mingkun; Mu Xinlin; Wang Qi; Cao Jie; Hu Ke; Yan Chunliang; Fan Hongwei; Li Xiangxin; Chen Yusheng; Wang Ruiqin; An Fucheng; An Shuchang; Luo Ming; Wang Ying; Xiao Yan; Xiang Zichun; Xiao Yan; Li Li; Huang Fang; Jin Qi(*); Gao Zhancheng(*); Wang Jianwei(*), Genotyping of human rhinovirus in adult patients with acute respiratory infections identified predominant infections of genotype A21, Scientific Reports, 2017.1.27,7: 41601
其他论文
- Cheng Sijin (#), Li Ziyi (#), Gao Ranran, Xing Baocai, Gao Yunong, Yang Yu, Qin Shishang, Zhang Lei, Ouyang Hanqiang, Du Peng, Jiang Liang, Zhang Bin, Yang Yue, Wang Xiliang, Ren Xianwen, Bei Jin-Xin, Hu Xueda, Bu Zhaode (*), Ji Jiafu (*), Zhang Zemin (*), A pan-cancer single-cell transcriptional atlas of tumor infiltrating myeloid cells, Cell, 2021.2.4, 184,3(792-809)
- Zhang Lei(#), Li Ziyi(#), Katarzyna M.Skrzypczynska(#), Fang Qiao, Zhang Wei, Sarah A.O’Brien, He Yao, Wang Lynn, Zhang Qiming, Kim Aeryon, Gao Ranran, Jessica Orf, Wang Tao, Deepali Sawant, Kang Jiajinlong, Dev Bhatt, Lu Daniel, Li Chi-Ming, Aaron S. Rapaport, Kristy Perez, Ye Yingjiang, Wang Shan, Hu Xueda, Ren Xianwen, Ouyang Wenjun, Shen Zhanlong(*), Jackson G. Egen(*), Zhang Zemin(*), Yu Xin(*), Single-Cell Analyses Inform Mechanisms of Myeloid-Targeted Therapies in Colon Cancer, Cell, 2020.4.16, 181,2(442-459)
- Zhang Lei(#); Yu Xin; Zheng Liangtao; Zhang Yuanyuan; Li Yansen; Fang Qiao; Gao Ranran; Kang Boxi; Zhang Qimin; Huang Y. Julie; Konno Hiroyasu; Guo Xinyi; Ye Yingjiang; Gao Songyuan; Wang Shan; Hu Xueda; Ren Xianwen; Shen Zhanlong(*); Ouyang Wenjun(*); Zhang Zemin(*), Lineage tracking reveals dynamic relationships of T cells in colorectal cancer, Nature, 2018.10.29, 564 (268-272)
- Guo Xinyi(#); Zhang Yuanyuan(#); Zheng Liangtao(#); Zheng Chunhong(#); Song Jintao(#); Zhang Qiming; Kang Boxi; Liu Zhouzerui; Jin Liang; Xing Rui; Gao Ranran; Zhang Lei; Dong Minghui; Hu Xueda; Ren Xianwen; Kirchhoff Dennis; Helge Gottfried Roider; Yan Tiansheng(*); Zhang Zemin(*), Global characterization of T cells in non-small-cell lung cancer by single-cell sequencing, Nature Medicine, 2018.06.25,24(978-985)
- Liu Baolin(#), Li Chenwei(#), Li Ziyi, Wang Dongfang, Ren Xianwen, Zhang Zemin(*), An entropy-based metric for assessing the purity of single cell populations, Nature Communications, 2020.6.22, 3155
- Zhang Yuanyuan(#), Zheng Liangtao, Zhang Lei, Hu Xueda, Ren Xianwen, Zhang Zemin(*), Deep single-cell RNA sequencing data of individual T cells from treatment-naïve colorectal cancer patients, Scientific data, 6(1):1-15
- Feng Zhanying(#), Ren Xianwen, Fang Yuan, Yin Yining, Huang Chutian, Zhao Yimin, Wang Yong(*), scTIM: Seeking Cell-Type-Indicative Marker from single cell RNA-seq data by consensus optimization, Bioinformatics, 2019.12.7:btz936
- Tang Zefang(#)(*), Chen Tianxiang, Ren Xianwen, Zhang Zemin(*), Identification of transcriptional isoforms associated with survival in cancer patient, Journal of Genetics and Genomics, 2019.9.20, 46(9):413-421
- Wang Xiliang(#), He Yao(#), Zhang Qiming, Ren Xianwen, Zhang Zemin(*), Direct Comparative Analyses of 10X Genomics Chromium and Smart-seq2, Genomics Proteomics Bioinformatics, 19 (2021) 253-266
- Wu Zhiqiang(#); Lu Liang(#); Du Jiang(#); Yang Li; Ren Xianwen; Liu Bo; Jiang Jinyong; Yang Jian; Dong Jie; Sun Lilian; Zhu Yafang; Li Yuhui; Zheng Dandan; Zhang Chi; Su Haoxiang; Zheng Yuting; Zhou Hongning; Zhu Guangjian; Li Hongying; Chmura Aleksei; Yang Fan; Daszak Peter; Wang Jianwei(*); Liu Qiyong(*); Jin Qi(*), Comparative analysis of rodent and small mammal viromes to better understand the wildlife origin of emerging infectious diseases, Microbiome, 2018.10.03,6(178)
- Sun Duanchen(#); Ren Xianwen; Ari Eszter; Korcsmaros Tamas; Csermely Peter; Wu Ling-Yun(*), Discovering cooperative biomarkers for heterogeneous complex disease diagnoses, Briefings in Bioinformatics, 2019.01.18, 20(-1):89~101
- Du Jiang(#); Lu Liang; Liu Feng; Su Haoxiang; Dong Jie; Sun Lilian; Zhu Yafang; Ren Xianwen; Yang Fan; Guo Fei; Liu Qiyong(*); Wu Zhiqiang(*); Jin Qi(*), Distribution and characteristics of rodent picornaviruses in China, Scientific Reports, 2016.9.29,6: 34381
- Du Jiang(#); Yang Li; Ren Xianwen; Zhang Junpeng; Dong Jie; Sun Lilian; Zhu Yafang; Yang Fan; Zhang Shuyi; Wu Zhiqiang(*); Jin Qi(*), Genetic diversity of coronaviruses in Miniopterus fuliginosus bats, Science China-Life Sciences, 2016.6, 59(6): 604~614
- Hu Yongfeng(#); Zhang Yan(#); Ren Xianwen; Liu Yingmei; Xiao Yan; Li Li; Yang Fan; Su Haoxiang; Liu Feng; Liu Haiying(*); Cao Bin(*); Jin Qi(*), A case report demonstrating the utility of next generation sequencing in analyzing serial samples from the lung following an infection with influenza A (H7N9) virus, Journal of Clinical Virology, 2016, 76
- Xin Jingxue(#); Ren Xianwen; Chen Luonan(*); Wang Yong(*), Identifying network biomarkers based on protein-protein interactions and expression data, BMC Medical Genomics, 2015.5.29, 8(Suppl 2)(S11)
- Yang Jian(#); Zhang Ting(#); Guo Li(#); Hu Yongfeng(#); Li Jinlin; Su Haoxiang; Xiao Yan; Ren Xianwen; Dong Jie; Sun Lilian; Xiao Yan; Li Li; Yang Fan; Wang Jianwei; Yuan Hui; Jin Qi(*), Mutations of Novel Influenza A(H10N8) Virus in Chicken Eggs and MDCK Cells, Emerging Infectious Diseases, 2014.9, 20(9): 1541~1543
- Zhang Yan(#); Liu Haiying(#); Wang Linghang; Yang Fan; Hu Yongfeng; Ren Xianwen; Li Guojun; Yu Yang; Sun Shaoxia; Li Yufen; Chen Xinchun; Li Xingwang(*); Jin Qi(*), Comparative Study of the Cytokine/Chemokine Response in Children with Differing Disease Severity in Enterovirus 71-Induced Hand, Foot, and Mouth Disease, PLoS One, 2013.6.28, 8(6): 0~e67430
- Zheng Jianhua(#); Ren Xianwen; Wei Candong; Yang Jian; Hu, Yongfeng; Liu Liguo; Xu Xingye; Wang Jin; Jin Qi(*),Analysis of the secretome and identification of novel constituents from culture filtrate of bacillus Calmette-Guerin using high-resolution mass spectrometry, Molecular & Cellular Proteomics, 2013.4.24, 12(8): 2081~95
- Wang Xia(#); Ren Xianwen; Li Beiping; Yue Junjie(*); Liang Long(*), Applying modularity analysis of PPI networks to sequenced organisms, Virulence, 2012.8.15, 3(5): 459~63
- Wang Xia(#); Yue Junjie(*); Ren Xianwen; Wang Yuelan; Tan Minfeng; Li Beiping; Liang Long(*), Modularity analysis based on predicted protein-protein interactions provides new insights into pathogenicity and cellular process of Escherichia coli O157:H7, Theor Biol Med Model, 2011.12.22, 8: 0~47
- Zhang Zhong-Yuan(#); Li Tao(*); Ding Chris; Ren Xianwen; Zhang, Xiang-Sun, Binary matrix factorization for analyzing gene expression data, Data Mining and Knowledge Discovery, 2010.1.10, 20(1): 28~52
- Chang C. C(#)(*); Zhou X; Taylor J. J.; Huang W. T.; Ren Xianwen; Monzon F.; Feng Y.; Rao P. H.; Lu X. Y.; Fabio F.; Hilsenbeck S.; Creighton C. J.; Jaffe E. S.; Lau C. C., Genomic profiling of plasmablastic lymphoma using array comparative genomic hybridization (aCGH): revealing significant overlapping genomic lesions with diffuse large B-cell lymphoma, Journal of Hematology & Oncology, 2009, 2: 0~47