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Xianwen Ren (任仙文)


BIOPIC, Peking University(北京大学生物动态光学成像中心)


Education (教育背景)

南开大学,生物科学,信息与计算科学,双学位
军事医学科学院,遗传学,硕士
中国科学院数学与系统科学研究院,运筹学与控制论,博士

Experience (工作经历)

康奈尔大学威尔医学院卫斯理医院,访问学生
中国医学科学院北京协和医学院病原生物学研究所, 助理研究员、副研究员
北京大学生命科学学院生物动态光学成像中心,副研究员

Honors(获得荣誉)


Publications(发表论文)

First and corresponding author publications
  1. Xianwen Ren(co-first), Hua Fu and Qi Jin.
    Integrating heterogeneous genomic data to accurately identify disease subtypes
    BMC Med Genomics. 2015, 8:78 DOI:10.1186/s12920-015-0154-5.
  2. Xianwen Ren and Qi Jin.
    Safe sequencing depth to estimate the intra-host heterogeneity of viruses
    Brief Funct Genomics. 2015. DOI:10.1093/bfgp/elv039
  3. Xianwen Ren(co-first), Yongfeng, Hu, Fan Yang, Yan Xiao, Li Li, Jie Dong, Lilian Sun, Yafang Zhu and Qi Jin.
    Clinical utility comparison of two benchtop deep sequencing instruments for rapid diagnosis of newly emergent influenza infections
    Clin Microbiol Infec. 21(3):290.e1–290.e4, 2015.http://dx.doi.org/10.1016/j.cmi.2014.10.016
  4. Xianwen Ren.
    Toward a more systematic understanding of bacterial virulence factors and establishing Koch postulates in silico
    Virulence, invited comment, 4(6):437-438.
  5. Xianwen Ren(co-first), Fan Yang, Yongfeng Hu, Ting Zhang, Liguo Liu, Jie Dong, Lilian Sun, Yafang Zhu, Yan Xiao, Li Li, Jian Yang, Jianwei Wang and Qi Jin.
    Full Genome of Influenza A (H7N9) Virus Derived by Direct Sequencing without Culture
    Emerg Infect Dis, 19(11):1881-1884, 2013.
  6. Xianwen Ren(co-first), Yong Wang, Xiang-Sun Zhang, Qi Jin.
    iPcc: a novel feature extraction method for accurate disease class discovery and prediction
    Nucleic Acids Research, 41(14):e143, 2013; doi: 10.1093/nar/gkt343.
  7. Xianwen Ren(co-first), Yong Wang, Luonan Chen, Xiang-Sun Zhang and Qi Jin.
    ellipsoidFN: a tool for identifying a heterogeneous set of cancer biomarkers based on gene expressions
    Nucleic Acids Research, 41(4): e53, 2013. software
  8. Xianwen Ren(co-first), Tao Liu, Jie Dong, Lilian Sun, Jian Yang, Yafang Zhu and Qi Jin.
    Evaluating de Bruijn graph assemblers on 454 transcriptomic data
    PLoS One, 7(12): e51188, 2012.
  9. Xianwen Ren, Yong Wang, Jiguang Wang and Xiang-Sun Zhang.
    A unified computational model for revealing and predicting subtle subtypes of cancers
    BMC Bioinformatics 13:70, 2012.
  10. Xianwen Ren(co-first), Yongcui Wang, Yong Wang, Nai-Yang Deng and Xiang-Sun Zhang.
    Improving accuracy of protein-protein interaction prediction by considering the converse problem for sequence representation
    BMC Bioinformatics 12:409, 2011.
  11. Xianwen Ren, Xiaobo Zhou and Chung-Che Chang.
    The network properties of Myelodysplastic Syndromes pathogenesis revealed by an integrative systems biological method
    Mol Biosyst. 2011, 7(6):2048-2054.
  12. Xianwen Ren, Xiaobo Zhou, Ling-Yun Wu and Xiang-Sun Zhang.
    An information-flow-based model with dissipation, saturation and direction for active pathway inference
    BMC Systems Biology, 4:72, 2010.
  13. Xianwen Ren and Xiang-Sun Zhang.
    A linear programming model based on network flow for pathway inference
    Journal of Systems Science and Complexity, 23(5), 971-977, 2010.
  14. Xianwen Ren, Yong Wang, Jiguang Wang and Xiang-Sun Zhang.
    An Optimization Model for Fuzzy Binary Clustering
    The Ninth International Symposium, ISORA'10, Chengdu-Jiuzhaigou, China, August 19-23, 2010

Co-first author publications
  1. Lili Ren, Donghong Yang, Xianwen Ren(co-first), Mingkun Li, Xinlin Mu, Qi Wang, Jie Cao, Ke Hu, Chunliang Yan, Hongwei Fan, Xiangxin Li, Yusheng Chen, Ruiqin Wang, Fucheng An, Shuchang An, Ming Luo, Ying Wang, Yan Xiao, Zichun Xiang, Yan Xiao, Li Li, Fang Huang, Qi Jin, Zhancheng Gao & Jianwei Wang.
    Genotyping of human rhinovirus in adult patients with acute respiratory infections identified predominant infections of genotype A21
    Scientific Reports. (2017) 7:41601
  2. Zhe Chen, Xianwen Ren(co-first), Jian Yang, Jie Dong, Ying Xue, Lilian Sun, Yafang Zhu and Qi Jin.
    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.
  3. Yongfeng Hu, Xianwen Ren(co-first), Li Li, Yan Xiao, Jie Dong, Lilian Sun, Yafang Zhu, Fan Yang, Xi Zhang and Qi Jin.
    Rapid genome sequencing and characterization of novel avian-origin influenza A H7N9 virus directly from clinical sample by semiconductor sequencing
    J Clin Virol. 2015 DOI:10.1016/j.jcv.2015.10.022
  4. Zhiqiang Wu, Li Yang, Xianwen Ren(co-first), Junpeng Zhang, Fan Yang, Shuyi Zhang and Qi Jin.
    ORF8-related genetic evidence for Chinese horseshoe bats as the source of human SARS coronavirus
    J Infect Dis. 213 (4): 579-583 2016.
  5. Zhiqiang Wu, Li Yang, Xianwen Ren(co-first), Guimei He, Junpeng Zhang, Jian Yang, Zhaohui Qian, Jie Dong, Lilian Sun, Yafang Zhu, Jiang Du, Fan Yang, Shuyi Zhang and Qi Jin.
    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 10(3):609-20 2016; doi:10.1038/ismej.2015.138
  6. Yongfeng Hu, Xianwen Ren(co-first), Yingmei Liu, Fan Yang, Haiying Liu, Bin Cao and Qi Jin.
    Serial high-resolution analysis of blood virome and host cytokines expression profile of a patient with fatal H7N9 infection by massively parallel RNA sequencing
    Clin Microbiol Infec. 21(7):713.e1–713.e4, 2015. http://dx.doi.org/10.1016/j.cmi.2015.03.006
  7. Xingye Xu, Tao Liu, Xianwen Ren(co-first), Bo Liu, Jian Yang, Lihong Chen, Candong Wei, Jianhua Zheng, Jie Dong, Lilian Sun, Yafang Zhu, and Qi Jin.
    A proteogenomic analysis of Trichophyton rubrum aided by RNA sequencing
    J. Proteome Res. 14 (5), pp 2207–2218, 2015. http://dx.doi.org/10.1021/acs.jproteome.5b00009
  8. Li Yang, Zhiqiang Wu, Xianwen Ren(co-first), Fan Yang, Junpeng Zhang, Guimei He, Jie Dong, Lilian Sun, Yafang Zhu, Shuyi Zhang and Qi Jin.
    MERS–Related Betacoronavirus in Vespertilio superans Bats, China
    Emerg Infect Dis. 2014 July [date cited]. http://dx.doi.org/10.3201/eid2007.140318
  9. Zhiqiang Wu, Li Yang, Fan Yang, Xianwen Ren(co-first), Jinyong Jiang, Jie Dong, Lilian Sun, Yafang Zhu, Hongning Zhou and Qi Jin.
    Novel Henipa-like Virus, Mojiang Paramyxovirus, in Rats, China, 2012
    Emerg Infect Dis, 2014 June [date cited]. http://dx.doi.org/10.3201/eid2006.131022
  10. Tao Liu, Xianwen Ren(co-first), Tengfei Xiao, Jian Yang, Xingye Xu, Jie Dong, Lilian Sun, Runsheng Chen and Qi Jin.
    Identification and Characterisation of Non-coding Small RNAs in the Pathogenic Filamentous Fungus Trichophyton rubrum
    BMC Genomics, 14:931, 2013.
  11. Yongcui Wang, Xianwen Ren(co-first), Chunhua Zhang, Naiyang Deng, Xiang-Sun Zhang.
    Interrogating noise in protein sequences from the perspective of protein–protein interactions prediction
    Journal of Theoretical Biology 315(21): 64-70, 2012.
  12. Zhiqiang Wu, Xianwen Ren(co-first), Li Yang, Yongfeng Hu, Jian Yang, Guimei He, Junpeng Zhang, Jie Dong, Lilian Sun, Jiang Du, Liguo Liu, Ying Xue, Jianmin Wang, Fan Yang, Shuyi Zhang, Qi Jin.
    Virome Analysis for Identification of Novel Mammalian Viruses in Bat Species from Chinese Provinces
    Journal of Virology 86(20): 10999-11012, 2012.
  13. Li Yang, Zhiqiang Wu, Xianwen Ren(co-first), Fan Yang, Guimei He, Junpeng Zhang, Jie Dong, Lilian Sun, Yafang Zhu, Jiang Du, Shuyi Zhang and Qi Jin.
    Novel SARS-like Betacoronaviruses in Bats, China, 2011
    Emerg Infect Dis, 19(6), 2013.

Co-author publications
  1. Duanchen Sun, Xianwen Ren, Eszter Ari, Tamas Korcsmaros, Peter Csermely and Ling-Yun Wu.
    Discovering cooperative biomarkers for heterogeneous complex disease diagnoses
    Briefings in Bioinformatics, bbx090, https://doi.org/10.1093/bib/bbx090
  2. Jiang Du, Liang Lu, Feng Liu, Haoxiang Su, Jie Dong, Lilian Sun, Yafang Zhu, Xianwen Ren, Fan Yang, Fei Guo, Qiyong Liu, Zhiqiang Wu and Qi Jin.
    Distribution and characteristics of rodent picornaviruses in China
    Scientific Reports. (2016) 6:34381.
  3. Jiang Du, Li Yang, Xianwen Ren, Junpeng Zhang, Jie Dong, Lilian Sun, Yafang Zhu, Fan Yang, Shuyi Zhang, Zhiqiang Wu and Qi Jin.
    Genetic diversity of coronaviruses in Miniopterus fuliginosus bats
    Sci. China Life Sci. (2016) 59: 604.
  4. Yongfeng Hu, Yan Zhang, Xianwen Ren, Yingmei Liu, Yan Xiao, Li Li, Fan Yang, Haoxiang Su, Feng Liu, Haiying Liu, Bin Cao and Qi Jin.
    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
    J Clin Virol. 2015 DOI:10.1016/j.jcv.2015.12.013
  5. Jingxue Xin, Xianwen Ren, Luonan Chen and Yong Wang.
    Identifying network biomarkers based on protein-protein interactions and expression data
    BMC Medical Genomics 2015, 8(Suppl 2):S11. http://doi:10.1186/1755-8794-8-S2-S11
  6. Jian Yang, Ting Zhang, Li Guo, Yongfeng Hu, Jinlin Li, Haoxiang Su, Yan Xiao, Xianwen Ren, Jie Dong, Lilian Sun, Yan Xiao, Li Li, Fan Yang, Jianwei Wang, Hui Yuan and Qi Jin.
    Mutations of Novel Influenza A(H10N8) Virus in Chicken Eggs and MDCK Cells
    Emerg Infect Dis. 2014 Sep [date cited]. http://dx.doi.org/10.3201/eid2009.140257
  7. Yan Zhang, Haiying Liu, Linghang Wang, Fan Yang, Yongfeng Hu, Xianwen Ren, Guojun Li, Yang Yu, Shaoxia Sun, Yufen Li, Xinchun Chen, Xingwang Li and Qi Jin.
    Comparative Study of the Cytokine/Chemokine Response in Children with Differing Disease Severity in Enterovirus 71-Induced Hand, Foot, and Mouth Disease
    PLoS One, 8(6): e67430, 2013; doi:10.1371/journal.pone.0067430.
  8. Jianhua Zheng, Xianwen Ren, Candong Wei, Jian Yang, Yongfeng Hu, Liguo Liu, Xingye Xu, Jin Wang and Qi Jin.
    Analysis of the secretome and identification of novel constituents from culture filtrate of bacillus Calmette-Guerin using high-resolution mass spectrometry
    Molecular & Cellular Proteomics, 24, 2013.
  9. Xia Wang, Junjie Yue, Xianwen Ren, Yuelan Wang, Mingfeng Tan, Beiping Li and Long Liang.
    Modularity analysis based on predicted protein-protein interactions provides new insights into pathogenicity and cellular process of Escherichia coli O157:H7
    Theoretical Biology and Medical Modelling 8:47, 2011.
  10. Zhong-Yuan Zhang, Tao Li, Chris Ding, Xianwen Ren, and Xiang-Sun Zhang.
    Binary matrix factorization for analyzing gene expression data
    Data Mining and Knowledge Discovery, 20(1), 28-52, 2010.
  11. Chung-Che Chang, Xiaobo Zhou, Jesalyn J Taylor, Wan-Ting Huang, Xianwen Ren, Federico Monzon, Yongdong Feng, Pulivarthi H Rao, Xin-Yan Lu, Facchetti Fabio, Susan Hilsenbeck, Chad J Creighton, Elaine S Jaffe and Ching-Ching Lau.
    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, 2:47, 2009.

Patents(申请专利)

1)[发明, 已授权]
基于宏基因组学的病毒感染检测及鉴定方法 - 申请号:201510583787.3
- 申请人:中国医学科学院病原生物学研究所 - 申请日:2015-09-14 - 主分类号:C12Q1/70(2006.01)I - 发明人:金奇;任仙文;杨剑;胡永峰;杨帆.

Softwares of Publications:



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