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    苏震 博士

    中国农业大学, 教授

    Email: zhensu@cau.edu.cn

    实验室网页

     

    1990年毕业于北京农业大学 应用物理专业,19901997在中国科学院生物物理所细胞生物物理室工作,从事光生物物理和辐射生物物理等领域的研究,其间发表论文20余篇;19972003就读于美国亚利桑那大学农业与生命科学学院,获得环境科学专业博士学位,副修材料工程专业,主要从事计算机分子模拟和生物信息数据挖掘的研究;其间自2001年起,先后就职于美国TORREY MESA生物技术研究所、Activx生物医学公司和Syngenta生物技术公司,从事功能基因组学和蛋白组学研究并负责基因芯片实验室信息管理系统的管理、维护和数据挖掘。

    从2004年5月到中国农业大学至今,建立生物信息平台并在中国农业大学招收生物信息学专业的研究生;参与中国农业大学功能基因组中心建设,为转录组学和蛋白质组学平台提供实验管理和数据分析支撑。并在此基础上展开植物分子系统生物学的研究,主要研究方向为:大规?;虮泶锲追治鏊惴?,基因表达调控网络构建,蛋白质功能预测与计算机生物活性分子高通量筛选等。

    曾参与973计划《植物应答高盐、低温胁迫的分子调控网络机制研究》(2010结题),863项目《网络海量RNA数据搜索、二次挖掘与应用集成软件的开发》(2010结题),主持国家自然科学基金《降解农药残留的水稻细胞色素P450的功能基因组研究》(2008结题) ,《拟南芥JAZ家族基因在茉莉酸和脱落酸间交互作用及协调水分胁迫适应性的分子机制研究》(2012结题)和《水稻籼粳亚种间细胞凋亡差异反应的分子机制研究》(2013结题)。目前有两项国家自然科学基金《棉花和拟南芥应答水分胁迫的转录组数据比较分析及基因表达调控网络的构建》和《植物表观基因组和转录组数据整合及其时序动态变化规律探索》正在执行,并参与973计划《草本能源植物培育及化学催化制备先进液体燃料的基础研究》。2009年入选教育部“新世纪优秀人才支持计划”。

     

    近期发表文章:* (通讯作者)

    Juan Yu, Zhenhai Zhang, Jiangang Wei, Yi Ling, Wenying Xu*, Zhen Su*. (2014) SFGD: a comprehensive platform for mining functional information from soybean transcriptome data and its use in identifying acyl-lipid metabolism pathways. BMC Genomics. 15:271.

    Chunchao Wang, Qiang Wei, Kang Zhang, Ling Wang, Fengxia Liu, Linna Zhao, Yuanjun Tan, Chao Di, Hong Yan, Jingjuan Yu, Chuanqing Sun, Wenqiong J Chen, Wenying Xu*, Zhen Su*. (2013) Down-regulation of OsSPX1 causes high sensitivity to cold and oxidative stresses in rice seedlings. PLoS ONE. doi:10.1371/journal.pone.0081849.

    Du Z, Fei T, Verhaak RGW, Su Z, Zhang Y, Brown M, Chen C, Liu XS. (2013) An integrated approach to identify clinically relevant long non-coding RNAs (IncRNAs) in cancer. Nat Struct Mol Biol. doi:10.1038/nsmb.2591.

    Xin Yi, Zhou Du*, Zhen Su*. (2013) PlantGSEA: a Gene Set Enrichment Analysis toolkit for plant community.  Nucleic Acids Research. doi:10.1093/nar/gkt281.

    Zhou Du, Hui Li, Qiang Wei, Xin Zhao, Chunchao Wang, Qilin Zhu, Xin Yi, Wenying Xu, X. Shirley Liu*, Weiwei Jin*, Zhen Su*. (2013) Genome-wide analysis of histone modifications: H3K4me2, H3K4me3, H3K9ac and H3K27ac, in Oryza sativa L. japonica.  Molecular Plant. doi:10.1093/mp/sst018.

    Xueyan Zhang, Dongxia Yao, Qianhua Wang, Wenying Xu, Qiang Wei, Chunchao Wang, Chuanliang Liu, Chaojun Zhang, Hong Yan, Yi Ling, Zhen Su*, Fuguang Li*. (2013) mRNA-seq analysis of the Gossypium arboreum transcriptome reveals tissue selective signaling in response to water stress during seedling stage. PLoS ONE. doi:10.1371/journal.pone.0054762.

    Fengxia Liu, Wenying Xu, Qian Song, Lubin Tan, Jiayong Liu, Zuofeng Zhu, Yongcai Fu, Zhen Su*, and Chuanqing Sun*. (2013) Microarray Assisted Fine-mapping of Quantitative Trait Loci for Cold Tolerance in Rice. Molecular Plant. doi:10.1093/mp/sss161.

    Gaihua Zhang, Yijing Zhang and Zhen Su*. (2012) CYPSI: a structure-based interface for cytochrome P450s and ligands in Arabidopsis thaliana. BMC Bioinformatics. 13:332.

    Gaihua Zhang and Zhen Su*. (2012) Inferences from structural comparison: flexibility, secondary structure wobble and sequence alignment optimization. BMC Bioinformatics. 13(Suppl 15):S12.

    Dongxia Yao, Qiang Wei, Wenying Xu, Ryan D Syrenne, Joshua S. Yuan, and Zhen Su*. (2012) Comparative genomic analysis of NAC transcriptional factors to dissect the regulatory mechanisms for cell wall biosynthesis. BMC Bioinformatics. 13(Suppl 15):S10.

    Zhenyan Miao, Daofeng Li, Zhenhai Zhang, Jiangli Dong, Zhen Su* and Tao Wang*. (2012) Medicago truncatula transporter database: a comprehensive database resource for M. truncatula transporters. BMC Genomics. 13:60.

    Daofeng Li, Yunqin Zhang, Xiaona Hu, Xiaoye Shen, Lei Ma, Zhen Su, Tao Wang and Jiangli Dong. (2011) Transcriptional profiling of Medicago truncatula under salt stress identified a novel CBF transcription factor MtCBF4 that plays an important role in abiotic stress responses. BMC Plant Biology. 11:109.

    Dongxia Yao, Wenying Xu, Joshua S. Yuan, and Zhen Su*. (2011) Comparative Genome Analysis and Network Modeling of NAC Transcriptional Factors to Dissect the Regulatory Mechanisms for Cell Wall Biosynthesis. the 33rd Symposium on Biotechnology for Fuels and Chemicals (May 2-5, 2011) Sheraton Seattle, Seattle, WA, USA.

    Dongxia Yao, Xueyan Zhang, Xinhua Zhao, Chuanliang Liu, Chunchao Wang, Zhenghai Zhang, Chaojun Zhang, Qiang Wei, Qianhua Wang, Hong Yan, Fuguang Li*, Zhen Su*. (2011) Transcriptome analysis reveals salt-stress-regulated biological processes and key pathways in roots of cotton (Gossypium hirsutum L.). Genomics. 98: 47–55

    Wenying Xu, Rendong Yang, Meina Li, Zhuo Xing, Wenqiang Yang, Guang Chen, Han Guo, Xiaojie Gong, Zhou Du, Zhenhai Zhang, Xingming Hu, Dong Wang, Qian Qian, Tai Wang, Zhen Su*, Yongbiao Xue*. (2011)   Transcriptome Phase Distribution Analysis Reveals Diurnal Regulated Biological Processes and Key Pathways in Rice Flag Leaves and Seedling Leaves. PLoS ONE doi:10.1371/journal.pone.0017613

    Rendong Yang, Chen Zhang, Zhen Su*. (2011)   LSPR: an integrated periodicity detection algorithm for unevenly sampled temporal microarray data. Bioinformatics. 27: 1023-1025

    Yi Ling, Zhou Du, Zhenhai Zhang and Zhen Su*. (2010) ProFITS of maize: a database of protein families involved in the transduction of signalling in the maize genome. BMC Genomics. 11:580.

    Chao Di, Wenying Xu, Zhen Su* and Joshua S Yuan*. (2010) Comparative genome analysis of PHB gene family reveals deep evolutionary origins and diverse gene function. BMC Bioinformatics. 11 (Suppl 6):S22.

    Li Q Wei, Wen Y Xu, Zhu Y Deng, Zhen Su, Yongbiao Xue and Tai Wang. (2010) Genome-scale Analysis and Comparison of Gene Expression Profiles in Developing and Germinated Pollen in Oryza sativa. BMC Genomics. 11:338.

    Rendong Yang and Zhen Su*. (2010) Analyzing circadian expression data by harmonic regression based on autoregressive spectral estimation. BIOINFORMATICS. 26: i168-i174.

    Zhou Du , Xin Zhou , Yi Ling , Zhenhai Zhang , and Zhen Su*. (2010) agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Research  38: W64-W70.

    Jie Zhang, Haibin Lu, Xinyan Li, Yan Li, Haitao Cui, Chi-Kuang Wen, Xiaoyan Tang, Zhen Su, and Jian-Min Zhou (2010) Effector-Triggered and Pathogen-Associated Molecular Pattern–Triggered Immunity Differentially Contribute to Basal Resistance to Pseudomonas syringae. Molecular Plant-Microbe Interactions. 23: 940–948.

    Liu F, Xu W, Wei Q, Zhang Z, Xing Z, Tan L, Di C, Yao D, Wang C, Tan Y, Yan H, Ling Y, Sun C, Xue Y*, Su Z.* (2010) Gene Expression Profiles Deciphering Rice Phenotypic Variation between Nipponbare (Japonica) and 93-11 (Indica) during Oxidative Stress. PLoS ONE 5(1): e8632.

    Zhenhai Zhang, Jingyin Yu, Daofeng Li, Zuyong Zhang, Fengxia Liu, Xin Zhou, Tao Wang, Yi Ling, and Zhen Su*. (2010)  PMRD: plant microRNA database. Nucleic Acids Research. 38: D806-D813

    Daofeng Li, Zhen Su, Jiangli Dong and Tao Wang. (2009)  An expression database for roots of the model legume Medicago truncatula under salt stress. BMC Genomics. 10:517

    Xin Zhou, Zhen Su, R Douglas Sammons, Yanhui Peng, Patrick J Tranel, C Neal Stewart Jr, and Joshua S Yuan. (2009) Novel software package for cross-platform transcriptome analysis (CPTRA). BMC Bioinformatics. 10 (Suppl 11):S16

    Fu-Qing Wu, Qi Xin, Zheng Cao, Zhi-Qiang Liu, Shu-Yuan Du, Chao Mei, Chen-Xi Zhao, Xiao-Fang Wang, Yi Shang, Tao Jiang, Xiao-Feng Zhang, Lu Yan, Rui Zhao, Zi-Ning Cui, Rui Liu, Hai-Li Sun, Xin-Ling Yang, Zhen Su, and Da-Peng Zhang. (2009) The Mg-Chelatase H Subunit Binds Abscisic Acid and Functions in Abscisic Acid Signaling: New Evidence in Arabidopsis. Plant Physiol. 150(4):1940-54

    Zhou Du, Xin Zhou, Li Li, Zhen Su*. (2009) plantsUPS: a database of plants' Ubiquitin Proteasome System. BMC Genomics. 10:227

    郭华军, 焦远年, 邸超, 姚冬霞, 张盖华, 郑雪, 刘岚, 张群莲, 郭蔼光*, 苏震* (2009). 拟南芥转录因子GRAS 家族基因群响应渗透和干旱胁迫的初步探索. 植物学报 44, 290-299.

    Linna Zhao, Fengxia Liu, Wenying Xu, Chao Di, Shaoxia Zhou, Yongbiao Xue, Jingjuan Yu*, Zhen Su*. (2009) Increased expression of OsSPX1 enhances cold/subfreezing tolerance in tobacco and Arabidopsis thaliana. Plant Biotechnology Journal. 7: 550-561.

    Hao Lin, Renxiao Wang, Qian Qian, Meixian Yan, Xiangbing Meng, Zhiming Fu, Cunyu Yan, Biao Jiang, Zhen Su, Jiayang Li, Yonghong Wang. (2009) DWARF27, an Iron-Containing Protein Required for the Biosynthesis of Strigolactones, Regulates Rice Tiller Bud Outgrowth through the MAX/RMS/D Pathway. Plant Cell. 21:1512-1525

    Zhi-yu Peng, Xin Zhou, Linchuan Li, Xiangchun Yu, Hongjiang Li, Zhiqiang Jiang, Guangyu Cao, Mingyi Bai, Xingchun Wang, Caifu Jiang, Haibin Lu, Xianhui Hou, Lijia Qu, Zhiyong Wang, Jianru Zuo, Xiangdong Fu, Zhen Su, Songgang Li, and Hongwei Guo. (2009) Arabidopsis Hormone Database: a comprehensive genetic and phenotypic information database for plant hormone research in Arabidopsis. Nucleic Acids Research. 37: D975-D982

    Xin Zhou, Zhen Su*. (2008) tCal: transcriptional probability calculator using thermodynamic model. Bioinformatics. 24: 2639 - 2640

    He Fei, Kang Juqing, Zhou Xin, Su Zhen, Qu Li-Jia, Gu Hongya. (2008) Variation at the transcriptional level among Chinese natural populations of Arabidopsis thaliana in response to cold stress. Chinese Science Bulletin. Vol.53  No. 19  pp.2989-2999

    Yi Wang, Wen-Zheng Zhang, Lian-Fen Song, Jun-Jie Zou, Zhen Su, and Wei-Hua Wu. (2008) Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in Arabidopsis. Plant Physiol.  148:1201-1211

    Liu, F., Xu, W.*, Tan, L., Xue, Y., Sun, C., Su, Z.* (2008) Case study for identification of indel-caused alternative expression isoforms in rice subspecies japonica and indica by integrative genome analysis. Genomics 91: 186–194

    Xin Zhou, Zhen Su*. (2007) EasyGO: Gene Ontology-based annotation and functional enrichment analysis tool for agronomical species, BMC Genomics 8:246

    Hou ZC, Xu GY, Su Z, Yang N. 2007Purifying selection and positive selection on the myxovirus resistance gene in mammals and chickens. Gene. 396(1):188-95.

    Xin Zhou, Fei He, Fengxia Liu, Xue Zheng, Chao Di, Shaoxia Zhou, Hongya Gu, Wenying Xu, and Zhen Su*. (2006) Integration of Cold Signal Transduction Pathway Related to ABA 8’-hydroxylase in Arabidopsis. Biotechnology and Sustainable Agriculture 2006 and Beyond, 471-474, Z. Xu et al. (eds.), 2007 Springer

    Jia J, Fu J, Zheng J, Zhou X, Huai J, Wang J, Wang M, Zhang Y, Chen X, Zhang J, Zhao J, Su Z, Lv Y, Wang G. (2006) Annotation and expression profile analysis of 2073 full-length cDNAs from stress-induced maize (Zea mays L.) seedlings. Plant J. 48(5):710-27.

    Zhang X, Zhou S, Fu Y, Su Z, Wang X, Sun C. (2006) Identification of a drought tolerant introgression line derived from Dongxiang common wild rice (O. rufipogon Griff.). Plant Mol Biol. 62(1-2):247-59.

    丁必为,田英杰,邓乃扬,苏震,蔡春. (2006) 基于支持向量机的拟南芥基因表达数据分析. 运筹学学报10(2):51-58

    刘云岩,苏震,董江丽,申小叶,李道丰,王涛 (2006) 截形苜蓿生物数据分析平台的构建与应用 草地学报 14(3): 231-235

    刘胜毅, 毛晗, 苏震, 董彩华, 徐文英, 冀瑞琴, 郭学兰. (2005)  油菜对菌核病和黑胫病的抗病机制分析. 西北农林科技大学学报(自然科学版)   2005z1

    Su Z, Cushman JH, Curry JE (2003) Computer simulation of anisotropic diffusion in monolayer films in mica slit pores. Journal of Chemical Physics, 118(3):1417-1422

     

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