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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 Perse 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. （2007）Purifying 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）》 2005年z1期
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
承担项目及课题：
水稻籼粳亚种间细胞凋亡差异反应的分子机制研究: 国家自然科学基金资助项目
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: 国家自然科学基金资助项目
能源高粱等能源植物选择性培育及遗传学规律: 国家重点基础研究发展计划（973计划）项目〈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〉子课题
植物应答高盐、低温胁迫的分子调控网络机制研究: 国家重点基础研究发展计划（973计划）项目〈作物适应高盐、低温胁迫的分子调控机理〉子课题，已结题
降解农药残留的水稻细胞色素P450的功能基因组研究: 国家自然科学基金资助项目，已结题
小RNA网络数据资源整合体系: 国家高技术研究发展计划(863计划)项目《网络海量RNA数据搜索、二次挖掘与应用集成软件开发》子课题，已结题
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: 国家自然科学基金资助项目，已结题
专利情况 ：
杨仁东，苏震，徐文英 ARSER表达谱波形分析软件计算机软件著作权登记号2010SRBJ3476
杨仁东，张臣，苏震，徐文英 基于Lomb-Scargle周期图回归算法软件计算机软件著作权登记号 2010SRBJ6734
孙传清，刘凤霞，谭禄宾，苏震，朱作峰，付永彩 “一种辅助筛选耐冷水稻的方法与其专用引物”，专利号ZL200610089799.1
孙传清，刘凤霞，谭禄宾，苏震，朱作峰，付永彩 “辅助筛选耐冷水稻的方法和它的专用引物” 专利号200610088805.1
孙传清，刘凤霞，谭禄宾，苏震，朱作峰，付永彩 “辅助筛选耐冷水稻的方法与其专用引物” 专利号200610088803.2
孙传清，刘凤霞，谭禄宾，苏震，朱作峰，付永彩 “一种辅助筛选耐冷水稻的方法及其专用引物” 专利号200610088801.3
孙传清，刘凤霞，谭禄宾，苏震，朱作峰，付永彩 “辅助筛选耐冷水稻的方法及其专用引物” 专利号200610089798.7
苏震，刘凤霞，徐文英，谭禄宾，邸超，张振海，孙传清，薛勇彪 “一种辅助筛选籼稻和粳稻的方法以及专用引物” 专利号200810056529.X
苏震，刘凤霞，徐文英，谭禄宾，邸超，张振海，孙传清，薛勇彪 “一种辅助筛选籼稻和粳稻的方法” 专利号200810056530.2
苏震，徐文英，于静娟，赵琳娜，刘凤霞，周少霞 “一种植物耐低温蛋白及其编码基因与应用” 专利号200810115174.7
苏震，徐文英，于静娟，赵琳娜，刘凤霞，周少霞 “植物耐低温蛋白及其编码基因与应用” 专利号200810115175.1
苏震，徐文英，邸超，周少霞，张盖华 “水稻细胞色素P450基因专用引物辅助鉴别植物培养基质中除草剂的残留” 专利号200810118016.7
苏震，徐文英，邸超，周少霞，张盖华 “水稻细胞色素P450基因专用引物辅助鉴别植物培养基质中除草剂的残留” 专利号200810118017.1
苏震，徐文英，邸超，周少霞，张盖华 “水稻细胞色素P450基因专用引物辅助鉴别植物培养基质中除草剂的残留” 专利号200810118021.8
苏震，徐文英，邸超，周少霞，张盖华 “水稻细胞色素P450基因专用引物辅助鉴别植物培养基质中除草剂的残留” 专利号200810118019.0
苏震，徐文英，邸超，周少霞，张盖华 “水稻细胞色素P450基因专用引物辅助鉴别植物培养基质中除草剂的残留” 专利号200810118020.3
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