Zhen Su Lab


| Research | People | Publication | Database | Chinese Version |
  


Publications:

[2017]

  • Qi You, Xin Yi, Kang Zhang, Chunchao Wang, Xuelian Ma, Xueyan Zhang, Wenying Xu, Fuguang Li, Zhen Su. (2017). Genome-wide comparative analysis of H3K4me3 profiles between diploid and allotetraploid cotton to refine genome annotation. Scientific Reports. doi:10.1038/s41598-017-09680-6. [Link, MOAP]

  • Yue Liu, Wenli Zhang, Kang Zhang, Qi You, Hengyu Yan, Yuannian Jiao, Jiming Jiang, Wenying Xu, Zhen Su. (2017). Genome-wide mapping of DNase I hypersensitive sites reveals chromatin accessibility changes in Arabidopsis euchromatin and heterochromatin regions under extended darkness. Scientific Reports. doi:10.1038/s41598-017-04524-9. [Link]

  • Tian Tian, Yue Liu, Hengyu Yan, Qi You, Xin Yi, Zhou Du, Wenying Xu, Zhen Su. (2017). agriGO v2.0: a GO analysis toolkit for the agricultural community, 2017 update. Nucleic Acids Research. doi:10.1093/nar/gkx382. [Link]

  • Kang Zhang, Wenying Xu, Chunchao Wang, Xin Yi, Zhen Su. (2017). Differential deposition of H2A.Z in rice seedling tissue during the day-night cycle. Plant Signaling & Behavior. doi:10.1080/15592324.2017.1286438. [Link]

[2016]

  • Qi You, Hengyu Yan, Yue Liu, Xin Yi, Kang Zhang, Wenying Xu and Zhen Su. (2016). A systemic identification approach for primary transcription start site of Arabidopsis miRNAs from multidimensional omics data. Functional & Integrative Genomics. Accepted doi:10.1007/s10142-016-0541-9. [Link]

  • Qi You, Wenying Xu, Kang Zhang, Liwei Zhang, Xin Yi, Dongxia Yao, Chunchao Wang, Xueyan Zhang, Xinhua Zhao, Nicholas Provart, Fuguang Li, Zhen Su. (2016). ccNET: Database of co-expression networks with functional modules for diploid and polyploid Gossypium. Nucleic Acids Research. Accepted doi:10.1093/nar/gkw910. [Link]

  • Qi You, Liwei Zhang, Xin Yi, Kang Zhang, Dongxia Yao, Xueyan Zhang, Qianhua Wang, Xinhua Zhao, Yi Ling, Wenying Xu, Fuguang Li, Zhen Su. (2016). Co-expression network analyses identify functional modules associated with development and stress response in Gossypium arboreum. Scientific Reports. 6, 38436; doi:10.1038/srep38436. [Link]

  • Zhang, K., Xu, W., Wang, C., Yi, X., Zhang, W. and Su, Z. (2016). Differential deposition of H2A.Z in combination with histone modifications within related genes in rice callus and seedling. Plant J. Accepted doi:10.1111/tpj.13381. [Link]

  • Yuan Fang, Lei Wang, Ximeng Wang, Qi You, Xiucai Pan, Jin Xiao, Xiu-e Wang, Yufeng Wu, Zhen Su, Wenli Zhang (2016). Histone modifications facilitate the coexpression of bidirectional promoters in rice. BMC Genomics. Accepted doi: 10.1186/s12864-016-3125-0. [Link]

  • Tian Tian, Qi You, Liwei Zhang, Xin Yi, Hengyu Yan, Wenying Xu, Zhen Su (2016). SorghumFDB: Sorghum Functional Genomics Database with multidimensional network analysis. Database doi:10.1093/database/baw099. [Link]

  • Xin Ma, Yongcai Fu, Xinhui Zhao, Liyun Jiang, Zuofeng Zhu, Ping Gu, Wenying Xu, Zhen Su, Chuanqing Sun & Lubin Tan (2016). Genomic structure analysis of a set of Oryza nivara introgression lines and identification of yield associated QTLs using wholegenome resequencing. Scientific Reports   doi: 10.1038/srep27425. [Link]

  • Kang Zhang, Qian Song, Qiang Wei, Chunchao Wang, Liwei Zhang, Wenying Xu, Zhen Su (2016). Down-regulation of OsSPX1 caused semi-male sterility, resulting in reduction of grain yield in rice. Plant Biotechnology Journal   doi:10.1111/pbi.12527. [Link]

[2015]

  • Juan Yu, Yixiang Zhang, Chao Di, Qunlian Zhang, Kang Zhang, Chunchao Wang, Qi You, Hong Yan, Susie Dai, Joshua Yuan, Wenying Xu, and Zhen Su (2015). JAZ7 negatively regulates dark-induced leaf senescence in Arabidopsis. Journal of Experimental Botany doi:10.1093/jxb/erv487. [Link]

  • Zhenyan Miao; Wei Xu; Daofeng Li; Xiaona Hu; Jiaxing Liu; Rongxue Zhang; Zongyong Tong; Jiangli Dong; Zhen Su; Liwei Zhang; Min Sun; Wenjie Li; Zhenglin Du; Songnian Hu; Tao Wang (2015). De novo transcriptome analysis of Medicago falcata reveals novel insights about the mechanisms underlying abiotic stress-responsive pathway. BMC Genomics 16:818. doi:10.1186/s12864-015-2019-x. [Link, FalcataBase]

  • Xu W, Di C, Zhou S, Liu J, Li L, Liu F, Yang X, Ling Y and Su Z (2015). Rice Transcriptome Analysis to Identify Possible Herbicide Quinclorac Detoxification Genes. Front. Genet. 6:306. doi: 10.3389/fgene.2015.00306. [Link]

  • Jinyan Guo, Gongyao Shi, Liwei Zhang, Wenying Xu, Yumei Wang, Zhen Su, Jinping Hua. (2015) Transcriptome analysis reveals that distinct metabolic pathways operate in salt-tolerant and salt-sensitive upland cotton varieties subjected to salinity stress. Plant Science. doi:10.1016/j.plantsci.2015.05.013. [Link]

  • Liwei Zhang, Jinyan Guo, Qi You, Xin Yi, Yi Ling, WenyingXu, Jinping Hua, Zhen Su. (2015) GraP: Platform for Functional Genomics Analysis of Gossypium raimondii. Database. doi:10.1093/database/bav047. [Link]

  • Qi You, Liwei Zhang, Xin Yi, Zhenghai Zhang, Wengying Xu, and Zhen Su. (2015) SIFGD: Setaria italica Functional Genomics Database. Molecular Plant. doi:10.1016/j.molp.2015.02.001. [Link]

  • Xin Yi, Zhenhai Zhang, Yi Ling, Wenying Xu, Zhen Su. (2015) PNRD: A plant non-coding RNA database. Nucleic Acids Research. 43: D982-D989. [Link]

[2014]

  • Yonglu Meng, Nan Ma, Qian Zhang, Qi You, Na Li, Muhammad Ali Khan, Xiaojing Liu, Lin Wu, Zhen Su and Junping Gao. (2014) Precise Spatio-Temporal modulation of ACC Synthase by MPK6 Cascade Mediates the Response of Rose Flower to Rehydration. The Plant Journal. doi:10.1111/tpj.12594. [Link]

  • Juan Yu, Zhenhai Zhang, Jiangang Wei, Yi Ling, Wenying Xu and 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. [Link]

[2013]

  • 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. [Link]

  • 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. [Link]

  • 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. [Link]

  • 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. [Link, UCSC Browser]

  • 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. [Link]

  • 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. [Link]

[2012]

  • 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. [Link]

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

  • 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. [Link]

  • 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. [Link]

[2011]

  • 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. [Link]

  • 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. [Link]

  • 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 6(3): e176133. [Link]

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

[2010]

  • 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. [Link]

  • 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. [Link]

  • 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. [Link]

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

  • 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. [Link]

  • 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. [Link]

  • 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. [Link]

  • 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. [Link]

[2009]

  • 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. [Link]

  • 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. [Link]

  • 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. [Link]

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

  • Guo HJ, Jiao YN, Di C, Yao DX, Zhang GH, Zheng X, Liu L, Zhang QL, Guo AG, Su Z (2009). Discovery of Arabidopsis GRAS family genes in response to osmotic and drought stresses. Chin Bull Bot  44, 290-299. [Link] (In Chinese)

  • 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. [Link]

  • 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. [Link]

  • 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. [Link]

[2008]

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

  • 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. [Link]

  • 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. [Link]

  • 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. [Link]

[2007]

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

  • 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. [Link]

  • 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

[2006]

  • 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. [Link]

  • 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. [Link]

  • Biwei Ding, Yingjie Tian, Naiyang Deng, Zhen Su, Chun Cai. (2006) Gene Expression Analysis with Support Vector Machines in Arabidopsis. Operations Research Transactions  10(2):51-58. [Link]  (In Chinese)

  • Yunyan Liu, Zhen Su, Jiangli Dong, Xiaoye Shen, Daofeng Li, Tao Wang (2006) Construction and Application of Medicago truncatula Bio-Data Analysis Platform  Acta Agristia Sinica 14(3): 231-235. [Link]  (In Chinese)

[2005]

  • LIU Sheng-yi, MAO Han, SU Zhen, DONG Cai-hua, XUWen-ying, JI Rui-qin, GUO Xue-lan. (2005)  Molecular pathways of defense reactions to Sclerotinia sclerotiorum and Leptosphaeria maculans in oilseed rape.  Jour. of Northwest Sci-Tech Univ. of Agri. and For. (Nat. Sci. Ed.)   Vol. 33 Supp l. [Link] (In Chinese)

 

 

Mail: #2 Yuanmingyuan Xilu, Beijing 100193, China | Tel: +86(10)62731214 | Email: genome01ATcau.edu.cn

Copyright | Zhen Su Lab | 2012 | All right reserved | Last updated: March, 2012