Work Experience
1/2012 - current: Senior Engineer in CHINA AGRICULTURAL UNIVERSITY (Beijing)
2004 -
2010: Senior Engineer in Institute of Genetics and Developmental Biology, Chinese Academy of Sciences (Beijing)
2003 - 2004:
Research Scientist in
SYNGENTA BIOTECHNOLOGY INC. (Research Triangle Park, NC, USA)
2001-2002:Senior Research Associate in TORREY MESA RESEARCH INSTITUTE, SYNGENTA
(San Diego, CA, USA)
1996-1997:
Assistant Researcher in Beijing Plant Cell Bioengineering Laboratory
(Beijing)
1990-1993:
Research Assistant in NATIONAL LAB OF BIOTECHNOLOGY FOR TROPICAL CROPS (Hainan)
Education
MS: 2001 in Department of Plant Sciences, University of Arizona, Tucson,
Arizona, USA
Title of Thesis:
Microarray-based analysis of gene expression in very large gene families: the cytochrome p450 gene superfamily of arabidopsis thaliana. (supervisor: David Galbraith)
MS:
1996 in Plant genetics and breeding, Graduate School
of Chinese Academy of Agricultural Sciences, Beijing
Title of Thesis:
Study of Appraising the Soybean Lipoxygenase Mutants in Chinese Soybean Germplasm. (supervisor: Fu Cui-Zhen)
B.Sc: 1990 in Department of Applied Physics, Beijing Agricultural University,
Beijing China
Publication (*
Co-first author; #
Corresponding author）
Nannan Zhao,
Kang Zhang, Chunchao Wang, Hengyu Yan, Yue Liu,
Wenying Xu#
and Zhen Su#.
(2020). Systematic analysis of differential H3K27me3
and H3K4me3 deposition in callus and seedling
reveals the epigenetic regulatory mechanisms
involved in callus formation in rice.
Frontiers in Genetics. 11:766.
Nannan Zhao,
Minghao Sheng, Jie Zhao, Xuelian Ma, Qiang Wei, Qian
Song, Kang Zhang, Wenying Xu, Chuanqing Sun,
Fengxia Liu#
and Zhen Su#.
(2020). Over-expression of HDA710 delays leaf
senescence in rice (Oryza sativa L.).
Frontiers in Bioengineering and Biotechnology. 8:471.
Jiongliang
Wang, Xuelian Ma, Jiaotong Yang, Wenying Xu,
Yanan Hui, Jiajie She, Tian Tian, Zhongqiu Li,
Zhimin Gao, Zhen Su#
and Hansheng Zhao#.
(2020). Co-expression network analysis reveals the
dynamic modules regulating the growth and
development of cirrus in the rattans (Calamus
simplicifolius and Daemonorops jenkinsiana).
Frontiers in Genetics. 11:378.
Ge Zhao, Yun
Song, Qianhua Wang, Dongxia Yao, Dongliang Li,
Wenqiang Qin, Xiaoyang Ge, Zuoren Yang, Wenying
Xu, Zhen Su, Xueyan Zhang, Fuguang Li, Jiahe Wu.
(2020). Gossypium hirsutum salt tolerance is
enhanced by overexpression of G. arboreum
JAZ1. Frontiers in Bioengineering and
Biotechnology. 8:157.
Lingling Da,
Yue Liu, Jiaotong Yang, Tian Tian, Jiajie She,
Xuelian Ma, Wenying Xu#,
Zhen Su#.
(2019). AppleMDO: A multi-dimensional omics database
for apple co-expression networks and chromatin
states. Frontiers in Plant Science. 10:1333.
Hengyu Yan,
Yue Liu, Kang Zhang, James Song, Wenying Xu#,
Zhen Su#.
(2019). Chromatin state-based analysis of epigenetic
H3K4me3 marks of Arabidopsis in response to dark
stress. Frontiers in Genetics. 10:306.
Hengyu Yan,
Minghao Sheng, Chunchao Wang, Yue Liu, Jiaotong
Yang, Fengxia Liu, Wenying Xu#,
Zhen Su#.
(2019). AtSPX1-mediated transcriptional regulation
during leaf senescence in Arabidopsis thaliana.
Plant Science.
doi:10.1016/j.plantsci.2019.03.005.
Jiajie She,
Hengyu Yan, Jiaotong Yang, Wenying Xu*, Zhen
Su*. (2019). croFGD: Catharanthus roseus
Functional Genomics Database. Frontiers in
Genetics. 10:238.
Jiaotong
Yang, Yue Liu, Hengyu Yan, Tian Tian, Qi You, Liwei
Zhang, Wenying Xu#,
Zhen Su#.
(2018). PlantEAR: functional analysis platform for
plant EAR motif-containing proteins. Frontiers
in Genetics. 9:590.
Xuelian Ma,
Hansheng Zhao, Wenying Xu, Qi You, Hengyu Yan,
Zhimin Gao#,
Zhen Su#.
(2018). Co-expression Gene Network Analysis and
Functional Module Identification in Bamboo Growth
and Development. Frontiers in Genetics.
9:574.
Tian Tian,
Qi You, Hengyu Yan, Wenying Xu#,
Zhen Su#.
(2018). MCENet: A database for maize conditional
co-expression network and network characterization
collaborated with multi-dimensional omics levels.
Journal of Genetics and Genomics. 45:
351-360.
Zhaobin
Dong, Juan Yu, Hui Li, Wei Huang, Ling Xu, Yue Zhao,
Tao Zhang, Wenying Xu, Jiming Jiang, Zhen Su#,
Weiwei Jin#.
(2018). Transcriptional and epigenetic adaptation of
maize chromosomes in Oat-Maize addition lines.
Nucleic Acids Research. 46: 5012–5028.
Yue Liu, Tian Tian, Kang Zhang, Qi You, Hengyu Yan, Nannan Zhao, Xin Yi,
Wenying Xu#, Zhen Su#. (2017). PCSD: A plant chromatin state database.
Nucleic Acids Research. doi:10.1093/nar/gkx919.
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.
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.
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.
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.
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.
doi:10.1007/s10142-016-0541-9.
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. 45:
D1090–D1099.
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
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. doi:10.1111/tpj.13381.
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.
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.
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.
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.
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.
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.
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.
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.
Xin Yi,
Zhenhai Zhang, Yi Ling, Wenying Xu#,
Zhen Su#.
(2015) PNRD: A plant non-coding RNA database.
Nucleic Acids Research. 43: D982-D989.
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.
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.
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.
Yuanlin Duan, Zhuo Xing,
Zhijuan Diao, Wenying Xu, Shengping Li,
Xiaoqiu Du, Guangheng Wu, huanlei Wang, Tao Lan,
Zheng Meng, Huaqing Liu, Feng Wang, Weiren Wu,
Yongbiao Xue (2012) Characterization of Osmads6-5, a
null allele, reveals that OsMADS6 is a critical
regulator for early flower development in rice (Oryza
sativa L.) Plant Mol Biol
80:429–442
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.
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.
Kejian Wang, Ding Tang,Lilan
Hong, Wenying Xu, Jian Huang, Ming Li,
Minghong Gu, Yongbiao Xue, Zhukuan Cheng. (2010) DEP
and AFO Regulate Reproductive Habit in Rice.
PLOS GENETICS.
DOI:10.1371/journal.pgen.1000818.
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.
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.
Li, H., Xue, D., Gao, Z., Yan,
M., Xu, W., Xing, Z., Huang, D., Qian, Q.,
and Xue, Y. (2009). A putative lipase gene EXTRA
GLUME1 regulates both empty-glume fate and spikelet
development in rice. Plant J 57,
593-605
Zhang, Y., Xu, W., Li,
Z., Deng, X.W., Wu, W., and Xue, Y. (2008). F-box
protein DOR functions as a novel inhibitory factor
for abscisic acid-induced stomatal closure under
drought stress in Arabidopsis. Plant
physiology 148, 2121-2133
Yang, W., Kong, Z.,
Omo-Ikerodah, E., Xu, W., Li, Q., Xue, Y.
(2008) A calcineurin B-like interacting protein
kinase OsCIPK23 functions in pollination and drought
stress responses in rice (Oryza sativa L.).
JGG 35:531-543
Yang, W., Lai, Y., Li, M.,
Xu, W., Xue, Y. (2008) A novel C2-domain
phospholipid binding protein, OsPBP1, is required
for pollen fertility in rice. Mol Plant
1:770-785
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.
Liu, B., Chen, Z., Song, X.,
Liu, C., Zhao, X., Fang, J., Xu, W., Zhang,
H., Wang,X., Chu, C., Deng, X. W., Xue, Y., Cao, X.
(2007) Oryza sativa Dicer-like 4 reveals a key role
for siRNA silencing in plant development.
Plant Cell 19:2705-2718
Li, M., Xu, W., Yang,
W., Kong, Z., Xue, Y. (2007) Genome-wide gene
expression profiling reveals conserved and novel
molecular functions of the stigam in rice (Oryza
sativa L.). Plant Physiol.
144:1797-1812
Kong, Z., Xu, W., Li,
Q., Xue, Y. (2007) Identification, expression and
functional analysis of a receptor-like cytoplasmic
kinase, OsRLCK1, in rice(Oryza sativa L.). J.
Integrative Plant Biol. 49:898-907
Dai, X., Xu, Y., Ma, Q., Xu,
W., Wang, T., Xue, Y., and Chong, K. (2007).
Overexpression of an R1R2R3 MYB gene, OsMYB3R-2,
increases tolerance to freezing, drought, and salt
stress in transgenic Arabidopsis. Plant
physiology 143, 1739-1751
Kong, Z., Li, M., Yang, W.,
Xu, W., and Xue, Y. (2006). A novel
nuclear-localized CCCH-type zinc finger protein,
OsDOS, is involved in delaying leaf senescence in
rice. Plant physiology 141, 1376-1388
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. Z.Xu et al. (eds.),
Biotechnology and Sustainable Agriculture and Beyond,
471-474,2007 Springer.
Chen, Y.A., Chou, C.C., Lu,
X., Slate, E.H., Peck, K., Xu, W., Voit, E.O.,
and Almeida, J.S. (2006). A multivariate prediction
model for microarray cross-hybridization. BMC
bioinformatics 7, 101
Lan, L., Li, M., Lai, Y.,
Xu, W., Kong, Z., Ying, K., Han, B., and Xue, Y.
(2005). Microarray analysis reveals similarities and
variations in genetic programs controlling
pollination/fertilization and stress responses in
rice (Oryza sativa L.). Plant molecular
biology 59, 151-164
András Guttman, Julia
Khandurina, Paul Budworth, Wenying Xu,
Yu-Ming Hou and Xun Wang. (2004) Analysis of
Combinatorial natural Products by HPLC and CE.
LCGC Europe, Feb 1, 2004; LCGC
NORTH AMERICA V22 ( 1); PharmaGenomics,
June 1, 2004
Xu, W., Bak, S.,
Decker, A., Paquette, S.M., Feyereisen, R., and
Galbraith, D.W. (2001). Microarray-based analysis of
gene expression in very large gene families: the
cytochrome P450 gene superfamily of Arabidopsis
thaliana. Gene 272, 61-74
Galbraith, D.W., Macas, J.,
Pierson, E.A., Xu, W., and Nouzová, M.
(2001). Printing DNA microarrays using the Biomek®
Laboratory Automation Workstation. In: DNA Arrays:
Methods and Protocols (J.B. Rampal, ed.).
Methods in Molecular Biology 170:131-140
Xiong, L., Gong, Z., Rock,
C.D., Subramanian, S., Guo, Y., Xu, W.,
Galbraith, D., and Zhu, J.K. (2001). Modulation of
abscisic acid signal transduction and biosynthesis
by an Sm-like protein in Arabidopsis.
Developmental Cell 1, 771-781
FU Cuizhen, CHANG Ruzhen, Xu
Wenying. (2000) Identification of lipoxygenase
lacking mutants of seeds in Chinese soybean
germplasm. Journal of Plant Genetic Resources.
vol. 1 No 3
David Galbraith, Elizabeth
Pierson, Michael Deyholos, Wenying Xu, George
Watts, Rene Feyereisen, Hans Bohnert, Ken Feldmann,
Virginia Walbot, Jiri Macas. (1999) Implementing
microarrays for the study of plant genomics. Nature
Genetics 45 (1999) doi: 10.1038/14307
Fu Cuizhen, Xu Wenying and Su Zhen. (1997)
Study of Identification on Soybean Lipoxygenase
Mutants in Chinese Soybean Germplasm Resources
SCIENTIA AGRICULTURA SINICA 97:1.
Zhang Xiaodong, Li Dongmei, Xu Wenying,
et al. (1997) Development of Transgenic Wheat by
Biolistic Bombardment Transfering Basta Resistance
Gene and Novel HMW Glutenin Subunit Genes ACTA
AGRICULTURE BOREAL-SINICA 97:1.
Su Zhen, Xu Wenying, Zhang Zhonglun, et
al. (1997) Study on Ultraweak Bioluminescence of
Soybean Seeds Lacking one or more Lipoxygenase
Isozymes SOYBEAN SCIENCE 97:3.
Xu Wenying, Fu Cuizhen and Su Zhen.
(1996) The Newest Development of Soybean
Lipoxygenase Research PLANT PHYSIOLOGY
COMMUNICATIONS 96:4.
Fu Cuizhen and Xu Wenying. (1996)
Research on β-Carotene Bleaching Tests for Detecting
Activity of Chinese Soybean Lipoxygenase
JOURNAL OF THE CHINESE CEREALS AND OILS ASSOCIATION
96:2.
Fu Cuizhen and Xu Wenying. (1996) Study
of Appraising the Chinese Soybean Lipoxygenase
Heterogeneity ACTA AGRICULTURE BOREAL-SINICA
96:1.
Fu Cuizhen and Xu Wenying. (1996) A new
technique of identification for lipoxidase in
soybean CROPS 96:3.
Xu Wenying, Su Zhen, Fu Cuizhen, et al.
(1995) Study of Appraising Different Lipoxygenase
Mutant Type by Chemiluminescence (CL) of Soybean
Seedlings Cotyledons and Leaves. SOYBEAN
SCIENCE 95:3.
Fu Cuizhen and Xu Wenying. (1995)
Continued Utilization and Comprehensive Exploitation
of Chinese High-quality Soybean Resources.
CHINESE AGRICULTURAL SCIENCE BULLETIN 95:5
(this article also took part in World Soybean
Research Conference II in Thailand).