Selected Publications (*
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.
Yuan Fang,
Lifen Chen, Kande Lin, Yilong Feng, Pengyue Zhang,
Xiucai Pan, Jennifer Sanders, Yufeng Wu, Xiu-e Wang,
Zhen Su, Caiyan Chen, Hairong Wei, Wenli
Zhang. (2019). Characterization of functional
relationships of R-loops with gene transcription and
epigenetic modifications in rice. Genome
Research. doi: 10.1101/gr.246009.118.
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.
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. 17:768
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.
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.
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.
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.
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 2012, 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, 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 6(3): e17613
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.
doi:10.1371/journal.pone.0008632
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.
10.1104/pp.109.140731
Zhou Du,
Xin Zhou, Li Li, Zhen Su*. (2009) plantsUPS: a database of
plants' Ubiquitin Proteasome System. BMC
Genomics. 10:227
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 responded to osmotic
and drought stress. Chin Bull Bot. 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. 10.1105/tpc.109.065987
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.
10.1104/pp.108.126375
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.
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.
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