Zhongqiu Li, Yiheng Hu, Xuelian Ma, Lingling Da, Jiajie She, Yue Liu, Xin Yi, Yaxin Cao, Wenying Xu, Yuannian Jiao*, Zhen Su*. (2022).
WheatCENet: A database for comparative co-expression networks analysis of allohexaploid wheat and its progenitors.
Genomics, Proteomics & Bioinformatics. doi: 10.1016/j.gpb.2022.04.007.
Minghao
Sheng, Lingling Da, Qian Song, Yue Liu, Xinyi Zhang,
Fengxia Liu, Wenying Xu, Zhen Su*. (2022).
Systems biology-based analysis indicates that
PHO1;H10 positively modulates high light-induced
anthocyanin biosynthesis in Arabidopsis leaves.
Genomics. doi:
10.1016/j.ygeno.2022.110363.
Jiaotong
Yang, Hengyu Yan, Yue Liu, LingLing Da, Wenying Xu*,
Qiaoqiao Xiao*, Zhen Su*. (2022). GURFAP: a
platform for gene function analysis in Glycyrrhiza
uralensis. Frontiers in Genetics.
doi: 10.3389/fgene.2022.823966.
Minghao
Sheng, Xuelian Ma, Jiyao Wang, Tianxi Xue, Zhongqiu
Li, Yaxin Cao, Xinyue Yu, Xinyi Zhang, Yonghong
Wang, Wenying Xu, Zhen Su*. (2022). KNOX II
Transcription Factor HOS59 Functions in Regulating
Rice Grain Size. Plant Journal.
doi:10.1111/tpj.15709.
Huawei Liu,
Li Jiang, Zhifeng Wen, Yingjun Yang, Stacy D.
Singer, Dennis Bennett, Wenying Xu, Zhen Su,
Zhifang Yu, Jonathan Cohn, Hyunsook Chae, Qiudeng
Que, Yue Liu, Chang Liu, Zongrang Liu. (2021). Rice
RS2-9, which is bound by transcription factor OSH1,
blocks enhancer-promoter interactions in plants.
Plant Journal. 109: 541–554.
Xuelian Ma,
Hengyu Yan, Jiaotong Yang, Yue Liu, Zhongqiu Li,
Minghao Sheng, Yaxin Cao, Xinyue Yu, Xin Yi, Wenying
Xu, Zhen Su*. (2021). PlantGSAD: a
comprehensive gene set annotation database for plant
species. Nucleic Acids Research. 50:
D1456–D1467.
Qiaoqiao
Xiao, Zhongqiu Li, Mengmeng Qu, Wenying Xu, Zhen
Su*, Jiaotong Yang*. (2021). LjaFGD: Lonicera
japonica functional genomics database. Journal
of Integrative Plant Biology. doi:
10.1111/jipb.13112.
Xuelian Ma,
Hansheng Zhao, Hengyu Yan, Minghao Sheng, Yaxin Cao,
Kebin Yang, Hao Xu, Wenying Xu*, Zhimin Gao*, Zhen
Su*. (2021). Refinement of bamboo genome
annotations through integrative analyses of
transcriptomic and epigenomic data.
Computational and Structural Biotechnology Journal. PII:
S2001-0370(21)00180-X. doi:
10.1016/j.csbj.2021.04.068.
Peng Yu,
Xiaoming He, Marcel Baer, Stien Beirinckx, Tian Tian,
Yudelsy A. T. Moya, Xuechen Zhang, Marion Deichmann,
Felix P. Frey, Verena Bresgen, Chunjian Li, Bahar S.
Razavi, Gabriel Schaaf, Nicolaus von Wirén, Zhen
Su, Marcel Bucher, Kenichi Tsuda, Sofie
Goormachtig, Xinping Chen and Frank Hochholdinger.
(2021). Plant flavones enrich rhizosphere
Oxalobacteraceae to improve maize performance under
nitrogen deprivation. Nature Plants.
7:481–499.
Jiaotong
Yang, Qiaoqiao Xiao, Jiao Xu, Lingling Da, Lanping
Guo, Luqi Huang, Yue Liu, Wenying Xu, Zhen Su,
Shiping Yang, Qi Pan, Weike Jiang and Tao Zhou.
(2020). GelFAP: Gene functional analysis platform
for Gastrodia elata. Frontiers in Plant
Science. 11:563237.
Minghao
Sheng, Jiajie She, Wenying Xu, Yan Hong, Zhen Su*
and Xiaodong Zhang*. (2020). HpeNet: Co-expression
Network Database for De Novo Transcriptome Assembly
of Paeonia lactiflora Pall. Frontiers in
Genetics. 11:570138.
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.
Hansheng
Zhao, Shancen Zhao, International Network for Bamboo
and Rattan, Benhua Fei, Huan Liu, Huanming Yang,
Honghai Dai, DanWang, Wei Jin, Feng Tang, Qiang Gao,
Hang Xun, Yuwei Wang, Lianghua Qi, Xianghua Yue,
Shuyan Lin, Lianfeng Gu, Lubin Li, Tiansheng Zhu,
Qiang Wei, Zhen Su, Tarmeze Bin Wanoup
Ariffin Wan, Daniel A. Ofori, George Mbeva Muthike,
Yigardu Mulatu Mengesha, Roberto Magno de Castro e
Silva, Antonio Ludovico Beraldo, Zhimin Gao, Xin
Liu, Zehui Jiang. (2017). Announcing the Genome
Atlas of Bamboo and Rattan (GABR) project: promoting
research in evolution and in economically and
ecologically beneficial plants. GigaScience.
6: 1–7.
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. 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 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.
(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
苏震,
徐文英, 张仲纶, 马玉琴, 傅翠真, 郑雁珍, 刘成祥. (1997)
大豆种子脂肪氧化酶同工酶缺失体的超弱发光研究 《大豆科学》
1997(3)
赵文恩, 韩雅珊, Saishi
Hirota, 苏震, 张仲纶, 郑雁珍. (1997) 类胡萝卜素对H2O2-NaOCl体系生成的1O2的猝灭作用
《生物物理学报》 1997(1) : 137-142
傅翠真, 徐文英, 苏震.
(1997) 中国大豆脂肪氧化酶缺失种质多样性鉴定研究《中国农业科学》1997(1)
章汴生, 牛玉中, 阎日成, 马玉琴,
张仲伦, 苏震. (1997) 人血清超弱发光水平与肿瘤关系的研究 《肿瘤研究与临床》
1997 (1)
徐文英, 傅翠真, 苏震.
(1996) 大豆脂肪氧化酶的研究动态 《植物生理学通讯》 1996
(4) : 308-313
Wang Yingyan, Wang
Jinguang, Ma Yuqin, Su Zhen, Zhang Zhonglun,
Zheng Yanzhen, Liu Chengxiang. (1996) Biophoton
emission, free radical and toxicity of benzene to
aquatic biosystems Journal of Environmental
Sciences. Vol.8 No.2: 218-227
徐文英, 付翠真, 丁安林, 苏震,
马玉琴, 张仲纶. (1995) 大豆脂肪氧化酶同工酶缺失体的苗期叶片超弱发光研究 《大豆科学》
1995 (3)
Ma Yuqin, Zhang
Zhonglun, Su Zhen, Ma Bin, Zheng Yanzhen, Liu
Chengxiang, Wang Yingyan, Wa Jiguang. (1995)
SO2-induced change of spectrum in Low-Level
Chemiluminescence from Populus tomentosa leaf.
Bull. Environ. Contam. Toxicol. Vol.
55: 136-141
王英彦, 马玉琴, 苏震,
张仲纶, 郑雁珍, 刘成祥. (1995)
苯、过渡金属离子和鱼肝微粒体相互作用过程中的生物光子发射 《科学通报》
1995 (20)
王英彦, 王继光;马玉琴, 苏震,
赵克俭, 张仲纶, 郑雁珍, 刘成祥. (1995)
60Coγ射线辐照诱发的苯水体系发光特性的实验研究 《化学通报》
1995 (1) 31-33
苏 震, 马玉琴,
张仲纶, 赵克俭, 郑雁珍, 马斌, 刘成祥. (1994)
血清的超弱发光对骨肿瘤术前术后监测的临床意义 《中国肿瘤临床》 1994
(12) 903-905
苏 震, 马玉琴,
张仲纶, 赵克俭, 宗小林, 郑雁珍, 刘成祥. (1994)
毛白杨叶片SO2急性损伤诱发的呼吸障碍与其低水平化学发光的相关性研究 《科学通报》
1994(20) 1893-1895
张仲纶, 郑雁珍, 苏震,
马玉琴, 赵克俭, 刘成祥, 马斌;卢绍婉, 孙象贤, 王淑贤, 叶元贞, 尹殿军;糜福顺, 苏学清.
(1994) 单片微机化微弱发光测量仪及其在肿瘤研究中的初步应用 《生物医学工程学杂志》
1994 (1) 24-30
马玉琴, 张仲纶, 苏震,
郑雁珍, 马斌, 刘成祥, 赵克俭;王英彦, 王继光. (1994) SO2诱导的毛白杨叶片LCL发射光谱变化
《科学通报》 1994 (6)
马玉琴, 赵克俭, 张仲纶, 苏震,
马斌, 郑雁珍, 杨光洁, 米志勇 (1994)
羟自由基(*OH)、超氧阴离子(O2)与线粒体低水平化学发光相关性的研究 《感光化学与光化学》
1994 (4) 312-317
常崴克, 唐锦华, 罗醒萱;张仲纶,
苏震, 刘成祥, 郑雁珍 (1994) 快中子治癌束剂量特性研究 《辐射防护》
1994 (4) 256-261
张仲纶, 苏震, 郑雁珍,
刘晓梅. (1993) LiF剂量计高剂量测量方法研究 《辐射研究与辐射工艺学报》
1993(3) 135-138
张仲纶, 郑雁珍, 苏震,
赵克俭, 刘成祥. (1993) 中国实验卫星中空间辐射剂量的热释光分析方法 《空间科学学报》
1993 (2)
Wang Yingyan, Ma
Yuqin, Su Zhen, Wang Jinguang, Zhao Keijian,
Zhang Zhonglun, Ma Bin, Zheng Yanzhen, Liu
Chengxiang. (1993) Changes of Low Level
Chemiluminescence Spectra from Plant Leaf Smoked by
Air Pollutants Fresenius Envir Bull
2: 588-595
王红霞, 袁润英, 相东, 王林,
吴捷, 徐万鹏;马玉琴, 赵克俭, 张仲纶, 苏震, 郑雁珍, 马斌. (1993)
骨肿瘤病人血清和尿液超微弱发光强度的研究 《中华肿瘤杂志》 1993
(2) 108-111
马斌, 马玉琴, 苏震,
赵克俭, 张仲纶, 郑雁珍, 刘成祥, 王英彦. (1992)
雨水对毛白杨树叶片低水平化学发光的影响 《科学通报》 1992 (24)
Ma Yuqin, Zhao
Kejian, Zhang Zhonglun, Su Zhen, Ma Bin,
Zheng Yanzhen, Liu Chengxiang. (1992) Influence of
Rain and Sulphur Dioxide on Low-Level
Chemiluminescence from leaf of Populus tomentosa
Bull. Environ. Contam. Toxicol.
Vol. 49 906-913
马玉琴, 赵克俭, 王英彦, 张仲纶,
郑雁珍, 苏震, 马斌, 刘成祥, 韩卫. (1992)
用斑马鱼的自发化学发光研究水域酚污染 《环境保护》 1992 (11)
33-34
Ma Yuqin, Song
Xueling, Zhao Kejing, Zhang Zhoglun, Ma Bin, Zhen
YanZhen, Liu Chengxiang, Su Zhen; Mi Fushun,
Su Xueqing, Shen Yu, Wang Jianzhang. (1992)
Investigation of Tumorigenic Effect on Ultraweak
Luminescence from Nude Mouse for Animal Model
Chinese Journal of Cancer Research Vol.
4 No. 4: 46-50
临床组 申文江等; 物理组 唐锦华,
常崴克, 张仲纶, 罗醒萱, 苏震. (1992) 快中子治疗临床实验研究 《中华放射肿瘤学杂志》
1992 (4)
张仲纶, 王英彦, 郑雁珍, 苏震,
马玉琴, 赵克俭, 刘成祥, 马斌. (1991) 用于环境生物监测的微弱发光测量仪 《环境保护》
1991 (10) 28-29
专利:
1.
张仲纶,付世密,郑雁珍,苏震,马玉琴,刘成祥,江丕栋
“微弱发光测量仪”,专利号ZL96241369.0
2.
Guangzhou Zou, Xun Wang, and Zhen Su. System
and Method for Clustering Data (2003) in USA,
PCT/US2003/001806
3.
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
4.
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
5.
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
6.
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
7.
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
8. 孙传清,刘凤霞,苏震,谭禄宾,刘家勇,付永彩,朱作峰
“一种与植物耐冷性相关的蛋白及其编码基因与应用” 专利号200810181172.8
9.
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
10.
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
11.
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
12.
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
13.
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
14.
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
15.
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
16.
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
17.
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
18. 孙传清,刘凤霞,谭禄宾,付永彩,朱作峰,谢道昕,苏震
“水稻冷诱导启动子p-LTT7 及其应用” 专利号 201010122399.2
19. 孙传清,刘加勇,刘凤霞,谭禄宾,付永彩,朱作峰,苏震
“植物耐冷相关蛋白LTT9及其编码基因和应用” 专利号 201210072826.X
20. 孙传清,张侠,刘凤霞,王娜,苏震,谭禄宾,朱作峰,付永彩,谢道昕
“耐旱相关蛋白DT1及其编码基因和应用” 专利号 201110296327.4
21. 苏震,徐文英,魏强,王玲,刘凤霞,于静娟,赵琳娜,张群莲,王春超
“水稻OsSPX1蛋白及其编码基因在调控植物种子结实率中的应用” 专利号 201210101772.5
22. 苏震,徐文英,魏强,王玲,刘凤霞,于静娟,赵琳娜,张力圩
“OsSPX1蛋白及其编码基因在调节植物花粉育性中的应用” 专利号201210253451.7
23. 苏震,徐文英,魏强,王玲,刘凤霞,于静娟,赵琳娜,谭远军
“水稻OsSPX1蛋白及其编码基因在调控植物抗氧化性中的应用” 专利号 201210166813.9
24. 李付广,王倩华,张雪妍,刘传亮,张朝军,武芝霞,王晔,孔德培,秦文强,苏震,徐文英,姚冬霞,张群莲,郑雪 “与植物抗逆性相关蛋白Gh01399 及其编码基因与应用” 专利号201210261882.8
25. 苏震,徐文英,杨教童,
张群莲,邸超,刘凤霞, 焦远年, 张康 “一种植物开花时间性状相关蛋白AtJAZ5及其编码基因和应用”
专利号 201910079723.8
26. 苏震,徐文英,闫恒宇,刘凤霞,王春超
“一种植物衰老相关蛋白AtSPX1及其编码基因和应用” 专利号 201811569253.5
27. 苏震,徐文英,赵楠楠,魏强,张群莲
“水稻组蛋白去乙酰化酶基因HDA710在延迟叶片衰老中的应用” 专利号 201911298782.0
28. 葛晓阳,李付广,苏震,徐文英,达玲玲,詹晶晶,姚冬霞,张力圩
“miR164a在应答亚洲棉耐盐中的应用” 专利号 202010952096.7
29. 葛晓阳,李付广,苏震,徐文英,达玲玲,詹晶晶,姚冬霞,张力圩
“一种亚洲棉miR172c在调控目的植物应答盐胁迫中的应用” 专利号 202010149664.X
30. 苏震,徐文英,达玲玲,
宋倩, 刘凤霞,张群莲 “拟南芥PHO1;H10蛋白及其编码基因在调控植物叶片花青素合成中的应用”
专利号 201911323001.9
软件著作权:
1.
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;证书号:BJ28859
2.
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;证书号:BJ28859
3. 张盖华,苏震
基于BMCD细胞色素P450同源结构建模流程软件 计算机软件著作权 登记号 2013SRBJ0529;证书号:BJ39206
4. 苏震,易欣 PlantGSEA植物GeneSet富集分析软件 计算机软件著作权 登记号 2013SRBJ0679;证书号:BJ39356
5. 苏震,徐文英,张振海,尤琪,于娟
顺式作用元件motif显著性分析软件 计算机软件著作权 登记号
:2015SRBJ0087;证书号:BJ40645
6. 苏震,尤琪,徐文英 同源基因共表达网络比较分析软件V1.0 计算机软件著作权 登记号
:2017SRBJ0778;证书号:BJ43322
7. 苏震,尤琪,徐文英,刘悦,田甜,马雪莲 共表达网络表达谱动态分析软件V1.0 计算机软件著作权 登记号
:2017SRBJ0683;证书号:BJ43227
8. 苏震,田甜,徐文英,刘悦,闫恒宇,尤琪 富集分析P值分布计算软件 计算机软件著作权 登记号
:2017SRBJ0838;证书号:BJ43382
9. 苏震,徐文英,易欣,尤琪,闫恒宇,佘加杰,赵楠楠 基于多维组学数据的植物新转录本预测软件V1.0 计算机软件著作权 登记号
:2017SRBJ0881;证书号:BJ43425
10. 苏震,张康,徐文英
染色质状态聚类及可视化查询分析软件V1.0 计算机软件著作权 登记号
:2017SRBJ1093;证书号:BJ43637
11. 苏震,刘悦,徐文英
染色质状态SOM聚类比较分析及可视化软件V1.0 计算机软件著作权 登记号
:2018SRBJ0863;证书号:BJ44693
12. 苏震,刘悦,徐文英
植物基因组调控元件预测软件V1.0 计算机软件著作权 登记号
:2018SRBJ1116;证书号:BJ44946
13. 苏震,田甜,徐文英
共表达网络自定义分析工具V1.0 计算机软件著作权 登记号
:2018SRBJ1117;证书号:BJ44947
14. 苏震,田甜,徐文英
基因组共线性图谱可视化分析工具V1.0 计算机软件著作权 登记号
:2018SRBJ1118;证书号:BJ44948
15. 苏震,佘加杰,徐文英
SNP数据查询和可视化软件 计算机软件著作权 登记号 :2020SRBJ0177;证书号:BJ46487
16. 苏震,马雪莲,徐文英
自定义基因集富集分析软件 计算机软件著作权 登记号 :2021SRBJ0509;证书号:BJ47637
17. 苏震,马雪莲,徐文英
基因集富集分析优化软件 计算机软件著作权 登记号 :2021SRBJ0558;证书号:BJ47686
18. 苏震,马雪莲,徐文英
基因集富集结果平行比较分析软件 计算机软件著作权 登记号
:2021SRBJ0563;证书号:BJ47691
学术奖励:
苏震,杜舟,杨仁东,周鑫,易欣,张振海
,徐文英,凌毅,尤琪 “组学大数据整合与解析的新技术和算法研究” 2018年获
教育部高等学校科学研究优秀成果奖自然科学二等奖
证书号 :2018-068