Xiu Jie Wang

Summary

Affiliation: Institute of Genetics and Developmental Biology
Country: China

Publications

  1. pmc PsRobot: a web-based plant small RNA meta-analysis toolbox
    Hua Jun Wu
    The State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
    Nucleic Acids Res 40:W22-8. 2012
  2. pmc GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis
    Qi Zheng
    State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences and Graduate University of the Chinese Academy of Sciences, Beijing 100101, China
    Nucleic Acids Res 36:W358-63. 2008
  3. pmc Identification of a small molecule 1,4-bis-[4-(3-phenoxy-propoxy)-but-2-ynyl]-piperazine as a novel inhibitor of the transcription factor p53
    Xin Liu
    Center for Molecular Systems Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
    Acta Pharmacol Sin 34:805-10. 2013
  4. pmc Combining metabolomics and transcriptomics to characterize tanshinone biosynthesis in Salvia miltiorrhiza
    Wei Gao
    National Resource Center for Chinese Materia Medica, Academy of Chinese Medical Sciences, Beijing 100700, China
    BMC Genomics 15:73. 2014
  5. pmc The response and recovery of the Arabidopsis thaliana transcriptome to phosphate starvation
    Jongchan Woo
    Laboratory of Plant and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
    BMC Plant Biol 12:62. 2012
  6. pmc Gene expression profile analysis of tobacco leaf trichomes
    Hong Cui
    Key Laboratory for Cultivation of Tobacco Industry, College of Tobacco Science, Henan, Agricultural University, Zhengzhou, 450002, PR China
    BMC Plant Biol 11:76. 2011
  7. pmc Complete sequence determination of a novel reptile iridovirus isolated from soft-shelled turtle and evolutionary analysis of Iridoviridae
    Youhua Huang
    State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat Sen University, 135 West Xingang Road, Guangzhou 510275, PR China
    BMC Genomics 10:224. 2009
  8. pmc Systematic identification and evolutionary features of rhesus monkey small nucleolar RNAs
    Yong Zhang
    National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, PR China
    BMC Genomics 11:61. 2010
  9. pmc Formation of a functional maize centromere after loss of centromeric sequences and gain of ectopic sequences
    Bing Zhang
    State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
    Plant Cell 25:1979-89. 2013
  10. pmc MicroRNA-323-3p regulates the activity of polycomb repressive complex 2 (PRC2) via targeting the mRNA of embryonic ectoderm development (Eed) gene in mouse embryonic stem cells
    Ying Zhang
    State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
    J Biol Chem 288:23659-65. 2013

Collaborators

Detail Information

Publications32

  1. pmc PsRobot: a web-based plant small RNA meta-analysis toolbox
    Hua Jun Wu
    The State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
    Nucleic Acids Res 40:W22-8. 2012
    ..The cross species conservation statuses and the multiplicity of smRNA target sites are also provided. PsRobot is freely accessible at http://omicslab.genetics.ac.cn/psRobot/...
  2. pmc GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis
    Qi Zheng
    State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences and Graduate University of the Chinese Academy of Sciences, Beijing 100101, China
    Nucleic Acids Res 36:W358-63. 2008
    ..GOEAST also provides rigorous statistical tests to enhance the reliability of analysis results. GOEAST is freely accessible at http://omicslab.genetics.ac.cn/GOEAST/..
  3. pmc Identification of a small molecule 1,4-bis-[4-(3-phenoxy-propoxy)-but-2-ynyl]-piperazine as a novel inhibitor of the transcription factor p53
    Xin Liu
    Center for Molecular Systems Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
    Acta Pharmacol Sin 34:805-10. 2013
    ..To identify novel small compound inhibitor of p53 protein...
  4. pmc Combining metabolomics and transcriptomics to characterize tanshinone biosynthesis in Salvia miltiorrhiza
    Wei Gao
    National Resource Center for Chinese Materia Medica, Academy of Chinese Medical Sciences, Beijing 100700, China
    BMC Genomics 15:73. 2014
    ..However, the often-inducible nature of such metabolic processes enables selection of those genes whose expression pattern indicates a role in production of the targeted natural product...
  5. pmc The response and recovery of the Arabidopsis thaliana transcriptome to phosphate starvation
    Jongchan Woo
    Laboratory of Plant and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
    BMC Plant Biol 12:62. 2012
    ..The work presented here describes a genome-wide resource on the molecular dynamics underpinning the response and recovery in roots and shoots of Arabidopsis thaliana to phosphate-starvation...
  6. pmc Gene expression profile analysis of tobacco leaf trichomes
    Hong Cui
    Key Laboratory for Cultivation of Tobacco Industry, College of Tobacco Science, Henan, Agricultural University, Zhengzhou, 450002, PR China
    BMC Plant Biol 11:76. 2011
    ..They contribute to plant defense response against biotic and abiotic stress, and also influence leaf aroma and smoke flavor. However, there is limited genomic information about trichomes of this non-model plant species...
  7. pmc Complete sequence determination of a novel reptile iridovirus isolated from soft-shelled turtle and evolutionary analysis of Iridoviridae
    Youhua Huang
    State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat Sen University, 135 West Xingang Road, Guangzhou 510275, PR China
    BMC Genomics 10:224. 2009
    ....
  8. pmc Systematic identification and evolutionary features of rhesus monkey small nucleolar RNAs
    Yong Zhang
    National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, PR China
    BMC Genomics 11:61. 2010
    ..However, most reports on these animals focus on the functional roles of protein-coding sequences, whereas very little is known about macaque ncRNAs...
  9. pmc Formation of a functional maize centromere after loss of centromeric sequences and gain of ectopic sequences
    Bing Zhang
    State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
    Plant Cell 25:1979-89. 2013
    ..Our results indicate that functional centromeres may be formed without the known centromere-specific sequences, yet the maintenance of a high DNA methylation level seems to be crucial for the proper function of a new centromere. ..
  10. pmc MicroRNA-323-3p regulates the activity of polycomb repressive complex 2 (PRC2) via targeting the mRNA of embryonic ectoderm development (Eed) gene in mouse embryonic stem cells
    Ying Zhang
    State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
    J Biol Chem 288:23659-65. 2013
    ..These findings identify miR-323-3p as a new regulator for PRC2 and provide a new approach for regulating PRC2 activity via microRNAs. ..
  11. pmc Widespread long noncoding RNAs as endogenous target mimics for microRNAs in plants
    Hua Jun Wu
    State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
    Plant Physiol 161:1875-84. 2013
    ..The effectiveness of eTMs for three other miRNAs was also confirmed by transient agroinfiltration assay...
  12. doi request reprint ISRNA: an integrative online toolkit for short reads from high-throughput sequencing data
    Guan Zheng Luo
    State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences and Graduate University of Chinese Academy of Sciences, Beijing 100101, China
    Bioinformatics 30:434-6. 2014
    ..A specialized genome browser is integrated to visualize the genomic distribution of short reads. ISRNA also supports management and comparison among multiple datasets...
  13. doi request reprint Genetic modification and screening in rat using haploid embryonic stem cells
    Wei Li
    State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China Key Laboratory of Translational Stem Cell Research, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
    Cell Stem Cell 14:404-14. 2014
    ..Overall, RahESCs represent a practical tool for functional genetic studies and production of transgenic lines in rat. ..
  14. doi request reprint Roles of DCL4 and DCL3b in rice phased small RNA biogenesis
    Xianwei Song
    State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
    Plant J 69:462-74. 2012
    ..Our results revealed significant roles of OsDCL4, OsDCL3b and OsDCL1 in the 21- and 24-nucleotide phased small RNA biogenesis pathway in rice...
  15. pmc Activation of the imprinted Dlk1-Dio3 region correlates with pluripotency levels of mouse stem cells
    Lei Liu
    State Key Laboratory of Reproductive Biology, Institute of Zoology, ChineseAcademy of Sciences, Beijing 100101, China
    J Biol Chem 285:19483-90. 2010
    ..These findings also provide a step forward toward understanding the operating mechanisms during reprogramming to produce iPS cells and can potentially promote the application of iPS cells in regenerative medicine and cancer therapy...
  16. doi request reprint Conserved miRNA analysis in Gossypium hirsutum through small RNA sequencing
    Meng Bin Ruan
    Key Laboratory of Molecular and Developmental Biology, National Center for Plant Gene Research Beijing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100080, China
    Genomics 94:263-8. 2009
    ..Multiple encoding loci of some miRNAs were identified by comparing the cloned miRNA and miR sequences...
  17. pmc Small RNA profiling in two Brassica napus cultivars identifies microRNAs with oil production- and development-correlated expression and new small RNA classes
    Ying Tao Zhao
    State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
    Plant Physiol 158:813-23. 2012
    ..A large number of 23-nucleotide small RNAs with specific nucleotide composition preferences were also identified, which may present new classes of functional small RNAs...
  18. pmc Genome-wide annotation and analysis of zebra finch microRNA repertoire reveal sex-biased expression
    Guan Zheng Luo
    State Kay Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
    BMC Genomics 13:727. 2012
    ....
  19. pmc Insights into salt tolerance from the genome of Thellungiella salsuginea
    Hua Jun Wu
    State Key Laboratory of Plant Genomics, National Center for Plant Gene Research Beijing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
    Proc Natl Acad Sci U S A 109:12219-24. 2012
    ..Comparative genomics and experimental analyses identified genes related to cation transport, abscisic acid signaling, and wax production prominent in T. salsuginea as possible contributors to its success in stressful environments...
  20. ncbi request reprint Endogenous small RNA clusters in plants
    Yong Xin Liu
    State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China University of Chinese Academy of Sciences, Beijing 100101, China
    Genomics Proteomics Bioinformatics 12:64-71. 2014
    ..Here, we summarize the features and functions of cluster-distributed sRNAs, aimed to not only provide a thorough picture of sRNA clusters (SRCs) in plants, but also shed light on the identification of new classes of functional sRNAs...
  21. ncbi request reprint Proteomic response to iron deficiency in tomato root
    Jie Li
    The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
    Proteomics 8:2299-311. 2008
    ..Most of the proteins affected by iron deficiency and fer mutation showed similar effect on individual proteins or pathways, but the independent function of FER to iron deficiency were statistically indicated...
  22. pmc LEAFY COTYLEDON1 is a key regulator of fatty acid biosynthesis in Arabidopsis
    Jinye Mu
    State Key Laboratory of Plant Genomics and National Plant Gene Research Center, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
    Plant Physiol 148:1042-54. 2008
    ..These results suggest that LEC1 and LEC1-like genes act as key regulators to coordinate the expression of fatty acid biosynthetic genes, thereby representing promising targets for genetic improvement of oil production plants...
  23. ncbi request reprint Comparative analysis of JmjC domain-containing proteins reveals the potential histone demethylases in Arabidopsis and rice
    Falong Lu
    State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, The Chinese Academy of Sciences, Beijing 100101, China
    J Integr Plant Biol 50:886-96. 2008
    ....
  24. pmc Direct reprogramming of Sertoli cells into multipotent neural stem cells by defined factors
    Chao Sheng
    State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
    Cell Res 22:208-18. 2012
    ..In addition, iNSCs can survive and generate synapses following transplantation into the dentate gyrus. Generation of iNSCs may have important implications for disease modeling and regenerative medicine...
  25. pmc Systematic identification of genes involved in divergent skeletal muscle growth rates of broiler and layer chickens
    Qi Zheng
    State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, PR China
    BMC Genomics 10:87. 2009
    ....
  26. doi request reprint Androgenetic haploid embryonic stem cells produce live transgenic mice
    Wei Li
    State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
    Nature 490:407-11. 2012
    ..Our findings show the developmental pluripotency of androgenentic haploids and provide a new tool to quickly produce genetic models for recessive traits. They may also shed new light on assisted reproduction...
  27. pmc Identification and functional characterization of small non-coding RNAs in Xanthomonas oryzae pathovar oryzae
    Hong Liang
    State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
    BMC Genomics 12:87. 2011
    ..Xanthomonas oryzae pathovar oryzae (Xoo) is an important plant pathogenic bacterium which causes serious bacterial blight of rice. However, little is known about the number, genomic distribution and biological functions of sRNAs in Xoo...
  28. doi request reprint Pseudogenes: pseudo or real functional elements?
    Wen Li
    State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
    J Genet Genomics 40:171-7. 2013
    ..A new nomenclature is desirable for the currently called 'pseudogenes' to better describe their functions...
  29. pmc Prediction of trans-antisense transcripts in Arabidopsis thaliana
    Huan Wang
    State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
    Genome Biol 7:R92. 2006
    ..Experimental and computational methods have demonstrated the widespread occurrence of NATs in eukaryotes. However, most previous studies only focused on cis-NATs with little attention being paid to NATs that originate in trans...
  30. pmc Identification and characterization of small RNAs in the hyperthermophilic archaeon Sulfolobus solfataricus
    Ning Xu
    State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
    PLoS ONE 7:e35306. 2012
    ..Archaea represent a unique life form next to Bacteria and Eukarya, and our results may provide a useful resource for further in-depth study on the regulation and evolution of smRNAs in this special organism...
  31. pmc Bidirectional processing of pri-miRNAs with branched terminal loops by Arabidopsis Dicer-like1
    Hongliang Zhu
    1 Department of Biochemistry and Biophysics, Texas A and M University, College Station, Texas, USA 2 Institute of Plant Genomics and Biotechnology, Texas A and M University, College Station, Texas, USA 3 College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
    Nat Struct Mol Biol 20:1106-15. 2013
    ..DCL1 also adjusts processing sites toward an internal loop through its helicase domain. These results provide new insight into the poorly understood processing mechanism of pri-miRNAs with complex secondary structures. ..
  32. pmc De novo centromere formation on a chromosome fragment in maize
    Shulan Fu
    State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
    Proc Natl Acad Sci U S A 110:6033-6. 2013
    ..Collectively, these results define the behavior and molecular features of de novo centromere formation in the Dp3a chromosome, which may shed light on the initiation of new centromere sites during evolution...