Xiu Jie Wang

Summary

Affiliation: The Rockefeller University
Country: USA

Publications

  1. pmc Prediction and identification of Arabidopsis thaliana microRNAs and their mRNA targets
    Xiu Jie Wang
    Laboratory of Computational Genomics, The Rockefeller University, New York, NY 10021, USA
    Genome Biol 5:R65. 2004
  2. pmc Genome-wide prediction and identification of cis-natural antisense transcripts in Arabidopsis thaliana
    Xiu Jie Wang
    Laboratory of Computational Genomics, The Rockefeller University, New York, NY 10021, USA
    Genome Biol 6:R30. 2005
  3. 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
  4. pmc Deep sequencing of small RNAs specifically associated with Arabidopsis AGO1 and AGO4 uncovers new AGO functions
    Huan Wang
    Laboratory of Plant Molecular Biology, The Rockefeller University, New York, NY 10065, USA
    Plant J 67:292-304. 2011
  5. pmc Genomic resources for songbird research and their use in characterizing gene expression during brain development
    Xiaoching Li
    The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
    Proc Natl Acad Sci U S A 104:6834-9. 2007
  6. 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
  7. pmc Prediction and identification of herpes simplex virus 1-encoded microRNAs
    Can Cui
    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA
    J Virol 80:5499-508. 2006
  8. doi 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
  9. pmc A complex system of small RNAs in the unicellular green alga Chlamydomonas reinhardtii
    Tao Zhao
    National Institute of Biological Sciences, Zhongguancun Life Science Park, Beijing 102206, China
    Genes Dev 21:1190-203. 2007
  10. ncbi request reprint Distinct catalytic and non-catalytic roles of ARGONAUTE4 in RNA-directed DNA methylation
    Yijun Qi
    Cold Spring Harbor Laboratory, Watson School of Biological Sciences and Howard Hughes Medical Institute, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
    Nature 443:1008-12. 2006

Collaborators

Detail Information

Publications12

  1. pmc Prediction and identification of Arabidopsis thaliana microRNAs and their mRNA targets
    Xiu Jie Wang
    Laboratory of Computational Genomics, The Rockefeller University, New York, NY 10021, USA
    Genome Biol 5:R65. 2004
    ..Extensive sequence complementarity between miRNAs and their target mRNAs is used to predict miRNA-regulated Arabidopsis transcripts...
  2. pmc Genome-wide prediction and identification of cis-natural antisense transcripts in Arabidopsis thaliana
    Xiu Jie Wang
    Laboratory of Computational Genomics, The Rockefeller University, New York, NY 10021, USA
    Genome Biol 6:R30. 2005
    ..Genome-wide identification of cis-NATs in human, mouse and rice has revealed their widespread occurrence in eukaryotes. However, little is known about cis-NATs in the model plant Arabidopsis thaliana...
  3. 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...
  4. pmc Deep sequencing of small RNAs specifically associated with Arabidopsis AGO1 and AGO4 uncovers new AGO functions
    Huan Wang
    Laboratory of Plant Molecular Biology, The Rockefeller University, New York, NY 10065, USA
    Plant J 67:292-304. 2011
    ....
  5. pmc Genomic resources for songbird research and their use in characterizing gene expression during brain development
    Xiaoching Li
    The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
    Proc Natl Acad Sci U S A 104:6834-9. 2007
    ..Networks among the regulated genes were also identified. These resources provide songbird biologists with tools for genome annotation, comparative genomics, and microarray gene expression analysis...
  6. 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...
  7. pmc Prediction and identification of herpes simplex virus 1-encoded microRNAs
    Can Cui
    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA
    J Virol 80:5499-508. 2006
    ..Three of these latter miRNA candidates were predicted to be conserved in HSV-2. Thus, HSV-1 encodes at least one miRNA. We hypothesize that HSV-1 miRNAs regulate viral and host gene expression...
  8. doi 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
    ....
  9. pmc A complex system of small RNAs in the unicellular green alga Chlamydomonas reinhardtii
    Tao Zhao
    National Institute of Biological Sciences, Zhongguancun Life Science Park, Beijing 102206, China
    Genes Dev 21:1190-203. 2007
    ..Our findings suggest that the miRNA pathway and some siRNA pathways are ancient mechanisms of gene regulation that evolved prior to the emergence of multicellularity...
  10. ncbi request reprint Distinct catalytic and non-catalytic roles of ARGONAUTE4 in RNA-directed DNA methylation
    Yijun Qi
    Cold Spring Harbor Laboratory, Watson School of Biological Sciences and Howard Hughes Medical Institute, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
    Nature 443:1008-12. 2006
    ..Second, AGO4 catalytic activity can be crucial for the generation of secondary siRNAs that reinforce its repressive effects...
  11. doi 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...
  12. 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/..