My research focus on development of databases and bioinformatics tools for genome analyses and gene annotations, predictions of genes responsive to environmental/developmental cues, and predictions of gene functions (subcellular localization, and protein motifs). Another focus of my research is the molecular mechanism controlling plant responses to abiotic stresses, seed dormancy and germination. I am also interested in the mechanism underlying tissue-specific and developmentally-regulated gene expression.
Genomics, Bioinformatics, Genetics, Molecular Biology, Seed Germination, Plant Response to Environmental Stresses
Ph.D. Washington University, St. Louis
The recent accomplishment in sequencing the genomes of thousands of organisms, including human being and important crops such as rice, is leading to a revolution in scientific research, medicine discovery, and improvement of the quality of our food. My lab is interested in developing (adopting, modifying, and inventing) bioinformatics tools for genome analyses and gene ontology studies. Gene ontology addresses: Biological Process (Why is this, such as cell enlargement, being done?), Molecular Function (What kind of molecule is this? Enzymes or transcription factors?), and Cellular Component (Where is this located? Nuclei or Mitochondria?).
- Rushton, P.J., Somssich, I.E., Ringler, P. and Shen, Q. J. : WRKY transcription factors (Feature Review). Trends in Plant Science, 2010, 15: 247-258.
- Jiang,Y., Cukic,B., Adjeroh,D.A., Skinner,H.D., Lin, J., Shen, Q. J. , and Bing-Hua Jiang: An Algorithm for Identifying Novel Targets of Transcription Factor Families: Application to Hypoxia-inducible Factor 1 Targets. Cancer Informatics, 2009, 7: 75-89. Full Text
- Zhang, Z.L., Shin, M., Zou, X.L., Huang, J.Z., Ho, T.H.D. and Shen, Q. J.: A negative regulator encoded by a rice WRKY gene represses both abscisic acid and gibberellin signaling in aleurone cells. Plant Mol. Biol., 2009, 70: 139-151.
- Zou, X., Neuman, D. and Shen, Q. J.: Interactions of two transcriptional repressors and two transcriptional activators in modulating gibberellin signaling in aleurone cells. Plant Physiol., 2008, 148: 176-186.
- Johnson, R.R., Shin, M, Shen, Q. J.: The wheat PKABA1-interacting factor TaABF1 mediates both abscisic acid-suppressed and abscisic acid-induced gene expression in bombarded aleurone cells. Plant Mol. Biol. 2008, 68: 93-103.
- Xie, Z., Zhang, Z.L., Hanzlik, S., Cook, E. and Shen, Q. J.: Salicylic acid inhibits gibberellin-induced alpha-amylase expression and seed germination via a pathway involving an abscisic-acid-inducible WRKY gene. Plant Mol. Biol., 2007, 64: 293-303.
- Ross, C.A, Liu, Y. and Shen, Q.J.: Invited Review, The WRKY Gene Family in Rice (Oryza sativa), In the Special Issue on Rice Breeding and Functional Genomics, J. Integr. Plant Boil., 2007, 49: 827-842. Most cited papers award.
- Zou, X., Shen, Q.J. and Neuman, D.: An ABA inducible WRKY gene integrates responses of creosote bush (Larrea tridentata) to elevated CO2 and abiotic stresses. Plant Science 2007, 172: 997-1004. PDF File
- Xie, Z., Zhang, Z.L., Zou, X.L., Yang, G.X., Komatsu, Setsuko and Shen, Q.J.: Interactions of two abscisic-acid induced WRKY genes in repressing gibberellin signaling in aleurone cells. Plant J., 2006, 46: 231-242.
- Ross C.A. and Shen, Q.J.: Computational prediction and experimental verification of HVA1-like abscisic acid responsive promoters in rice (Oryza sativa)., Plant Mol. Biol., 2006, 62:233-246.
- Shen, Q.J. and Wang J.: Engineering for drought tolerance in horticultural and ornamental plants: lessons from the studies with model plants. In Journal of Crop Improvement, Edited by Yi Li and Yan Pei, Haworth Press, Inc, Binghamton, NY. 2006, 17(1): 121-153. This volume is simultaneously published as a book entitled Plant Biotechnology in Ornamental Horticulture.
- Xie, Z., Zhang, Z.L., Zou, X.L., Huang, J., Ruas, P., Thompson, D., and Shen, Q.J.: Annotations and functional analyses of the rice WRKY gene superfamily reveal positive and negative regulators of abscisic acid signaling in aleurone cells. Plant Physiol., 2005. 137: 176-189.
- Xie, Z., Ruas, P. and Shen, Q.J.: Regulatory networks of phytohormone abscisic acid. In Vitamins and Hormones, Edited by Gerald Litwack, Academic Press/Elsevier Science. 2005. 72: 235-269.