PUBLICATIONS

• Xu, C., Hao, B.W., Sun, G.L., Mei, Y.Y., Sun, L.F., Sun, Y. M., Wang, Y.B., Zhang, Y.Y., Zhang, W., Zhang, M.Y., Zhang, Y., Wang, D., Rao, Z.H., Shen, Q.J., and Wang, N. N.: Dual activities of ACC synthase: Novel clues regarding the molecular evolution of ACS genes, Science Advances, 2021, 7:eabg8752. PDF, doi: 10.1126/sciadv.abg8752
• Villacastin, A.J., Adams, K.S., Boonjue, R., Rushton, P.J., Han, M., Shen, Q.J.: Dynamic differential evolution schemes of WRKY transcription factors in domesticated and wild rice, Scientific Reports, 2021, 11:14887, PDF, doi: 10.1038/s41598-021-94109-4.
• Cheng, J.X., Chen, L., Li, Y., Yue, M., Cloe, A., Wei, J., Watanabe, K.A., Shammo, J. M., Anastasi, J., Shen, Q.J., Larson, R.A, He, C., Le Beau, M.M, and Vardiman, J.M.: RNA cytosine methylation and methyltransferases mediate chromatin organization and 5-azacytidine response and resistance in leukemia, Nature Communications, 2018, PDF, doi:10.1038/s41467-018-03513-4.
• Watanabe, K., Homayouni, A., Gu, L., Huang, K.Y., Ho, T.D., Shen, Q.J.: Transcriptomic analysis of rice aleurone cells identified a novel abscisic acid response element. Plant, Cell & Environment, 2017, 40(9): 2004-2016, PDF, doi: 10.1111/pce.13006.
• Jiang, C., Shen, Q.J., Wang, B., Xiao, S., Chen, L., Yu, T., Ke, X., Zhong, Q., Fu, J., Chen, Y., Wang, L., Yin, F., Zhang, D., Ghidan, W., Huang, X., Cheng, Z.: Transcriptome analysis of WRKY gene family in Oryza officinalis Wall ex Watt and WRKY genes involved in responses to Xanthomonas oryzae pv. oryzae stress, PLOS One, 2017,. 12(11):e0188742, PDF, doi: 10.1371/journal.pone.0188742
• Xu, H., Watanabe, K., Zhang, L. and Shen, Q. J.: WRKY transcription factor genes in wild rice Oryza nivara. DNA Research, 2016, 23(4), 311–323, PDF doi:10.1093/dnares/dsw025.
• Watanabe, K., Ma, K., Homayouni, A., Rushton, P.J. and Shen, Q.J.: Transcript structure and domain display: a customizable transcript visualization tool. Bioinformatics, 2016, 32 (13): 2024-2025, PDF, doi:10.1093/bioinformatics/btw095
• Tripathi, P., Rabara, R.C., Reese, R.N., Miller, M.A., Rohila, J.S., Subramanian, S., Shen, Q.J., Morandi, D., Bücking, H., Shulaev, V. and Rushton, P.J.: A toolbox of genes, proteins, metabolites and promoters for improving drought tolerance in soybean includes the metabolite coumestrol and stomatal development genes. BMC Genomics, 2016, 17:102.
• Watanabe, K.A., Homayouni, A., Tufano, T., Lopez, J., Ringler, P., Rushton, P. and Shen, Q.J.: Tiling Assembly: a new tool for reference annotation independent transcript assembly and novel gene identification by RNA-sequencing. DNA Research, 2015, 22(5):319-329, PDF
• Zhang, L., Gu, L, Ringler, P., Smith, S.D., Rushton, P.J. and Shen, Q.J.: Three WRKY transcription factors additively repress abscisic acid and gibberellin signaling in aleurone cells. Plant Science, 2015, 236:214-222.
• Tripathi, P., Rabara, R.C., Shulaev, V. Shen, Q.J. and  Rushton, P.J.: Understanding water-stress responses in soybean using hydroponics system - A systems biology perspective. Front Plant Sci., 2015, Front. Plant Sci. | doi: 10.3389/fpls.2015.01145
• Rinerson, C.I., Scully, E.D., Palmer, N.A., Donze-Reiner, T., Rabara, R.C., Tripathi, P., Shen, Q.J., Sattler, S.E., Rohila, J.S., Sarath, G., Rushton P.J.: The WRKY transcription factor family and senescence in switchgrass. BMC Genomics, 2015, 16:912.
• Rabara, R.C., Tripathi, P., Reese, R. N., Rushton, D.L., Alexander, D., Timko, M.P., Shen, Q.J., and Rushton, P.J.: Tobacco drought stress responses reveal new targets for Solanaceae crop improvement. BMC Genomics, 2015, 16:484.
• Rinerson, C.I., Rabara, R.C., Tripathi, P., Shen, Q.J. and Rushton, P.J.: The evolution of WRKY transcription factors. BMC Plant Biology, 2015, 15:66.
• Tripathi, P., Rabara, R.C., Choudhary, M.K., Kant, M., Miller, M.A., Huang, Y.S., Shen, Q.J. and Ruston, P.J.: The interactome of soybean GmWRKY53 using yeast 2-hybrid library screening to saturation. Plant Signaling & Behavior, 2015, 10:10(7):e1028705.
• Tripathi, P., Rabara, R.C., Shen, Q.J. and Ruston, P.J.: Transcriptomics analyses of soybean leaves and roots sample during water-deficit. Genomic Data, 2015, 5:164-166.
• Rabara, R.C., Tripathi, P., Choudhary, M.K., Timko, M.P., Shen, Q.J. and Ruston, P.J.: Transcriptome profiling of tobacco under water deficit conditions. Genomic Data, 2015, 5:61-63.
• Rinerson, C.I., Rabara, R.C., Tripathi, P., Shen, Q.J. and Rushton, P.J.: Structure and evolution of WRKY transcription factors. In Plant Transcription Factors: Evolutionary, Structural and Functional Aspects, Edited by Daniel H. Gonzalez, Elsevier, 2015, 163-182.
• Jiang, C., Cheng Z., Zhang, C., Yu T., Zhong, Q., Shen J.Q., Huang, X.: Proteomic analysis of seed storage proteins in wild rice species of the Oryza genus. Proteome Sci., 2014, 12:51.
• Watanabe, K.A, Ringler, P., Gu, L. and Shen, Q.J.: RNA-sequencing reveals previously unannotated protein- and microRNA-coding genes expressed in aleurone cells of rice seeds. Genomics, 2014, 103: 122-134.
• Cheng, J., Anastasi, J., Watanabe, K., Shen, Q.J., and Vardiman, J.: Genome-wide profiling reveals epigenetic inactivation of the PU.1 pathway by histone H3 lysine 27 trimethylation in cytogenetically normal myelodysplastic syndrome. Leukemia, 2013, 27: 1291-1300.
• Fu J., Gu, L.,Guo Y., Zhang, L., Wang, L., Li D., Wang B., Shen, Q.J., Cheng, Z.: Construction and high-efficient screenings of a yeast two-hybrid cDNA library from the drought-stressed roots of rice. Chinese Journal of Rice Science, 2013, 27(2):198-202.
• Rice WRKY Working Group: Nomenclature report on rice WRKY's - Conflict regarding gene names and its solution. Rice 2012, 5:3 .
• Rushton, D.L., Tripathi, P., Rabara, R.C., Lin, J., Ringler, P., Boken, A. k., Langum, T. J., Smidt, L., Boomsma, D.D., Emme, N.J., Chen, X.F., John J. Finer, J.J., Shen, Q.J., and Rushton, P.J.: WRKY transcription factors: key components in abscisic acid signaling. Plant Biotech. J., 2012, 10：2-11.
• 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.
• 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.
• 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. Full Text
• 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. PDF File.
• Zou, X., Seemann, J.R., Neuman, D., and Shen, Q.J.: A WRKY gene from creosote bush encodes an activator of the ABA signaling pathway. J. Biol. Chem. 2004. 279: 55770-55779. PDF File
• Zhang, Z.L., Xie, Z., Zou, X.L., Casaretto, J.A, Ho, T.H.D. and Shen, Q.J.: A rice WRKY gene encodes a transcriptional repressor of the gibberellin signaling pathway in aleurone cells. Plant Physiol.  2004. 134: 1500-1513. Full Text
• Zhang, Z.L., Cook, E., Zhao, H.Y., Song, Y.R. and Shen, Q.J.: Symmetrical directional cloning: an efficient method to prepare hairpin RNA interference constructs. Progress in Natural Science, 2004. 14: 1053-1059. PDF File.
• Zhao, H.Y., Shen, Q.J., and Song, Y.R.: Characterization of three rice CCoAOMT genes. Chinese Science Bulletin. 2004. 49: 1602-1606. PDF File.
• Shen, Q.J., Casaretto, J.A., Zhang, P. and Ho, T.H.D.: Functional definition of ABA response complexes, the promoter units necessary and sufficient for ABA induction of gene expression in barley (Hordeum vulgare L.). Plant Mol. Biol. 2004. 54: 111-124. PDF File.
• Shen, Q., Gomez-Cadenas,A., Zhang, P.M. and Walker-Simmons M.K., Sheen, J., Ho, T.H.D.: : Dissection of abscisic acid signal transduction pathways in barley aleurone layers.Plant Mol. Biol. 2001. 47: 437-448. PDF File
• Shen, Q, Chen, C.N., Brands A., Pan, S.M. and Ho, T.H.D.: The stress and abscisic acid induced barley gene HVA22: developmental regulation and homologs in diverse organisms. Plant Mol. Biol. 2001. 45: 327-340. PDF File
• Gomez-Cadenas, A, Verhey SD, Holappa, LD, Shen, Q, Ho T.H. D., Walker-Simmons MK: An abscisic acid- induced protein kinase, PKABA1, mediates abscisic acid-suppressed gene expression in barley aleurone layers. Proc. Natl. Acad. Sci. U S A. 1999. 96: 1767-72. PDF File
• Shen, Q., and Ho, T.H.D.: Abscisic acid- and stress-induced promoter switches in the control of gene expression. In Inducible Gene Expression in Plants. Edited by P.H.S. Reynolds, CABI Publishing . 1998. 187- 218.
• Su, J. Shen, Q., Ho, T.H.D and Wu, R.: Dehydration-stress-regulated transgene expression in stably transformed rice plants. Plant Physiol. 1998. 117: 913-922. PDF File
• Shen, Q., and Ho, T.H.D.: Promoter switches specific for abscisic acid (ABA)-induced gene expression in cereals. Physiol. Plant. 1997. 101: 653-664. PDF File
• Shen, Q., Zhang, P. and Ho, T.H.D.: Modular nature of abscisic acid (ABA) response complexes: Composite promoter units that are necessary and sufficient for ABA induction of gene expression in Barley. Plant Cell. 1996. 8: 1107-1119. PDF File
• Shen, Q. and Ho, T.H.D.: Functional dissection of an abscisic acid (ABA)-inducible gene reveals two independent response complexes each containing a G-box and a novel cis-acting element. Plant Cell. 1995. 7: 295-307. PDF File
• Shen, Q. and Ho, T.H.D.: Abscisic acid response complex (ABRC): a promoter unit necessary and sufficient for ABA-induced gene expression in barley seeds. The 7th International Symposium on Pre-Harvest Sprouting in Cereals. 1995. 99-108. PDF File
• Straub, P.F, Shen, Q. and Ho, T.H.D.: Structure and promoter analysis of an ABA- and stress-regulated barley gene, HVA1. Plant Mol. Biol. 1994. 26: 617-630. PDF File
• Shen, Q., Uknes, S.J. and Ho, T.H.D.: Hormone response complex in a novel abscisic acid and cycloheximide inducible barley gene. J. Biol. Chem. 1993 (268): 23652-23660. PDF File
• Hood, E.E., Shen, Q. and Varner, J.E.: A developmentally regulated hydroxyproline-rich glycoprotein in maize pericarp cell walls. Plant Physiol.  1988. 87: 138-142. PDF File