Publications

54) Bimal Paudel,  Aayudh Das, Michaellong Tran, Arvid Boe,  Nathan Palmer,  Gautam Sarath,  Jose Luis Gonzalez,  Paul Rushton and  Jai S Rohila (2016) Proteomic responses of switchgrass and prairie cordgrass to senescence Front. Plant Sci. doi: 10.3389/fpls.2016.00293

53) Watanabe, K., Ma, K., Homayouni, A., Rushton, P.J., and Shen, Q. J (2016) Transcript Structure and Domain Display: A Customizable Transcript Visualization Tool Bioinformatics doi: 10.1093/bioinformatics/btw095

52) Prateek Tripathi, Roel C. Rabara, R. Neil Reese, Marissa A. Miller, Jai S. Rohila, Senthil Subramanian, Qingxi J. Shen, Dominique Morandi, Heike Bucking, Vladimir Shulaev, and Paul J. Rushton. (2016) A toolbox of genes, proteins, metabolites and promoters for improving drought tolerance in soybean includes the metabolite coumestrol and stomatal development genes. BMC Genomics 17:102 DOI: 10.1186/s12864-016-2420-0

51) Prateek Tripathi,  Roel C Rabara,  Vladimir Shulaev,  Qingxi J Shen and  Paul J Rushton (2015) Understanding water-stress responses in Soybean using Hydroponics system – A Systems Biology Perspective Perspective, Front. Plant Sci. – Plant Biotechnology doi: 10.3389/fpls.2015.01145

50) Charles I. Rinerson, Erin D. Scully, Nathan A. Palmer, Teresa Donze-Reiner, Roel C. Rabara, Prateek Tripathi, Qingxi J Shen, Scott E. Sattler, Jai S. Rohila, Gautam Sarath, and Paul J. Rushton (2015) The WRKY transcription factor family and senescence in switchgrass. BMC Genomics. 16:912  doi:10.1186/s12864-015-2057-4

49) Ross L. Tellam, Paul Rushton, Peter Schuerman, Irene Pala, and Derek Anane (2015) The primary reasons behind data sharing, its wider benefits and how to cope with the realities of commercial data. BMC Genomics. 16:626

48) Kenneth A. Watanabe, Arielle Homayouni, Tara Tufano, Jennifer Lopez, Patricia Ringler, Paul Rushton and Jeffery Q. Shen (2015) Tiling Assembly: A New Tool for Reference Annotation Independent Transcript Assembly and Novel Gene Identification by RNA-Sequencing DNA Research. doi: 10.1093/dnares/dsv015

47) Prateek Tripathi, Roel C. Rabara, Qingxi J. Shen and Paul J. Rushton. (2015) Transcriptomics Analyses of soybean leaves and roots sample during water-deficit. Genomics Data. 5, Pages 164-166

46) Roel C Rabara; Prateek Tripathi; Mani Kant Choudhary; Michael P Timko; Qingxi J Shen, and Paul Rushton (2015). Transcriptome profiling of tobacco under water deficit conditions. Genomics Data. 5, Pages 61-63

45) Liyuan Zhang, Lingkun Gu, Patricia Ringler, Stanley Smith, Paul Rushton, and Qingxi J. Shen (2015). Three WRKY transcription factors repress abscisic acid signaling additively and gibberellin signaling synergistically in aleurone cells. In the press. Plant Science 236, July 2015, Pages 214-222

44) Prateek Tripathi, Roel C. Rabara, Mani Kant Choudhary, Marissa A. Miller, Ying-Sheng Huang, Qingxi J Shen, and Paul J. Rushton (2015). The Interactome of Soybean GmWRKY53 using Yeast 2-Hybrid Library Screening to Saturation. Plant signaling & Behavior. DOI:10.1080/15592324.2015.1028705

43) Roel C. Rabara, Prateek Tripathi, R. Neil Reese, Deena L. Rushton, Danny Alexander, Michael P. Timko, Qingxi J Shen, and Paul J. Rushton (2015). Tobacco Drought Stress Responses Reveal New Targets for Solanaceae Crop Improvement. BMC Genomics 16:484  doi:10.1186/s12864-015-1575-4

42) Charles I. Rinerson, Roel C. Rabara, Prateek Tripathi Qingxi J Shen, and Paul J. Rushton (2015) The evolution of WRKY transcription factors. BMC Plant Biology 2015, 15:66  doi:10.1186/s12870-015-0456-y

41) Charles I. Rinerson, Roel C. Rabara, Prateek Tripathi Qingxi J Shen, and Paul J. Rushton (2015) Structure and evolution of WRKY transcription factors. In Plant Transcription Factors: Evolutionary, Structural and Functional Aspects Edited by: Daniel H. Gonzalez. Elsevier

40) Prateek Tripathi, Aravind Galla,Roel C. Rabara, and Paul J. Rushton (2015) Transcription factors that regulate defence responses and their use in increasing disease resistance. In Biotechnology for Plant Disease Control. Edited by David B. Collinge.

39) Roel C. Rabara, Prateek Tripathi and Paul J. Rushton (2014) The potential of transcription factor-based genetic engineering in improving crop tolerance to drought. OMICS: A Journal of Integrative Biology 18(10):601-14. doi:10.1089/omi.2013.0177.

38) Prateek Tripathi, Roel C Rabara, and Paul J Rushton (2013) A systems biology perspective on the role of WRKY transcription factors in drought responses in crops. Planta. 239(2):255-66. PMID: 24146023.

37) Sears, M.T., Zhang, H., Rushton, P. J., Kudithipudi, C., Han, S., Spano, A., Hayes, A., Timko, M. P. (2013) NtERF2, a non-NIC locus AP2/ERF transcription factor that activates early jasmonate responses of nicotine biosynthesis gene expression in tobacco. Plant Molecular Biology 84(1-2):49-66. PMID 23934400

36) Prateek Tripathi, Roel C. Rabara, Jun Lin and Paul J. Rushton (2013). GmWRKY53, a water- and salt-inducible soybean gene for rapid dissection of regulatory elements in BY-2 cell culture. Plant Signaling & Behavior 8 (5)  eLocation ID: e24097

35) Prateek Tripathi, Roel C Rabara, and Paul J Rushton (2012). Emergence of omics-approaches for crop improvement during abiotic stress. International Journal of Environmental Science and Technology. 1(2):125-128.

34) Roel C Rabara, Prateek Tripathi, Jun Lin, and Paul J Rushton (2012). Dehydration-Induced WRKY Genes from Tobacco and Soybean Respond to Jasmonic Acid Treatments in By-2 Cell Culture.  Biochemical and Biophysical Research Communications. 01/2013; DOI:doi: 10.1016/j.bbrc.2012.12.156.

33) Prateek Tripathi, Roel C. Rabara, Tanner J. Langum, Ashley K. Boken, Deena L. Rushton, Darius D. Boomsma, Charles I. Rinerson, Jennifer Rabara, R. Neil Reese, Xianfeng Chen, Jai S. Rohila, and Paul J. Rushton (2012). The WRKY transcription factor family from Brachypodium distachyon. BMC Genomics 13:270.

32) Maurice HT Ling, Roel C Rabara, Prateek Tripathi, Paul J Rushton, and Xijin Ge. Extending MapMan Ontology to Tobacco for Visualization of Gene Expression. (2012) Dataset Papers in Biology. 706465. doi:  10.7167/2013/706465

31)Rushton, P.J., Li, W., and Hansen, S. (2011) Using Molecular Biology for Management and Genetic Enhancements. In iGrow wheat, South Dakota State University, College of Agriculture and Biological Sciences, AgBio Communications Unit, Brookings, South Dakota.

30) 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., Finer, J.J., Shen, Q.J., and Rushton P.J. (2011) WRKY transcription factors: key components in abscisic acid signalling. The Plant Biotechnology Journal. 10(1):2-11.

29) Zhang, H., Bokowiec, M.T., Rushton, P.J., Han, S., and Timko, M.P. (2011) Tobacco Transcription Factors NtMYC2a and NtMYC2b Form Nuclear Complexes with the NtJAZ1 Repressor and Regulate Multiple Jasmonate-inducible Steps in Nicotine Biosynthesis. Molecular Plant. 5(1) 73-84.

28) Roy, A., Rushton, P.J., and Rohila, J.S. (2011) The Potential of Proteomic Technologies for Crop Improvement under Drought Environments. Critical Reviews in Plant Science. 30:5, 471-490.

27) Hernandez-Garcia, C.M., Bouchard, R.A., Rushton, P.J., Jones, M.L., Chen, X., Timko, M.P., and Finer, J.J. (2010) High level transgenic expression of soybean (Glycine max) GmERF and Gmubi gene promoters isolated by a novel promoter analysis pipeline. BMC Plant Biology 10:237.

26) Timko, M.P., Rushton, P.J., Bokowiec, M.T., and Zhang, H. (2010) Functional genomic approaches to harm reduction in tobacco products. In: Robertson R, Robinson E, and  Siminszky B (eds.), Recent Advances in Tobacco Science, Vol. 36, Tobacco Research in the Era of Biotechnology and Genomics, Proceedings 64th Tobacco Science Research Conference. Tobacco Science Research Conference Communication Services, pp. 25-43.

25) Rushton, P.J., Somssich, I.E., Ringler, P., and Shen, J. (2010) WRKY transcription factors. Trends in Plant Science 15, 247-58.

24) Rushton, P.J., Bokowiec, M.T., Han, S., Zhang, H., Chen, X., Laudeman, T.W., Brannock, J.F. and Timko, M.P. (2008) Tobacco transcription factors. Plant Physiology, 147(1): 280-95.

23) Michael P. Timko, Paul J. Rushton, Thomas W. Laudeman, Marta T. Bokowiec, Edmond Chipumuro, Foo Chueng, Christopher D. Town, and Xianfeng Chen (2008) Sequencing and Analysis of the Gene-Rich Space of Cowpea. BMC Genomics 9:103.

22) Stefan A. Rensing, Daniel Lang, Andreas Zimmer, Astrid Terry, Asaf Salamov, Harris Shapiro, Tomoaki Nishiyama, Pierre-François Perroud, Erika Lindquist, Yasuko Kamisugi, Takako Tanahashi, Keiko Sakakibara, Tomomichi Fujita, Kazuko Oishi, Tadasu Shin-I, Yoko Kuroki, Atsushi Toyoda, Yutaka Suzuki, Shinichi, Hashimoto, Kazuo Yamaguchi,, Sumio Sugano, Yuji Kohara, Asao Fujiyama, Aldwin Anterola, Setsuyuki Aoki, Neil Ashton, W. Brad Barbazuk, Elizabeth Barker, Jeffrey Bennetzen, Robert Blankenship, Sung Hyun Cho, Susan Dutcher, Mark Estelle, Jeffrey A. Fawcett, Heidrun Gundlach, Kosuke Hanada, Alexander Heyl, Karen A. Hicks, Jon Hughes, Martin Lohr, Klaus Mayer, Alexander Melkozernov, Takashi Murata,, David Nelson, Birgit Pils, Michael Prigge, Bernd Reiss, Tanya Renner, Stephane Rombauts, Paul J. Rushton, Anton Sanderfoot, Gabriele Schween, Shin-Han Shiu, Kurt Stueber, Frederica L. Theodoulou, Hank Tu, Yves Van de Peer, Paul J. Verrier, Elizabeth Waters, Andrew Wood, Lixing Yang, David Cove,, Andrew C. Cuming, Mitsuyasu Hasebe, Susan Lucas, Brent D. Mishler, Ralf Reski, Igor Grigoriev, Ralph S. Quatrano, Jeffrey L. Boore. (2008).

The genome of the moss Physcomitrella patens reveals evolutionary insights into the conquest of land by plants. Science 319:64-9 (Published online December 13th 2007. DOI: 10.1126/science.1150646).

21) Rushton, P.J., Bokowiec, M.T., Laudeman, T.W., Brannock, J.F., Chen, X., and Timko, M.P. (2008) TOBFAC: The database of tobacco transcription factors. BMC Bioinformatics 9:53.

20) Chen, X., Laudeman, T.W., Rushton, P.J., Spraggins, T.A. and Timko, M.P. (2007) CGKB: an annotation knowledge base for cowpea (Vigna unguiculata L.) methylation filtered genomic genespace sequences. BMC Bioinformatics 8:129.

19) Gurr, S.J. and Rushton, P.J. (2005)a Engineering plants with increased disease resistance: What are we going to express? Trends in Biotechnology 23: 275-282.

18) Gurr, S.J. and Rushton, P.J. (2005)b Engineering plants with increased disease resistance: How are we going to express it? Trends in Biotechnology 23: 283-290.

17) Rushton, P.J. (2002) Exciting prospects for plants with greater disease resistance. Trends in Plant Science 7. 325.

16) Rushton, P.J., Reinstädler, A., Lipka, V., Lippok, B., Hahlbrock, K. and Somssich, I.E. (2002) Synthetic plant promoters containing defined regulatory elements provide novel insights into pathogen- and wound-induced signalling. Plant Cell 14: 749-762.

This work was the subject of the following commentary:

– Synthetic promoters illuminate roles of cis-acting elements in plant defence. (2002) Trends in Plant Science 7. 315

15) Cormack, R.S., Eulgem, T., Rushton, P.J., Köchner, P., Hahlbrock, K. and Somssich, I.E. (2002) Leuzine zipper containing WRKY proteins widen the spectrum of immediate early elicitor-induced WRKY transcription factors in parsley. Biochimica et Biophysica Acta 1576: 92-100.

14) Rushton, P.J. and Weißhaar, B. (2002) DNA-protein interactions. In: Molecular Plant Biology Volume 2: A Practical Approach (Gilmartin, P. and Bowler, C. eds.) Oxford University Press. Pp. 77-95.

13) Eulgem, T., Rushton, P.J., Robatzek, S. and Somssich, I.E. (2000) The WRKY superfamily of plant transcription factors. Trends in Plant Science 5: 199-206. Cited 1,000 times in Google Scholar, this was the second most cited review to come from the Max-Planck Society in 2000.

12) Eulgem, T., Rushton, P.J., Schmelzer, E., Hahlbrock, K. and Somssich, I.E. (1999) Early nuclear events in plant defense signaling: rapid gene activation by WRKY transcription factors. EMBO J. 18: 4689-4699.

11) Rushton, P.J. and Somssich, I.E. (1999) Transcriptional regulation of plant genes responsive to pathogens and elicitors. In: Plant-Microbe Interactions Vol. 4 (Stacey, G. and Keen, N. eds.), APS Press, pp. 251-274.

10) Rushton, P.J. and Somssich, I.E. (1998) Transcriptional control of plant genes responsive to pathogens. Curr. Opin. Plant Biol. 1: 311-315.

9) Willmott, R.L., Rushton, P.J., Hooley, R. and Lazarus, C.M. (1998) DNase1 footprints suggest the involvement of at least three types of transcription factors in the regulation of a-Amy2/A by gibberellin. Plant Molecular Biology 38: 817-825.

8) Rushton, P.J., Torres, J.T., Parniske, M., Wernert, P., Hahlbrock, K. and Somssich, I.E. (1996) Interaction of elicitor-induced DNA-binding proteins with elicitor response elements in the promoters of parsley PR1 genes. EMBO J. 15: 5690-5700.

7) Rushton, P.J., Macdonald, H., Huttly, A.K., Lazarus, C.M. and Hooley, R. (1995) Members of a new family of DNA-binding proteins bind to a conserved cis-element in the promoters of alpha-Amy2 genes. Plant Molecular Biology 29: 691-702.

6) Hooley, R., Beale, M.H., Smith, S.J., Walker, R.P., Rushton, P.J., Whitford P.N. and Lazarus,  C.M. (1992b) In: Transport and Receptor Proteins of Plant Membranes: Molecular structure and Function, (Cooke, D.T. and Clarkson, D.T. eds.) Plenum Press, New York, pp.157-167.

5) Hooley. R., Beale, M.H. Smith, S.J. Walker, R.P., Rushton, P.J., Whitford P.N. and Lazarus, C.M. (1992a) Gibberellin perception and the Avena fatua aleurone – Do our molecular keys fit the correct locks? Biochemical Society Transactions 20: 85-89.

4) Rushton, P.J., Hooley, R. and Lazarus, C.M. (1992) Aleurone nuclear proteins bind to similar elements in the promoter regions of 2 gibberellin-regulated a-amylase genes. Plant Molecular Biology 19: 891-901.

3) Bray, C.M. Blowers, L.E., Rushton, P.J. and Smith, C.A.D. (1992) In: Advances in the Science and Technology of Seeds (Fu, J.R. and Khan, A.A. eds.)  Science Press, Beijing and New York, pp 91-97.

2) Rushton, P.J. and Bray, C.M. (1987) Stored and de novo synthesised polyadenylated RNA and loss of vigor and viability in wheat seed. Plant Science 51: 51-59.

1) Smith, C.A.D., Rushton, P.J. and Bray, C.M. (1986) Polyadenylated RNA-metabolism and loss of vigor and viability in germinating wheat embryos. Physiologia Plantarum 67: 310-314.

Conference Presentations:

12) Rushton, P.J., Tripathi,P.,  Boken, A.K., Langum, T.J.,  Bokoweic, M.T., Sutton, F., Meyerink, B., Geraets, R.,  Lang, D., Chen, X.,  Shen, Q.J., Timko, M.P., and Rensing, S.A., The Evolution of WRKY Transcription Factors In the Green Lineage. (W398) Plants and Animal Genome conference JXVIII, San Diego, CA, USA.

11) Tripathi, P., Rabara, R. C., Langum, T.J., Boken, A.K., Rushton, D.L., Smidt, L., and Rushton, P.J. (2011) The molecular and physiological responses of soybean to water stress. Proceedings of the South Dakota Academy of Science, Vol. 90 173.

10) Rabara, R. C., Lin, J., Tripathi, P., Langum, T.J., Boken, A.K., Rushton, D.L., Smidt, L., and Rushton, P.J. (2011) Drought inducible WRKY genes in tobacco (Nicotiana tabacum L.) Proceedings of the South Dakota Academy of Science, Vol. 90

9) Tripathi, P., Rabara, R. C., Boken, A.K., Langum, T.J., Smidt, L., Rushton, D.L., and Rushton, P.J. (2011) The Molecular Responses of Soybean in Water Deificit.”  Plant Biology 2011, Annual Meeting   of The American Society of Plant Biology, Minneapolis, MN, USA (Abstract # P13020): pL68.

8) Rabara, R. C., Lin, J., Tripathi, P., Boken, A.K., Langum, T.J., Smidt, L., Rushton, D.L., and Rushton, P.J. (2011) Promoter Analysis of drought induced WRKY genes in tobacco (Nicotiana tabacum L.) Plant Biology 2011, Annual Meeting   of The American Society of Plant Biology, Minneapolis, MN, USA (Abstract # P13006): pL68.

7) Rabara, R. C., Tripathi, P., Lin, J., Parett, J., and  Rushton, P.J.  (2012). A tobacco BY-2 cell system for the identification of drought responsive regulatory elements in plants. American Society of Plant Biology Mid-Westerm Section Meeting, Lincoln, Nebraska, USA. P-39.

6) Tripathi, P., Rabara, R. C., Reese, R.N., Shen, Q.J., and Rushton, P.J. (2012) Global gene expression in Tobacco in water deficit condition. Plant Biology 2012, Annual meeting of American Society of Plant Biology, Austin, Texas, USA. (Abstract # 14018): pR118.

5) Rabara, R. C., Tripathi, P., Lin, J., Reese, R.N., Shen, Q.J., and Rushton, P.J. (2012). Global gene expression in Tobacco in water deficit condition. Plant Biology 2012, Annual meeting of American Society of Plant Biology, Austin, Texas, USA. (Abstract # 14020): pR118

4) Tripathi, P., Rabara, R. C., Reese, R.N., Shen, Q.J., and Rushton, P.J. (2012) Understanding water stress responses at systems level in Soybean (Glycine Max.)”  International Conference of Systems Biology 2012, Toronto, ON, Canada (Abstract  #  469D): pQ196.

3) Tripathi, P., Rabara, R. C., Reese, R.N., Shen, Q.J., and Rushton, P.J. (2012) Systems wide identification of WRKY transcription factors regulating water stress responses in Soybean (Glycine Max.) 14^th Annual Fall Symposia Exploration in Synthetic System Biology, Danforth Plant Science Center, St. Louis, Missouri, USA (PX08).

2) Rabara, R. C., Tripathi, P., Reese, R.N., Shen, Q.J., and Rushton, P.J. (2012) Systems wide identification of WRKY transcription factors regulating water stress responses in Soybean (Glycine Max.) 14th Annual Fall Symposia Exploration in Synthetic System Biology, Danforth Plant Science Center, St. Louis, Missouri, USA (PX09)

1) Tripathi, P., Rabara, R. C., Reese, R.N., Shen, Q.J., and Rushton, P.J. (2013) Systems Biology of Drought Tolerance in Soybean (Glycine Max). International Conference on Bio-resource and Stress Management (ICBSM-2013) Kolkata, India.

Databases:

1) The WRKY Wide Web: The database of WRKY transcription factors (http://systemsbiology.usm.edu/BrachyWRKY/WRKY/Species.html).

2) The Database of Brachypodium distachyon WRKY Transcription Factors http://www.igece.org/WRKY/BrachyWRKY/BrachyWRKYIndex.html

3) WRKY.org A WRKY Wide Web (http://www.wrky.org/)