Bioinformatics

2008

Journals

• Breland, A, Nasser, S, Schlauch, K, Harris, FC. Influenza A Virus (H3N2) Genomic Sequence Difference Measures Based on Word Absence and Expression Levels. 2008. Proceedings of CAINE 2008.
• Cushman JC, Agarie S, Albion RL, Elliot SM, Taybi T, Borland AM. (2008) Isolation and characterization of mutants of ice plant, Mesembryanthemum crystallinum, deficient in Crassulacean acid metabolism. 147: 228-238.
• Cushman JC, Tillett RL, Wood JA, Branco JA, Schlauch KA (2008) Large-scale mRNA expression profiling in the common ice plant, Mesembryanthemum crystallinum, performing C3 photosynthesis and Crassulacean acid metabolism (CAM). J. Exp. Botany. 59:1875-1894.
• Heyden M, Heugen U, Bründermann E, Niehues G, Leitner DM, Havenith M. The long range influence of carbohydrates on the solvation dynamics of water — answers from THz absorption measurements and molecular modelling simulations. Journal of the American Chemical Society
• Horan K, Jang C, Bailey-Serres J, Mittler R, Shelton C, Harper JF, Zhu J-K, Cushman JC, Gollery M, Girke T. (2008) Annotating genes of known and unknown function by large-scale co-expression analysis. Plant Physiol. 147: 41-57.
• Morsy MR, Gouthu S, Orchard S, Thorneycroft D, Harper JF, Mittler R, Cushman JC. (2008) Charting Plant Interactomes: Possibilities and Challenges. Trends in Plant Science. 13: 183-191.
• Ross CA, Liu Y, and Shen QJ. The WRKY Gene Family in Oryza sativa. J. Integrative Plant Biology, in press
• Song L, Ciftci-Yilmaz S, Harper J, Cushman JC, Mittler R. (2008) Enhanced tolerance to oxidative stress in transgenic Arabidopsis thaliana plants expressing proteins of unknown function. Plant Physiol. 148: 280-292.

Posters

• Facemyer, K. C., Herald, C. H., Kenyon, J., Schlauch,, K., Baker, J. E., & Cremo, C. R. (2008). Computational Dissection of Intramolecular Interface Binding Energies in Various Myosin States, 5Res. 52nd Annual Meeting of the Biophysics Society & 16th Annual International Biophysical Congress. Long Beach, CA, February 3, 2008.
• Hooft, A. M., Smith, R. D., Shannon, S. F., Facemyer, K. C., Cremo, C. R., & Baker, J. E. (2008). The Mechanism of Blebbistatin Inhibition on Actin-Myosin Mechanics, 2279/B395. 52nd Annual Meeting of the Biophysics Society & 16th Annual International Biophysical Congress. Long Beach, CA, February 5, 2008.

Abstracts

• Singer, C. A., Kuhn, A.R., Schlauch, K., Gerthoffer, W. T. MicroRNA expression following inflammatory stimulation of human airway smooth muscle cells. Proc.Am.Thorac.Soc., A324, 2008.
• Gerthoffer, W.T., Kuhn, A.R., Schlauch, K., Singer, C. A. MicroRNA expression in human tracheal smooth muscle. Proc.Am.Thorac.Soc., A494, 2008.
• Kuhn, A.R., Elorza, M., Miano, J., Gerthoffer, W. T., Singer, C. A. Myocardin controls miRNA expression in human airway smooth muscle cells. Proc.Am.Thorac.Soc., A322, 2008.

Presentations

• Cramer, G.R., (Presenter Only), Academic, “Water and Salinity Stress in Grapevines: A Systems Biology Approach.” Invited speaker to Graduate Seminar program at South Dakota State University, March 7th, 2008.
• Cramer, G.R., (Presenter Only), Academic, “Transcriptomic and metabolite analyses of Cabernet Sauvignon grape berry development.” Invited speaker at the 2^nd Annual National Viticulture Research Conference, University of Californica, Davis. July 9 -11th, 2008.
• Cramer, G.R., (Presenter Only), Academic, “Transcriptomic and metabolite analyses of Cabernet Sauvignon grape berry development.” Invited speaker at the Istituto Agrario San Michele all'Adige, Trento, Italy, August 29th, 2008.
• Cramer, G.R., (Presenter Only), Academic, “Systems Biology of Abiotically-Stressed Grapes.” Keynote speaker at the 11th International Meeting of the Microarray and Gene Expression Data Society, Riva del Garda, Italy. September 1-4, 2008.
• Cramer, G.R., (Presenter Only), Academic, “Abiotic stress & plant responses - from the whole vine to the genes.” Keynote speaker at the 8th International Symposium on Grapevine Physiology & Biotechnology, Adelaide, Australia, November 23-28, 2008.
• Facemyer, K. C., Herald, C. H., Kenyon, J., Schlauch,, K., Baker, J. E., & Cremo, C. R. (2008). Computational Dissection of Intramolecular Interface Binding Energies in Various Myosin States, 5Res. 52nd Annual Meeting of the Biophysics Society & 16th Annual International Biophysical Congress. Long Beach, CA, February 3, 2008.
• Facemyer, K. C. (2008). Interface Energetics inside Myosin during the Actomyosin Cycle, (Invited Talk) Motility Subgroup Meeting of the 52nd Annual Meeting of the Biophysics Society & 16th Annual International Biophysical Congress. Long Beach, CA, February 2, 2008.
• Kuhn, A.R., Role of miR-25 in regulation of airway smooth muscle remodeling. 2009 Bierkamper Symposium.
• C. Tittiger, T. Aw, K. Schlauch, S. Young, C.I. Keeling and G.J. Blomquist. 2008. Functional Genomics: Clues to Mountain Pine Beetle Biology. Entomology Society of America Annual Meeting. Reno, NV, November 2008.

2007

Books

• Grimplet J, Deluc LG, Cramer GR, Cushman JC. (2007) Integrating functional genomics with salinity and water-defict stress responses in wine grape — Vitis vinifera. In: Advances in molecular-breeding toward drought and salt tolerant crops. Eds: Matthew A. Jenks, Paul M. Hasegawa, and S. Mohan Jain. Springer, Dordrecht, The Netherlands.

Journals

• Cramer Grant R, Ergül Ali, Grimplet Jerome, Tillett Richard L, Tattersall Elizabeth A R, Bohlman Marlene C, Vincent Delphine, Sonderegger Justin, Evans Jason, Osborne Craig, Quilici David, Schlauch Karen A, Schooley David A, Cushman John C. Water and salinity stress in grapevines: early and late changes in transcript and metabolite profiles. Funct Integr Genomics 7 2, 2007 Apr pp.111-34
• Vincent Delphine, Ergül Ali, Bohlman Marlene C, Tattersall Elizabeth A R, Tillett Richard L, Wheatley Matthew D, Woolsey Rebekah, Quilici David R, Joets Johann, Schlauch Karen, Schooley David A, Cushman John C, Cramer Grant R. Proteomic analysis reveals differences between Vitis vinifera L. cv. Chardonnay and cv. Cabernet Sauvignon and their responses to water deficit and salinity. J Exp Bot 58 7, 2007 pp.1873-92
• Deluc LG, Grimplet J, Wheatley MD, Tillett RL, Quilici DR, Osborne C,Schooley DA, Schlauch KA, Cushman JC, Cramer GR. Transcriptomic and metabolite analyses of Cabernet Sauvignon grape berrydevelopment.BMC Genomics. 2007 Nov 22;8:429.
• Elekonich, M.M., (in press) Honey Bees as a Biomedical Model, in Sourcebook of Models for Biomedical Research, Michael Conn, ed.; Totowa NJ: Humana Press.
• Gollery Martin, Harper Jeff, Cushman John, Mittler Taliah, Mittler Ron. POFs: what we don't know can hurt us. Trends Plant Sci 12 11, 2007 Nov pp.492-6
• Grimplet J, Deluc LG, Tillett RL, Wheatley MD, Schlauch KA, Cramer GR,Cushman JC. Tissue-specific mRNA expression profiling in grape berry tissues.BMC Genomics. 2007 Jun 21;8:187.
• Tattersall EA, Grimplet J, DeLuc L, Wheatley MD, Vincent D, Osborne C,Ergül A, Lomen E, Blank RR, Schlauch KA, Cushman JC, Cramer GR. Transcript abundance profiles reveal larger and more complex responses ofgrapevine to chilling compared to osmotic and salinity stress.Funct Integr Genomics. 2007 Oct;7(4):317-33. Epub 2007 Jun 20.
• Ross, C.A., Liu, Y., and Shen, Q.J.: The WRKY Gene Family in Oryza sativa. J. Integrative Plant Biology, in press
• 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 Molecular Biology, in press.
• Zou, X.L., 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, in press (doi:10.1016/j.plantsci.2007.02.003).

2006

Books

• Shen, Q.J. and Wang J. 2006. Engineering for drought tolerance in horticultural and ornamental plants: lessons from the studies with model plants. Journal of Crop Improvement, Edited by Yi Li and Yan Pei, Haworth Press, Inc, Binghamton, NY. 17(1): 121-153.

Journals

• Bearfield, J. C., Keeling, C. I., Young, S., Blomquist, G. J., Tittiger, C. (2006) Isolation, endocrine regulation and mRNA distribution of the 3-hydroxy-3-methylglutaryl coenzyme A synthase (HMG-S) gene from the pine engraver, Ips pini (Coleoptera: Scolytidae) Insect Molecular Biology 15 (2), 187195.
• Borland AM, Elliott S, Pater B, Taybi T, Cushman JC, Barnes B. 2006, Are the metabolic components of crassulacean acid metabolism up-regulated in response to an increase in oxidative burden? J. Exp. Bot. 57:319-328.
• Chen C, Beck, BW, Krause K, Pettitt BM. (2006) Solvent participation in Serratia marcescens endonuclease complexes. Proteins. 62(4):982-995.
• Chen, C., Beck, B.W., Krause, K., Warth, T., and Pettitt, B.M. (2006) The Effects of Dimerization of Serratia marcescens Endonuclease on Water Dynamics. Accepted by Biopolymers.
• Gollery M, Harper J, Cushman J, Mittler T, Girke T, Zhu J-K, Bailey-Serres J, Mittler R. (2006) What Makes Species Unique? A Role for Genes with Unknown Function. Genomic Research. 7:R57.
• Gollery, M., J. Harper, T. Mittler, J. Cushman, T. Girke, J. Bailey-Serres, R. Mittler (2006) What Makes Species Unique? The Contribution of Proteins with Obscure Features. Genome Biology, 7:R57.
• Grimplet J, Deluc LG, Wheatley M, Schlauch KA, Cramer GR, Cushman JC. (2006) Tissue-specific mRNA expression profile in grape berry tissues. Proceedings of the Macrowine 2006 Conference, Reims, France (in press).
• Grzymski, J.J. , Carter, B.J. , DeLong, E.F. , Feldman, R.A. ,Ghadiri A. , and Murray, A.E. "Comparative Genomics of DNA Fragments from Six AntarcticMarine Planktonic Bacteria",APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Feb. 2006, p. 15321541 Vol. 72, No. 2.
• Honeybee genome sequencing consortium. Insights into social insects from the genome of the honeybee Apis mellifera. Nature. 2006 Oct 26; 443(7114):931-49.
• Iturriaga, G, Cushman MAF, Cushman JC (2006) An EST catalogue from the resurrection plant Selaginella lepidophylla reveals stress-adaptive genes. Plant Science. 170: 1173-1184.
• Kishore VK, Velasco P, Shintani DK, Rowe J, Rosato C, Adair N, Slabaugh MB, Knapp SJ. Conserved simple sequence repeats for the Limnanthaceae (Brassicales). Theoretical and Applied Genetics. Miller G, Mittler R (2006) Could plant HSFs function as hydrogen peroxide sensors? Ann. Bot. in press.
• Mittler R (2006) Abiotic Stress, the Field Environment and Stress Combination. Trends Plant Sci. 11: 15-19.
• Rodriguez Milla MA, Uno Y, Townsend J, Maher E, Cushman JC. 2006, A novel yeast two-hybrid approach to identify CDPK substrates: Characterization of the interaction between AtCPK11 and AtDi19, a nuclear zinc finger protein1 FEBS Lett. 580: 904-911.
• Ross C, Pybus C, Pedraza-Reyes M, Sung HM, Yasbin RE, Robleto E. Novel role of mfd: effects on stationary-phase mutagenesis in Bacillussubtilis.J Bacteriol. 2006 Nov;188(21):7512-20. Epub 2006 Sep 1.
• Ross C, Shen QJ. Computational prediction and experimental verification of HVA1-like abscisicacid responsive promoters in rice (Oryza sativa).Plant Mol Biol. 2006 Sep;62(1-2):233-46. Epub 2006 Jul 15.
• Salzameda B, Facemyer KC, Beck BW, Cremo CR. The N-terminal lobes of both regulatory light chains interact with the taildomain in the 10 S-inhibited conformation of smooth muscle myosin.J Biol Chem. 2006 Dec 15;281(50):38801-11. Epub 2006 Sep 29.
• Suzuki N, Mittler R (2006) Reactive oxygen species and temperature stresses: A delicate balance between signaling and destruction. Physiol. Plant. 126: 45-51.
• Xie, Z., Zhang, Z.L., Zou, X.L., Yang, G.X., Komatsu, S. and Shen, Q.J. 2006. Interactions of two abscisic-acid induced WRKY genes in repressing gibberellin signaling in aleurone cells. Plant Journal, 46: 231-242.

2005

Journals

• Boxall SF, Foster JM, Bohnert HJ, Cushman JC, Nimmo HG, Hartwell J. 2005, Conservation and divergence of the central circadian clock in the stress-inducible CAM plant Mesembryanthemum crystallinum: clock operation in a CAM halophyte reveals clock compensation against abiotic stress. Plant Physiol. 137: 969-982.
• Cramer GR, Cushman JC, Schooley DA, Quilici D, Vincent D, Bohlman MC, Ergül A, Tattersall EAT, Tillett R, Evans J, Delacruz R, Schlauch K, Mendes P. (2005). Progress in bioinformatics – the challenge of integrating transcriptomic, proteomic and metabolomic information. Acta Hort 689: 417-425.
• Davletova S, Rizhsky L, Liang H, Shengqiang Z, Oliver DJ, Coutu J, Shulaev V, Schlauch K, Mittler R (2005) Cytosolic ascorbate peroxidase 1 is a central component of the reactive oxygen gene network of Arabidopsis. Plant Cell 17: 268-281. 0004
• Davletova S, Schlauch K, Coutu J, Mittler R (2005) The zinc-finger protein Zat12 plays a central role in reactive oxygen and abiotic stress signaling in Arabidopsis. Plant Physiol. 139: 847-856.
• Gehrig HH, Wood J, Cushman MA, Virgo A, Cushman JC, Winter K. 2005, Large gene family of phosphoenolpyruvate carboxylase in the Crassulacean acid metabolism plant Kalanchoe pinnata (Crassulaceae). Functional Plant Biology. 32: 467-472. 0002,
• Goes da Silva F, Iandolino A, Lim H, Baek JM, Leslie A, Xu J, Cook DR, and Al-Kayal F, Bohlman MC, Cushman MA, Ergül A, Figueroa R, Kabuloglu EK, Osborne C, Rowe J, Tattersall EA, Cramer GR, Cushman JC. 2005. Characterizing the grape transcriptome: analysis of ESTs from multiple Vitis species and development of a compendium of gene expression during berry development. Plant Physiol. 139: 574-597.
• Kidd T, Abu-Shumays R, Katzen A, Sisson JC, Jimenez G, Pinchin S, Sullivan W, Ish-Horowicz D. 2005. The epsilon-subunit of mitochondrial ATP synthase is required for normal spindle orientation during the Drosophila embryonic divisions. Genetics. 170(2):697-708.
• Kore-eda S, Noake C, Ohishi M, Ohnishi J, Cushman JC. 2005, Transcriptional regulation of organellar metabolite transporters during induction of crassulacean acid metabolism in Mesembryanthemum crystallinum. Functional Plant Biology. 32:451-466.
• Suzuki N, Rizhsky L, Liang H, Shuman J, Shulaev V, Mittler R (2005) Enhanced tolerance to environmental stresses in transgenic plants expressing the transcriptional co-activator MBF1. Plant Physiol. 139, 1313-1322.
• Tattersall EAR, Ergül A, AlKayal F, DeLuc L, Cushman JC, Cramer, Grant R.. 2005, Comparison of methods for isolating high-quality RNA from leaves of grapevine. Amer. J. Vitic. Enol. 56:400-406.
• Xie, Z., Ruas, P. and Shen, Q.J. (2005) Regulatory networks of phytohormone abscisic acid. In Vitamins and Hormones, Edited by Gerald Litwack, Academic Press/Elsevier Science. 2005. 72: 235-269
• Zhen Xie, Zhong-Lin Zhang, Xiaolu Zou, Jie Huang, Paul Ruas, Daniel Thompson and Qingxi J. Shen (2005) Annotations and Functional Analyses of the Rice WRKY Gene Superfamily Reveal Positive and Negative Regulators of Abscisic Acid Signaling in Aleurone Cells.Plant Physiology 137:176-189

Proceedings

• Lyle NJ, Williams I, Brar KR, Beck BW, and Dascalu SM. 2005. Specification of AutomN:An Automatic Protein Sequence to Protein-Protein Interaction Software System. Proceedings of the 2005 International Conference on Software Engineering Research and Practice (SERP'05) Las Vegas, NV; June 27-30, 2005.

2004

• Chen, C, Beck, B. W., Krause,K., and Pettitt, B. M. (2004) Solvent participation in Serratia marcescens endonuclease complexes with DNA. Proteins: Structure, Function, and Bioinformatics 62(4):982-995.
• Dolan, E., Yelle, R., Beck, B., Fischer, J, and Ichiye, T. (2004) Protein Control of Electron Transfer Rates via Polarization: Molecular Dynamics Studies of Rubredoxin. Biophys J. 86(4):2030-2036.
• R. Mittler, S.Vaderauwera, M. Gollery and F. Van Breusegem (2004) The Reactive Oxygen Gene Network of Plants. Trends in Plant Science, Volume 9, Issue 10, October 2004, Pages 490-498.