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Publications

1. Arora, R., C. Manisseri, et al. (2010). "Monitoring and Analyzing Process Streams Towards Understanding Ionic Liquid Pretreatment of Switchgrass (Panicum virgatum L.)." Bioenergy Research 3(2): 134-145.
2. Atmodjo, M. A., Y. Sakuragi, et al. (2011). "GAUT1 and GAUT7 are the core of a plant cell wall pectin biosynthetic homogalacturonan:galacturonosyltransferase complex." Proceedings of the National Academy of Sciences.*
3. Banks, J. A., T. Nishiyama, et al. (2011). "The Selaginella genome identifies genetic changes associated with the evolution of vascular plants." Science 332(6032): 960-963.
4. Bart, R. S., M. Chern, et al. (2010). "Rice Snl6, a cinnamoyl-CoA reductase-like gene family member, is required for NH1-mediated immunity to Xanthomonas oryzae pv. oryzae." PLoS Genet 6(9).
5. Bartley, L. E. and P. C. Ronald (2009). "Plant and microbial research seeks biofuel production from lignocellulose." California Agriculture 63(4): 178-184.
6. Bernal, A. J., C. M. Yoo, et al. (2008). "Functional Analysis of the Cellulose Synthase-Like Genes CSLD1, CSLD2, and CSLD4 in Tip-Growing Arabidopsis Cells." Plant Physiology 148(3): 1238-1253.
7. Blanch, H. W. (2011). "Bioprocessing for biofuels." Current Opinion in Biotechnology 23: 1-6.*
8. Blanch, H. W., P. D. Adams, et al. (2008). "Addressing the need for alternative transportation fuels: The Joint BioEnergy Institute." ACS Chemical Biology 3(1): 17-20.
9. Cao, P. J., L. E. Bartley, et al. (2008). "Construction of a rice glycosyltransferase phylogenomic database and identification of rice-diverged glycosyltransferases." Molecular Plant 1(5): 858-877.
10. Cao, P. J., K. H. Jung, et al. (2010). "A Survey of Databases for Analysis of Plant Cell Wall-Related Enzymes." Bioenergy Research 3(2): 108-114.
11. Chou, H. H., A. Trisiriroj, et al. (2009). "Direct calibration of PICKY-designed microarrays." BMC Bioinformatics 10(347): 1-11.
12. Christensen, U., A. Alonso-Simon, et al. (2010). "Characterization of the primary cell walls of seedlings of Brachypodium distachyon - A potential model plant for temperate grasses." Phytochemistry 71(1): 62-69.
13. Christensen, U. and H. V. Scheller (2011). "Regulation of (1,3;1,4)-ß-D-glucan synthesis in developing endosperm of barley lys mutants." Journal of Cereal Science: 1-8.*
14. Durek, P., R. Schmidt, et al. (2010). "PhosPhAt: the Arabidopsis thaliana phosphorylation site database. An update." Nucleic Acids Research 38: D828-D834.
15. Eudes, A., E. E. Baidoo, et al. (2011). "Production of tranilast [N-(3',4'-dimethoxycinnamoyl)-anthranilic acid] and its analogs in yeast Saccharomyces cerevisiae." Applied Microbiology and Biotechnology 89(4): 989-1000.
16. Fedoroff, N. V., D. S. Battisti, et al. (2010). "Radically Rethinking Agriculture for the 21st Century." Science 327(5967): 833-834.
17. Geshi, N., B. L. Petersen, et al. (2010). "Toward tailored synthesis of functional polysaccharides in plants." Foods for Health in the 21st Century: A Road Map for the Future 1190: 50-57.
18. Harholt, J., I. C. Bach, et al. (2010). "Generation of transgenic wheat (Triticum aestivum L.) accumulating heterologous endo-xylanase or ferulic acid esterase in the endosperm." Plant Biotechnology Journal 8(3): 351-362.
19. Harholt, J., A. Suttangkakul, et al. (2010). "Biosynthesis of Pectin." Plant Physiology 153(2): 384-395.
20. Heazlewood, J. L. (2011). "The Green proteome: challenges in plant proteomics." Frontiers in Plant Proteomics: 1-5.
21. Heazlewood, J. L. and C. J. Petzold (2011). Proteomics - Applications in Biology. Rijeka, Croatia, InTech.*
22. Ito, J., T. S. Batth, et al. (2011). "Analysis of the Arabidopsis cytosolic proteome highlights subcellular partitioning of central plant metabolism." Journal of Proteome Research 10(4): 1571-1582.
23. Ito, J., C. J. Petzold, et al. (2010). "The Role of Proteomics in the Development of Cellulosic Biofuels." Current Proteomics 7(2): 121-134.
24. Ito, J., N. L. Taylor, et al. (2009). "A survey of the Arabidopsis thaliana mitochondrial phosphoproteome." Proteomics 9(17): 4229-4240.
25. Jensen, J. K., S. O. Sorensen, et al. (2008). "Identification of a xylogalacturonan xylosyltransferase involved in pectin biosynthesis in Arabidopsis." Plant Cell 20(5): 1289-1302.
26. Joshi, H. J., M. Hirsch-Hoffmann, et al. (2011). "MASCP Gator: an aggregation portal for the visualization of Arabidopsis proteomics data." Plant Physiology 155(1): 259-270.
27. Jung, K. H., L. E. Bartley, et al. (2009). "Analysis of Alternatively Spliced Rice Transcripts Using Microarray Data." Rice 2(1): 44-55.
28. Jung, K. H., P. Cao, et al. (2010). "The Rice Kinase Phylogenomics Database: a guide for systematic analysis of the rice kinase super-family." Trends in Plant Science 15(11).
29. Jung, K. H., C. Dardick, et al. (2008). "Refinement of Light-Responsive Transcript Lists Using Rice Oligonucleotide Arrays: Evaluation of Gene-Redundancy." Plos One 3(10): e3337.
30. Jung, K. H., Y. S. Seo, et al. (2010). "The Submergence Tolerance Regulator Sub1A Mediates Stress-Responsive Expression of AP2/ERF Transcription Factors." Plant Physiology 152(3): 1674-1692.
31. Lalonde, S., A. Sero, et al. (2010). "A membrane protein/signaling protein interaction network for Arabidopsis version AMPv2." Frontiers in Physiology 1: 24.
32. Landau, A. M., H. Lokstein, et al. (2009). "A cytoplasmically inherited barley mutant is defective in photosystem I assembly due to a temperature-sensitive defect in ycf3 splicing." Plant Physiology 151: 1802-1811.
33. Lee, I., Y. S. Seo, et al. (2011). "Genetic dissection of the biotic stress response using a genome-scale gene network for rice." Proceedings of National Academy of Sciences 108(45): 18548-18553.
34. Li, C., B. Knierim, et al. (2010). "Comparison of dilute acid and ionic liquid pretreatment of switchgrass: Biomass recalcitrance, delignification and enzymatic saccharification." Bioresource Technology 101(13): 4900-4906.
35. Liepman, A. H., R. Wightman, et al. (2010). "Arabidopsis - a powerful model system for plant cell wall research." Plant Journal 61(6): 1107-1121.
36. Loque, D., A. Eudes, et al. (2011). Biomass Availability and Sustainability for BioFuels. Chemical and Biochemical Catalysis for Next Generation Biofuels. B. A. Simmons, Royal Society of Chemistry: 5-32.
37. Loque, D., S. I. Mora, et al. (2009). "Pore mutations in ammonium transporter AMT1 with increased electrogenic ammonium transport activity." Journal of Biological Chemistry 284(37): 24988-24995.
38. Manabe, Y., M. Nafisi, et al. (2011). "Loss-of-Function Mutation of REDUCED WALL ACETYLATION2 in Arabidopsis Leads to Reduced Cell Wall Acetylation and Increased Resistance to Botrytis cinerea." Plant Physiology 155(3): 1068-1078.
39. Meng, M., M. Geisler, et al. (2009). "UDP-glucose pyrophosphorylase is not rate limiting, but is essential in Arabidopsis." Plant Cell Physiology 50(5): 998-1011.
40. Oikawa, A., H. J. Joshi, et al. (2010). "An integrative approach to the identification of Arabidopsis and rice genes involved in xylan and secondary wall development." PLoS One 5(11): e15481.
41. Parsons, H. T., J. Ito, et al. (2011). The current state of the Golgi proteomes. Proteomics - Applications in Biology. J. L. Heazlewood and C. J. Petzold. Rijeka, Croatia, InTech.*
42. Petersen, B. L., J. Egelund, et al. (2009). "Assay and heterologous expression in Pichia pastoris of plant cell wall type-II membrane anchored glycosyltransferases." Glycoconjugate Journal 26(9): 1235-1246.
43. Rautengarten, C., E. Baidoo, et al. (2010). "A Simple Method for Enzymatic Synthesis of Unlabeled and Radiolabeled Hydroxycinnamate-CoA." BioEnergy Research 3(2): 115-122.
44. Rautengarten, C., B. Ebert, et al. (2011). "The interconversion of UDP-arabinopyranose and UDP-arabinofuranose is indispensable for plant development in Arabidopsis." Plant Cell 23(4): 1373-1390.
45. Ronald, P. (2011). "Plant genetics, sustainable agriculture and global food security." Genetics 188(1): 11-20.
46. Ronald, P. and R. Adamchak (2010). "The future of sustainable food production." Annals of the New York Academy of Sciences 1190(1): 184-185.
47. Ronald, P. C. and B. Beutler (2010). "Plant and animal sensors of conserved microbial signatures." Science 330(6007): 1061-1064.
48. Sakuragi, Y., M. H. Norholm, et al. (2011). Visual mapping of cell wall biosynthesis. The Plant Cell Wall: Methods and Protocols. Z. A. Popper. Berlin, Germany, Springer Science. 715: 153-167.
49. Scheller, H. V., S. Singh, et al. (2010). "The Joint BioEnergy Institute (JBEI): Developing New Biofuels by Overcoming Biomass Recalcitrance." BioEnergy Research 3(2): 105-107.
50. Scheller, H. V. and P. Ulvskov (2010). "Hemicelluloses." Annual Review of Plant Biology 61: 263-289.
51. Seo, Y. S., M. Chern, et al. (2011). "Towards establishment of a rice stress response interactome." PLoS Genet 7(4): e1002020.
52. Sharma, R., F. Tan, et al. (2011). "Transcriptional dynamics during cell wall removal and regeneration reveals key genes involved in cell wall development in rice." Plant Molecular Biology 77(4-5): 391-406.
53. Simmons, B. A., D. Loque, et al. (2008). "Next-generation biomass feedstocks for biofuel production." Genome Biology 9(12): 242.
54. Simmons, B. A., D. Loque, et al. (2010). "Advances in modifying lignin for enhanced biofuel production." Current Opinion in Plant Biology 13(3): 313-320.
55. Smith-Moritz, A. M., C. Mawsheng, et al. (2011). "Combining multivariate analysis and monosaccharide composition modeling to identify plant cell wall variations by Fourier Transform Near Infrared spectroscopy." Plant Methods 7(26).
56. Sun, L., P. Varanasi, et al. (2011). "Rapid determination of syringyl: Guaiacyl ratios using FT-Raman spectroscopy." Biotechnology and Bioengineering.*
57. Taylor, N. L., J. L. Heazlewood, et al. (2011). "The Arabidopsis thaliana 2-D gel mitochondrial proteome: Refining the value of reference maps for assessing protein abundance, contaminants and post-translational modifications." Proteomics 11(9): 1720–1733.
58. Vega-Sanchez, M. E. and P. C. Ronald (2010). "Genetic and biotechnological approaches for biofuel crop improvement." Current Opinion Biotechnology 21(2): 218-224.
59. Verhertbruggen, Y., L. Yin, et al. (2011). "Mannan synthase activity in the CSLD family." Plant Signaling & Behavior 6(10): 1620-1623.
60. Vogel, J., D. Garvin, et al. (2010). "Genome sequence analysis of the model grass Brachypodium distachyon: insights into grass genome evolution." Nature 463(2): 763-768.
61. Weckwerth, W., S. Baginsky, et al. (2008). "The multinational Arabidopsis steering subcommittee for proteomics assembles the largest proteome database resource for plant systems biology." Journal of Proteome Research 7(10): 4209-4210.
62. Yin, L., Y. Verhertbruggen, et al. (2011). "The Cooperative Activities of CSLD2, CSLD3, and CSLD5 Are Required for Normal Arabidopsis Development." Molecular Plant 4(6): 1024-1037.