| Fiscal Year 2013 |
| Chiniquy, D., Sharma, V., Schultink, A., Baidoo, E. E., Rautengarten, C., Cheng, K., Carroll, A., Ulvskov, P., Harholt, J., Keasling, J. D., Pauly, M., Scheller, H. V. and Ronald, P. C. (2012). "XAX1 from glycosyltransferase family 61 mediates xylosyltransfer to rice xylan." Proc Natl Acad Sci U S A 109(42): 17117-17122. |
| Chivian, D., Dehal, P. S., Keller, K. and Arkin, A. P. (2013). "MetaMicrobesOnline: phylogenomic analysis of microbial communities." Nucleic Acids Res 41(Database issue): D648-654. |
| Dietrich, J.A., Shis, D.L., Alikhani , A. and Keasling, J.D. (2012). "Transcription Factor-Based Screens and Synthetic Selections for Microbial Small-Molecule Biosynthesis." ACS Synth Biol. DOI: 10.1021/sb300091d |
| Goldberg, A., Linshiz, G., Koudritsky, M., Chemodanov, A., and Hillson, N.J. (2012). "Distributed marine biorefineries for developing economies". Proceedings of the ASME 2012 International Mechanical Engineering Congress & Exposition. IMECE2012-86051. |
| Linshiz, G., Goldberg, A., Konry, T., and Hillson, N.J. (2013). "The Fusion of Biology, Computer Science, and Engineering – towards efficient and successful synthetic biology." Perspectives in Biology and Medicine 55 (4), 503-520. DOI: 10.1353/pbm.2012.0044 |
| Paap, S. M., T. H. West, D. K. Manley, E. J. Steen, H. R. Beller, J. D. Keasling, D. C. Dibble, S. Chang, B. A. Simmons. 2013. "Biochemical production of ethanol and fatty acid ethyl esters from switchgrass: analysis of environmental and economic performance." Biomass and Bioenergy 49:49-62 |
| Parsons, H. T., Drakakaki, G. and Heazlewood, J. L. (2012). "Proteomic dissection of the Arabidopsis Golgi and trans-Golgi network." Front Plant Sci 3: 298. |
| Pereira, J. H., Goh, E. B., Keasling, J. D., Beller, H. R. and Adams, P. D. (2012). "Structure of FabH and factors affecting the distribution of branched fatty acids in Micrococcus luteus." Acta Crystallogr D Biol Crystallogr 68(Pt 10): 1320-1328. |
| Perez-Pimienta, J. A., Lopez-Ortega, M. G., Varanasi, P., Stavila, V., Cheng, G., Singh, S. and Simmons, B. A. (2013). "Comparison of the impact of ionic liquid pretreatment on recalcitrance of agave bagasse and switchgrass." Bioresour Technol 127: 18-24. |
| Persil-Cetinkol O, Smith-Moritz AM, Cheng G, Lao J, George A, Hong K, Henry R, Simmons B, Heazlewood JL, Holmes BM (2012) "Structural and chemical characterization of hardwood from tree species with applications as bioenergy feedstocks." PLOS ONE. 7: e52820. doi: 52810.51371/journal.pone.0052820. |
| Petersen PD, Lau J, Ebert B, Yang F, Verhertbruggen Y, Kim JS, Varanasi P, Suttangkakul A, Auer M, Loqué D, Scheller HV (2012). "Engineering of plants with improved properties as biofuels feedstocks by vessel-specific complementation of xylan biosynthesis mutants." Biotechnology for Biofuels. 2012 Nov 26;5(1):84. doi: 10.1186/1754-6834-5-84 |
| Reddy, A. P., Simmons, C. W., Claypool, J., Jabusch, L., Burd, H., Hadi, M. Z., Simmons, B. A., Singer, S. W. and Vandergheynst, J. S. (2012). "Thermophilic enrichment of microbial communities in the presence of the ionic liquid 1-ethyl-3-methylimidazolium acetate." J Appl Microbiol ;113(6):1362-70 |
| Shi, J., Thompson, V. S., Yancey, N. A., Stavila, V., Simmons, B. A. and Singh, S. (2013). "Impact of mixed feedstocks and feedstock densification on ionic liquid pretreatment efficiency." Biofuels 4(1): 63-72. |
| Varanasi, P., Singh, P., Arora, R., Adams, P. D., Auer, M., Simmons, B. A. and Singh, S. (2012). "Understanding changes in lignin of Panicum virgatum and Eucalyptus globulus as a function of ionic liquid pretreatment." Bioresour Technol 126C: 156-161. |
| Varanasi, P., Singh, P., Auer, M., Adams, P. D., Simmons, B. A. and Singh, S. (2013). "Survey of renewable chemicals produced from lignocellulosic biomass during ionic liquid pretreatment." Biotechnol Biofuels 6(1): 14. |
| Vega-Sanchez ME, Verhertbruggen Y, Scheller HV, Ronald PC. 2013. "Abundance of mixed linkage glucan in mature tissues and secondary cell walls of grasses." Plant Signaling and Behavior, 8:2, e23143 |
| Yeh, Y. C., Muller, J., Bi, C., Hillson, N. J., Beller, H. R., Chhabra, S. R. and Singer, S. W. (2013). "Functionalizing bacterial cell surfaces with a phage protein." Chem Commun (Camb) 49(9): 910-912. |
| Zhang, F., Ouellet, M., Batth, T. S., Adams, P. D., Petzold, C. J., Mukhopadhyay, A. and Keasling, J. D. (2012). "Enhancing fatty acid production by the expression of the regulatory transcription factor FadR." Metab Eng 14(6): 653-660. |
| Fiscal Year 2012 |
| Agrawal, G. K., Sarkar, A., Agrawal, R., Ndimba, B. K., Tanou, G., Dunn, M. J., Kieselbach, T., Cramer, R., Wienkoop, S., Chen, S., Rafudeen, M. S., Deswal, R., Barkla, B. J., Weckwerth, W., Heazlewood, J. L., Renaut, J., Job, D., Chakraborty, N. and Rakwal, R. (2012). "Boosting the globalization of plant proteomics through INPPO: current developments and future prospects." Proteomics 12(3): 359-368. |
| Atmodjo, M. A., Sakuragi, Y., Zhu, X., Burrell, A. J., Mohanty, S. S., Atwood, J. A., 3rd, Orlando, R., Scheller, H. V. and Mohnen, D. (2011). "Galacturonosyltransferase (GAUT)1 and GAUT7 are the core of a plant cell wall pectin biosynthetic homogalacturonan:galacturonosyltransferase complex." Proceedings of the National Academy of Sciences 108(50): 20225-20230. |
| Batth, T. S., Keasling, J. D. and Petzold, C. J. (2012). Targeted Proteomics for Metabolic Pathway Optimization. |
| Beller, H. R., T. C. Legler, and S. R. Kane. 2012 (Book chapter). "Genetic manipulation of the obligate chemolithoautotrophic bacterium Thiobacillus denitrificans", vol. 881, pp. 99-136, In Microbial Systems Biology: Methods and Protocols [Methods in Molecular Biology series], A. Navid (ed.), Springer Science. DOI 10.1007/978-1-61779-827-6_5. |
| Bennetzen, J. L., Schmutz, J., Wang, H., Percifield, R., Hawkins, J., Pontaroli, A. C., Estep, M., Feng, L., Vaughn, J. N., Grimwood, J., Jenkins, J., Barry, K., Lindquist, E., Hellsten, U., Deshpande, S., Wang, X., Wu, X., Mitros, T., Triplett, J., Yang, X., Ye, C. Y., Mauro-Herrera, M., Wang, L., Li, P., Sharma, M., Sharma, R., Ronald, P. C., Panaud, O., Kellogg, E. A., Brutnell, T. P., Doust, A. N., Tuskan, G. A., Rokhsar, D. and Devos, K. M. (2012). "Reference genome sequence of the model plant Setaria." Nat Biotechnol 30(6): 555-561. |
| Blanch, H. W. (2012). "Bioprocessing for biofuels." Curr Opin Biotechnol 23(3): 390-395. |
| Bokinsky, G., Peralta-Yahya, P. P., George, A., Holmes, B. M., Steen, E. J., Dietrich, J., Soon Lee, T., Tullman-Ercek, D., Voigt, C. A., Simmons, B. A. and Keasling, J. D. (2011). "Synthesis of three advanced biofuels from ionic liquid-pretreated switchgrass using engineered Escherichia coli." Proceedings of the National Academy of Sciences 108(50): 19949-19954. |
| Cao, P. J. and Ronald, P. C. (2012). "The rice oligonucleotide array database: an atlas of rice gene expression." Rice. |
| Carothers, J. M., Goler, J. A., Juminaga, D. and Keasling, J. D. (2011). "Model-driven engineering of RNA devices to quantitatively program gene expression." Science 334(6063): 1716-1719. |
| Casler, M., Tobias, C., Kaeppler, S., Buell, C. R., Wang, Z.-Y., Cao, P., Schmutz, J. and Ronald, P. (2011). "The Switchgrass Genome: Tools and Strategies." Plant Genome 4(3): 273-282. |
| Chen, J., Densmore, D., Ham, T. S., Keasling, J. D. and Hillson, N. J. (2012). "DeviceEditor visual biological CAD canvas." J Biol Eng 6(1): 1. |
| Chen, Z., Friedland, G. D., Pereira, J. H., Reveco, S., Chan, R., Park, J. I., Thelen, M. P., Adams, P. D., Arkin, A. P., Keasling, J. D., Blanch, H. W., Simmon, B. A., Sale, K., Chivian, D. and Chhabra, S. R. (2012). "Tracing the determinants of dual-substrate specificity in a diverse subfamily of family 5 glycoside hydrolases." J Bio Chem. |
| Cheng, G., Datta, S., Liu, Z., Wang, C., Murton, J. K., Brown, P. A., Jablin, M. S., Dubey, M., Majewski, J., Halbert, C. E., Browning, J. F., Esker, A. R., Watson, B. J., Zhang, H., Hutcheson, S. W., Huber, D. L., Sale, K. L., Simmons, B. A. and Kent, M. S. (2012). "Interactions of endoglucanases with amorphous cellulose films resolved by neutron reflectometry and quartz crystal microbalance with dissipation monitoring." Langmuir 28(22): 8348-8358. |
| Cheng, G., Kent, M. S., He, L., Varanasi, P., Dibble, D., Arora, R., Deng, K., Hong, K., Melnichenko, Y. B., Simmons, B. A. and Singh, S. (2012). "Effect of ionic liquid treatment on the structures of lignins in solutions: molecular subunits released from lignin." Langmuir 28(32): 11850-11857. |
| Cheng, G., Varanasi, P., Arora, R., Stavila, V., Simmons, B. A., Kent, M. S. and Singh, S. (2012). "Impact of Ionic Liquid Pretreatment Conditions on Cellulose Crystalline Structure Using 1-Ethyl-3-methylimidazolium Acetate." Journal of Physical Chemistry B 116(33): 10049-10054. |
| Christensen, U. and Scheller, H. V. (2012). "Regulation of (1,3;1,4)-β-D-glucan synthesis in developing endosperm of barley lys mutants." Journal of Cereal Science 55(1): 69-76. |
| Chuck, G. S., Tobias, C., Sun, L., Kraemer, F., Li, C., Dibble, D., Arora, R., Bragg, J. N., Vogel, J. P., Singh, S., Simmons, B. A., Pauly, M. and Hake, S. (2011). "Overexpression of the maize Corngrass1 microRNA prevents flowering, improves digestibility, and increases starch content of switchgrass." Proceedings of National Academy of Sciences 108(42): 17550-17555. |
| De Michele, R., Loque, D., Lalonde, S. and Frommer, W. B. (2012). "Ammonium and urea transporter inventory of the selaginella and physcomitrella genomes." Front Plant Sci 3(62): 62. |
| DeAngelis, K. M., Fortney, J. L., Borglin, S., Silver, W. L., Simmons, B. A. and Hazen, T. C. (2012). "Anaerobic decomposition of switchgrass by tropical soil-derived feedstock-adapted consortia." MBio 3(1). |
| Deng K, George KW, Reindl W, Keasling JD, Adams PA, Lee TS, Singh AK, Northen TR, Encoding substrates with mass tags to resolve stereospecific reactions using Nimzyme, RCM 2012 Mar 30;26(6):611-5. doi: 10.1002/rcm.6134. |
| Dibble, D., Li , C., Sun, L., George, A., Cheng, A., Çetinkol, O., Benke, P., Holmes, B., Singh, S. and Simmons, B. A. (2011). "A facile method for the recovery of ionic liquid and lignin from biomass pretreatment." Green Chemistry 13(11): 3255-3264. |
| Dougherty, M. J., D'Haeseleer, P., Hazen, T. C., Simmons, B. A., Adams, P. D. and Hadi, M. Z. (2012). "Glycoside Hydrolases from a targeted Compost Metagenome, activity-screening and functional characterization." BMC Biotechnol 12: 38. |
| Eudes, A., George, A., Mukerjee, P., Kim, J. S., Pollet, B., Benke, P. I., Yang, F., Mitra, P., Sun, L., Cetinkol, O. P., Chabout, S., Mouille, G., Soubigou-Taconnat, L., Balzergue, S., Singh, S., Holmes, B. M., Mukhopadhyay, A., Keasling, J. D., Simmons, B. A., Lapierre, C., Ralph, J. and Loque, D. (2012). "Biosynthesis and incorporation of side-chain-truncated lignin monomers to reduce lignin polymerization and enhance saccharification." Plant Biotechnol J 10(5): 609-620. |
| George, A., Tran, K., Morgan, T. J., Benke, P., Berrueco, C., Lorente, E., Wu, B., Keasling, J. D., Simmon, B. A. and Holmes, B. (2011). "The effect of ionic liquid cation and anion combinations on the macromolecular structure of lignins." Green Chemistry 13(12): 3375-3385. |
| Gladden, J. M., Eichorst, S. A., Hazen, T. C., Simmons, B. A. and Singer, S. W. (2012). "Substrate perturbation alters the glycoside hydrolase activities and community composition of switchgrass-adapted bacterial consortia." Biotechnol Bioeng 109(5): 1140-1145. |
| Goh, E. B., Baidoo, E. E., Keasling, J. D. and Beller, H. R. (2012). "Engineering of bacterial methyl ketone synthesis for biofuels." Applied and Environmental Microbiology 78(1): 70-80. |
| Greving, M., Cheng, X. L., Reindl, W., Bowen, B., Deng, K., Louie, K., Nyman, M., Cohen, J., Singh, A., Simmons, B., Adams, P., Siuzdak, G. and Northen, T. (2012). "Acoustic deposition with NIMS as a high-throughput enzyme activity assay." Analytical and Bioanalytical Chemistry 403(3): 707-711. |
| Groff, D., Benke, P. I., Batth, T. S., Bokinsky, G., Petzold, C. J., Adams, P. D. and Keasling, J. D. (2012). "Supplementation of intracellular XylR leads to coutilization of hemicellulose sugars." Appl Environ Microbiol 78(7): 2221-2229. |
| Ham, T. S., Dmytriv, Z., Plahar, H., Chen, J., Hillson, N. J. and Keasling, J. D. (2012). "Design, implementation and practice of JBEI-ICE: an open source biological part registry platform and tools." Nucleic Acids Res 40(18): e141. |
| Hansen, S. F., Harholt, J., Oikawa, A. and Scheller, H. V. (2012). "Plant Glycosyltransferases Beyond CAZy: A Perspective on DUF Families." Front Plant Sci 3(59): 59. |
| Harholt, J., Jensen, J. K., Verhertbruggen, Y., Sogaard, C., Bernard, S., Nafisi, M., Poulsen, C. P., Geshi, N., Sakuragi, Y., Driouich, A., Knox, J. P. and Scheller, H. V. (2012). "ARAD proteins associated with pectic Arabinan biosynthesis form complexes when transiently overexpressed in planta." Planta 236(1): 115-128. |
| Harholt, J., Sorensen, I., Fangel, J., Roberts, A., Willats, W. G., Scheller, H. V., Petersen, B. L., Banks, J. A. and Ulvskov, P. (2012). "The glycosyltransferase repertoire of the spikemoss Selaginella moellendorffii and a comparative study of its cell wall." PLoS One 7(5): e35846. |
| Heazlewood, J. L. and Petzold, C. J. (2012). Proteomics - Applications in Biology. Rijeka, Croatia, InTech. |
| Hillson, N. J., Rosengarten, R. D. and Keasling, J. D. (2012). "j5 DNA Assembly Design Automation Software." ACS Synthetic Biology 1(1): 14-21. |
| Jones, A. M., Aebersold, R., Ahrens, C. H., Apweiler, R., Baerenfaller, K., Baker, M., Bendixen, E., Briggs, S., Brownridge, P., Brunner, E., Daube, M., Deutsch, E. W., Grossniklaus, U., Heazlewood, J., Hengartner, M. O., Hermjakob, H., Jovanovic, M., Lawless, C., Lochnit, G., Martens, L., Ravnsborg, C., Schrimpf, S. P., Shim, Y. H., Subasic, D., Tholey, A., Wijk, K., Mering, C., Weiss, M. and Zheng, X. (2012). "The HUPO initiative on Model Organism Proteomes, iMOP." Proteomics 12(3): 340-345. |
| Joshi, H. J., Christiansen, K. M., Fitz, J., Cao, J., Lipzen, A., Martin, J., Smith-Moritz, A. M., Pennacchio, L. A., Schackwitz, W. S., Weigel, D. and Heazlewood, J. L. (2012). "1001 Proteomes: a functional proteomics portal for the analysis of Arabidopsis thaliana accessions." Bioinformatics 28(10): 1303-1306. |
| Juminaga, D., Baidoo, E. E., Redding-Johanson, A. M., Batth, T. S., Burd, H., Mukhopadhyay, A., Petzold, C. J. and Keasling, J. D. (2012). "Modular Engineering of L-Tyrosine Production in Escherichia coli." Applied and Environmental Microbiology 78(1): 89-98. |
| Khudyakov, J., D'Haeseleer, P., Borglin, S., DeAngelis, K. M., H., W., Lindquist, E., Hazen, T., Simmons, B. S. and Thelen, M. P. (2012). "Global transcriptome response to ionic liquid by a tropical rain forest soil bacterium, Enterobacter lignolyticus SCF1." Proceedings of National Academy of Sciences 109(32): E2173-E2182. |
| Klein-Marcuschamer, D., Oleskowicz-Popiel, P., Simmons, B. A. and Blanch, H. W. (2012). "The challenge of enzyme cost in the production of lignocellulosic biofuels." Biotechnology and Bioengineering 109(4): 1083-1087. |
| Knight, R., Jansson, J., Field, D., Fierer, N., Desai, N., Fuhrman, J. A., Hugenholtz, P., van der Lelie, D., Meyer, F., Stevens, R., Bailey, M. J., Gordon, J. I., Kowalchuk, G. A. and Gilbert, J. A. (2012). "Unlocking the potential of metagenomics through replicated experimental design." Nature Biotechnology 30(6): 513-520. |
| Lee, I., Seo, Y. S., Coltrane, D., Hwang, S., Oh, T., Marcotte, E. M. and Ronald, P. C. (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. |
| Li, C., Sun, L., Simmons, B. A. and Singh, S. (2012). "Comparing the Recalcitrance of Eucalyptus, Pine, and Switchgrass Using Ionic Liquid and Dilute Acid Pretreatments." Bioenergy Research. |
| Linshiz, G., Stawski, N., Poust, S., Bi, C., Keasling, J.D., and Hillson, N.J. (2012). "PaR-PaR Laboratory Automation platform." ACS Synthetic Biology. DOI: 10.1021/sb300075t |
| Liu, H., Cheng, G., Kent, M., Stavila, V., Simmons, B. A., Sale, K. L. and Singh, S. (2012). "Simulations Reveal Conformational Changes of Methylhydroxyl Groups during Dissolution of Cellulose I(beta) in Ionic Liquid 1-Ethyl-3-methylimidazolium Acetate." J Phys Chem B 116(28): 8131-8138. |
| McAndrew, R. P., Peralta-Yahya, P. P., Degiovanni, A., Pereira, J. H., Hadi, M. Z., Keasling, J. D. and Adams, P. D. (2011). "Structure of a three-domain sesquiterpene synthase: a prospective target for advanced biofuels production." Structure 19(12): 1876-1884. |
| McClendon, S. D., Baath, T., Petzold, C. J., Adams, P. D., Simmons, B. A. and Singer, S. W. (2012). "Thermoascus aurantiacus is a promising source of enzymes for biomass deconstruction under thermophilic conditions." Biotechnol Biofuels 5(1): 54. |
| McKee, A. E., Rutherford, B. J., Chivian, D. C., Baidoo, E. K., Juminaga, D., Kuo, D., Benke, P. I., Dietrich, J. A., Ma, S. M., Arkin, A. P., Petzold, C. J., Adams, P. D., Keasling, J. D. and Chhabra, S. R. (2012). "Manipulation of the carbon storage regulator system for metabolite remodeling and biofuel production in Escherichia coli." Microb Cell Fact 11(1): 79. |
| Mukhopadhyay, A., Hillson, N. J. and Keasling, J. D. (2012). Control of Stress Tolerance in Bacterial Host Organisms for Bioproduction of Fuels. Microbial Stress Tolerance: From Genomics to Biofuels. Z. L. Liu. Berlin / Heidelberg, Springer-Verlag. 22: 209-238. |
| Oikawa, A., Lund, C. H., Sakuragi, Y. and Scheller, H. V. (2012). "Golgi-localized enzyme complexes for plant cell wall biosynthesis." Trends Plant Sci. |
| Oleskowicz-Popiel, P., Kadar, Z., Heiske, S., Klein-Marcuschamer, D., Simmons, B. A., Blanch, H. W. and Schmidt, J. E. (2012). "Co-production of ethanol, biogas, protein fodder and natural fertilizer in organic farming--evaluation of a concept for a farm-scale biorefinery." Bioresour Technol 104(2012): 440-446. |
| Orfila, C., Degan, F. D., Jorgensen, B., Scheller, H. V., Ray, P. M. and Ulvskov, P. (2012). "Expression of mung bean pectin acetyl esterase in potato tubers: effect on acetylation of cell wall polymers and tuber mechanical properties." Planta 236(1): 197. |
| Ouellet, M., Datta, S., Dibble, D. C., Tamrakar, P. R., Benke, P., Li, C., Singh, S., Sale, K. L., Adams, P. D., Keasling, J. D., Simmons, B. A., Holmes, B. M. and Mukhopadhyay, A. (2011). "Impact of ionic liquid pretreated plant biomass on Saccharomyces cerevisiae growth and biofuel production." Green Chemistry 13(10): 2743-2749. |
| Ozaydin, B., Burd, H., Lee, T. S. and Keasling, J. D. (2012). "Carotenoid-based phenotypic screen of the yeast deletion collection reveals new genes with roles in isoprenoid production." Metab Eng. |
| Papa, G., Varanasi, P., Sun, L., Cheng, G., Stavila, V., Holmes, B., Simmons, B. A., Adani, F. and Singh, S. (2012). "Exploring the effect of different plant lignin content and composition on ionic liquid pretreatment efficiency and enzymatic saccharification of Eucalyptus globulus L. mutants." Bioresour Technol 117: 352-359. |
| Park, J. I., Steen, E. J., Burd, H., Evans, S. S., Redding-Johnson, A. M., Batth, T., Benke, P. I., D'Haeseleer, P., Sun, N., Sale, K. L., Keasling, J. D., Lee, T. S., Petzold, C. J., Mukhopadhyay, A., Singer, S. W., Simmons, B. A. and Gladden, J. M. (2012). "A thermophilic ionic liquid-tolerant cellulase cocktail for the production of cellulosic biofuels." PLoS One 7(5): e37010. |
| Parsons, H. T., Christiansen, K., Knierim, B., Carroll, A., Ito, J., Batth, T. S., Smith-Moritz, A. M., Morrison, S., McInerney, P., Hadi, M. Z., Auer, M., Mukhopadhyay, A., Petzold, C. J., Scheller, H. V., Loque, D. and Heazlewood, J. L. (2012). "Isolation and proteomic characterization of the Arabidopsis Golgi defines functional and novel components involved in plant cell wall biosynthesis." Plant Physiol 159(1): 12-26. |
| Parsons, H. T., Ito, J., Park, E., Carroll, A. W., Joshi, H. J., Petzold, C. J., Drakakaki, G. and Heazlewood, J. L. (2012). The current state of the Golgi proteomes. Proteomics - Applications in Biology. J. L. Heazlewood and C. J. Petzold. Rijeka, Croatia, InTech. |
| Rautengarten, C., Ebert, B., Ouellet, M., Nafisi, M., Baidoo, E. E., Benke, P., Stranne, M., Mukhopadhyay, A., Keasling, J. D., Sakuragi, Y. and Scheller, H. V. (2012). "Arabidopsis Deficient in Cutin Ferulate encodes a transferase required for feruloylation of omega-hydroxy fatty acids in cutin polyester." Plant Physiol 158(2): 654-665. |
| Rennie, E. A., Hansen, S. F., Baidoo, E. E., Hadi, M. Z., Keasling, J. D. and Scheller, H. V. (2012). "Three members of the Arabidopsis glycosyltransferase family 8 are xylan glucuronosyltransferases." Plant Physiol 159(4): 1408-1417. |
| Rutherford, B. J. and Mukhopadhyay, A. (2012). "Host Engineering for Biofuel-Tolerant Phenotypes." Microbial Biotechnology: Energy and Environment. R. Arora. Wallingford, UK, CABI. |
| Satoh, Y., Tajima, K., Munekata, M., Keasling, J. D. and Lee, T. S. (2012). "Engineering of a tyrosol-producing pathway, utilizing simple sugar and the central metabolic tyrosine, in Escherichia coli." J Agric Food Chem 60(4): 979-984. |
| Satoh, Y., Tajima, K., Munekata, M., Keasling, J. D. and Lee, T. S. (2012). "Engineering of l-tyrosine oxidation in Escherichia coli and microbial production of hydroxytyrosol." Metab Eng 14(6): 603-610. |
| Schrimpf, S. P., von Mering, C., Bendixen, E., Heazlewood, J. L., Bumann, D., Omenn, G. and Hengartner, M. O. (2012). "The initiative on Model Organism Proteomes (iMOP) Session September 6, 2011, Geneva, Switzerland." Proteomics 12(3): 346-350. |
| Sharma, M. K., Sharma, R., Cao, P., Jenkins, J., Bartley, L. E., Qualls, M., Grimwood, J., Schmutz, J., Rokhsar, D. and Ronald, P. C. (2012). "A genome-wide survey of switchgrass genome structure and organization." PLoS One 7(4): e33892. |
| Sharma, R., Tan, F., Jung, K. H., Sharma, M. K., Peng, Z. and Ronald, P. C. (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. |
| Shepherd, M., Bartle, J., Lee, D. J., Brawner, J., Bush, D., Turnbull, P., Macdonel, P., Brown, T. R., Simmon, B. A. and Henry, R. (2011). "Eucalypts as a biofuel feedstock." Biofuels 2(6): 639-657. |
| Simmons, B. A. (2011). Bioenergy from Plants and Plant Residues. Plant Biotechnology and Agriculture - Prospects for the 21st Century. A. Altman and P. M. Hasegawa. Oxford, Academic Press: 495-506. |
| Singh, P., Batth, T. S., Juminaga, D., Dahl, R. H., Keasling, J. D., Adams, P. D. and Petzold, C. J. (2012). "Application of targeted proteomics to metabolically engineered Escherichia coli." Proteomics 12(8): 1289-1299. |
| Sogaard, C., Stenbaek, A., Bernard, S., Hadi, M., Driouich, A., Scheller, H. V. and Sakuragi, Y. (2012). "GO-PROMTO illuminates protein membrane topologies of glycan biosynthetic enzymes in the Golgi apparatus of living tissues." PLoS One 7(2): e31324. |
| Sun, L., Varanasi, P., Yang, F., Loque, D., Simmons, B. A. and Singh, S. (2012). "Rapid determination of syringyl: guaiacyl ratios using FT-Raman spectroscopy." Biotechnol Bioeng 109(3): 647-656. |
| Sun, L., Li, C., Xue, Z., Simmons, B. A. and Singh, S. (2012). "Unveiling High-resolution tissue specific dynamic changes in corn stover during ionic liquid pretreatment". RSC Advances |
| Torr, K. M., Love, K. T., Cetinkol, O. P., Donaldson, L. A., George, A., Holmes, B. M. and Simmons, B. A. (2012). "The impact of ionic liquid pretreatment on the chemistry and enzymatic digestibility of Pinus radiata compression wood." Green Chemistry 14(3): 778-787. |
| Varanasi, P., Katsnelson, J., Larson, D. M., Sharma, R., Sharma, M. K., Vega-Sanchez, M. E., Zemla, M., Loque, D., Ronald, P. C., Simmons, B. A., Singh, S., Adams, P. D. and Auer, M. (2012). "Mechanical stress analysis as a method to understand the impact of genetically engineered rice and arabidopsis plants." Industrial Biotechnology 8(4): 238-244. |
| Vega-Sanchez, M. E., Verhertbruggen, Y., Christensen, U., Chen, X., Sharma, V., Varanasi, P., Jobling, S. A., Talbot, M., White, R. G., Joo, M., Singh, S., Auer, M., Scheller, H. V. and Ronald, P. C. (2012). "Loss of Cellulose Synthase-Like F6 function affects mixed-linkage glucan deposition, cell wall mechanical properties and defense responses in vegetative tissues of rice." Plant Physiology 159: 56-69. |
| Verhertbruggen, Y., Yin, L., Oikawa, A. and Scheller, H. V. (2011). "Mannan synthase activity in the CSLD family." Plant Signaling & Behavior 6(10): 1620-1623. |
| Vickers, C. E., Klein-Marcuschamer, D. and Kromer, J. O. (2012). "Examining the feasibility of bulk commodity production in Escherichia coli." Biotechnology Letters 34(4): 585-596. |
| Welz, O., Zador, J., Savee, J. D., Ng, M. Y., Meloni, G., Fernandes, R. X., Sheps, L., Simmons, B. A., Lee, T. S., Osborn, D. L. and Taatjes, C. A. (2012). "Low-temperature combustion chemistry of biofuels: pathways in the initial low-temperature (550 K-750 K) oxidation chemistry of isopentanol." Physical Chemistry Chemical Physics 14(9): 3112-3127. |
| Wipat, A., Villalobos, A., Stan, G.-B., Smith, T., Sauro, H., Roehner, N., Pocock, M., Plahar, H., Peccoud, J., Myers, C., Misirli, G., Madsen, C., Lux, M., Kuchinsky, A., Ham, T., Grünberg, R., Gennari, J., Endy, D., Drory, O., Densmore, D., Chandran, D., Beal, J., Anderson, J. C., Adler, A., Adam, L., Rodriguez, C., Wilson, M. and Galdzicki, M. (2011). Synthetic Biology Open Language (SBOL) Version 1.0.0. BioBricks Foundation Request for Comments. |
| Wipf, D., Loque, D., Lalonde, S. and Frommer, W. B. (2012). "Amino acid transporter inventory of the Selaginella genome." Frontiers in Plant Science 3(36). |
| Xiao, Y., Savchenko, T., Baidoo, E. E., Chehab, W. E., Hayden, D. M., Tolstikov, V., Corwin, J. A., Kliebenstein, D. J., Keasling, J. D. and Dehesh, K. (2012). "Retrograde signaling by the plastidial metabolite MEcPP regulates expression of nuclear stress-response genes." Cell 149(7): 1525-1535. |
| Zendejas, F. J., Benke, P. I., Lane, P. D., Simmons, B. A. and Lane, T. W. (2012). "Characterization of the acylglycerols and resulting biodiesel derived from vegetable oil and microalgae (Thalassiosira pseudonana and Phaeodactylum tricornutum)." Biotechnol Bioeng 109(5): 1146-1154. |
| Zhang, F., Rodriguez, S. and Keasling, J. D. (2011). "Metabolic engineering of microbial pathways for advanced biofuels production." Current Opinion Biotechnology 22(6): 775-783. |
| Zhang, F., Carothers, J. M. and Keasling, J. D. (2012). "Design of a dynamic sensor-regulator system for production of fatty acid-based chemicals and fuels." Nature Biotechnol. 30(4): 354-359. |
| Fiscal Year 2011 |
| Achyuthan, K. E., A. M. Achyuthan, P. D. Adams, S. M. Dirk, J. C. Harper, B. A. Simmons and A. K. Singh (2010). "Supramolecular Self-Assembled Chaos: Polyphenolic Lignin's Barrier to Cost-Effective Lignocellulosic Biofuels." Molecules 15(12): 8641-8688. |
| Banks, J. A., T. Nishiyama, M. Hasebe, J. L. Bowman, M. Gribskov, C. dePamphilis, V. A. Albert, N. Aono, T. Aoyama, B. A. Ambrose, N. W. Ashton, M. J. Axtell, E. Barker, M. S. Barker, J. L. Bennetzen, N. D. Bonawitz, C. Chapple, C. Cheng, L. G. Correa, M. Dacre, J. DeBarry, I. Dreyer, M. Elias, E. M. Engstrom, M. Estelle, L. Feng, C. Finet, S. K. Floyd, W. B. Frommer, T. Fujita, L. Gramzow, M. Gutensohn, J. Harholt, M. Hattori, A. Heyl, T. Hirai, Y. Hiwatashi, M. Ishikawa, M. Iwata, K. G. Karol, B. Koehler, U. Kolukisaoglu, M. Kubo, T. Kurata, S. Lalonde, K. Li, Y. Li, A. Litt, E. Lyons, G. Manning, T. Maruyama, T. P. Michael, K. Mikami, S. Miyazaki, S. Morinaga, T. Murata, B. Mueller-Roeber, D. R. Nelson, M. Obara, Y. Oguri, R. G. Olmstead, N. Onodera, B. L. Petersen, B. Pils, M. Prigge, S. A. Rensing, D. M. Riano-Pachon, A. W. Roberts, Y. Sato, H. V. Scheller, B. Schulz, C. Schulz, E. V. Shakirov, N. Shibagaki, N. Shinohara, D. E. Shippen, I. Sorensen, R. Sotooka, N. Sugimoto, M. Sugita, N. Sumikawa, M. Tanurdzic, G. Theissen, P. Ulvskov, S. Wakazuki, J. K. Weng, W. W. Willats, D. Wipf, P. G. Wolf, L. Yang, A. D. Zimmer, Q. Zhu, T. Mitros, U. Hellsten, D. Loque, R. Otillar, A. Salamov, J. Schmutz, H. Shapiro, E. Lindquist, S. Lucas, D. Rokhsar and I. V. Grigoriev (2011). "The Selaginella genome identifies genetic changes associated with the evolution of vascular plants." Science 332(6032): 960-963. |
| Bates, J. T., D. Chivian and A. P. Arkin (2011). "GLAMM: Genome-Linked Application for Metabolic Maps." Nucleic Acids Research 39(Web Server issue): W400-405. |
| Beller, H. R., E. B. Goh and J. D. Keasling (2011). "Definitive alkene identification needed for in vitro studies with ole (olefin biosynthesis) proteins." Journal of Biological Chemistry 286(26): le11. |
| Bharadwaj, R., Z. Chen, S. Datta, B. M. Holmes, R. Sapra, B. A. Simmons, P. D. Adams and A. K. Singh (2010). "Microfluidic Glycosyl Hydrolase Screening for Biomass-to-Biofuel Conversion." Analytical Chemistry 82(22): 9513–9520. |
| Bharadwaj, R., A. Wong, B. Knierim, S. Singh, B. M. Holmes, M. Auer, B. A. Simmons, P. D. Adams and A. K. Singh (2011). "High-throughput enzymatic hydrolysis of lignocellulosic biomass via in-situ regeneration." Bioresource Technology 102(2): 1329-1337. |
| Blanch, H. W., B. A. Simmons and D. Klein-Marcuschamer (2011). "Biomass deconstruction to sugars." Biotechnology Journal 6(9): 1086-1102. |
| Chandrasekaran, A., R. Bharadwaj, J. I. Park, R. Sapra, P. D. Adams and A. K. Singh (2010). "A Microscale Platform For Integrated Cell-Free Expression And Activity Screening Of Cellulases." Journal of Proteome Research 9(11): 5677-5683. |
| Cheng, G., Z. Liu, J. K. Murton, M. Jablin, M. Dubey, J. Majewski, C. Halbert, J. Browning, J. Ankner, B. Akgun, C. Wang, A. R. Esker, K. L. Sale, B. A. Simmons and M. S. Kent (2011). "Neutron Reflectometry and QCM-D Study of the Interaction of Cellulases with Films of Amorphous Cellulose." Biomacromolecules 12(6): 2216-2224. |
| Cheng, G., P. Varanasi, C. Li, H. Liu, Y. B. Melnichenko, B. A. Simmons, M. S. Kent and S. Singh (2011). "Transition of cellulose crystalline structure and surface morphology of biomass as a function of ionic liquid pretreatment and its relation to enzymatic hydrolysis." Biomacromolecules 12(4): 933-941. |
| Chertkov, O., A. Copeland, S. Lucas, A. Lapidus, K. W. Berry, J. C. Detter, T. G. Del Rio, N. Hammon, E. Dalin, H. Tice, S. Pitluck, P. Richardson, D. Bruce, L. Goodwin, C. Han, R. Tapia, E. Saunders, J. Schmutz, T. Brettin, F. Larimer, M. Land, L. Hauser, S. Spring, M. Rohde, N. C. Kyrpides, N. Ivanova, M. Göker, H. R. Beller, H.-P. Klenk and T. Woyke (2011). "Complete genome sequence of Tolumonas auensis type strain (TA 4T)." Standards in Genomic Sciences 5(1). ), doi:10.4056/sigs.2184986. |
| Chhabra, S. R., M. P. Joachimiak, C. J. Petzold, G. M. Zane, M. N. Price, S. A. Reveco, V. Fok, A. R. Johanson, T. S. Batth, M. Singer, J. M. Chandonia, D. Joyner, T. C. Hazen, A. P. Arkin, J. D. Wall, A. K. Singh and J. D. Keasling (2011). "Towards a Rigorous Network of Protein-Protein Interactions of the Model Sulfate Reducer Desulfovibrio vulgaris Hildenborough." PLoS One 6(6): e21470. |
| Chhabra, S. R. and J. Keasling (2011). The Biological Basis | Metabolic Design and Control for Production in Prokaryotes. Comprehensive Biotechnology. M. Moo-Young, Elsevier. 1: 243–255. |
| Chhabra, S. R., G. Butland, D. A. Elias, J. M. Chandonia, O. Y. Fok, T. R. Juba, A. Gorur, S. Allen, C. M. Leung, K. L. Keller, S. Reveco, G. M. Zane, E. Semkiw, R. Prathapam, B. Gold, M. Singer, M. Ouellet, E. D. Szakal, D. Jorgens, M. N. Price, H. E. Witkowska, H. R. Beller, A. P. Arkin, T. C. Hazen, M. D. Biggin, M. Auer, J. D. Wall and J. D. Keasling (2011). "Generalized Schemes for High-Throughput Manipulation of the Desulfovibrio vulgaris Genome." Applied and Environmental Microbiology 77(21): 7595-7604. |
| Datta, S. and R. Sapra. (2011). Cellulases and Hemicellulases for Biomass Degradation: An Introduction. Chemical and Biochemical Catalysis for Next Generation Biofuels. B. A. Simmons, Royal Society of Chemistry.: 115-135. |
| DeAngelis, K., P. D'Haeseleer, D. Chivian, J. L. Fortney, J. Khudyakov, B. A. Simmons, H. Woo, A. P. Arkin, K. W. Davenport, L. Goodwin, A. Chen, N. Ivanova, N. Kyrpides, K. Mavromatis, T. Woyke and T. Hazen (2011). "Complete genome sequence of Enterobacter lignolyticus SCF1." Standards in Genomic Sciences 5(1): 69-85. |
| DeAngelis, K. M., M. Allgaier, Y. Chavarria, J. L. Fortney, P. Hugenholtz, B. A. Simmons, K. Sublette, W. L. Silver and T. C. Hazen (2011). "Characterization of Trapped Lignin-Degrading Microbes in Tropical Forest Soil." PLoS ONE 6(4): e19306. |
| DeAngelis, K. M., C. H. Wu, H. R. Beller, E. L. Brodie, R. Chakraborty, T. Z. Desantis, J. L. Fortney, T. C. Hazen, S. R. Osman, M. E. Singer, L. M. Tom and G. L. Andersen (2011). "PCR amplification-independent methods for detection of microbial communities by the high-density microarray PhyloChip." Applied and Environmental Microbiology 77(18): 6313-6322. |
| Dunlop, M. J., Z. Y. Dossani, H. L. Szmidt, H. C. Chu, T. S. Lee, J. D. Keasling, M. Z. Hadi and A. Mukhopadhyay (2011). "Engineering microbial biofuel tolerance and export using efflux pumps." Molecular Systems Biology 7: 487. |
| Eudes, A., E. E. Baidoo, F. Yang, H. Burd, M. Z. Hadi, F. W. Collins, J. D. Keasling and D. Loque (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. |
| Gladden, J. M., M. Allgaier, C. S. Miller, T. C. Hazen, J. S. Vandergheynst, P. Hugenholtz, B. A. Simmons and S. W. Singer (2011). "Glycoside hydrolase activities of thermophilic bacterial consortia adapted to switchgrass." Applied and Environmental Microbiology 77(16): 5804-5812. |
| Heazlewood, J. L. (2011). "The Green proteome: challenges in plant proteomics." Frontiers in Plant Proteomics: 1-5. |
| Hillson, N. J. (2011). DNA Assembly Method Standardization for Synthetic Biomolecular Circuits and Systems. Design and Analysis of Biomolecular Circuits: Engineering Approaches to Systems and Synthetic Biology. H. Koeppl, D. Densmore, M. di Bernardo and G. Setti. New York, Springer-Verlag: 295-314. |
| Ito, J., T. S. Batth, C. J. Petzold, A. M. Redding-Johanson, A. Mukhopadhyay, R. Verboom, E. H. Meyer, A. H. Millar and J. L. Heazlewood (2011). "Analysis of the Arabidopsis cytosolic proteome highlights subcellular partitioning of central plant metabolism." Journal of Proteome Research 10(4): 1571-1582. |
| Joshi, H. J., M. Hirsch-Hoffmann, K. Baerenfaller, W. Gruissem, S. Baginsky, R. Schmidt, W. X. Schulze, Q. Sun, K. J. van Wijk, V. Egelhofer, S. Wienkoop, W. Weckwerth, C. Bruley, N. Rolland, T. Toyoda, H. Nakagami, A. M. Jones, S. P. Briggs, I. Castleden, S. K. Tanz, A. H. Millar and J. L. Heazlewood (2011). "MASCP Gator: an aggregation portal for the visualization of Arabidopsis proteomics data." Plant Physiology 155(1): 259-270. |
| Joshua, C. J., R. Dahl, P. I. Benke and J. D. Keasling (2011). "Absence of Diauxie during Simultaneous Utilization of Glucose and Xylose by Sulfolobus acidocaldarius." Journal of Bacteriology 193(6): 1293-1301. |
| Jung, K. H., P. Cao, Y. S. Seo, C. Dardick and P. C. Ronald (2010). "The Rice Kinase Phylogenomics Database: a guide for systematic analysis of the rice kinase super-family." Trends in Plant Science 15(11): 595-599. |
| Keasling, J. (2011). "Joint BioEnergy Institute." Industrial Biotechnology 7(4): 259-260. |
| Keasling, J. D. (2010). "Manufacturing molecules through metabolic engineering." Science 330(6009): 1355-1358. |
| Keller, K. L., J. D. Wall and S. Chhabra (2011). "Methods for engineering sulfate reducing bacteria of the genus desulfovibrio." Methods in Enzymology 497: 503-517. |
| Klein-Marcuschamer, D., B. Holmes, B. A. Simmons and H. W. Blanch (2011). Biofuel Economics. Plant Biomass Conversion. E. Hood, R. Powell and N. P. New York, John Wiley & Sons: 329-348. |
| Klein-Marcuschamer, D., P. Oleskowicz-Popiel, B. A. Simmons and H. W. Blanch (2010). "Technoeconomic analysis of biofuels: A wiki-based platform for lignocellulosic biorefineries." Biomass & Bioenergy 34(12): 1914-1921. |
| Klein-Marcuschamer, D., B. A. Simmons and H. W. Blanch (2011). "Techno-economic analysis of a lignocellulosic ethanol biorefinery with ionic liquid pre-treatment." Biofuels, Bioproducts and Biorefining 5(5): 562-569. |
| Lee, T. S., R. A. Krupa, F. Zhang, M. Hajimorad, W. J. Holtz, N. Prasad, S. K. Lee and J. D. Keasling (2011). "BglBrick vectors and datasheets; a synthetic biology platform for gene expression." Journal of Biological Engineering 5(1): 12. |
| Li, C., G. Cheng, V. Balan, M. S. Kent, M. Ong, S. P. Chundawat, L. D. Sousa, Y. B. Melnichenko, B. E. Dale, B. A. Simmons and S. Singh (2011). "Influence of physico-chemical changes on enzymatic digestibility of ionic liquid and AFEX pretreated corn stover." Bioresource Technology 102(13): 6928-6936. |
| Liu, H., K. L. Sale, B. A. Simmons and S. Singh (2011). "Molecular Dynamics Study of Polysaccharides in Binary Solvent Mixtures of an Ionic Liquid and Water." Journal of Physical Chemistry B 115(34): 10251-10258. |
| Loque, D., A. Eudes and F. Yang (2011). Biomass Availability and Sustainability for BioFuels. Chemical and Biochemical Catalysis for Next Generation Biofuels. B. A. Simmons, Royal Society of Chemistry: 5-32. |
| Ma, S. M., D. E. Garcia, A. M. Redding-Johanson, G. D. Friedland, R. Chan, T. S. Batth, J. R. Haliburton, D. Chivian, J. D. Keasling, C. J. Petzold, T. S. Lee and S. R. Chhabra (2011). "Optimization of a heterologous mevalonate pathway through the use of variant HMG-CoA reductases." Metabolic Engineering 13(5): 588-597. |
| Manabe, Y., M. Nafisi, Y. Verhertbruggen, C. Orfila, S. Gille, C. Rautengarten, C. Cherk, S. E. Marcus, S. Somerville, M. Pauly, J. P. Knox, Y. Sakuragi and H. V. Scheller (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. |
| Miller, C. S., B. J. Baker, B. C. Thomas, S. W. Singer and J. F. Banfield (2011). "EMIRGE: Reconstruction of full length ribosomal genes from microbial community short read sequencing data." Genome Biology 12(5): R44. |
| Nielsen, J. and J. D. Keasling (2011). "Synergies between synthetic biology and metabolic engineering." Nature Biotechnology 29(8): 693-695. |
| Oikawa, A., H. J. Joshi, E. A. Rennie, B. Ebert, C. Manisseri, J. L. Heazlewood and H. V. Scheller (2010). "An integrative approach to the identification of Arabidopsis and rice genes involved in xylan and secondary wall development." PLoS One 5(11): e15481. |
| Park, J. I., M. S. Kent, S. Datta, B. M. Holmes, Z. Huang, B. A. Simmons, K. L. Sale and R. Sapra (2011). "Enzymatic hydrolysis of cellulose by the cellobiohydrolase domain of CelB from the hyperthermophilic bacterium Caldicellulosiruptor saccharolyticus." Bioresource Technology 102(10): 5988-5994. |
| Peralta-Yahya, P. P., M. Ouellet, R. Chan, A. Mukhopadhyay, J. D. Keasling and T. S. Lee (2011). "Identification and microbial production of a terpene-based advanced biofuel." Nature Communications 2: 483. |
| Pereira, J. H., Z. Chen, R. P. McAndrew, R. Sapra, S. R. Chhabra, K. L. Sale, B. A. Simmons and P. D. Adams (2010). "Biochemical characterization and crystal structure of endoglucanase Cel5A from the hyperthermophilic Thermotoga maritima." Journal of Structural Biology 172(3): 372-379. |
| Rautengarten, C., B. Ebert, T. Herter, C. J. Petzold, T. Ishii, A. Mukhopadhyay, B. Usadel and H. V. Scheller (2011). "The interconversion of UDP-arabinopyranose and UDP-arabinofuranose is indispensable for plant development in Arabidopsis." Plant Cell 23(4): 1373-1390. |
| Redding-Johanson, A. M., T. S. Batth, R. Chan, R. Krupa, H. L. Szmidt, P. D. Adams, J. D. Keasling, T. S. Lee, A. Mukhopadhyay and C. J. Petzold (2011). "Targeted proteomics for metabolic pathway optimization: Application to terpene production." Metabolic Engineering 13(2): 194-203. |
| Reddy, A. P., M. Allgaier, S. W. Singer, T. C. Hazen, B. A. Simmons, P. Hugenholtz and J. S. Vandergheynst (2011). "Bioenergy feedstock-specific enrichment of microbial populations during high-solids thermophilic deconstruction." Biotechnology and Bioengineering 108(9): 2088-2098. |
| Reindl, W., K. Deng, J. M. Gladden, G. Cheng, A. Wong, S. W. Singer, S. Singh, J. C. Lee, C. H. Yao, T. C. Hazen, A. K. Singh, B. A. Simmons, P. D. Adams and T. R. Northen (2011). "Colloid-based multiplexed screening for plant biomass-degrading glycoside hydrolase activities in microbial communities." Energy & Environmental Science 4(8): 2884-2893. |
| Rezaei, F., L. D. Joh, H. Kashima, A. P. Reddy and J. S. Vandergheynst (2011). "Selection of Conditions for Cellulase and Xylanase Extraction from Switchgrass Colonized by Acidothermus cellulolyticus." Applied Biochemistry and Biotechnology 164(6): 793-803. |
| Ronald, P. (2011). "Plant genetics, sustainable agriculture and global food security." Genetics 188(1): 11-20. |
| Ronald, P. C. and B. Beutler (2010). "Plant and animal sensors of conserved microbial signatures." Science 330(6007): 1061-1064. |
| Sakuragi, Y., M. H. Norholm and H. V. Scheller (2011). Visual mapping of cell wall biosynthesis. The Plant Cell Wall: Methods and Protocols. Z. A. Popper. Berlin, Germany, Springer Science. 715: 153-167. |
| Seo, Y. S., M. Chern, L. E. Bartley, M. Han, K. H. Jung, I. Lee, H. Walia, T. Richter, X. Xu, P. Cao, W. Bai, R. Ramanan, F. Amonpant, L. Arul, P. E. Canlas, R. Ruan, C. J. Park, X. Chen, S. Hwang, J. S. Jeon and P. C. Ronald (2011). "Towards establishment of a rice stress response interactome." PLoS Genet 7(4): e1002020. |
| Simmons, B. A. (2011). "Synthetic enzymes: catalysis on demand." Microbial Biotechnology 4(2): 130-131. |
| Simmons, B. A. (2011). Introduction to Catalysis for Biofuels. Chemical and Biochemical Catalysis for Next Generation Biofuels. B. A. Simmons. Cambridge Royal Society of Chemistry: 1-4. |
| Simmons, B. A. (2011). "Rethinking renewable energy in Japan." Biofuels 2(4): 365–367. |
| Simmons, B. A. (2011). "Opportunities and challenges in advanced biofuel production: the importance of synthetic biology and combustion science." Biofuels 2(1): 5-7. |
| Singer, S. W., A. P. Reddy, J. M. Gladden, H. Guo, T. C. Hazen, B. A. Simmons and J. S. Vandergheynst (2011). "Enrichment, Isolation and Characterization of Fungi Tolerant to 1-Ethyl-3-Methylimadazolium Acetate." Journal of Applied Microbiology 110(4): 1023-1031. |
| Smith-Moritz, A. M., C. Mawsheng, J. Lao, W. H. Sze-To, J. L. Heazlewood, P. Ronald and M. E. Vega-Sanchez (2011). "Combining multivariate analysis and monosaccharide composition modeling to identify plant cell wall variations by Fourier Transform Near Infrared spectroscopy." Plant Methods 7(26). |
| Sun, L., B. A. Simmons and S. Singh (2011). "Understanding tissue specific compositions of bioenergy feedstocks through hyperspectral Raman imaging." Biotechnology and Bioengineering 108(2): 286-295. |
| Taylor, N. L., J. L. Heazlewood and A. H. Millar (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. |
| Varanasi, P., L. Sun, B. Knierim, E. Bosneaga, P. Sakar, S. Singh and M. Auer (2011). Quantifying Bio-Engineering: The Importance of Biophysics in Biofuel Research. Biofuel's Engineering Process Technology. M. A. dos Santos Bernades, InTech: 493-520. |
| Yang, Y., J. Dec, N. Dronniou and B. A. Simmons (2010). "Characteristics of Isopentanol as a Fuel for HCCI Engines." Society of Automobile Engineers International Journal of Fuels and Lubricants 3(2): 725-741. |
| Yilmaz, S., M. Allgaier and P. Hugenholtz (2010). "Multiple displacement amplification compromises quantitative analysis of metagenomes." Nature Methods 7(12): 943-944. |
| Yin, L., Y. Verhertbruggen, A. Oikawa, C. Manisseri, B. Knierim, L. Prak, J. K. Jensen, J. P. Knox, M. Auer, W. G. Willats and H. V. Scheller (2011). "The Cooperative Activities of CSLD2, CSLD3, and CSLD5 Are Required for Normal Arabidopsis Development." Molecular Plant 4(6): 1024-1037. |
| Zhang, F. and J. Keasling (2011). "Biosensors and their applications in microbial metabolic engineering." Trends in Microbiology 19(7): 323-329. |
| Zhang, T., S. Datta, J. Eichler, N. Ivanova, S. D. Axen, C. A. Kerfeld, F. Chen, N. Kyrpides, P. Hugenholtz, J.-F. Cheng, K. L. Sale, B. A. Simmons and E. Rubin (2011). "Identification of a haloalkaliphilic and thermostable cellulase with improved ionic liquid tolerance." Green Chemistry 13(8): 2083-2090. |
| Fiscal Year 2010 |
| Achyuthan, K. E., P. D. Adams, S. Datta, B. A. Simmons and A. K. Singh (2010). "Hitherto Unrecognized Fluorescence Properties of Coniferyl Alcohol." Molecules 15(3): 1645-1667. |
| Achyuthan, K. E., P. D. Adams, B. A. Simmons and A. K. Singh (2009). "Spectroscopic Analyses of the Biofuels-Critical Phytochemical Coniferyl Alcohol and Its Enzyme-Catalyzed Oxidation Products." Molecules 14(11): 4758-4778. |
| Allgaier, M., A. Reddy, J. I. Park, N. Ivanova, P. D'haeseleer, S. Lowry, R. Sapra, T. C. Hazen, B. A. Simmons, J. S. VanderGheynst and P. Hugenholtz (2010). "Targeted Discovery of Glycoside Hydrolases from a Switchgrass-Adapted Compost Community." Plos One 5(1): e8812. |
| Arora, R., C. Manisseri, C. L. Li, M. D. Ong, H. V. Scheller, K. Vogel, B. A. Simmons and S. Singh (2010). "Monitoring and Analyzing Process Streams Towards Understanding Ionic Liquid Pretreatment of Switchgrass (Panicum virgatum L.)." Bioenergy Research 3(2): 134-145. |
| Bart, R. S., M. Chern, M. E. Vega-Sanchez, P. Canlas and P. C. Ronald (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). |
| Bartley, L. E. and P. C. Ronald (2009). "Plant and microbial research seeks biofuel production from lignocellulose." California Agriculture 63(4): 178-184. |
| Beller, H. R., E. B. Goh and J. D. Keasling (2010). "Genes Involved in Long-Chain Alkene Biosynthesis in Micrococcus luteus." Applied and Environmental Microbiology 76(4): 1212-1223. |
| Brennan, T. C. R., S. Datta, H. W. Blanch, B. A. Simmons and B. M. Holmes (2010). "Recovery of Sugars from Ionic Liquid Biomass Liquor by Solvent Extraction." Bioenergy Research 3(2): 123-133. |
| Cao, P. J., K. H. Jung and P. C. Ronald (2010). "A Survey of Databases for Analysis of Plant Cell Wall-Related Enzymes." Bioenergy Research 3(2): 108-114. |
| Cetinkol, O. P., D. C. Dibble, G. Cheng, M. S. Kent, B. Knierim, M. Auer, D. E. Wemmer, J. G. Pelton, Y. B. Melnichenko, J. Ralph, B. A. Simmons and B. M. Holmes (2010). "Understanding the impact of ionic liquid pretreatment on eucalyptus." Biofuels 1(1): 33-46. |
| Chou, H. H., A. Trisiriroj, S. Park, Y. I. C. Hsing, P. C. Ronald and P. S. Schnable (2009). "Direct calibration of PICKY-designed microarrays." BMC Bioinformatics 10(347): 1-11. |
| Christen, B., M. J. Fero, N. J. Hillson, G. Bowman, S. H. Hong, L. Shapiro and H. H. McAdams (2010). "High-throughput identification of protein localization dependency networks." Proceedings of the National Academy of Sciences 107(10): 4681-4686. |
| Christensen, U., A. Alonso-Simon, H. V. Scheller, W. G. T. Willats and J. Harholt (2010). "Characterization of the primary cell walls of seedlings of Brachypodium distachyon - A potential model plant for temperate grasses." Phytochemistry 71(1): 62-69. |
| Cong, Y., M. L. Baker, J. Jakana, D. Woolford, E. J. Miller, S. Reissmann, R. N. Kumar, A. M. Redding-Johanson, T. S. Batth, A. Mukhopadhyay, S. J. Ludtke, J. Frydman and W. Chiu (2010). "4.0-A resolution cryo-EM structure of the mammalian chaperonin TRiC/CCT reveals its unique subunit arrangement." Proceedings of the National Academy of Sciences 107(11): 4967-4972. |
| Datta, S., B. Holmes, J. I. Park, Z. W. Chen, D. C. Dibble, M. Hadi, H. W. Blanch, B. A. Simmons and R. Sapra (2010). "Ionic liquid tolerant hyperthermophilic cellulases for biomass pretreatment and hydrolysis." Green Chemistry 12(2): 338-345. |
| DeAngelis, K. M., J. M. Gladden, M. Allgaier, P. D'haeseleer, J. L. Fortney, A. Reddy, P. Hugenholtz, S. W. Singer, J. S. Vander Gheynst, W. L. Silver, B. A. Simmons and T. C. Hazen (2010). "Strategies for Enhancing the Effectiveness of Metagenomic-based Enzyme Discovery in Lignocellulolytic Microbial Communities." Bioenergy Research 3(2): 146-158. |
| Dehal, P. S., M. P. Joachimiak, M. N. Price, J. T. Bates, J. K. Baumohl, D. Chivian, G. D. Friedland, K. H. Huang, K. Keller, P. S. Novichkov, I. L. Dubchak, E. J. Alm and A. P. Arkin (2010). "MicrobesOnline: an integrated portal for comparative and functional genomics." Nucleic Acids Research 38: D396-D400. |
| Dunlop, M. J., J. D. Keasling and A. Mukhopadhyay (2010). "A model for improving microbial biofuel production using a synthetic feedback loop." Synthetic and Systems Biology 4(2): 95-104. |
| Durek, P., R. Schmidt, J. L. Heazlewood, A. Jones, D. MacLean, A. Nagel, B. Kersten and W. X. Schulze (2010). "PhosPhAt: the Arabidopsis thaliana phosphorylation site database. An update." Nucleic Acids Research 38: D828-D834. |
| Fedoroff, N. V., D. S. Battisti, R. N. Beachy, P. J. M. Cooper, D. A. Fischhoff, C. N. Hodges, V. C. Knauf, D. Lobell, B. J. Mazur, D. Molden, M. P. Reynolds, P. C. Ronald, M. W. Rosegrant, P. A. Sanchez, A. Vonshak and J. K. Zhu (2010). "Radically Rethinking Agriculture for the 21st Century." Science 327(5967): 833-834. |
| Geshi, N., B. L. Petersen and H. V. Scheller (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. |
| Han, J., S. Singh, L. Sun, B. A. Simmons, M. Auer and B. Parvin (2010). "Chemical profiling of the plant cell wall through Raman microspectroscopy in 2010 IEEE International Symposium on Biomedical Imaging: From Nano to Macro." IEEE ISBI: 1273-1276. |
| Harholt, J., I. C. Bach, S. Lind-Bouquin, K. J. Nunan, S. M. Madrid, H. Brinch-Pedersen, P. B. Holm and H. V. Scheller (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. |
| Harholt, J., A. Suttangkakul and H. V. Scheller (2010). "Biosynthesis of Pectin." Plant Physiology 153(2): 384-395. |
| Holtz, W. J. and J. D. Keasling (2010). "Engineering Static and Dynamic Control of Synthetic Pathways." Cell 140(1): 19-23. |
| Ito, J., C. J. Petzold, A. Mukhopadhyay and J. L. Heazlewood (2010). "The Role of Proteomics in the Development of Cellulosic Biofuels." Current Proteomics 7(2): 121-134. |
| Jung, K. H., Y. S. Seo, H. Walia, P. J. Cao, T. Fukao, P. E. Canlas, F. Amonpant, J. Bailey-Serres and P. C. Ronald (2010). "The Submergence Tolerance Regulator Sub1A Mediates Stress-Responsive Expression of AP2/ERF Transcription Factors." Plant Physiology 152(3): 1674-1692. |
| Kent, M. S., G. Cheng, J. K. Murton, E. L. Carles, D. C. Dibble, F. Zendejas, M. A. Rodriquez, H. Tran, B. Holmes, B. A. Simmons, B. Knierim, M. Auer, J. L. Banuelos, J. Urquidi and R. P. Hjelm (2010). "Study of Enzymatic Digestion of Cellulose by Small Angle Neutron Scattering." Biomacromolecules 11(2): 357-368. |
| Lacayo, C. I., A. J. Malkin, H. Y. Holman, L. Chen, S. Y. Ding, M. S. Hwang and M. P. Thelen (2010). "Imaging cell wall architecture in single Zinnia elegans tracheary elements." Plant Physiology 154(1): 121-133. |
| Lalonde, S., A. Sero, R. Pratelli, G. Pilot, J. Chen, M. I. Sardi, S. A. Parsa, D. Y. Kim, B. R. Acharya, E. V. Stein, H. C. Hu, F. Villiers, K. Takeda, Y. Yang, Y. S. Han, R. Schwacke, W. Chiang, N. Kato, D. Loque, S. M. Assmann, J. M. Kwak, J. I. Schroeder, S. Y. Rhee and W. B. Frommer (2010). "A membrane protein/signaling protein interaction network for Arabidopsis version AMPv2." Frontiers in Physiology 1: 24. |
| Landau, A. M., H. Lokstein, H. V. Scheller, V. Lainez, S. Maldonado and A. R. Prina (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. |
| Li, C., B. Knierim, C. Manisseri, R. Arora, H. V. Scheller, M. Auer, K. P. Vogel, B. A. Simmons and S. Singh (2010). "Comparison of dilute acid and ionic liquid pretreatment of switchgrass: Biomass recalcitrance, delignification and enzymatic saccharification." Bioresource Technology 101(13): 4900-4906. |
| Liepman, A. H., R. Wightman, N. Geshi, S. R. Turner and H. V. Scheller (2010). "Arabidopsis - a powerful model system for plant cell wall research." Plant Journal 61(6): 1107-1121. |
| Liu, H., J. H. Pereira, P. D. Adams, R. Sapra, B. A. Simmons and K. L. Sale (2010). "Molecular simulations provide new insights into the role of the accessory immunoglobulin-like domain of Cel9A." FEBS Letters 584(15): 3431-3435. |
| Liu, H., K. L. Sale, B. M. Holmes, B. A. Simmons and S. Singh (2010). "Understanding the interactions of cellulose with ionic liquids: a molecular dynamics study." Journal of Physical Chemistry B 114(12): 4293-4301. |
| Ouellet, M., P. D. Adams, J. D. Keasling and A. Mukhopadhyay (2009). "A rapid and inexpensive labeling method for microarray gene expression analysis." BMC Biotechnology 9: 97. |
| Peralta-Yahya, P. P. and J. D. Keasling (2010). "Advanced biofuel production in microbes." Biotechnology Journal 5(2): 147-162. |
| Petzold, C. J. and J. D. Keasling (2010). Metabolic engineering of E.coli for the production of a precursor to artemisinin, an anti-malarial drug. The Manual of Industrial Microbiology and Biotechnology. R. Balz. Washington, DC, ASM Press: 364-379. |
| Rautengarten, C., E. Baidoo, J. D. Keasling and H. V. Scheller (2010). "A Simple Method for Enzymatic Synthesis of Unlabeled and Radiolabeled Hydroxycinnamate-CoA." BioEnergy Research 3(2): 115-122. |
| Ronald, P. and R. Adamchak (2010). "The future of sustainable food production." Annals of the New York Academy of Sciences 1190(1): 184-185. |
| Rutherford, B. J., R. H. Dahl, R. E. Price, H. L. Szmidt, P. I. Benke, A. Mukhopadhyay and J. D. Keasling (2010). "Functional genomic study of exogenous n-butanol stress in Escherichia coli." Applied and Environmental Microbiology 76(6): 1935-1945. |
| Scheller, H. V., S. Singh, H. Blanch and J. D. Keasling (2010). "The Joint BioEnergy Institute (JBEI): Developing New Biofuels by Overcoming Biomass Recalcitrance." BioEnergy Research 3(2): 105-107. |
| Scheller, H. V. and P. Ulvskov (2010). "Hemicelluloses." Annual Review of Plant Biology 61: 263-289. |
| Shaikh, A. S., Y. J. Tang, A. Mukhopadhyay, H. G. Martin, J. Gin, P. I. Benke and J. D. Keasling (2010). "Study of stationary phase metabolism via isotopomer analysis of amino acids from an isolated protein." Biotechnology Progress 26(1): 52-56. |
| Simmons, B. A., D. Loque and J. Ralph (2010). "Advances in modifying lignin for enhanced biofuel production." Current Opinion in Plant Biology 13(3): 313-320. |
| Simmons, B. A., S. Singh, B. M. Holmes and H. W. Blanch (2010). "Ionic liquid pretreatment." Chemical Engineering Progress: 50-55. |
| Steen, E. J., Y. Kang, G. Bokinsky, Z. Hu, A. Schirmer, A. McClure, S. B. Del Cardayre and J. D. Keasling (2010). "Microbial production of fatty-acid-derived fuels and chemicals from plant biomass." Nature 463(7280): 559-562. |
| Vega-Sanchez, M. E. and P. C. Ronald (2010). "Genetic and biotechnological approaches for biofuel crop improvement." Current Opinion Biotechnology 21(2): 218-224. |
| Vogel, J., D. Garvin, T. Mockler, J. Schmutz, D. Rokhsar, M. Bevan, K. Barry, S. Lucas, M. Harmon-Smith, K. Lail, H. Tice, J. Grimwood, N. McKenzie, N. Huo, Y. Gu, G. Lazo, O. Anderson, F. You, M.-C. Luo, J. Dvorak, J. Wright, M. Febrer, D. Idziak, R. Hasterok, E. Lindquist, M. Wang, S. Fox, H. Priest, S. Filichkin, S. Givan, D. Bryant, J. Chang, T. Mockler, H. Wu, W. Wu, A.-P. Hsia, P. Schnable, A. Kalyanaraman, B. Barbazuk, T. Michael, S. Hazen, J. Bragg, D. Laudencia-Chingcuanco, Y. Weng, G. Haberer, M. Spannagl, K. Mayer, T. Rattei, T. Mitros, S.-J. Lee, J. Rose, L. Mueller, T. York, T. Wicker, J. Buchmann, J. Tanskanen, A. Schulman, H. Gundlach, A. de Oliveira, L. Maia, W. Belknap, N. Jiang, J. Lai, L. Zhu, J. Ma, J. Salse, F. Murat, M. Abrouk, R. Bruggmann, N. Fahlgren, C. Sullivan, J. Carrington, E. Chapman, G. May, J. Zhai, M. Ganssmann, G. Gurazada, M. German, B. Meyers, P. Green, L. Tyler, J. Thomson, S. Chen, H. Scheller, J. Harholt, P. Ulvskov, J. Kimbrel, J. Chang, L. Bartley, P. Cao, K.-H. Jung, M. Sharma, M. Vega-Sanchez, P. Ronald, C. Dardick, S. DeBodt, W. Verelst, D. Inzé, M. Heese, A. Schnittger, X. Yang, U. Kalluri, G. Tuskan, Z. Hua, R. Vierstra, Y. Cui, S. Ouyang, Q. Sun, Z. Liu, A. Yilmaz, E. Grotewold, R. Sibout, K. Hematy, G. Mouille, H. Höfte, T. Michael, J. Pelloux, D. O'Connor, J. Schnable, S. Rowe, F. Harmon, C. Cass, J. Sedbrook, M. Byrne, S. Walsh, J. Higgins, P. Li, T. Brutnell, U. Turgay, H. Budak, H. Belcram, M. Charles, B. Chalhoub and I. Baxter (2010). "Genome sequence analysis of the model grass Brachypodium distachyon: insights into grass genome evolution." Nature 463(2): 763-768. |
| Wurtzel, O., R. Sapra, F. Chen, Y. Zhu, B. A. Simmons and R. Sorek (2010). "A single-base resolution map of an archaeal transcriptome." Genome Research 20(1): 133-141. |
| Young, M., V. Artsatbanov, H. R. Beller, G. Chandra, K. F. Chater, L. G. Dover, E. B. Goh, T. Kahan, A. S. Kaprelyants, N. Kyrpides, A. Lapidus, S. R. Lowry, A. Lykidis, J. Mahillon, V. Markowitz, K. Mavromatis, G. V. Mukamolova, A. Oren, J. S. Rokem, M. C. Smith, D. I. Young and C. L. Greenblatt (2010). "Genome sequence of the Fleming strain of Micrococcus luteus, a simple free-living actinobacterium." Journal of Bacteriology 192(3): 841-860. |
| Yu, E., S. P. Gaucher and M. Z. Hadi (2010). "Probing conformational changes in Ape1 during the progression of base excision repair."Biochemistry 49(18): 3786-3796. |
| Yu, E. T. and M. Z. Hadi (2010). "Bioinformatic processing to identify single nucleotide polymorphism that potentially affect Ape1 function."Mutation Research 722(2): 140-146. |
| Fiscal Year 2009 |
| Bernal, A. J., C. M. Yoo, M. Mutwil, J. K. Jensen, G. Hou, C. Blaukopf, I. Sorensen, E. B. Blancaflor, H. V. Scheller and W. G. T. Willats (2008). "Functional Analysis of the Cellulose Synthase-Like Genes CSLD1, CSLD2, and CSLD4 in Tip-Growing Arabidopsis Cells." Plant Physiology 148(3): 1238-1253. |
| Dietrich, J. A., Y. Yoshikuni, K. J. Fisher, F. X. Woolard, D. Ockey, D. J. McPhee, N. S. Renninger, M. C. Y. Chang, D. Baker and J. D. Keasling (2009). "A Novel Semi-biosynthetic Route for Artemisinin Production Using Engineered Substrate-Promiscuous P450(BM3)." ACS Chemical Biology 4(4): 261-267. |
| Dougherty, M. J. and F. H. Arnold (2009). "Directed evolution: new parts and optimized function." Current Opinion in Biotechnology 20(4): 486-491. |
| Dueber, J. E., G. C. Wu, G. R. Malmirchegini, T. S. Moon, C. J. Petzold, A. V. Ullal, K. L. J. Prather and J. D. Keasling (2009). "Synthetic protein scaffolds provide modular control over metabolic flux." Nature Biotechnology 27(8): 753-U107. |
| Harper, J. C., S. M. Brozik, J. H. Flemming, J. L. McClain, R. Polsky, D. Raj, G. A. Ten Eyck, D. R. Wheeler and K. E. Achyuthan (2009). "Fabrication and testing of a microneedles sensor array for p-cresol detection with potential biofuel applications." ACS Applied Materials & Interfaces 1(7): 1591-1598. |
| Ito, J., N. L. Taylor, I. Castleden, W. Weckwerth, A. H. Millar and J. L. Heazlewood (2009). "A survey of the Arabidopsis thaliana mitochondrial phosphoproteome." Proteomics 9(17): 4229-4240. |
| Jung, K. H., L. E. Bartley, P. J. Cao, P. E. Canlas and P. C. Ronald (2009). "Analysis of Alternatively Spliced Rice Transcripts Using Microarray Data." Rice 2(1): 44-55. |
| Jung, K. H., C. Dardick, L. E. Bartley, P. J. Cao, J. Phetsom, P. Canlas, Y. S. Seo, M. Shultz, S. Ouyang, Q. Yuan, B. C. Frank, E. Ly, L. Zheng, Y. Jia, A. P. Hsia, K. An, H. H. Chou, D. Rocke, G. C. Lee, P. S. Schnable, G. An, C. R. Buell and P. C. Ronald (2008). "Refinement of Light-Responsive Transcript Lists Using Rice Oligonucleotide Arrays: Evaluation of Gene-Redundancy." Plos One 3(10): e3337. |
| Kent, M. S., J. K. Murton, D. C. Dibble, F. Zendejas, J. L. Banuelos, J. Urquidi, R. P. Hjelm and B. A. Simmons (2009). "Effect of Agitation/Flow on the Enzymatic Digestion of Cellulose: a Structural Study by SANS." Polymer Preprints, ACS-PMSE symposium on Small Angle Neutron Scattering from Polymers and Complex Fluids, 238th ACS National Meeting, Washington DC, Aug 16-20, 2009. : 2. |
| Kirby, J. and J. D. Keasling (2009). "Biosynthesis of plant isoprenoids: perspectives for microbial engineering." Annual Review of Plant Biology 60: 335-355. |
| Lee, S. K., H. Chou, T. S. Ham, T. S. Lee and J. D. Keasling (2008). "Metabolic engineering of microorganisms for biofuels production: from bugs to synthetic biology to fuels." Current Opinion in Biotechnology 19(6): 556-563. |
| Loque, D., S. I. Mora, S. L. Andrade, O. Pantoja and W. B. Frommer (2009). "Pore mutations in ammonium transporter AMT1 with increased electrogenic ammonium transport activity." Journal of Biological Chemistry 284(37): 24988-24995. |
| Marner, W. D., 2nd, A. S. Shaikh, S. J. Muller and J. D. Keasling (2009). "Enzyme immobilization via silaffin-mediated autoencapsulation in a biosilica support." Biotechnology Progress 25(2): 417-423. |
| Meng, M., M. Geisler, H. Johansson, J. Harholt, H. V. Scheller, E. J. Mellerowicz and L. A. Kleczkowski (2009). "UDP-glucose pyrophosphorylase is not rate limiting, but is essential in Arabidopsis." Plant Cell Physiology 50(5): 998-1011. |
| Pereira, J. H., R. Sapra, J. V. Volponi, C. L. Kozina, B. Simmons and P. D. Adams (2009). "Structure of endoglucanase Cel9A from the thermoacidophilic Alicyclobacillus acidocaldarius." Acta Crystallographica Section D Biological Crystallography 65(Pt 8): 744-750. |
| Petersen, B. L., J. Egelund, I. Damager, K. Faber, J. K. Jensen, Z. Yang, E. P. Bennett, H. V. Scheller and P. Ulvskov (2009). "Assay and heterologous expression in Pichia pastoris of plant cell wall type-II membrane anchored glycosyltransferases." Glycoconjugate Journal 26(9): 1235-1246. |
| Sarkar, P., E. Bosneaga and M. Auer (2009). "Plant cell walls throughout evolution: towards a molecular understanding of their design principles." Journal of Experimental Botany 60(13): 3615-3635. |
| Shui, W., L. Sheu, J. Liu, B. Smart, C. J. Petzold, T. Y. Hsieh, A. Pitcher, J. D. Keasling and C. R. Bertozzi (2008). "Membrane proteomics of phagosomes suggests a connection to autophagy." Proceedings of the National Academy of Sciences 105(44): 16952-16957. |
| Simmons, B. A., D. Loque and H. W. Blanch (2008). "Next-generation biomass feedstocks for biofuel production." Genome Biology 9(12): 242. |
| Singh, S., B. A. Simmons and K. P. Vogel (2009). "Visualization of biomass solubilization and cellulose regeneration during ionic liquid pretreatment of switchgrass." Biotechnology and Bioengineering 104(1): 68-75. |
| Steen, E. J., R. Chan, N. Prasad, S. Myers, C. J. Petzold, A. Redding, M. Ouellet and J. D. Keasling (2008). "Metabolic engineering of Saccharomyces cerevisiae for the production of n-butanol." Microbial Cell Factories 7: 36. |
| Tang, Y. J., H. G. Martin, P. S. Dehal, A. Deutschbauer, X. Llora, A. Meadows, A. Arkin and J. D. Keasling (2009). "Metabolic flux analysis of Shewanella spp. reveals evolutionary robustness in central carbon metabolism." Biotechnology and Bioengineering 102(4): 1161-1169. |
| Tang, Y. J., H. G. Martin, S. Myers, S. Rodriguez, E. E. Baidoo and J. D. Keasling (2009). "Advances in analysis of microbial metabolic fluxes via (13)C isotopic labeling." Mass Spectrometry Reviews 28(2): 362-375. |
| Tang, Y. J., R. Sapra, D. Joyner, T. C. Hazen, S. Myers, D. Reichmuth, H. Blanch and J. D. Keasling (2009). "Analysis of metabolic pathways and fluxes in a newly discovered thermophilic and ethanol-tolerant Geobacillus strain." Biotechnology and Bioengineering 102(5): 1377-1386. |
| Tang, Y. J., S. Yi, W. Q. Zhuang, S. H. Zinder, J. D. Keasling and L. Alvarez-Cohen (2009). "Investigation of carbon metabolism in "Dehalococcoides ethenogenes" strain 195 by use of isotopomer and transcriptomic analyses." Journal of Bacteriology 191(16): 5224-5231. |
| Weckwerth, W., S. Baginsky, K. van Wijk, J. L. Heazlewood and H. Millar (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. |
| Fiscal Year 2008 |
| Blanch, H. W., P. D. Adams, K. M. Andrews-Cramer, W. B. Frommer, B. A. Simmons and J. D. Keasling (2008). "Addressing the need for alternative transportation fuels: The Joint BioEnergy Institute." ACS Chemical Biology 3(1): 17-20. |
| Cao, P. J., L. E. Bartley, K. H. Jung and P. C. Ronald (2008). "Construction of a rice glycosyltransferase phylogenomic database and identification of rice-diverged glycosyltransferases." Molecular Plant 1(5): 858-877. |
| Fortman, J. L., S. Chhabra, A. Mukhopadhyay, H. Chou, T. S. Lee, E. Steen and J. D. Keasling (2008). "Biofuel alternatives to ethanol: pumping the microbial well." Trends in Biotechnology 26(7): 375-381. |
| Garcia, D. E., E. E. Baidoo, P. I. Benke, F. Pingitore, Y. J. Tang, S. Villa and J. D. Keasling (2008). "Separation and mass spectrometry in microbial metabolomics." Current Opinion in Microbiology 11(3): 233-239. |
| Jensen, J. K., S. O. Sorensen, J. Harholt, N. Geshi, Y. Sakuragi, I. Moller, J. Zandleven, A. J. Bernal, N. B. Jensen, C. Sorensen, M. Pauly, G. Beldman, W. G. T. Willats and H. V. Scheller (2008). "Identification of a xylogalacturonan xylosyltransferase involved in pectin biosynthesis in Arabidopsis." Plant Cell 20(5): 1289-1302. |
| Keasling, J. D. (2008). "Synthetic biology for synthetic chemistry." ACS Chemical Biology 3(1): 64-76. |
| Keasling, J. D. and H. Chou (2008). "Metabolic engineering delivers next-generation biofuels." Nature Biotechnology 26(3): 298-299. |
| Mukhopadhyay, A., A. M. Redding, B. J. Rutherford and J. D. Keasling (2008). "Importance of systems biology in engineering microbes for biofuel production." Current Opinion in Biotechnology 19(3): 228-234. |
| Shaikh, A. S., Y. J. Tang, A. Mukhopadhyay and J. D. Keasling (2008). "Isotopomer distributions in amino acids from a highly expressed protein as a proxy for those from total protein." Analytical Chemistry 80(3): 886-890. |
