Achyuthan, K. E., A. M. Achyuthan, et al. (2010). "Supramolecular Self-Assembled Chaos: Polyphenolic Lignin's Barrier to Cost-Effective Lignocellulosic Biofuels." Molecules 15(12): 8641-8688.

Achyuthan, K. E., P. D. Adams, et al. (2010). "Hitherto Unrecognized Fluorescence Properties of Coniferyl Alcohol." Molecules 15(3): 1645-1667.

Achyuthan, K. E., P. D. Adams, et al. (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, et al. (2010). "Targeted Discovery of Glycoside Hydrolases from a Switchgrass-Adapted Compost Community." Plos One 5(1): e8812.

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.

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.*

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.

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).

Bartley, L. E. and P. C. Ronald (2009). "Plant and microbial research seeks biofuel production from lignocellulose." California Agriculture 63(4): 178-184.

Bates, J. T., D. Chivian, et al. (2011). "GLAMM: Genome-Linked Application for Metabolic Maps." Nucleic Acids Research 39(Web Server issue): W400-405.

Beller, H. R., E. B. Goh, et al. (2010). "Genes Involved in Long-Chain Alkene Biosynthesis in Micrococcus luteus." Applied and Environmental Microbiology 76(4): 1212-1223.

Beller, H. R., E. B. Goh, et al. (2011). "Definitive alkene identification needed for in vitro studies with ole (olefin biosynthesis) proteins." Journal of Biological Chemistry 286(26): le11.

Beller, H. R., T. C. Legler, et al. (2011). Genetic manipulation of the obligate chemolithoautotrophic bacterium Thiobacillus denitrificans. Microbial Systems Biology: Methods and Protocols (Methods in Molecular Biology series), Humana Press.*

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.

Bharadwaj, R., Z. Chen, et al. (2010). "Microfluidic Glycosyl Hydrolase Screening for Biomass-to-Biofuel Conversion." Analytical Chemistry 82(22): 9513–9520.

Bharadwaj, R., A. Wong, et al. (2011). "High-throughput enzymatic hydrolysis of lignocellulosic biomass via in-situ regeneration." Bioresource Technology 102(2): 1329-1337.

Blanch, H. W. (2011). "Bioprocessing for biofuels." Current Opinion in Biotechnology 23: 1-6.*

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.

Blanch, H. W., B. A. Simmons, et al. (2011). "Biomass deconstruction to sugars." Biotechnology Journal 6(9): 1086-1102.

Bokinsky, G., P. Peralta-Yahya, et al. (2011). "Synthesis of three advanced biofuels from ionic liquid-pretreated switchgrass using engineered." Proceedings of the National Academy of Sciences.*

Brennan, T. C. R., S. Datta, et al. (2010). "Recovery of Sugars from Ionic Liquid Biomass Liquor by Solvent Extraction." Bioenergy Research 3(2): 123-133.

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.

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.

Carothers, J. M., J. A. Goler, et al. (2011). "Model-driven engineering of RNA devices to quantitatively-program gene expression." Science.*

Cetinkol, O. P., D. C. Dibble, et al. (2010). "Understanding the impact of ionic liquid pretreatment on eucalyptus." Biofuels 1(1): 33-46.

Chandrasekaran, A., R. Bharadwaj, et al. (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, et al. (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, et al. (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, et al. (2011). "Complete genome sequence of Tolumonas auensis type strain (TA 4T)." Standards in Genomic Sciences 5(1).

Chhabra, S. R., G. Butland, et al. (2011). "Generalized Schemes for High-Throughput Manipulation of the Desulfovibrio vulgaris Genome." Applied and Environmental Microbiology 77(21): 7595-7604.

Chhabra, S. R., M. P. Joachimiak, et al. (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.

Chou, H. H., A. Trisiriroj, et al. (2009). "Direct calibration of PICKY-designed microarrays." BMC Bioinformatics 10(347): 1-11.

Christen, B., M. J. Fero, et al. (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, 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.

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.*

Chuck, G. S., C. Tobias, et al. (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.

Cong, Y., M. L. Baker, et al. (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, et al. (2010). "Ionic liquid tolerant hyperthermophilic cellulases for biomass pretreatment and hydrolysis." Green Chemistry 12(2): 338-345.

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, et al. (2011). "Complete genome sequence of Enterobacter lignolyticus SCF1." Standards in Genomic Sciences 5(1): 69-85.

DeAngelis, K. M., M. Allgaier, et al. (2011). "Characterization of Trapped Lignin-Degrading Microbes in Tropical Forest Soil." PLoS ONE 6(4): e19306.

DeAngelis, K. M., J. M. Gladden, et al. (2010). "Strategies for Enhancing the Effectiveness of Metagenomic-based Enzyme Discovery in Lignocellulolytic Microbial Communities." Bioenergy Research 3(2): 146-158.

DeAngelis, K. M., C. H. Wu, et al. (2011). "PCR amplification-independent methods for detection of microbial communities by the high-density microarray PhyloChip." Applied and Environmental Microbiology 77(18): 6313-6322.

Dehal, P. S., M. P. Joachimiak, et al. (2010). "MicrobesOnline: an integrated portal for comparative and functional genomics." Nucleic Acids Research 38: D396-D400.

Dibble, D., C. Li , et al. (2011). "A facile method for the recovery of ionic liquid and lignin from biomass pretreatment." Green Chemistry 13(11): 3255-3264.

Dietrich, J. A., Y. Yoshikuni, et al. (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, et al. (2009). "Synthetic protein scaffolds provide modular control over metabolic flux." Nature Biotechnology 27(8): 753-U107.

Dunlop, M. J., Z. Y. Dossani, et al. (2011). "Engineering microbial biofuel tolerance and export using efflux pumps." Molecular Systems Biology 7: 487.

Dunlop, M. J., J. D. Keasling, et al. (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, et al. (2010). "PhosPhAt: the Arabidopsis thaliana phosphorylation site database. An update." Nucleic Acids Research 38: D828-D834.

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.

Fedoroff, N. V., D. S. Battisti, et al. (2010). "Radically Rethinking Agriculture for the 21st Century." Science 327(5967): 833-834.

Fortman, J. L., S. Chhabra, et al. (2008). "Biofuel alternatives to ethanol: pumping the microbial well." Trends in Biotechnology 26(7): 375-381.

Garcia, D. E., E. E. Baidoo, et al. (2008). "Separation and mass spectrometry in microbial metabolomics." Current Opinion in Microbiology 11(3): 233-239.

George, A., K. Tran, et al. (2011). "The effect of ionic liquid cation and anion combinations on the macromolecular structure of lignins." Green Chemistry.*

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.

Gladden, J. B., S. A. Eichorst, et al. (2011). "Substrate Perturbation Alters the Glycoside Hydrolase Activities and Community Composition of Switchgrass-Adapted Bacterial Consortia." Biotechnology and Bioengineering.*

Gladden, J. M., M. Allgaier, et al. (2011). "Glycoside hydrolase activities of thermophilic bacterial consortia adapted to switchgrass." Applied and Environmental Microbiology 77(16): 5804-5812.

Goh, E. B., E. E. Baidoo, et al. (2011). "Engineering of bacterial methyl ketone synthesis for biofuels." Applied and Environmental Microbiology.*

Han, J., S. Singh, et al. (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, 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.

Harholt, J., A. Suttangkakul, et al. (2010). "Biosynthesis of Pectin." Plant Physiology 153(2): 384-395.

Harper, J. C., S. M. Brozik, et al. (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.

Heazlewood, J. L. (2011). "The Green proteome: challenges in plant proteomics." Frontiers in Plant Proteomics: 1-5.

Heazlewood, J. L. and C. J. Petzold (2011). Proteomics - Applications in Biology. Rijeka, Croatia, InTech.*

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.

Holtz, W. J. and J. D. Keasling (2010). "Engineering Static and Dynamic Control of Synthetic Pathways." Cell 140(1): 19-23.

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.

Ito, J., C. J. Petzold, et al. (2010). "The Role of Proteomics in the Development of Cellulosic Biofuels." Current Proteomics 7(2): 121-134.

Ito, J., N. L. Taylor, et al. (2009). "A survey of the Arabidopsis thaliana mitochondrial phosphoproteome." Proteomics 9(17): 4229-4240.

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.

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.

Joshua, C. J., R. Dahl, et al. (2011). "Absence of Diauxie during Simultaneous Utilization of Glucose and Xylose by Sulfolobus acidocaldarius." Journal of Bacteriology 193(6): 1293-1301.

Juminaga, D., E. E. Baidoo, et al. (2011). "Modular Engineering of L-Tyrosine Production in Escherichia coli." Applied and Environmental Microbiology.*

Jung, K. H., L. E. Bartley, et al. (2009). "Analysis of Alternatively Spliced Rice Transcripts Using Microarray Data." Rice 2(1): 44-55.

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).

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.

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.

Keasling, J. (2011). "Joint BioEnergy Institute." Industrial Biotechnology 7(4): 259-260.

Keasling, J. D. (2008). "Synthetic biology for synthetic chemistry." ACS Chemical Biology 3(1): 64-76.

Keasling, J. D. (2010). "Manufacturing molecules through metabolic engineering." Science 330(6009): 1355-1358.

Keasling, J. D. and H. Chou (2008). "Metabolic engineering delivers next-generation biofuels." Nature Biotechnology 26(3): 298-299.

Keller, K. L., J. D. Wall, et al. (2011). "Methods for engineering sulfate reducing bacteria of the genus desulfovibrio." Methods in Enzymology 497: 503-517.

Kent, M. S., G. Cheng, et al. (2010). "Study of Enzymatic Digestion of Cellulose by Small Angle Neutron Scattering." Biomacromolecules 11(2): 357-368.

Kent, M. S., J. K. Murton, et al. (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.

Klein-Marcuschamer, D., B. Holmes, et al. (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, et al. (2010). "Technoeconomic analysis of biofuels: A wiki-based platform for lignocellulosic biorefineries." Biomass & Bioenergy 34(12): 1914-1921.

Klein-Marcuschamer, D., P. Oleskowicz-Popiel, et al. (2011). "The challenge of enzyme cost in the production of lignocellulosic biofuels." Biotechnology and Bioengineering.*

Klein-Marcuschamer, D., B. A. Simmons, et al. (2011). "Techno-economic analysis of a lignocellulosic ethanol biorefinery with ionic liquid pre-treatment." Biofuels, Bioproducts and Biorefining 5(5): 562-569.

Lacayo, C. I., A. J. Malkin, et al. (2010). "Imaging cell wall architecture in single Zinnia elegans tracheary elements." Plant Physiology 154(1): 121-133.

Lalonde, S., A. Sero, et al. (2010). "A membrane protein/signaling protein interaction network for Arabidopsis version AMPv2." Frontiers in Physiology 1: 24.

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.

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.

Lee, S. K., H. Chou, et al. (2008). "Metabolic engineering of microorganisms for biofuels production: from bugs to synthetic biology to fuels." Current Opinion in Biotechnology 19(6): 556-563.

Lee, T. S., R. A. Krupa, et al. (2011). "BglBrick vectors and datasheets; a synthetic biology platform for gene expression." Journal of Biological Engineering 5(1): 12.

Li, C., G. Cheng, et al. (2011). "Influence of physico-chemical changes on enzymatic digestibility of ionic liquid and AFEX pretreated corn stover." Bioresource Technology 102(13): 6928-6936.

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.

Liepman, A. H., R. Wightman, et al. (2010). "Arabidopsis - a powerful model system for plant cell wall research." Plant Journal 61(6): 1107-1121.

Liu, H., J. H. Pereira, et al. (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, et al. (2010). "Understanding the interactions of cellulose with ionic liquids: a molecular dynamics study." Journal of Physical Chemistry B 114(12): 4293-4301.

Liu, H., K. L. Sale, et al. (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, 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.

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.

Ma, S. M., D. E. Garcia, et al. (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, 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.

Marner, W. D., 2nd, A. S. Shaikh, et al. (2009). "Enzyme immobilization via silaffin-mediated autoencapsulation in a biosilica support." Biotechnology Progress 25(2): 417-423.

McAndrew, R. P., P. P. Peralta-Yahya, et al. (2011). "Structure of a Three-Domain Sesquiterpene Synthase: A Prospective Target for Advanced Biofuels Production." Structure 19: 1-9.*

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.

Miller, C. S., B. J. Baker, et al. (2011). "EMIRGE: Reconstruction of full length ribosomal genes from microbial community short read sequencing data." Genome Biology 12(5): R44.

Mukhopadhyay, A., N. J. Hillson, et al. (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.*

Mukhopadhyay, A., A. M. Redding, et al. (2008). "Importance of systems biology in engineering microbes for biofuel production." Current Opinion in Biotechnology 19(3): 228-234.

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, 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.

Ouellet, M., P. D. Adams, et al. (2009). "A rapid and inexpensive labeling method for microarray gene expression analysis." BMC Biotechnology 9: 97.

Ouellet, M., S. Datta, et al. (2011). "Impact of ionic liquid pretreated plant biomass on Saccharomyces cerevisiae growth and biofuel production." Green Chemistry 13(10): 2743-2749.

Park, J. I., M. S. Kent, et al. (2011). "Enzymatic hydrolysis of cellulose by the cellobiohydrolase domain of CelB from the hyperthermophilic bacterium Caldicellulosiruptor saccharolyticus." Bioresource Technology 102(10): 5988-5994.

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.*

Peralta-Yahya, P. P. and J. D. Keasling (2010). "Advanced biofuel production in microbes." Biotechnology Journal 5(2): 147-162.

Peralta-Yahya, P. P., M. Ouellet, et al. (2011). "Identification and microbial production of a terpene-based advanced biofuel." Nature Communications 2: 483.

Pereira, J. H., Z. Chen, et al. (2010). "Biochemical characterization and crystal structure of endoglucanase Cel5A from the hyperthermophilic Thermotoga maritima." Journal of Structural Biology 172(3): 372-379.

Pereira, J. H., R. Sapra, et al. (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, 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.

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, et al. (2010). "A Simple Method for Enzymatic Synthesis of Unlabeled and Radiolabeled Hydroxycinnamate-CoA." BioEnergy Research 3(2): 115-122.

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.

Redding-Johanson, A. M., T. S. Batth, et al. (2011). "Targeted proteomics for metabolic pathway optimization: Application to terpene production." Metabolic Engineering 13(2): 194-203.

Reddy, A. P., M. Allgaier, et al. (2011). "Bioenergy feedstock-specific enrichment of microbial populations during high-solids thermophilic deconstruction." Biotechnology and Bioengineering 108(9): 2088-2098.

Reindl, W., K. Deng, et al. (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, et al. (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. and R. Adamchak (2010). "The future of sustainable food production." Annals of the New York Academy of Sciences 1190(1): 184-185.

Ronald, P. C. and B. Beutler (2010). "Plant and animal sensors of conserved microbial signatures." Science 330(6007): 1061-1064.

Rutherford, B. J., R. H. Dahl, et al. (2010). "Functional genomic study of exogenous n-butanol stress in Escherichia coli." Applied and Environmental Microbiology 76(6): 1935-1945.

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.

Sarkar, P., E. Bosneaga, et al. (2009). "Plant cell walls throughout evolution: towards a molecular understanding of their design principles." Journal of Experimental Botany 60(13): 3615-3635.

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.

Scheller, H. V. and P. Ulvskov (2010). "Hemicelluloses." Annual Review of Plant Biology 61: 263-289.

Seo, Y. S., M. Chern, et al. (2011). "Towards establishment of a rice stress response interactome." PLoS Genet 7(4): e1002020.

Shaikh, A. S., Y. J. Tang, et al. (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.

Shaikh, A. S., Y. J. Tang, et al. (2010). "Study of stationary phase metabolism via isotopomer analysis of amino acids from an isolated protein." Biotechnology Progress 26(1): 52-56.

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.

Shepherd, M., J. Bartle, et al. (2011). "Eucalypts as a biofuel feedstock." Biofuels 2(6): 639-657.

Shui, W., L. Sheu, et al. (2008). "Membrane proteomics of phagosomes suggests a connection to autophagy." Proceedings of the National Academy of Sciences 105(44): 16952-16957.

Simmons, B. A. (2011). "Opportunities and challenges in advanced biofuel production: the importance of synthetic biology and combustion science." Biofuels 2(1): 5-7.

Simmons, B. A. (2011). "Synthetic enzymes: catalysis on demand." Microbial Biotechnology 4(2): 130-131.

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.*

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., D. Loque, et al. (2008). "Next-generation biomass feedstocks for biofuel production." Genome Biology 9(12): 242.

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.

Simmons, B. A., S. Singh, et al. (2010). "Ionic liquid pretreatment." Chemical Engineering Progress: 50-55.

Singer, S. W., A. P. Reddy, et al. (2011). "Enrichment, Isolation and Characterization of Fungi Tolerant to 1-Ethyl-3-Methylimadazolium Acetate." Journal of Applied Microbiology 110(4): 1023-1031.

Singh, S., B. A. Simmons, et al. (2009). "Visualization of biomass solubilization and cellulose regeneration during ionic liquid pretreatment of switchgrass." Biotechnology and Bioengineering 104(1): 68-75.

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).

Steen, E. J., R. Chan, et al. (2008). "Metabolic engineering of Saccharomyces cerevisiae for the production of n-butanol." Microbial Cell Factories 7: 36.

Steen, E. J., Y. Kang, et al. (2010). "Microbial production of fatty-acid-derived fuels and chemicals from plant biomass." Nature 463(7280): 559-562.

Sun, L., B. A. Simmons, et al. (2011). "Understanding tissue specific compositions of bioenergy feedstocks through hyperspectral Raman imaging." Biotechnology and Bioengineering 108(2): 286-295.

Sun, L., P. Varanasi, et al. (2011). "Rapid determination of syringyl: Guaiacyl ratios using FT-Raman spectroscopy." Biotechnology and Bioengineering.*

Tang, Y. J., H. G. Martin, et al. (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, et al. (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, et al. (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, et al. (2009). "Investigation of carbon metabolism in "Dehalococcoides ethenogenes" strain 195 by use of isotopomer and transcriptomic analyses." Journal of Bacteriology 191(16): 5224-5231.

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.

Varanasi, P., L. Sun, et al. (2011). Quantifying Bio-Engineering: The Importance of Biophysics in Biofuel Research. Biofuel's Engineering Process Technology. M. A. dos Santos Bernades, InTech: 493-520.

Vega-Sanchez, M. E. and P. C. Ronald (2010). "Genetic and biotechnological approaches for biofuel crop improvement." Current Opinion Biotechnology 21(2): 218-224.

Verhertbruggen, Y., L. Yin, et al. (2011). "Mannan synthase activity in the CSLD family." Plant Signaling & Behavior 6(10): 1620-1623.

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.

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.

Wipat, A., A. Villalobos, et al. (2011). Synthetic Biology Open Language (SBOL) Version 1.0.0. BioBricks Foundation Request for Comments.

Wurtzel, O., R. Sapra, et al. (2010). "A single-base resolution map of an archaeal transcriptome." Genome Research 20(1): 133-141.

Yang, Y., J. Dec, et al. (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, et al. (2010). "Multiple displacement amplification compromises quantitative analysis of metagenomes." Nature Methods 7(12): 943-944.

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.

Young, M., V. Artsatbanov, et al. (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, et al. (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.

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, et al. (2011). "Identification of a haloalkaliphilic and thermostable cellulase with improved ionic liquid tolerance." Green Chemistry 13(8): 2083-2090.