1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13. 14. 15. 16. 17. 18. 19. 20. 21. 22. 23. 24. 25. 26. 27. J. D. Keasling, et al., Metabolic engineering delivers next-generation biofuels, Nature Biotechnology, 2008 J. E. Dueber, et al., Synthetic protein scaffolds provide modular control over metabolic flux, Nature Biotechnology, 2009 J. Nielsen, et al., Synergies between synthetic biology and metabolic engineering, Nature Biotechnology, 2011 R. Knight, et al., Unlocking the potential of metagenomics through replicated experimental design, Nature Biotechnology, 2012 R. Dahl, et al., Engineering dynamic pathway regulation using stress-response promoters, nature biotechnology, 2013 W. J. Holtz, et al., Engineering Static and Dynamic Control of Synthetic Pathways, Cell, 2010 Y. Xiao, et al., Retrograde signaling by the plastidial metabolite MEcPP regulates expression of nuclear stress-response genes, Cell, 2012 J. C. Way, et al., Integrating Biological Redesign: Where Synthetic Biology Came From and Where It Needs to Go, Cell, 2014 N. V. Fedoroff, et al., Radically Rethinking Agriculture for the 21st Century, Science, 2010 J. D. Keasling, Manufacturing molecules through metabolic engineering, Science, 2010 P. C. Ronald, et al., Plant and animal sensors of conserved microbial signatures, Science, 2010 J. A. Banks, et al., The Selaginella genome identifies genetic changes associated with the evolution of vascular plants, Science, 2011 J. M. Carothers, et al., Model-driven engineering of RNA devices to quantitatively program gene expression, Science, 2011 J. A. Dietrich, et al., High-throughput metabolic engineering: advances in small-molecule screening and selection, Annu Rev Biochem, 2010 E. J. Steen, et al., Microbial production of fatty-acid-derived fuels and chemicals from plant biomass, Nature, 2010 JP Vogel, et al., Genome sequence analysis of the model grass Brachypodium distachyon: insights into grass genome evolution, Nature, 2010 S. Yilmaz, et al., Multiple displacement amplification compromises quantitative analysis of metagenomes, Nature Methods, 2010 J. D. Keasling, et al., Synthesis: A constructive debate, Nature, 2012 P. P. Peralta-Yahya, et al., Microbial engineering for the production of advanced biofuels, Nature, 2012 C. C. Liu, et al., An adaptor from translational to transcriptional control enables predictable assembly of complex regulation, Nature Methods, 2012 V. K. Mutalik, et al., Precise and reliable gene expression via standard transcription and translation initiation elements, Nat Methods, 2013 V. K. Mutalik, et al., Quantitative estimation of activity and quality for collections of functional genetic elements, Nat Methods, 2013 J. Kirby, et al., Biosynthesis of plant isoprenoids: perspectives for microbial engineering, Annual Review of Plant Biology, 2009 H. V. Scheller, et al., Hemicelluloses, Annual Review of Plant Biology, 2010 J. K. Jansson and N. Tas, The microbial ecology of permafrost, Nature Reviews Microbiology, 2014 J. L. Bennetzen, et al., Reference genome sequence of the model plant Setaria, Nat Biotechnol, 2012 F. Zhang, et al., Design of a dynamic sensor-regulator system for production of chemicals and fuels derived from fatty acids, Nat Biotechnol, 2012 28. 29. 30. 31. 32. 33. 34. 35. 36. 37. 38. 39. 40. 41. 42. 43. 44. 45. 46. 47. 48. 49. 50. 51. 52. W. Reindl, et al., Colloid-based multiplexed screening for plant biomass-degrading glycoside hydrolase activities in microbial communities, Energy & Environmental Science, 2011 O. Wurtzel, et al., A single-base resolution map of an archaeal transcriptome, Genome Research, 2010 K. H. Jung, et al., The Rice Kinase Phylogenomics Database: a guide for systematic analysis of the rice kinase super-family, Trends in Plant Science, 2010 Oikawa, et al., Golgi-localized enzyme complexes for plant cell wall biosynthesis, Trends Plant Sci, 2013 J. Keasling, From yeast to alkaloids, Nature Chemical Biology, 2008 V. K. Mutalik, et al., Rationally designed families of orthogonal RNA regulators of translation, Nature Chemical Biology, 2012 J. Nielsen, et al., Engineering synergy in biotechnology, Nature Chemical Biology, 2014 P.C. Ronald, Lab to Farm: Applying Research on Plant Genetics and Genomics to Crop Improvement, PLoS Biology, 2014 M. J. Dunlop, et al., Engineering microbial biofuel tolerance and export using efflux pumps, Molecular Systems Biology, 2011 H. H. Chou and J. D. Keasling, Programming adaptive control to evolve increased metabolite production, Nature Communications, 2013 T. L. Ruegg, et al., An auto-inducible mechanism for ionic liquid resistance in microbial biofuel production, Nature Communications, 2014 J. K. Jensen, et al., Identification of a xylogalacturonan xylosyltransferase involved in pectin biosynthesis in Arabidopsis, Plant Cell, 2008 Rautengarten, et al., The interconversion of UDP-arabinopyranose and UDP-arabinofuranose is indispensable for plant development in Arabidopsis, Plant Cell, 2011 J. Liwanag, et al., Pectin biosynthesis: GALS1 in Arabidopsis thaliana is a beta-1,4-galactan beta-1,4galactosyltransferase, Plant Cell, 2012 K. Baerenfaller, et al., Arabidopsis, Taking the Next Step: Building an Arabidopsis Information Portal, Plant Cell, 2012 L. Yuan, et al., Allosteric regulation of transport activity by heterotrimerization of Arabidopsis ammonium transporter complexes in vivo, Plant Cell, 2013 A. Simmons, et al., Next-generation biomass feedstocks for biofuel production, Genome Biology, 2008 S. Miller, et al., EMIRGE: Reconstruction of full length ribosomal genes from microbial community short read sequencing data, Genome Biology, 2011 P. P. Peralta-Yahya, et al., Identification and microbial production of a terpene-based advanced biofuel, Nature Communications , 2011 F. Zhang, and J. Keasling, Biosensors and their applications in microbial metabolic engineering, Trends in Microbiology, 2011 A. Simmons, et al., Advances in modifying lignin for enhanced biofuel production, Current Opinion in Plant Biology , 2010 M. Socha, et al., Efficient biomass pretreatment using ionic liquids derived from lignin and hemicellulose, PNAS, 2014 Rautengarten, et al., The Golgi localized bifunctional UDP-rhamnose/UDP-galactose transporter family of Arabidopsis, PNAS, 2014 J. L. Fortman, et al., Biofuel alternatives to ethanol: pumping the microbial well, Trends in Biotechnology, 2008 A. Rennie, et al., Identification of a sphingolipid alpha-glucuronosyltransferase that is essential for pollen function in Arabidopsis, Plant Cell, 2014 53. 54. 55. 56. 57. 58. 59. 60. 61. 62. 63. 64. 65. 66. 67. 68. 69. 70. 71. 72. 73. 74. 75. 76. R. D. Rosengarten and M. L. Nicotra, Model Systems of Invertebrate Allorecognition, Current Biology, 2011 P. C. Ronald and K. Shirasu, Front-runners in plant-microbe interactions, Current Opinion in Plant Biology, 2012 O. U. Mason, et al., Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill, ISME Journal, 2014 E. Graham, et al., Microbes in thawing permafrost: the unknown variable in the climate change equation, ISME Journal, 2012 Lauck, et al., Rosetta Backrub-a web server for flexible backbone protein structure modeling and design, Nucleic Acids Research, 2010 Densmore, et al., Algorithms for automated DNA assembly, Nucleic Acids Research, 2010 R. De Michele, et al., Fluorescent sensors reporting the activity of ammonium transceptors in live cells, eLife, 2013 S. K. Lee, et al., Metabolic engineering of microorganisms for biofuels production: from bugs to synthetic biology to fuels, Current Opinion in Biotechnology, 2008 Mukhopadhyay, et al., Importance of systems biology in engineering microbes for biofuel production, Current Opinion in Biotechnology, 2008 J. M. Carothers, et al., Chemical synthesis using synthetic biology, Current Opinion in Biotechnology, 2009 M. J. Dougherty, and F. H. Arnold, Directed evolution: new parts and optimized function, Current Opinion in Biotechnology, 2009 M. E. Vega-Sanchez, and P. C. Ronald, Genetic and biotechnological approaches for biofuel crop improvement, Current Opinion Biotechnology, 2010 Zhang, et al., Metabolic engineering of microbial pathways for advanced biofuels production, Current Opinion Biotechnology, 2011 W. Blanch, et al., Bioprocessing for biofuels, Curr Opin Biotechnol, 2012 S. Yuzawa, et al., Heterologous production of polyketides by modular type I polyketide synthases in Escherichia coli, Curr Opin Biotechnol, 2012 T. de Rond, et al., High throughput screening of enzyme activity with mass spectrometry imaging, Curr Opin Biotechnol, 2014 M. Carothers, et al., Selecting RNA aptamers for synthetic biology: investigating magnesium dependence and predicting binding affinity, Nucleic Acids Res, 2010 P. S. Dehal, et al., MicrobesOnline: an integrated portal for comparative and functional genomics, Nucleic Acids Research, 2010 P. Durek, et al., PhosPhAt: the Arabidopsis thaliana phosphorylation site database. An update, Nucleic Acids Research, 2010 T. Bates, et al., GLAMM: Genome-Linked Application for Metabolic Maps, Nucleic Acids Research, 2011 T. S. Ham, et al., Design, implementation and practice of JBEI-ICE: an open source biological part registry platform and tools, Nucleic Acids Res, 2012 Chivian, et al., MetaMicrobesOnline: phylogenomic analysis of microbial communities, Nucleic Acids Res, 2013 S. Kumar, et al., Remodeling the isoprenoid pathway in tobacco by expressing the cytoplasmic mevalonate pathway in chloroplasts, Metabolic Engineering, 2012 W. Runguphan and J. D. Keasling, Metabolic engineering of Saccharomyces cerevisiae for production of fatty acid-derived biofuels and chemicals, Metabolic Engineering, 2014 77. R. S. Bart, et al., Rice Snl6, a cinnamoyl-CoA reductase-like gene family member, is required for NH1mediated immunity to Xanthomonas oryzae pv. oryzae, PLoS Genet, 2010 78.Y. S. Seo, et al., Towards establishment of a rice stress response interactome, PLoS Genet, 2011 79. Y. J. Tang, et al., Advances in analysis of microbial metabolic fluxes via (13)C isotopic labeling, Mass Spectrometry Reviews, 2009 80. R. Lamendella, et al., Omics' of the mammalian gut - new insights into function, Current Opinion in Biotechnology, 2012 81. S. Borglin, et al., Application of phenotypic microarrays to environmental microbiology, Current Opinion in Biotechnology, 2012 82. Eudes, Y., et al., Lignin bioengineering, Current Opinion in Biotechnology, 2014 83. S. Rodriguez, et al., Production and quantification of sesquiterpenes in Saccharomyces cerevisiae, including extraction, detection and quantification of terpene products and key related metabolites, Nature Protocols, 2014 84. G. M. Estavillo, et al., Isolation of the plant cytosolic fraction for proteomic analysis, Plant Proteomics: Methods and Protocols, 2013 85. H. T. Parsons, et al., Separation of the plant golgi apparatus and endoplasmic reticulum by free-flow electrophoresis, Plant Proteomics: Methods and Protocols, 2013 86. E. Garcia, et al., Separation and mass spectrometry in microbial metabolomics, Current Opinion in Microbiology, 2008 87. A. Rennie and H. V. Scheller, Xylan biosynthesis, Current Opinion in Biotechnology, 2014 88. J. Bernal, et al., Functional Analysis of the Cellulose Synthase-Like Genes CSLD1, CSLD2, and CSLD4 in Tip-Growing Arabidopsis Cells, Plant Physiology, 2008 89. M. Landau, et al., A cytoplasmically inherited barley mutant is defective in photosystem I assembly due to a temperature-sensitive defect in ycf3 splicing, Plant Physiology, 2009 90. Harholt, et al., Biosynthesis of Pectin, Plant Physiology, 2010 91. H. Jung, et al., The Submergence Tolerance Regulator Sub1A Mediates Stress-Responsive Expression of AP2/ERF Transcription Factors, Plant Physiology, 2010 92. I. Lacayo, et al., Imaging cell wall architecture in single Zinnia elegans tracheary elements, Plant Physiology, 2010 93. J. Joshi, et al., MASCP Gator: an aggregation portal for the visualization of Arabidopsis proteomics data, Plant Physiology, 2011 94. Y. Manabe, et al., Loss-of-Function Mutation of REDUCED WALL ACETYLATION2 in Arabidopsis Leads to Reduced Cell Wall Acetylation and Increased Resistance to Botrytis cinerea, Plant Physiology, 2011 95. T. Parsons, et al., Isolation and proteomic characterization of the Arabidopsis Golgi defines functional and novel components involved in plant cell wall biosynthesis, Plant Physiol, 2012 96. Rautengarten, et al., Arabidopsis Deficient in Cutin Ferulate encodes a transferase required for feruloylation of omega-hydroxy fatty acids in cutin polyester, Plant Physiol, 2012 97. A. Rennie, et al., S. F. Hansen, et al., E. E. Baidoo, et al., M. Z. Hadi, et al., J. D. Keasling, et al., H. V. Scheller, Three members of the Arabidopsis glycosyltransferase family 8 are xylan glucuronosyltransferases, Plant Physiol, 2012 98. E. Vega-Sanchez, et al., 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, 2012 99. L. E. Bartley, et al., Overexpression of a BAHD Acyltransferase, OsAt10, alters rice cell wall hydroxycinnamic acid content and saccharification, Plant Physiol, 2013 100. 101. 102. 103. 104. 105. 106. 107. 108. 109. 110. 111. 112. 113. 114. 115. 116. 117. 118. 119. 120. 121. 122. Y. Manabe, et al., RWA Proteins Play Vital and Distinct Roles in Cell Wall O-Acetylation in Arabidopsis thaliana, Plant Physiology, 2013 S. S. Dey, et al., Mutual Information Analysis Reveals Coevolving Residues in Tat That Compensate for Two Distinct Functions in HIV-1 Gene Expression, Journal of Biological Chemistry, 2012 H. Pereira, et al., Structure of endoglucanase Cel9A from the thermoacidophilic Alicyclobacillus acidocaldarius, Acta Crystallographica Section D Biological Crystallography, 2009 H. Pereira, et al., Structure of FabH and factors affecting the distribution of branched fatty acids in Micrococcus luteus, Acta Crystallogr D Biol Crystallogr, 2012 R. McAndrew, et al., Structure of the OsSERK2 leucine-rich repeat extracellular domain, Acta Crystallogr D Biol Crystallogr, 2014 M. DeAngelis, et al., Anaerobic decomposition of switchgrass by tropical soil-derived feedstockadapted consortia, MBio, 2012 S. Datta, et al., Ionic liquid tolerant hyperthermophilic cellulases for biomass pretreatment and hydrolysis, Green Chemistry, 2010 Dibble, et al., A facile method for the recovery of ionic liquid and lignin from biomass pretreatment, Green Chemistry, 2011 George, et al., The effect of ionic liquid cation and anion combinations on the macromolecular structure of lignins, Green Chemistry, 2011 Ouellet, et al., Impact of ionic liquid pretreated plant biomass on Saccharomyces cerevisiae growth and biofuel production, Green Chemistry, 2011 T. Zhang, et al., Identification of a haloalkaliphilic and thermostable cellulase with improved ionic liquid tolerance, Green Chemistry, 2011 K. M. Torr, et al., The impact of ionic liquid pretreatment on the chemistry and enzymatic digestibility of Pinus radiata compression wood, Green Chemistry, 2012 Groff, et al., Acid enhanced ionic liquid pretreatment of biomass, Green Chemistry, 2013 Jian Shi, et al., One-pot ionic liquid pretreatment and saccharification of switchgrass, Green Chemistry, 2013 Sun, et al., Understanding pretreatment efficacy of four cholinium and imidazolium ionic liquids by chemistry and computation, Green Chemistry, 2014 J. Shi, et al., Understanding the Role of Water during Ionic Liquid Pretreatment of Lignocellulose: Cosolvent or Anti-solvent?, Green Chemistry, 2014 Sathitsuksanoh, et al., Lignin fate and characterization during ionic liquid biomass pretreatment for renewable chemicals and fuels production, Green Chemistry, 2014 Knoch, et al., A beta-glucuronosyltransferase from Arabidopsis thaliana involved in biosynthesis of type II arabinogalactan has a role in cell elongation during seedling growth, Plant Journal, 2013 J. Lao, et al., The plant glycosyltransferase clone collection for functional genomics, Plant Journal, 2014 R. P. McAndrew, et al., Structure of a three-domain sesquiterpene synthase: a prospective target for advanced biofuels production, Structure, 2011 Y. Kung, et al., Constructing tailored isoprenoid products by structure-guided modification of geranylgeranyl reductase, Structure, 2014 Chandrasekaran, et al., K. Deng, et al., C. Y. Koh, et al., T. Takasuka, et al., L. F. Bergeman, et al., B. G. Fox, et al., P. D. Adams, et al., A. K. Singh, A universal flow cytometry assay for screening carbohydrate-active enzymes using glycan microspheres, Chem Commun (Camb), 2013 Y. C. Yeh, et al., Functionalizing bacterial cell surfaces with a phage protein, Chem Commun (Camb), 2013 123. 124. 125. 126. 127. 128. 129. 130. 131. 132. 133. 134. 135. 136. 137. 138. 139. 140. 141. 142. 143. 144. 145. 146. J. Cao, et al., Construction of a rice glycosyltransferase phylogenomic database and identification of rice-diverged glycosyltransferases, Molecular Plant, 2008 L. Yin, et al., The Cooperative Activities of CSLD2, CSLD3, and CSLD5 Are Required for Normal Arabidopsis Development, Molecular Plant, 2011 X. Chen, et al., Inactivation of OsIRX10 leads to decreased xylan content in rice culm cell walls and improved biomass saccharification, Mol Plant, 2013 S. Gille, et al., Arabinosylation of a Yariv-Precipitable Cell Wall Polymer Impacts Plant Growth as Exemplified by the Arabidopsis Glycosyltransferase Mutant ray1, Mol Plant, 2013 R. Sharma, et al., Recent advances in dissecting stress-regulatory crosstalk in rice, Mol Plant, 2013 X. Chen, et al., An XA21-associated kinase (OsSERK2) regulates immunity mediated by the XA21 and XA3 immune receptors, Molecular Plant, 2014 H. Liepman, et al., Arabidopsis - a powerful model system for plant cell wall research, Plant Journal, 2010 Geshi, et al., A galactosyltransferase acting on arabinogalactan protein glycans is essential for embryo development in Arabidopsis, Plant J, 2013 Y. Tobimatsu, et al., Visualization of Plant Cell Wall Lignification Using Fluorescence-tagged Monolignols, Plant J, 2013 J. Y. Zhang, et al., Development of an integrated transcript sequence database and a gene expression atlas for gene discovery and analysis in switchgrass (Panicum virgatum L.), Plant J, 2013 M. Frederix and A. J. Downie, Quorum Sensing: Regulating the Regulators, Advances in Microbial Physiology, Vol 58, 2011 S. Okumoto, et al., Quantitative imaging for discovery and assembly of the metabo-regulome, New Phytologist, 2008 J. Harholt, et al., Generation of transgenic wheat (Triticum aestivum L.) accumulating heterologous endo-xylanase or ferulic acid esterase in the endosperm, Plant Biotechnology Journal, 2010 Eudes, et al., Biosynthesis and incorporation of side-chain-truncated lignin monomers to reduce lignin polymerization and enhance saccharification, Plant Biotechnol J, 2012 Yang, et al., Engineering secondary cell wall deposition in plants, Plant Biotechnol J, 2013 S. A. Eichorst, et al., Community dynamics of cellulose-adapted thermophilic bacterial consortia, Environ Microbiol, 2013 S. D. McClendon, et al., Thermoascus aurantiacus is a promising source of enzymes for biomass deconstruction under thermophilic conditions, Biotechnol Biofuels, 2012 D. Petersen, et al., Engineering of plants with improved properties as biofuels feedstocks by vesselspecific complementation of xylan biosynthesis mutants, Biotechnol Biofuels, 2012 G. Cruz, et al., Impact of high biomass loading on ionic liquid pretreatment, Biotechnol Biofuels, 2013 V. Reyes-Ortiz, et al., Addition of a carbohydrate-binding module enhances cellulase penetration into cellulose substrates, Biotechnol Biofuels, 2013 M. Socha, et al., Comparison of sugar content for ionic liquid pretreated Douglas-fir woodchips and forestry residues, Biotechnol Biofuels, 2013 N. Sun, et al., Production and extraction of sugars from switchgrass hydrolyzed in ionic liquids, Biotechnol Biofuels, 2013 Varanasi, et al., Survey of renewable chemicals produced from lignocellulosic biomass during ionic liquid pretreatment, Biotechnol Biofuels, 2013 Li, D. Tanjore, et al., Scale-up and evaluation of high solid ionic liquid pretreatment and enzymatic hydrolysis of switchgrass, Biotechnology for Biofuels, 2013 147. 148. 149. 150. 151. 152. 153. 154. 155. 156. 157. 158. 159. 160. 161. 162. 163. 164. 165. 166. 167. 168. 169. N. Uppugundla, et al., A comparative study of ethanol production using dilute acid, ionic liquid and AFEX pretreated corn stover, Biotechnology for Biofuels, 2014 J. S. Lupoi, et al., High-throughput prediction of eucalypt lignin syringyl/guaiacyl content using multivariate analysis: a comparison between mid-infrared, near-infrared, and Raman spectroscopies for model development, Biotechnology for Biofuels, 2014 M. Konda, et al., Understanding cost drivers and economic potential of two variants of ionic liquid pretreatment for cellulosic biofuel production, Biotechnology for Biofuels, 2014 J. M. Gladden, et al., Discovery and characterization of ionic liquid-tolerant thermophilic cellulases from a switchgrass-adapted microbial community, Biotechnology for Biofuels, 2014 X. Gao, et al., Comparison of enzymatic reactivity of corn stover solids prepared by dilute acid, AFEX, and ionic liquid pretreatments, Biotechnology for Biofuels, 2014 J. C. Harper, et al., Fabrication and testing of a microneedles sensor array for p-cresol detection with potential biofuel applications, ACS Applied Materials & Interfaces, 2009 S. Shaikh, et al., Isotopomer distributions in amino acids from a highly expressed protein as a proxy for those from total protein, Analytical Chemistry, 2008 Bharadwaj, et al., Microfluidic Glycosyl Hydrolase Screening for Biomass-to-Biofuel Conversion, Analytical Chemistry, 2010 M. S. Kent, et al., Study of Enzymatic Digestion of Cellulose by Small Angle Neutron Scattering, Biomacromolecules, 2010 Cheng, et al., Neutron Reflectometry and QCM-D Study of the Interaction of Cellulases with Films of Amorphous Cellulose, Biomacromolecules, 2011 Cheng, et al., Transition of cellulose crystalline structure and surface morphology of biomass as a function of ionic liquid pretreatment and its relation to enzymatic hydrolysis, Biomacromolecules, 2011 Chang, et al., Droplet-based microfluidic platform for heterogeneous enzymatic assays, Lab Chip, 2013 M. Ma, et al., Optimization of a heterologous mevalonate pathway through the use of variant HMGCoA reductases, Metabolic Engineering, 2011 M. Redding-Johanson, et al., Targeted proteomics for metabolic pathway optimization: Application to terpene production, Metabolic Engineering, 2011 D. Keasling, Synthetic biology and the development of tools for metabolic engineering, Metab Eng, 2012 Y. Satoh, et al., Engineering of l-tyrosine oxidation in Escherichia coli and microbial production of hydroxytyrosol, Metab Eng, 2012 Zhang, et al., Enhancing fatty acid production by the expression of the regulatory transcription factor FadR, Metab Eng, 2012 Alonso-Gutierrez, et al., Metabolic engineering of Escherichia coli for limonene and perillyl alcohol production, Metab Eng, 2013 Ozaydin, et al., Carotenoid-based phenotypic screen of the yeast deletion collection reveals new genes with roles in isoprenoid production, Metab Eng, 2013 W. Runguphan, et al., Metabolic engineering of Saccharomyces cerevisiae for production of fatty acidderived biofuels and chemicals, Metab Eng, 2013 S. Batth, et al., A targeted proteomics toolkit for high-throughput absolute quantification of Escherichia coli proteins, Metab Eng, 2014 E. B. Goh et al., Substantial improvements in methyl ketone production in E. coli and insights on the pathway from in vitro studies, Metab Eng, 2014 R. W. Haushalter, et al., Production of anteiso-branched fatty acids in Escherichia coli, et al., next generation biofuels with improved cold-flow properties, Metab Eng, 2014 170. 171. 172. 173. 174. 175. 176. 177. 178. 179. 180. 181. 182. 183. 184. 185. 186. 187. 188. 189. 190. 191. 192. B. Lucks, et al., Engineering mRNA structural regulation of transcription using an RNA-sensing riboregulator, Faseb Journal, 2010 Butland, et al., Functional interactions of a monothiol glutaredoxin and an iron sulfur cluster carrier protein with the radical SAM enzyme MiaB, Faseb Journal, 2013 W. Blanch, et al., Addressing the need for alternative transportation fuels: The Joint BioEnergy Institute, ACS Chemical Biology, 2008 D. Keasling, Synthetic biology for synthetic chemistry, ACS Chemical Biology, 2008 A. Dietrich, et al., A Novel Semi-biosynthetic Route for Artemisinin Production Using Engineered Substrate-Promiscuous P450(BM3), ACS Chemical Biology, 2009 Heins RA, et al., Phylogenomically Guided Identification of Industrially Relevant GH1 β-Glucosidases through DNA Synthesis and Nanostructure-Initiator Mass Spectrometry, ACS Chemical Biology, 2014 Deng, et al., Rapid Kinetic Characterization of Glycosyl Hydrolases Based on Oxime Derivatization and Nanostructure-Initiator Mass Spectrometry (NIMS), ACS Chemical Biology, 2014 Hajimorad, et al., A framework and model system to investigate linear system behavior in Escherichia coli, J Biol Eng, 2011 J. Chen, et al., Device Editor visual biological CAD canvas, J Biol Eng, 2012 Li, et al., Comparison of dilute acid and ionic liquid pretreatment of switchgrass: Biomass recalcitrance, delignification and enzymatic saccharification, Bioresource Technology, 2010 R. Bharadwaj, et al., High-throughput enzymatic hydrolysis of lignocellulosic biomass via in-situ regeneration, Bioresource Technology, 2011 Li, et al., Influence of physico-chemical changes on enzymatic digestibility of ionic liquid and AFEX pretreated corn stover, Bioresource Technology, 2011 J. I. Park, et al., Enzymatic hydrolysis of cellulose by the cellobiohydrolase domain of CelB from the hyperthermophilic bacterium Caldicellulosiruptor saccharolyticus, Bioresource Technology, 2011 Oleskowicz-Popiel, et al., Co-production of ethanol, biogas, protein fodder and natural fertilizer in organic farming--evaluation of a concept for a farm-scale biorefinery, Bioresour Technol, 2012 G. Papa, et al., 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, 2012 Varanasi, et al., Understanding changes in lignin of Panicum virgatum and Eucalyptus globulus as a function of ionic liquid pretreatment, Bioresour Technol, 2012 J. A. Perez-Pimienta, et al., Comparison of the impact of ionic liquid pretreatment on recalcitrance of agave bagasse and switchgrass, Bioresour Technol, 2013 P. Oleskowicz-Popiel, et al., Lignocellulosic ethanol production without enzymes--technoeconomic analysis of ionic liquid pretreatment followed by acidolysis, Bioresource Technology, 2014 Scullin, et al., Optimization of renewable pinene production from the conversion of macroalgae Saccharina latissima, Bioresour Technol, 2014 W. Weckwerth, et al., The multinational Arabidopsis steering subcommittee for proteomics assembles the largest proteome database resource for plant systems biology, Journal of Proteome Research, 2008 Chandrasekaran, et al., A Microscale Platform For Integrated Cell-Free Expression And Activity Screening Of Cellulases, Journal of Proteome Research, 2010 J. Ito, et al., Analysis of the Arabidopsis cytosolic proteome highlights subcellular partitioning of central plant metabolism, Journal of Proteome Research, 2011 Meng, et al., UDP-glucose pyrophosphorylase is not rate limiting, but is essential in Arabidopsis, Plant Cell Physiology, 2009 193. 194. 195. 196. 197. 198. 199. 200. 201. 202. 203. 204. 205. 206. 207. 208. 209. 210. 211. 212. 213. 214. 215. 216. Y. Chiu, et al., AtAPY1 and AtAPY2 function as Golgi-localized nucleoside diphosphatases in Arabidopsis thaliana, Plant Cell Physiol, 2012 O.P. Cetinkol, et al., Understanding the impact of ionic liquid pretreatment on eucalyptus, Biofuels, 2010 Shepherd, et al., Eucalypts as a biofuel feedstock, Biofuels, 2011 B.A. Simmons, Opportunities and challenges in advanced biofuel production: the importance of synthetic biology and combustion science, Biofuels, 2011 B.A. Simmons, Rethinking renewable energy in Japan, Biofuels, 2011 Jian Shi, et al., Impact of mixed feedstocks and feedstock densification on ionic liquid pretreatment efficiency, Biofuels, 2013 Ronald, et al., Plant genetics, sustainable agriculture and global food security, Genetics, 2011 Ghosh, et al., A peptide-based method for 13C Metabolic Flux Analysis in microbial communities, PLoS Comput Biol, 2014 Rotavera, et al., Photoionization mass spectrometric measurements of initial reaction pathways in lowtemperature oxidation of 2,5-dimethylhexane, J Phys Chem A, 2014 Loque, et al., Pore mutations in ammonium transporter AMT1 with increased electrogenic ammonium transport activity, Journal of Biological Chemistry, 2009 H. R. Beller, et al., Definitive alkene identification needed for in vitro studies with ole (olefin biosynthesis) proteins, Journal of Biological Chemistry, 2011 Casler, et al., The Switchgrass Genome: Tools and Strategies, Plant Genome, 2011 Z. Chen, et al., Tracing determinants of dual substrate specificity in glycoside hydrolase family 5, J Biol Chem, 2012 P. McAndrew, et al., From soil to structure, a novel dimeric beta-glucosidase belonging to glycoside hydrolase family 3 isolated from compost using metagenomic analysis, J Biol Chem, 2013 H. J. Joshi, et al., 1001 Proteomes: a functional proteomics portal for the analysis of Arabidopsis thaliana accessions, Bioinformatics, 2012 Kristen M. DeAngelis, et al., Changes in microbial dynamics during long-term decomposition in tropical forests, Soil Biology and Biochemistry, 2013 Y. B. Melnichenko, et al., Monitoring Phase Behavior of Sub- and Supercritical CO2 Confined in Porous Fractal Silica with 85% Porosity, Langmuir, 2010 G. Cheng, et al., Interactions of endoglucanases with amorphous cellulose films resolved by neutron reflectometry and quartz crystal microbalance with dissipation monitoring, Langmuir, 2012 G. Cheng, et al., Effect of ionic liquid treatment on the structures of lignins in solutions: molecular subunits released from lignin, Langmuir, 2012 Ronald, and R. Adamchak, The future of sustainable food production, Annals of the New York Academy of Sciences, 2010 S. Scullin and L. D. Partridge, Modulation by pregnenolone sulfate of filtering properties in the hippocampal trisynaptic circuit, Hippocampus, 2012 Klein-Marcuschamer, et al., Techno-economic analysis of a lignocellulosic ethanol biorefinery with ionic liquid pre-treatment, Biofuels, Bioproducts and Biorefining, 2011 Goldberg, et al., Proposed design of distributed macroalgal biorefineries: thermodynamics, bioconversion technology, and sustainability implications for developing economies, biofuels, Bioproducts and Biorefining, 2013 Daniel Klein-Marcuschamer, et al., Technoeconomic analysis of renewable aviation fuel from microalgae,Pongamia pinnata, and sugarcane, Biofuels, Bioproducts and Biorefining, 2013 217. 218. 219. 220. 221. 222. 223. 224. 225. 226. 227. 228. 229. 230. 231. 232. 233. 234. 235. 236. 237. 238. Golberg, et al., Proposed design of distributed macroalgal biorefineries: thermodynamics, bioconversion technology, and sustainability implications for developing economies, Biofuels Bioproducts & Biorefining, et al., Biofpr, 2014 K. Cox, et al., Environmental life cycle assessment (LCA) of aviation biofuel from microalgae, Pongamia pinnata, and sugarcane molasses, Biofuels Bioproducts & Biorefining, et al., Biofpr, 2014 J. Morgan, et al., Estimating molecular masses of petroleum-derived fractions: High mass (> 2000 u) materials in maltenes and asphaltenes from Maya crude oil, Journal of Chromatography A, 2010 E. McKee, et al., Manipulation of the carbon storage regulator system for metabolite remodeling and biofuel production in Escherichia coli, Microb Cell Fact, 2012 Eudes, et al., Production of hydroxycinnamoyl anthranilates from glucose in Escherichia coli, Microb Cell Fact, 2013 Bi, et al., Development of a broad-host synthetic biology toolbox for Ralstonia eutropha and its application to engineering hydrocarbon biofuel production, Microbial Cell Factories, 2013 O. Welz, et al., Low-temperature combustion chemistry of biofuels: pathways in the initial lowtemperature (550 K-750 K) oxidation chemistry of isopentanol, Physical Chemistry Chemical Physics, 2012 J. H. Mack, et al., Investigation of biofuels from microorganism metabolism for use as anti-knock additives, Fuel, 2014 Singh, et al., Visualization of biomass solubilization and cellulose regeneration during ionic liquid pretreatment of switchgrass, Biotechnology and Bioengineering, 2009 Y. J. Tang, et al., Metabolic flux analysis of Shewanella spp. reveals evolutionary robustness in central carbon metabolism, Biotechnology and Bioengineering, 2009 Y. J. Tang, et al., Analysis of metabolic pathways and fluxes in a newly discovered thermophilic and ethanol-tolerant Geobacillus strain, Biotechnology and Bioengineering, 2009 P. Reddy, et al., Bioenergy feedstock-specific enrichment of microbial populations during high-solids thermophilic deconstruction, Biotechnology and Bioengineering, 2011 Sun, et al., Understanding tissue specific compositions of bioenergy feedstocks through hyperspectral Raman imaging, Biotechnology and Bioengineering , 2011 J. M. Gladden, et al., Substrate perturbation alters the glycoside hydrolase activities and community composition of switchgrass-adapted bacterial consortia, Biotechnol Bioeng, 2012 L. Sun, et al., Rapid determination of syringyl: guaiacyl ratios using FT-Raman spectroscopy, Biotechnol Bioeng, 2012 J. Zendejas, et al., Characterization of the acylglycerols and resulting biodiesel derived from vegetable oil and microalgae (Thalassiosira pseudonana and Phaeodactylum tricornutum), Biotechnol Bioeng, 2012 Klein-Marcuschamer, et al., The challenge of enzyme cost in the production of lignocellulosic biofuels, Biotechnology and Bioengineering, 2012 Klein-Marcuschamer, et al., A matter of detail: Assessing the true potential of microalgal biofuels, Biotechnol Bioeng, 2013 L. J. Weaver, et al., A kinetic-based approach to understanding heterologous mevalonate pathway function in E. coli., Biotechnology and Bioengineering, 2014 K. W. George, et al., Correlation analysis of targeted proteins and metabolites to assess and engineer microbial isopentenol production, Biotechnology and Bioengineering, 2014 Sharma, et al., Transcriptional dynamics during cell wall removal and regeneration reveals key genes involved in cell wall development in rice, Plant Molecular Biology, 2011 J. Ito, et al., A survey of the Arabidopsis thaliana mitochondrial phosphoproteome, Proteomics, 2009 239. 240. 241. 242. 243. 244. 245. 246. 247. 248. 249. 250. 251. 252. 253. 254. 255. 256. 257. 258. 259. 260. 261. 262. 263. N.L. Taylor, et al., The Arabidopsis thaliana 2-D gel mitochondrial proteome: Refining the value of reference maps for assessing protein abundance, contaminants and post-translational modifications, Proteomics, 2011 K. Agrawal, et al., Boosting the globalization of plant proteomics through INPPO: current developments and future prospects, Proteomics, 2012 M. Jones, et al., The HUPO initiative on Model Organism Proteomes, iMOP, Proteomics, 2012 P. Schrimpf, et al., The initiative on Model Organism Proteomes (iMOP) Session September 6, 2011, Geneva, Switzerland, Proteomics, 2012 P. Singh, et al., Application of targeted proteomics to metabolically engineered Escherichia coli, Proteomics, 2012 E. K. Baidoo and J. D. Keasling, Microbial metabolomics: welcome to the real world!, Metabolomics, 2013 R. Beller, et al., Genes Involved in Long-Chain Alkene Biosynthesis in Micrococcus luteus, Applied and Environmental Microbiology, 2010 J. Rutherford, et al., Functional genomic study of exogenous n-butanol stress in Escherichia coli, Applied and Environmental Microbiology, 2010 R. Chhabra, et al., Generalized Schemes for High-Throughput Manipulation of the Desulfovibrio vulgaris Genome, Applied and Environmental Microbiology, 2011 K. M. DeAngelis, et al., PCR amplification-independent methods for detection of microbial communities by the high-density microarray PhyloChip, Applied and Environmental Microbiology, 2011 M. Gladden, et al., Glycoside hydrolase activities of thermophilic bacterial consortia adapted to switchgrass, Applied and Environmental Microbiology, 2011 Rezaei, et al., Selection of Conditions for Cellulase and Xylanase Extraction from Switchgrass Colonized by Acidothermus cellulolyticus, Applied Biochemistry and Biotechnology, 2011 Eudes, et al., Production of tranilast [N-(3',4'-dimethoxycinnamoyl)-anthranilic acid] and its analogs in yeast Saccharomyces cerevisiae, Applied Microbiology and Biotechnology, 2011 Jeffrey A. Dietrich, et al., Transcription Factor-Based Screens and Synthetic Selections for Microbial Small-Molecule Biosynthesis, ACS Synthetic Biology, 2012 J. Hillson, et al., j5 DNA Assembly Design Automation Software, ACS Synthetic Biology, 2012 H. Chou and J. D. Keasling, Synthetic pathway for production of five-carbon alcohols from isopentenyl diphosphate, Appl Environ Microbiol, 2012 Groff, et al., Supplementation of intracellular XylR leads to coutilization of hemicellulose sugars, Appl Environ Microbiol, 2012 B. Goh, et al., Engineering of bacterial methyl ketone synthesis for biofuels, Applied and Environmental Microbiology, 2012 Juminaga, et al., Modular Engineering of L-Tyrosine Production in Escherichia coli, Applied and Environmental Microbiology, 2012 Y. Kung, et al., From fields to fuels: recent advances in the microbial production of biofuels, ACS Synth Biol, 2013 Linshiz, et al., PaR-PaR laboratory automation platform, ACS Synth Biol, 2013 Muller, et al., Engineering of Ralstonia eutropha H16 for Autotrophic and Heterotrophic Production of Methyl Ketones, Appl Environ Microbiol, 2013 J. Hillson, j5 DNA assembly design automation, ACS Synthetic Biology, 2013 Sarria, et al., Microbial Synthesis of Pinene, ACS Synthetic Biology, 2014 R. M. Phelan, Engineering Terpene Biosynthesis in Streptomyces for Production of the Advanced Biofuel Precursor Bisabolene, ACS Synthetic Biology, 2014 264. 265. 266. 267. 268. 269. 270. 271. 272. 273. 274. 275. 276. 277. 278. 279. 280. 281. 282. 283. 284. 285. 286. Linshiz, et al., PR-PR: Cross-Platform Laboratory Automation System, ACS Synthetic Biology, 2014 Javidpour, et al., Biochemical and Structural Studies of NADH-Dependent FabG Used To Increase the Bacterial Production of Fatty Acids under Anaerobic Conditions, Applied and Environmental Microbiology, 2014 L. Cote, et al., Gene family structure, expression and functional analysis of HD-Zip III genes in angiosperm and gymnosperm forest trees, BMC Plant Biology, 2010 M. DeAngelis, et al., Evidence supporting dissimilatory and assimilatory lignin degradation in Enterobacter lignolyticus SCF1, Frontiers in Microbial Physiology and Metabolism, 2013 Nyyssoenen, et al., Coupled high-throughput functional screening and next generation sequencing for identification of plant polymer decomposing enzymes in metagenomic libraries, Frontiers in Microbiology, 2013 X. Cheng, et al., High throughput nanostructure-initiator mass spectrometry screening of microbial growth conditions for maximal beta-glucosidase production, Frontiers in Microbiology, 2013 S. A. Eichorst, et al., Substrate-Specific Development of Thermophilic Bacterial Consortia Using Chemically Pretreated Switchgrass, Appl Environ Microbiol, 2014 J. Kirby, et al., Use of non-ionic surfactants for improvement of terpene production in Saccharomyces cerevisiae, Appl Environ Microbiol, 2014 J. Ito, et al., Analysis of plant nucleotide sugars by hydrophilic interaction liquid chromatography and tandem mass spectrometry, Analytical Biochemistry, 2014 Greving, et al., Acoustic deposition with NIMS as a high-throughput enzyme activity assay, Analytical and Bioanalytical Chemistry, 2012 de Rond, et al., Versatile synthesis of probes for high-throughput enzyme activity screening, Anal Bioanal Chem, 2013 M. Smith, et al., Fluorescent Lifetime Imaging of Lignin in the Plant Cell Wall, Biophysical Journal, 2010 Liu, et al., The N-Terminal Ig Domain of Endoglucanase Cel9A from the Thermoacidophilic Alicyclobacillus Acidocaldarius Enhances Protein Stability, Biophysical Journal, 2010 Knierim, et al., TEM/FISH Imaging of Microbial Communities, Biophysical Journal, 2010 M. Smith-Moritz, et al., Dependence of Plant Cell Wall Composition and Structure on Cellulose Synthase-Like Knock Out Mutant, Biophysical Journal, 2012 F. Nowroozi, et al., Metabolic pathway optimization using ribosome binding site variants and combinatorial gene assembly, Applied Microbial Biotechnology, 2014 M.-K. Kang, et al., Synthetic biology platform of CoryneBrick vectors for gene expression in Corynebacterium glutamicum and its application to xylose utilization, Applied Microbiology and Biotechnology, 2014 C.-J. Park, et al., The endoplasmic reticulum-quality control component SDF2 is essential for XA21mediated immunity in rice, Plant Science, 2013 Geshi, et al., Glycosyltranfserases Involved in the Plant Cell Wall Polysaccharides Biosynthesis, Glycobiology, 2008 S. F. Hansen, et al., Structural Comparison of Plant Glycosyltransferases, Glycobiology, 2011 K. H. Jung, et al., Refinement of Light-Responsive Transcript Lists Using Rice Oligonucleotide Arrays: Evaluation of Gene-Redundancy, Plos One, 2008 Shui, et al., Membrane proteomics of phagosomes suggests a connection to autophagy, Proceedings of the National Academy of Sciences, 2008 M. Allgaier, et al., Targeted Discovery of Glycoside Hydrolases from a Switchgrass-Adapted Compost Community, Plos One, 2010 287. 288. 289. 290. 291. 292. 293. 294. 295. 296. 297. 298. 299. 300. 301. 302. 303. 304. 305. 306. 307. Oikawa, et al., An integrative approach to the identification of Arabidopsis and rice genes involved in xylan and secondary wall development, PLoS One, 2010 Christen, et al., High-throughput identification of protein localization dependency networks, Proceedings of the National Academy of Sciences, 2010 Y. Cong, et al., 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, 2010 S. R. Chhabra, et al., Towards a Rigorous Network of Protein-Protein Interactions of the Model Sulfate Reducer Desulfovibrio vulgaris Hildenborough, PLoS One, 2011 K. M. DeAngelis, et al., Characterization of Trapped Lignin-Degrading Microbes in Tropical Forest Soil, PLoS ONE , 2011 S. Chuck, et al., Overexpression of the maize Corngrass1 microRNA prevents flowering, improves digestibility, and increases starch content of switchgrass, Proceedings of National Academy of Sciences, 2011 Lee, et al., Genetic dissection of the biotic stress response using a genome-scale gene network for rice, Proceedings of National Academy of Sciences, 2011 M. A. Atmodjo, et al., 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, 2011 Bokinsky, et al., Synthesis of three advanced biofuels from ionic liquid-pretreated switchgrass using engineered Escherichia coli, Proceedings of the National Academy of Sciences, 2011 P. Cetinkol, et al., Structural and chemical characterization of hardwood from tree species with applications as bioenergy feedstocks, PLoS One, 2012 Harholt, et al., The glycosyltransferase repertoire of the spikemoss Selaginella moellendorffii and a comparative study of its cell wall, PLoS One, 2012 I. Park, et al., A thermophilic ionic liquid-tolerant cellulase cocktail for the production of cellulosic biofuels, PLoS One, 2012 J. Perez-Gil, et al., Mutations in Escherichia coli aceE and ribB genes allow survival of strains defective in the first step of the isoprenoid biosynthesis pathway, PLoS One, 2012 K. Sharma, et al., A genome-wide survey of switchgrass genome structure and organization, PLoS One, 2012 Sogaard, et al., GO-PROMTO illuminates protein membrane topologies of glycan biosynthetic enzymes in the Golgi apparatus of living tissues, PLoS One, 2012 Chiniquy, et al., XAX1 from glycosyltransferase family 61 mediates xylosyltransfer to rice xylan, Proc Natl Acad Sci U S A, 2012 J. Khudyakov, et al., Global transcriptome response to ionic liquid by a tropical rain forest soil bacterium, Enterobacter lignolyticus SCF1, Proceedings of National Academy of Sciences, 2012 Ying Xu, et al., Proteogenomic Analysis of a Thermophilic Bacterial Consortium Adapted to Deconstruct Switchgrass, PLoS One, 2013 J. A. Rodrigues, et al., Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm, Proceedings of the National Academy of Sciences of the United States of America, 2013 P. Reddy, et al., Discovery of Microorganisms and Enzymes Involved in High-Solids Decomposition of Rice Straw Using Metagenomic Analyses, PLoS One, 2013 T. Parsons, et al., Golgi enrichment and proteomic analysis of developing Pinus radiata xylem by freeflow electrophoresis, PLoS One, 2013 308. 309. 310. 311. 312. 313. 314. 315. 316. 317. 318. 319. 320. 321. 322. 323. 324. 325. 326. 327. 328. 329. 330. J. Joshua, et al., Functional characterization of the origin of replication of pRN1 from Sulfolobus islandicus REN1H1, PLoS One, 2013 Z. Chen, et al., Improved activity of a thermophilic cellulase, Cel5A, from Thermotoga maritima on ionic liquid pretreated switchgrass, PLoS One, 2013 Golberg, et al., Cloud-enabled microscopy and droplet microfluidic platform for specific detection of Escherichia coli in water, PLoS One, 2014 E. Garcia and J. D. Keasling, Kinetics of Phosphomevalonate Kinase from Saccharomyces cerevisiae, PLoS One, 2014 Frederix, et al., Development of a Native Escherichia coli Induction System for Ionic Liquid Tolerance, PLoS One, 2014 J. Dougherty, et al., Cellulosic Biomass Pretreatment and Sugar Yields as a Function Of Biomass Particle Size, PLoS One, 2014 P. Peralta-Yahya, et al., Advanced biofuel production in microbes, Biotechnology Journal, 2010 W. Blanch, et al., Biomass deconstruction to sugars, Biotechnology Journal, 2011 L. Sun, et al., Unveiling high-resolution, tissue specific dynamic changes in corn stover during ionic liquid pretreatment, Rsc Advances, 2013 M. Rhee, et al., Versatile on-demand droplet generation for controlled encapsulation, Biomicrofluidics, 2014 De Michele, et al., Ammonium and urea transporter inventory of the selaginella and physcomitrella genomes, Front Plant Sci, 2012 F. Hansen, et al., Plant Glycosyltransferases Beyond CAZy: A Perspective on DUF Families, Front Plant Sci, 2012 T. Parsons, et al., Proteomic dissection of the Arabidopsis Golgi and trans-Golgi network, Front Plant Sci, 2012 L. Heazlewood, et al., The Green proteome: challenges in plant proteomics, Frontiers in Plant Proteomics, 2011 Wipf, et al., Amino acid transporter inventory of the Selaginella genome, Frontiers in Plant Science, 2012 Chiniquy, et al., Three novel rice genes closely related to the Arabidopsis IRX9, IRX9L, and IRX14 genes and their roles in xylan biosynthesis, Frontiers in Plant Science, 2013 Rita Sharma, et al., Construction of a rice glycoside hydrolase phylogenomic database and identification of targets for biofuel research, Frontiers in Plant Science, 2013 W. Mann, et al., MASCP gator: an overview of the Arabidopsis proteomic aggregation portal, Frontiers in Plant Science, 2013 W. Carroll, et al., Managing the green proteomes for the next decade of plant research, Frontiers in Plant Science, 2013 Ito, et al., The Arabidopsis cytosolic proteome: the metabolic heart of the cell, Frontiers in Plant Science, 2014 Lee, et al., Characterization of wastewater treatment plant microbial communities and the effects of carbon sources on diversity in laboratory models, PLoS One, 2014 S. Parreiras, et al., Engineering and Two-Stage Evolution of a Lignocellulosic Hydrolysate-Tolerant Saccharomyces cerevisiae Strain for Anaerobic Fermentation of Xylose from AFEX Pretreated Corn Stover, PLoS One, 2014 Y. Ren, et al., Site-directed mutagenesis of IRX9, IRX9L and IRX14 proteins involved in xylan biosynthesis: glycosyltransferase activity is not required for IRX9 function in Arabidopsis, PLoS One, 2014 331. 332. 333. 334. 335. 336. 337. 338. 339. 340. 341. 342. 343. 344. 345. 346. 347. 348. 349. 350. 351. 352. 353. T. Yu, et al., Bioinformatic processing to identify single nucleotide polymorphism that potentially affect Ape1 function, Mutation Research, 2010 L. Woo, et al., Enzyme activities of aerobic lignocellulolytic bacteria isolated from wet tropical forest soils, Systematic and applied microbiology, 2014 Barcon, J. Alonso-Gutierrez, et al., Molecular and physiological approaches to understand the ecology of methanol degradation during the biofiltration of air streams, Chemosphere, 2012 Liu, et al., Molecular simulations provide new insights into the role of the accessory immunoglobulinlike domain of Cel9A, FEBS Letters, 2010 Y. B. Melnichenko, et al., Accessibility of pores in coal to methane and carbon dioxide, Fuel, 2012 R. Arora, et al., Monitoring and Analyzing Process Streams Towards Understanding Ionic Liquid Pretreatment of Switchgrass (Panicum virgatum L.), Bioenergy Research, 2010 C. R. Brennan, et al., Recovery of Sugars from Ionic Liquid Biomass Liquor by Solvent Extraction, Bioenergy Research, 2010 J. Cao, et al., A Survey of Databases for Analysis of Plant Cell Wall-Related Enzymes, Bioenergy Research, 2010 M. DeAngelis, et al., Strategies for Enhancing the Effectiveness of Metagenomic-based Enzyme Discovery in Lignocellulolytic Microbial Communities, Bioenergy Research, 2010 Rautengarten, et al., A Simple Method for Enzymatic Synthesis of Unlabeled and Radiolabeled Hydroxycinnamate-CoA, BioEnergy Research, 2010 V. Scheller, et al., The Joint BioEnergy Institute (JBEI): Developing New Biofuels by Overcoming Biomass Recalcitrance, BioEnergy Research, 2010 Chenlin Li, et al., Comparing the Recalcitrance of Eucalyptus, Pine, and Switchgrass Using Ionic Liquid and Dilute Acid Pretreatments, Bioenergy Research, 2012 Jason S. Lupoi, et al., Assessment of Lignocellulosic Biomass Using Analytical Spectroscopy: an Evolution to High-Throughput Techniques, Bioenergy Research, 2013 S. Lupoi, et al., Assessment of Lignocellulosic Biomass Using Analytical Spectroscopy: an Evolution to High-Throughput Techniques, Bioenergy Research, 2014 H. Liu, et al., Understanding the interactions of cellulose with ionic liquids: a molecular dynamics study, Journal of Physical Chemistry B, 2010 H. Liu, et al., Molecular Dynamics Study of Polysaccharides in Binary Solvent Mixtures of an Ionic Liquid and Water, Journal of Physical Chemistry B, 2011 H. Liu, et al., 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, 2012 Cheng, et al., Impact of Ionic Liquid Pretreatment Conditions on Cellulose Crystalline Structure Using 1Ethyl-3-methylimidazolium Acetate, Journal of Physical Chemistry B, 2012 Harholt, et al., ARAD proteins associated with pectic Arabinan biosynthesis form complexes when transiently overexpressed in planta, Planta, 2012 Orfila, et al., Expression of mung bean pectin acetyl esterase in potato tubers: effect on acetylation of cell wall polymers and tuber mechanical properties, Planta, 2012 Stoppel and J. Meurer, Complex RNA metabolism in the chloroplast: an update on the psbB operon, Planta, 2013 N. Mac Dowell, et al., New Experimental Density Data and Soft-SAFT Models of Alkylimidazolium ([CnC1im](+)) Chloride (Cl(-)), Methylsulfate ([MeSO4](-)), and Dimethylphosphate ([Me2PO4](-)) Based Ionic Liquids, Journal of Physical Chemistry: B, 2014 H. Pereira, et al., Biochemical characterization and crystal structure of endoglucanase Cel5A from the hyperthermophilic Thermotoga maritima, Journal of Structural Biology, 2010 354. 355. 356. 357. 358. 359. 360. 361. 362. 363. 364. 365. 366. 367. 368. 369. 370. 371. 372. 373. 374. 375. 376. J. Steen, et al., Metabolic engineering of Saccharomyces cerevisiae for the production of n-butanol, Microbial Cell Factories, 2008 A. Simmons, Synthetic enzymes: catalysis on demand, Microbial Biotechnology, 2011 Yu, et al., Probing conformational changes in Ape1 during the progression of base excision repair, Biochemistry, 2010 Yuzawa, et al., Construction of a part of a 3-hydroxypropionate cycle for heterologous polyketide biosynthesis in Escherichia coli, Biochemistry, 2012 Yuzawa, et al., Broad substrate specificity of the loading didomain of the lipomycin polyketide synthase, Biochemistry, 2013 Hagen, S., et al., In Vitro Analysis of Carboxyacyl Substrate Tolerance in the Loading and First Extension Modules of Borrelidin Polyketide Synthase, Biochemistry, 2014 Muyzer, et al., Complete genome sequence of "Thioalkalivibrio sulfidophilus" HL-EbGr7, Standards in Genomic Sciences, 2011 Chertkov, et al., Complete genome sequence of Tolumonas auensis type strain (TA 4T), Standards in Genomic Sciences, 2011 DeAngelis, et al., Complete genome sequence of Enterobacter lignolyticus SCF1, Standards in Genomic Sciences, 2011 DeAngelis, et al., Metagenomes of tropical soil-derived anaerobic switchgrass-adapted consortia with and without iron, Standards in Genomic Sciences, 2013 Y. Satoh, et al., Engineering of a tyrosol-producing pathway, utilizing simple sugar and the central metabolic tyrosine, in Escherichia coli, J Agric Food Chem, 2012 M. Lafreniere, et al., Multiplexed extraction and quantitative analysis of pharmaceuticals from DBS samples using digital microfluidics, Bioanalysis, 2014 Sarkar, et al., Plant cell walls throughout evolution: towards a molecular understanding of their design principles, Journal of Experimental Botany, 2009 Simmons, Characterization of bacterial communities in solarized soil amended with lignocellulosic organic matter, Applied Soil Ecology, 2013 C. S. Hastrup, et al., Differences in crystalline cellulose modification due to degradation by brown and white rot fungi, Fungal Biology, 2012 M. Winger, et al., Secretome analysis of the thermophilic xylanase hyper-producer Thermomyces lanuginosus SSBP cultivated on corn cobs, J Ind Microbiol Biotechnol, 2014 S. Kumar, et al., Metabolic reconstruction of the archaeon methanogen Methanosarcina Acetivorans, BMC Systems Biology, 2011 Y. Lee, et al., Mass spectrometry-based metabolomics, analysis of metabolite-protein interactions, and imaging, Biotechniques, 2010 Woo, et al., Draft Genome Sequence of the Lignin-Degrading Burkholderia sp. Strain LIG30, Isolated from Wet Tropical Forest Soil, Genome Announcements, 2014 J. C. Bergmann, et al., Discovery of two novel beta-glucosidases from an Amazon soil metagenomic library, FEMS Microbiology Letters, 2014 Y. J. Tang, et al., Investigation of carbon metabolism in "Dehalococcoides ethenogenes" strain 195 by use of isotopomer and transcriptomic analyses, Journal of Bacteriology, 2009 Young, et al., Genome sequence of the Fleming strain of Micrococcus luteus, a simple free-living actinobacterium, Journal of Bacteriology, 2010 J. Joshua, et al., Absence of Diauxie during Simultaneous Utilization of Glucose and Xylose by Sulfolobus acidocaldarius, Journal of Bacteriology, 2011 377. 378. 379. 380. 381. 382. 383. 384. 385. 386. 387. 388. 389. 390. 391. 392. 393. 394. 395. 396. 397. 398. 399. Bokinsky, et al., HipA-Triggered Growth Arrest and beta-Lactam Tolerance in Escherichia coli Are Mediated by RelA-Dependent ppGpp Synthesis, J Bacteriol, 2013 H. Chou, et al., Direct calibration of PICKY-designed microarrays, BMC Bioinformatics, 2009 Ouellet, et al., A rapid and inexpensive labeling method for microarray gene expression analysis, BMC Biotechnology, 2009 J. Dougherty, et al., Glycoside Hydrolases from a targeted Compost Metagenome, activity-screening and functional characterization, BMC Biotechnol, 2012 Deng, et al., Encoding substrates with mass tags to resolve stereospecific reactions using Nimzyme, Rapid Commun Mass Spectrom, 2012 A.M. Smith-Moritz, et al., Combining multivariate analysis and monosaccharide composition modeling to identify plant cell wall variations by Fourier Transform Near Infrared spectroscopy, Plant Methods, 2011 Klein-Marcuschamer and H. W. Blanch, Survival of the Fittest: An Economic Perspective on the Production of Novel Biofuels, AiChe Journal, 2013 Frear, et al., Biogas potential and microbial population distributions in flushed dairy manure and implications on anaerobic digestion technology, Journal of Chemical Technology and Biotechnology, 2011 Sathitsuksanoh, et al., New lignocellulose pretreatments using cellulose solvents: a review, Journal of Chemical Technology and Biotechnology, 2013 E. Achyuthan, et al., Spectroscopic High Throughput Screening of Laccase-Catalyzed p-Cresol Oxidation, Combinatorial Chemistry & High Throughput Screening, 2009 H. Jung, et al., Analysis of Alternatively Spliced Rice Transcripts Using Microarray Data, Rice, 2009 Peijian Cao, et al., The Rice Oligonucleotide Array Database: an atlas of rice gene expression, Rice, 2012 Yang, et al., Monolignol Transporters and Cell Wall Oxidases Screens, Plant Biology, 2009 Eudes, et al., Synthesis of phenylpropanoid-esters and -amides in Arabidopsis thaliana to engineer a cleavable lignin, Plant Biology, 2009 W. Singer, et al., Enrichment, Isolation and Characterization of Fungi Tolerant to 1-Ethyl-3Methylimadazolium Acetate, Journal of Applied Microbiology, 2011 P. Reddy, et al., Thermophilic enrichment of microbial communities in the presence of the ionic liquid 1ethyl-3-methylimidazolium acetate, J Appl Microbiol, 2012 W. Simmons, et al., , Effect of inoculum source on the enrichment of microbial communities on two lignocellulosic bioenergy crops under thermophilic and high-solids conditions, Journal of Applied Microbiology, 2014 K. E. Achyuthan, et al., Spectroscopic Analyses of the Biofuels-Critical Phytochemical Coniferyl Alcohol and Its Enzyme-Catalyzed Oxidation Products, Molecules, 2009 K. E. Achyuthan, et al., Supramolecular Self-Assembled Chaos: Polyphenolic Lignin's Barrier to CostEffective Lignocellulosic Biofuels, Molecules, 2010 K. E. Achyuthan, et al., Hitherto Unrecognized Fluorescence Properties of Coniferyl Alcohol, Molecules, 2010 Yuzawa, et al., Enzyme analysis of the polyketide synthase leads to the discovery of a novel analog of the antibiotic alpha-lipomycin, Journal of Antibiotics, 2014 Y. Verhertbruggen, et al., Mannan synthase activity in the CSLD family, Plant Signaling & Behavior, 2011 Vega-Sanchez, et al., Abundance of mixed linkage glucan in mature tissues and secondary cell walls of grasses, Plant Signal Behav, 2013 400. 401. 402. 403. 404. 405. 406. 407. 408. 409. 410. 411. 412. 413. 414. 415. 416. 417. 418. 419. 420. 421. 422. L. Petersen, et al., Assay and heterologous expression in Pichia pastoris of plant cell wall type-II membrane anchored glycosyltransferases, Glycoconjugate Journal , 2009 K. L. Keller, et al., Methods for engineering sulfate reducing bacteria of the genus desulfovibrio, Methods in Enzymology, 2011 Y. J. Tang, et al., Invariability of central metabolic flux distribution in Shewanella oneidensis MR-1 under environmental or genetic perturbations, Biotechnol Prog, 2009 D. Marner, 2nd, et al., Enzyme immobilization via silaffin-mediated autoencapsulation in a biosilica support, Biotechnology Progress, 2009 S. Shaikh, et al., Study of stationary phase metabolism via isotopomer analysis of amino acids from an isolated protein, Biotechnology Progress, 2010 W. Simmons, et al., Bacillus coagulans tolerance to 1-ethyl-3-methylimidazolium-based ionic liquids in aqueous and solid-state thermophilic culture, Biotechnology Progress, 2014 Heather L. Szmidt-Middleton, et al., Utilizing a highly responsive gene, yhjX, in E. coli based production of 1,4-butanediol, chemical engineering science, 2013 Han Min Woo, et al., Application of targeted proteomics and biological parts assembly in E. coli to optimize the biosynthesis of an anti-malarial drug precursor, amorpha-4,11-diene, chemical engineering science, 2013 Klein-Marcuschamer, et al., Technoeconomic analysis of biofuels: A wiki-based platform for lignocellulosic biorefineries, Biomass & Bioenergy, 2010 M. Paap, et al., Biochemical production of ethanol and fatty acid ethyl esters from switchgrass: A comparative analysis of environmental and economic performance, Biomass & Bioenergy, 2013 Seema Singh, et al., Understanding the impact of ionic liquid pretreatment on cellulose and lignin via thermochemical analysis, Biomass and Bioenergy, 2013 E. Vickers, et al., D. Klein-Marcuschamer, et al., J. O. Kromer, Examining the feasibility of bulk commodity production in Escherichia coli, Biotechnology Letters, 2012 Galdzicki, K. P., et al., The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology, Computational Biology, 2014 Christensen, et al., Characterization of the primary cell walls of seedlings of Brachypodium distachyon A potential model plant for temperate grasses, Phytochemistry, 2010 Xie, J. Kirby and J. D. Keasling, Functional characterization of four sesquiterpene synthases from Ricinus communis (Castor bean), Phytochemistry, 2012 W. Simmons, et al., Characterization of bacterial communities in solarized soil amended with lignocellulosic organic matter, Applied Soil Ecology, 2014 Christensen, et al., Regulation of (1,3, et al., 1,4)-β-D-glucan synthesis in developing endosperm of barley lys mutants, Journal of Cereal Science, 2012 Linshiz, et al., The fusion of biology, computer science, and engineering: towards efficient and successful synthetic biology, Perspect Biol Med, 2012 Sharma, tools for developing glycosyl-transferase assays and methods for xylan profiling in plants, pharmaceutical biology, 2012 McInerney, et al., Error Rate Comparison during Polymerase Chain Reaction by DNA Polymerase, Mol Biol Int, 2014 E. Baidoo, et al., Mass spectrometry-based microbial metabolomics, Methods Mol Biol, 2012 S. Batth, et al., Targeted proteomics for metabolic pathway optimization, Methods Mol Biol, 2012 R. Beller, et al., Genetic manipulation of the obligate chemolithoautotrophic bacterium Thiobacillus denitrificans, Methods Mol Biol, 2012 423. 424. 425. 426. 427. 428. 429. 430. 431. 432. 433. 434. 435. 436. 437. 438. 439. 440. 441. 442. 443. 444. 445. T. Parsons, et al., Separation of the plant golgi apparatus and endoplasmic reticulum by free-flow electrophoresis, Methods in Molecular Biology, 2014 M. Estavillo, et al., Isolation of the plant cytosolic fraction for proteomic analysis, Plant Proteomics: Methods and Protocols, 2014 K.-H. Jung, et al., Genome-wide Identification and Analysis of Early Heat Stress Responsive Genes in Rice, Journal of Plant Biology, 2012 Pradhan Mitra, et al., Histochemical Staining of Arabidopsis thaliana Secondary Cell Wall Elements, Journal of Visualized Experiments, JOVE, 2014 Keasling, Engineering Microorganisms with Plant-derived Genes to Produce Drugs and Fuels, In Vitro Cellular & Developmental Biology Animal, 2010 W. Mann, et al., Proteome coverage of the model plant Arabidopsis thaliana: implications for shotgun proteomic studies, J Proteomics, 2013 Ito, et al., The Role of Proteomics in the Development of Cellulosic Biofuels, Current Proteomics, 2010 E. Bartley, et al., Plant and microbial research seeks biofuel production from lignocellulose, California Agriculture, 2009 B.A. Simmons, et al., Ionic liquid pretreatment, Chemical Engineering Progress, 2010 M.S. Kent, et al., 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. , 2009 Geshi, et al., Toward tailored synthesis of functional polysaccharides in plants, Foods for Health in the 21st Century: A Road Map for the Future, 2010 S. Lalonde, et al., A membrane protein/signaling protein interaction network for Arabidopsis version AMPv2, Frontiers in Physiology, 2010 J. Han, et al., Chemical profiling of the plant cell wall through Raman microspectroscopy in 2010 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, IEEE ISBI, 2010 Yang, et al., Characteristics of Isopentanol as a Fuel for HCCI Engines, Society of Automobile Engineers International Journal of Fuels and Lubricants, 2010 M.J. Dunlop, et al., A model for improving microbial biofuel production using a synthetic feedback loop, Synthetic and Systems Biology, 2010 C.J. Petzold, et al., Metabolic engineering of E.coli for the production of a precursor to artemisinin, an anti-malarial drug, The Manual of Industrial Microbiology and Biotechnology, 2010 Anil Wipat, et al., Synthetic Biology Open Language (SBOL) Version 1.0.0, BioBricks Foundation Request for Comments, 2011 Varanasi, et al., Quantifying Bio-Engineering: The Importance of Biophysics in Biofuel Research, Biofuel's Engineering Process Technology, 2011 Datta, et al., Cellulases and Hemicellulases for Biomass Degradation: An Introduction, Chemical and Biochemical Catalysis for Next Generation Biofuels, 2011 Loque, et al., Biomass Availability and Sustainability for BioFuels, Chemical and Biochemical Catalysis for Next Generation Biofuels, 2011 B.A. Simmons, Introduction to Catalysis for Biofuels, Chemical and Biochemical Catalysis for Next Generation Biofuels, 2011 S.R. Chhabra, et al., The Biological Basis | Metabolic Design and Control for Production in Prokaryotes, Comprehensive Biotechnology, 2011 N.J. Hillson, DNA Assembly Method Standardization for Synthetic Biomolecular Circuits and Systems, Design and Analysis of Biomolecular Circuits: Engineering Approaches to Systems and Synthetic Biology, 2011 446. 447. 448. 449. 450. 451. 452. 453. 454. 455. 456. 457. 458. 459. 460. 461. 462. J. D. Keasling, Joint BioEnergy Institute, Industrial Biotechnology, 2011 S. Lee, et al., BglBrick vectors and datasheets, et al., a synthetic biology platform for gene expression, Journal of Biological Engineering , 2011 Klein-Marcuschamer, et al., Biofuel Economics, Plant Biomass Conversion, 2011 B.A. Simmons, Bioenergy from Plants and Plant Residues, Plant Biotechnology and Agriculture Prospects for the 21st Century, 2011 Sakuragi, et al., Visual mapping of cell wall biosynthesis, The Plant Cell Wall: Methods and Protocols, 2011 Reindl, et al., Nanostructure-initiator mass spectrometry (NIMS) for the analysis of enzyme activities, Curr protoc chem biol, 2012 Patanjali Varanasi, et al., Mechanical Stress Analysis as a Method to Understand the Impact of Genetically Engineered Rice and Arabidopsis Plants, Industrial Biotechnology, 2012 B.J Rutherford, et al., Engineering Stress Tolerance in Microbial Systems for Bioproduction of Fuels, Microbial Biotechnology: Energy and Environment, 2012 Mukhopadhyay, et al., Control of Stress Tolerance in Bacterial Host Organisms for Bioproduction of Fuels, Microbial Stress Tolerance: From Genomics to Biofuels, 2012 T. Parsons, et al., The current state of the Golgi proteomes, Proteomics - Applications in Biology, 2012 Bokinsky, et al., Synthetic biology of microbial biofuel production: From enzymes to pathways to organisms, Synthetic Biologu: Tools and Applications, 2012 Goldberg, et al., Distributed marine biorefineries for developing economies., , 2012 L. Heazlewood, et al., Proteomics - Applications in Biology, , 2012 Seema Singh, et al., Ionic Liquid Pretreatment: Mechanism, Performance, and Challenges, Aqueous Pretreatment of Plant Biomass for Biological and Chemical Conversion to Fuels and Chemicals, 2013 R. E. Paull, et al., Lotus Cell Walls and the Genes Involved in its Synthesis and Modification, Tropical Plant Biology, 2013 N.J. Hillson, J5 DNA Closing and Assembly Methods, Methods and Protocols, 2014 Chandrasekaran and A. K. Singh, One-Pot, Microscale Cell-Free Enzyme Expression and Screening, Cell-Free Protein Synthesis: Methods and Protocols, 2014