Genomic Science Program
U.S. Department of Energy | Office of Science | Biological and Environmental Research Program

Archival Publications List: The First DOE Bioenergy Research Centers (2007-2018)

201810.1002/bit.26530Alonso-Gutierrez, J., D. Koma, Q. Hu, Y. Yang, L. J. G. Chan, C. J. Petzold, P. D. Adams, C. E. Vickers, L. K. Nielsen, J. D. Keasling, and T. S. Lee. 2018. Toward industrial production of isoprenoids in Escherichia coli: Lessons learned from CRISPR-Cas9 based optimization of a chromosomally integrated mevalonate pathway, Biotechnol Bioeng 115(4), 1000-1013. JBEI
201810.1007/s11101-017-9530-4Banerjee, A., and B. Hamberger. 2018. P450s controlling metabolic bifurcations in plant terpene specialized metabolism, Phytochem Rev 17(1), 81-111. GLBRC
201810.1111/pbi.12747Baxter, H. L., M. Mazarei, A. Dumitrache, J. M. Natzke, M. Rodriguez, Jr., J. Gou, C. Fu, R. W. Sykes, G. B. Turner, M. F. Davis, S. D. Brown, B. H. Davison, Z. Y. Wang, and C. N. Stewart, Jr. 2018. Transgenic miR156 switchgrass in the field: growth, recalcitrance and rust susceptibility, Plant Biotechnol J 16(1), 39-49. BESC
201810.1002/yea.3292Dossani, Z. Y., A. Reider Apel, H. Szmidt-Middleton, N. J. Hillson, S. Deutsch, J. D. Keasling, and A. Mukhopadhyay. 2018. A combinatorial approach to synthetic transcription factor-promoter combinations for yeast strain engineering, Yeast 35(3), 273-280. JBEI
201810.1093/nar/gkx893Eng, C. H., T. W. H. Backman, C. B. Bailey, C. Magnan, H. Garcia Martin, L. Katz, P. Baldi, and J. D. Keasling. 2018. ClusterCAD: a computational platform for type I modular polyketide synthase design, Nucleic Acids Res 46(D1), D509-D515. JBEI
2018 10.1111/pbi.12841Gou, J., S. Debnath, L. Sun, A. Flanagan, Y. Tang, Q. Jiang, J. Wen, and Z. Y. Wang. 2018. From model to crop: functional characterization of SPL8 in M. truncatula led to genetic improvement of biomass yield and abiotic stress tolerance in alfalfa, Plant Biotechnol J 16(4), 951-962. BESC
201810.1016/j.copbio.2017.10.004Hittinger, C. T., J. L. Steele, and D. S. Ryder. 2018. Diverse yeasts for diverse fermented beverages and foods, Curr Opin Biotechnol 49, 199-206. GLBRC
201810.1038/s41564-017-0052-zKolinko, S., Y. W. Wu, F. Tachea, E. Denzel, J. Hiras, R. Gabriel, N. Backer, L. J. G. Chan, S. A. Eichorst, D. Frey, Q. Chen, P. Azadi, P. D. Adams, T. R. Pray, D. Tanjore, C. J. Petzold, J. M. Gladden, B. A. Simmons, and S. W. Singer. 2018. A bacterial pioneer produces cellulase complexes that persist through community succession, Nat Microbiol 3(1), 99-107. 10.1038/s41564-017-0052-z.JBEI
201810.1016/j.biombioe.2017.02.003Landis, D. A., C. Gratton, R. D. Jackson, K. L. Gross, D. S. Duncan, C. Liang, T. D. Meehan, B. A. Robertson, T. M. Schmidt, K. A. Stahlheber, J. M. Tiedje, and B. P. Werling. 2018. Biomass and biofuel crop effects on biodiversity and ecosystem services in the North Central US, Biomass and Bioenergy 114, 18-29. GLBRC
201810.1002/cssc.201701902Liu, D., K. H. Kim, J. Sun, B. A. Simmons, and S. Singh. 2018. Cascade Production of Lactic Acid from Universal Types of Sugars Catalyzed by Lanthanum Triflate, ChemSusChem 11(3), 598-604. JBEI
201810.1002/biot.201600433.Meadows, C. W., A. Kang, and T. S. Lee. 2018. Metabolic Engineering for Advanced Biofuels Production and Recent Advances Toward Commercialization, Biotechnol J 13(1). JBEI
201810.1093/bioinformatics/btx564Mendoza, B. J., and C. T. Trinh. 2018. Enhanced guide-RNA design and targeting analysis for precise CRISPR genome editing of single and consortia of industrially relevant and non-model organisms, Bioinformatics 34(1), 16-23. BESC
201810.1002/bbb.1821.Ng, R. T. L., S. Patchin, W. Wu, N. Sheth, and C. T. Maravelias. 2018. An optimization-based web application for synthesis and analysis of biomass-to-fuel strategies, Biofuels, Bioproducts and Biorefining 12(2), 170-176. GLBRC
201810.1007/s10529-017-2467-2Oguntimein, G. B., M. Rodriguez, Jr., A. Dumitrache, T. Shollenberger, S. R. Decker, B. H. Davison, and S. D. Brown. 2018. Anaerobic microplate assay for direct microbial conversion of switchgrass and Avicel using Clostridium thermocellum, Biotechnol Lett 40(2), 303-308. BESC
201810.1111/1477-9552.12233Skevas, T., I. Skevas, and S. M. Swinton. 2018. Does Spatial Dependence Affect the Intention to Make Land Available for Bioenergy Crops?, Journal of Agricultural Economics 69(2), 393-412. GLBRC
201810.1002/cssc.201701798Sun, J., D. Liu, R. P. Young, A. G. Cruz, N. G. Isern, T. Schuerg, J. R. Cort, B. A. Simmons, and S. Singh. 2018. Solubilization and Upgrading of High Polyethylene Terephthalate Loadings in a Low-Costing Bifunctional Ionic Liquid, ChemSusChem 11(4), 781-792. JBEI
201810.1093/molbev/msx315Vakirlis, N., A. S. Hebert, D. A. Opulente, G. Achaz, C. T. Hittinger, G. Fischer, J. J. Coon, and I. Lafontaine. 2018. A Molecular Portrait of De Novo Genes in Yeasts, Mol Biol Evol 35(3), 631-645. GLBRC
201810.1016/j.ymben.2017.12.007Wong, J., T. de Rond, L. d'Espaux, C. van der Horst, I. Dev, L. Rios-Solis, J. Kirby, H. Scheller, and J. Keasling. 2018. High-titer production of lathyrane diterpenoids from sugar by engineered Saccharomyces cerevisiae, Metab Eng 45, 142-148. JBEI
201810.1002/bbb.1825Yang, B., L. Tao, and C. E. Wyman. 2018. Strengths, challenges, and opportunities for hydrothermal pretreatment in lignocellulosic biorefineries, Biofuels, Bioproducts and Biorefining 12(1), 125-138. BESC
201810.1093/jxb/erx241Yang, J., and M. Udvardi. 2018. Senescence and nitrogen use efficiency in perennial grasses for forage and biofuel production, J Exp Bot 69(4), 855-865. BESC
201710.1016/j.coisb.2017.11.001Adamczyk, P. A., and J. L. Reed. 2017. Escherichia coli as a model organism for systems metabolic engineering, Current Opinion in Systems Biology 6, 80-88. GLBRC
20171111/1751-7915.12463.Adams, M. W., and R. M. Kelly. 2017. The renaissance of life near the boiling point - at last, genetics and metabolic engineering, Microb Biotechnol 10(1), 37-39. 10.BESC
201710.1021/acssuschemeng.7b01203Akinosho, H. O., C. G. Yoo, A. Dumitrache, J. Natzke, W. Muchero, S. D. Brown, and A. J. Ragauskas. 2017. Elucidating the Structural Changes to Populus Lignin during Consolidated Bioprocessing with Clostridium thermocellum, ACS Sustainable Chemistry & Engineering 5(9), 7486-7491. BESC
201710.1021/acssuschemeng.7b00449Akinosho, H., A. Dumitrache, J. Natzke, W. Muchero, S. S. Jawdy, G. A. Tuskan, S. D. Brown, and A. J. Ragauskas. 2017. Effects of Biomass Accessibility and Klason Lignin Contents during Consolidated Bioprocessing in Populus trichocarpa, ACS Sustainable Chemistry & Engineering 5(6), 5075-5081. BESC
201710.1016/j.indcrop.2017.07.021Alameldin, H., A. Izadi-Darbandi, S. A. Smith, V. Balan, A. D. Jones, and M. Sticklen. 2017. Production of Seed-Like Storage Lipids and Increase in Oil Bodies in Corn (Maize; Zea mays L.) Vegetative Biomass, Industrial Crops and Products 108, 526-534. GLBRC
201710.1126/sciadv.1603301Alonso, D. M., S. H. Hakim, S. Zhou, W. Won, O. Hosseinaei, J. Tao, V. Garcia-Negron, A. H. Motagamwala, M. A. Mellmer, K. Huang, C. J. Houtman, N. Labbe, D. P. Harper, C. Maravelias, T. Runge, and J. A. Dumesic. 2017. Increasing the revenue from lignocellulosic biomass: Maximizing feedstock utilization, Sci Adv 3(5), e1603301. GLBRC
201710.1371/journal.pone.0189604Amaike Campen, S., J. Lynn, S. J. Sibert, S. Srikrishnan, P. Phatale, T. Feldman, J. M. Guenther, J. Hiras, Y. T. A. Tran, S. W. Singer, P. D. Adams, K. L. Sale, B. A. Simmons, S. E. Baker, J. K. Magnuson, and J. M. Gladden. 2017. Expression of naturally ionic liquid-tolerant thermophilic cellulases in Aspergillus niger, PLoS One 12(12), e0189604. JBEI
201710.1101/110825Anderson, W., R. Apweiler, A. Bateman, G. A. Bauer, H. Berman, J. A. Blake, N. Blomberg, S. K. Burley, G. Cochrane, V. Di Francesco, T. Donohue, C. Durinx, A. Game, E. Green, T. Gojobori, P. Goodhand, A. Hamosh, H. Hermjakob, M. Kanehisa, R. Kiley, J. McEntyre, R. McKibbin, S. Miyano, B. Pauly, N. Perrimon, M. A. Ragan, G. Richards, Y.-Y. Teo, M. Westerfield, E. Westhof, and P. F. Lasko. 2017. Towards a global support of core data resources for the life sciences, bioRxiv. .GLBRC
2017Ando, D., and H. Garcia Martin. 2017. Two-Scale 13C Metabolic Flux Analysis for Metabolic Engineering. In Synthetic Metabolic Pathways: Methods and Protocols, 333-352. Eds. M. K. Jensen, and J. D. Keasling. Springer New York.JBEI
201710.1111/tpj.13449Angelos, E., C. Ruberti, S. J. Kim, and F. Brandizzi. 2017. Maintaining the factory: the roles of the unfolded protein response in cellular homeostasis in plants, Plant J 90(4), 671-682. GLBRC
201710.1111/gcbb.12428Austin, E. E., K. Wickings, M. D. McDaniel, G. P. Robertson, and A. S. Grandy. 2017. Cover crop root contributions to soil carbon in a no-till corn bioenergy cropping system, GCB Bioenergy 9(7), 1252-1263. GLBRC
201710.1039/c6ee03748hBalch, M. L., E. K. Holwerda, M. F. Davis, R. W. Sykes, R. M. Happs, R. Kumar, C. E. Wyman, and L. R. Lynd. 2017. Lignocellulose fermentation and residual solids characterization for senescent switchgrass fermentation by Clostridium thermocellum in the presence and absence of continuous in situ ball-milling, Energy & Environmental Science 10(5), 1252-1261. BESC
201710.1016/j.carbpol.2016.11.085Bhagia, S., R. Kumar, and C. E. Wyman. 2017. Effects of dilute acid and flowthrough pretreatments and BSA supplementation on enzymatic deconstruction of poplar by cellulase and xylanase, Carbohydr Polym 157, 1940-1948. BESC
201710.1186/s12859-017-1615-yBirkel, G. W., A. Ghosh, V. S. Kumar, D. Weaver, D. Ando, T. W. H. Backman, A. P. Arkin, J. D. Keasling, and H. G. Martin. 2017. The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism, BMC Bioinformatics 18(1), 205. JBEI
201710.1186/s13068-017-0866-1Biswal, A. K., L. Tan, M. A. Atmodjo, J. DeMartini, I. Gelineo-Albersheim, K. Hunt, I. M. Black, S. S. Mohanty, D. Ryno, C. E. Wyman, and D. Mohnen. 2017. Comparison of four glycosyl residue composition methods for effectiveness in detecting sugars from cell walls of dicot and grass tissues, Biotechnol Biofuels 10, 182. BESC
201710.1186/s13068-016-0684-xBiswas, R., C. M. Wilson, R. J. Giannone, D. M. Klingeman, T. Rydzak, M. B. Shah, R. L. Hettich, S. D. Brown, and A. M. Guss. 2017. Improved growth rate in Clostridium thermocellum hydrogenase mutant via perturbed sulfur metabolism, Biotechnol Biofuels 10, 6. BESC
201710.1111/1751-7915.12494Blumer-Schuette, S. E., J. V. Zurawski, J. M. Conway, P. Khatibi, D. L. Lewis, Q. Li, V. L. Chiang, and R. M. Kelly. 2017. Caldicellulosiruptor saccharolyticus transcriptomes reveal consequences of chemical pretreatment and genetic modification of lignocellulose, Microb Biotechnol 10(6), 1546-1557. BESC
201710.1016/j.cbpa.2017.10.013Bomble, Y. J., C. Y. Lin, A. Amore, H. Wei, E. K. Holwerda, P. N. Ciesielski, B. S. Donohoe, S. R. Decker, L. R. Lynd, and M. E. Himmel. 2017. Lignocellulose deconstruction in the biosphere, Curr Opin Chem Biol 41, 61-70. BESC
201710.1104/pp.16.01322Bouche, F., D. P. Woods, and R. M. Amasino. 2017. Winter Memory throughout the Plant Kingdom: Different Paths to Flowering, Plant Physiol 173(1), 27-35. GLBRC
201710.1021/acs.est.6b04591Breunig, H. M., L. Jin, A. Robinson, and C. D. Scown. 2017. Bioenergy Potential from Food Waste in California, Environ Sci Technol 51(3), 1120-1128. JBEI
201710.1038/s41598-017-08985-wBrunecky, R., B. S. Donohoe, J. M. Yarbrough, A. Mittal, B. R. Scott, H. Ding, L. E. Taylor Ii, J. F. Russell, D. Chung, J. Westpheling, S. A. Teter, M. E. Himmel, and Y. J. Bomble. 2017. The Multi Domain Caldicellulosiruptor bescii CelA Cellulase Excels at the Hydrolysis of Crystalline Cellulose, Sci Rep 7(1), 9622. BESC
201710.1128/mSystems.00015-17Burger, B. T., S. Imam, M. J. Scarborough, D. R. Noguera, and T. J. Donohue. 2017. Combining Genome-Scale Experimental and Computational Methods To Identify Essential Genes in Rhodobacter sphaeroides, mSystems 2(3). GLBRC
201710.1038/srep44150Cao, H., D. Wei, Y. Yang, Y. Shang, G. Li, Y. Zhou, Q. Ma, and Y. Xu. 2017. Systems-level understanding of ethanol-induced stresses and adaptation in E. coli, Sci Rep 7, 44150. BESC
201710.1093/bib/bbx088Cao, H., Q. Ma, X. Chen, and Y. Xu. 2017. DOOR: a prokaryotic operon database for genome analyses and functional inference, Brief Bioinform. BESC
201710.1104/pp.17.00362Carlos Del Rio, J., J. Rencoret, A. Gutierrez, H. Kim, and J. Ralph. 2017. Hydroxystilbenes Are Monomers in Palm Fruit Endocarp Lignins, Plant Physiol 174(4), 2072-2082. GLBRC
201710.1038/srep43925Chen, X., W. C. Chou, Q. Ma, and Y. Xu. 2017. SeqTU: A Web Server for Identification of Bacterial Transcription Units, Sci Rep 7, 43925. BESC
201710.1186/s13068-017-0849-2.Choi, J., D. M. Klingeman, S. D. Brown, and C. D. Cox. 2017. The LacI family protein GlyR3 co-regulates the celC operon and manB in Clostridium thermocellum, Biotechnol Biofuels 10, 163. BESC
201710.1038/npjsba.2016.35Chubukov, V., J. J. Desmarais, G. Wang, L. J. G. Chan, E. E. Baidoo, C. J. Petzold, J. D. Keasling, and A. Mukhopadhyay. 2017. Engineering glucose metabolism of Escherichia coli under nitrogen starvation, NPJ Syst Biol Appl 3, 16035. JBEI
201710.3389/fenrg.2017.00009Chundawat, S. P. S., N. Uppugundla, D. Gao, P. G. Curran, V. Balan, and B. E. Dale. 2017. Shotgun Approach to Increasing Enzymatic Saccharification Yields of Ammonia Fiber Expansion Pretreated Cellulosic Biomass, Frontiers in Energy Research 5. GLBRC
201710.1101/094805Clarkson, S. M., D. M. Kridelbaugh, J. G. Elkins, A. M. Guss, and J. Michener. 2017. Construction and optimization of a heterologous pathway for protocatechuate catabolism in Escherichia coli enables rapid bioconversion of model lignin monomers, bioRxiv. BESC
201710.1002/wsbm.1377Counts, J. A., B. M. Zeldes, L. L. Lee, C. T. Straub, M. W. W. Adams, and R. M. Kelly. 2017. Physiological, metabolic and biotechnological features of extremely thermophilic microorganisms, Wiley Interdiscip Rev Syst Biol Med 9(3). BESC
201710.1016/j.ymben.2017.06.004d'Espaux, L., A. Ghosh, W. Runguphan, M. Wehrs, F. Xu, O. Konzock, I. Dev, M. Nhan, J. Gin, A. Reider Apel, C. J. Petzold, S. Singh, B. A. Simmons, A. Mukhopadhyay, H. Garcia Martin, and J. D. Keasling. 2017. Engineering high-level production of fatty alcohols by Saccharomyces cerevisiae from lignocellulosic feedstocks, Metab Eng 42, 115-125. JBEI
201710.1111/nph.14306da Costa, R. M., S. Pattathil, U. Avci, S. J. Lee, S. P. Hazen, A. Winters, M. G. Hahn, and M. Bosch. 2017. A cell wall reference profile for Miscanthus bioenergy crops highlights compositional and structural variations associated with development and organ origin, New Phytol 213(4), 1710-1725. BESC
201710.1007/10_2016_45Dahal, S., S. Poudel, and R. A. Thompson. 2017. Genome-Scale Modeling of Thermophilic Microorganisms, Adv Biochem Eng Biotechnol 160, 103-119. BESC
201710.1002/bbb.1745Dale, B. 2017. A sober view of the difficulties in scaling cellulosic biofuels, Biofuels, Bioproducts and Biorefining 11(1), 5-7. GLBRC
201710.1186/s13068-017-0700-9Daly, P., J. M. van Munster, M. J. Blythe, R. Ibbett, M. Kokolski, S. Gaddipati, E. Lindquist, V. R. Singan, K. W. Barry, A. Lipzen, C. Y. Ngan, C. J. Petzold, L. J. G. Chan, S. T. Pullan, S. Delmas, P. R. Waldron, I. V. Grigoriev, G. A. Tucker, B. A. Simmons, and D. B. Archer. 2017. Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments, Biotechnol Biofuels 10, 35. JBEI
201710.1016/j.carbpol.2017.03.062Damm, T., S. Pattathil, M. Gunl, N. D. Jablonowski, M. O'Neill, K. S. Grun, P. M. Grande, W. Leitner, U. Schurr, B. Usadel, and H. Klose. 2017. Insights into cell wall structure of Sida hermaphrodita and its influence on recalcitrance, Carbohydr Polym 168, 94-102. BESC
201710.1021/acs.analchem.6b05004de Raad, M., T. de Rond, O. Rubel, J. D. Keasling, T. R. Northen, and B. P. Bowen. 2017. OpenMSI Arrayed Analysis Toolkit: Analyzing Spatially Defined Samples Using Mass Spectrometry Imaging, Anal Chem 89(11), 5818-5823. JBEI
201710.1038/nchembio.2471de Rond, T., P. Stow, I. Eigl, R. E. Johnson, L. J. G. Chan, G. Goyal, E. E. K. Baidoo, N. J. Hillson, C. J. Petzold, R. Sarpong, and J. D. Keasling. 2017. Oxidative cyclization of prodigiosin by an alkylglycerol monooxygenase-like enzyme, Nat Chem Biol 13(11), 1155-1157. JBEI
201710.1111/gcbb.12407DeBruyn, J. M., D. A. Bevard, M. E. Essington, J. Y. McKnight, S. M. Schaeffer, H. L. Baxter, M. Mazarei, D. G. J. Mann, R. A. Dixon, F. Chen, C. Zhuo, Z.-Y. Wang, and C. N. Stewart. 2017. Field-grown transgenic switchgrass (Panicum virgatum L.) with altered lignin does not affect soil chemistry, microbiology, and carbon storage potential, GCB Bioenergy 9(6), 1100-1109. BESC
201710.1016/j.ymben.2017.03.002Degreif, D., T. de Rond, A. Bertl, J. D. Keasling, and I. Budin. 2017. Lipid engineering reveals regulatory roles for membrane fluidity in yeast flocculation and oxygen-limited growth, Metab Eng 41, 46-56. JBEI
2017Dulys-Nusbaum, E. 2017. Timber residue supply for bioenergy in the northern tier of the Great Lakes: determinants and availability. Michigan State University East Lansing, MI.GLBRC
201710.1039/c7gc00346cDumitrache, A., A. Tolbert, J. Natzke, S. D. Brown, B. H. Davison, and A. J. Ragauskas. 2017. Cellulose and lignin colocalization at the plant cell wall surface limits microbial hydrolysis of Populus biomass, Green Chemistry 19(9), 2275-2285. BESC
201710.1038/srep43583Dumitrache, A., D. M. Klingeman, J. Natzke, M. Rodriguez, Jr., R. J. Giannone, R. L. Hettich, B. H. Davison, and S. D. Brown. 2017. Specialized activities and expression differences for Clostridium thermocellum biofilm and planktonic cells, Sci Rep 7, 43583. BESC
201710.1111/pbi.12666Dumitrache, A., J. Natzke, M. Rodriguez, Jr., K. L. Yee, O. A. Thompson, C. R. Poovaiah, H. Shen, M. Mazarei, H. L. Baxter, C. Fu, Z. Y. Wang, A. K. Biswal, G. Li, A. C. Srivastava, Y. Tang, C. N. Stewart, Jr., R. A. Dixon, R. S. Nelson, D. Mohnen, J. Mielenz, S. D. Brown, and B. H. Davison. 2017. Transgenic switchgrass (Panicum virgatum L.) targeted for reduced recalcitrance to bioconversion: a 2-year comparative analysis of field-grown lines modified for target gene or genetic element expression, Plant Biotechnol J 15(6), 688-697. BESC
201710.1021/acssuschemeng.7b02123Dutta, T., N. G. Isern, J. Sun, E. Wang, S. Hull, J. R. Cort, B. A. Simmons, and S. Singh. 2017. Survey of Lignin-Structure Changes and Depolymerization during Ionic Liquid Pretreatment, ACS Sustainable Chemistry & Engineering 5(11), 10116-10127. JBEI
201710.1080/19336950.2016.1222760Ebert, B., C. Rautengarten, and J. L. Heazlewood. 2017. GDP-L-fucose transport in plants: The missing piece, Channels (Austin) 11(1), 8-10. JBEI
201710.1104/pp.16.01108Eloy, N. B., W. Voorend, W. Lan, M. L. Saleme, I. Cesarino, R. Vanholme, R. A. Smith, G. Goeminne, A. Pallidis, K. Morreel, J. Nicomedes, Jr., J. Ralph, and W. Boerjan. 2017. Silencing CHALCONE SYNTHASE in Maize Impedes the Incorporation of Tricin into Lignin and Increases Lignin Content, Plant Physiol 173(2), 998-1016. GLBRC
201710.1371/journal.pone.0178160Eudes, A., T. Dutta, K. Deng, N. Jacquet, A. Sinha, V. T. Benites, E. E. K. Baidoo, A. Richel, S. E. Sattler, T. R. Northen, S. Singh, B. A. Simmons, and D. Loque. 2017. SbCOMT (Bmr12) is involved in the biosynthesis of tricin-lignin in sorghum, PLoS One 12(6), e0178160. JBEI
201710.1038/s41598-017-00234-4Farahi, R. H., A. M. Charrier, A. Tolbert, A. L. Lereu, A. Ragauskas, B. H. Davison, and A. Passian. 2017. Plasticity, elasticity, and adhesion energy of plant cell walls: nanometrology of lignin loss using atomic force microscopy, Sci Rep 7(1), 152. BESC
201710.1016/j.mbs.2016.08.004Faraji, M., and E. O. Voit. 2017. Nonparametric dynamic modeling, Mathematical Biosciences 287, 130-146. BESC
201710.1093/bioinformatics/btx126Faraji, M., and E. O. Voit. 2017. Stepwise inference of likely dynamic flux distributions from metabolic time series data, Bioinformatics 33(14), 2165-2172. BESC
201710.1016/j.jes.2016.10.005Fernandez-Bayo, J. D., J. Toniato, B. A. Simmons, and C. W. Simmons. 2017. Structure and activity of thermophilic methanogenic microbial communities exposed to quaternary ammonium sanitizer, J Environ Sci (China) 56, 164-168. JBEI
201710.3390/molecules22060981.Forman, V., R. Callari, C. Folly, H. Heider, and B. Hamberger. 2017. Production of Putative Diterpene Carboxylic Acid Intermediates of Triptolide in Yeast, Molecules 22(6). GLBRC
201710.1021/jacs.7b06560Fukushima, T., S. Gupta, B. Rad, J. A. Cornejo, C. J. Petzold, L. J. G. Chan, R. A. Mizrahi, C. Y. Ralston, and C. M. Ajo-Franklin. 2017. The Molecular Basis for Binding of an Electron Transfer Protein to a Metal Oxide Surface, J Am Chem Soc 139(36), 12647-12654. JBEI
201710.1039/c7lc00576hGach, P. C., K. Iwai, P. W. Kim, N. J. Hillson, and A. K. Singh. 2017. Droplet microfluidics for synthetic biology, Lab on a Chip 17(20), 3388-3400. JBEI
201710.1186/s13007-017-0172-8Gage, J. L., N. D. Miller, E. P. Spalding, S. M. Kaeppler, and N. de Leon. 2017. TIPS: a system for automated image-based phenotyping of maize tassels, Plant Methods 13, 21. GLBRC
201710.1016/j.copbio.2017.02.015Gall, D. L., J. Ralph, T. J. Donohue, and D. R. Noguera. 2017. Biochemical transformation of lignin for deriving valued commodities from lignocellulose, Curr Opin Biotechnol 45, 120-126. GLBRC
201710.1371/journal.pbio.2004050Gasch, A. P., F. B. Yu, J. Hose, L. E. Escalante, M. Place, R. Bacher, J. Kanbar, D. Ciobanu, L. Sandor, I. V. Grigoriev, C. Kendziorski, S. R. Quake, and M. N. McClean. 2017. Single-cell RNA sequencing reveals intrinsic and extrinsic regulatory heterogeneity in yeast responding to stress, PLoS Biol 15(12), e2004050. GLBRC
201710.1093/femsyr/fox038Gibson, B., J. A. Geertman, C. T. Hittinger, K. Krogerus, D. Libkind, E. J. Louis, F. Magalhaes, and J. P. Sampaio. 2017. New yeasts-new brews: modern approaches to brewing yeast design and development, FEMS Yeast Res 17(4). GLBRC
201710.1371/journal.pone.0177189Gontang, E. A., F. O. Aylward, C. Carlos, T. Glavina Del Rio, M. Chovatia, A. Fern, C. C. Lo, S. A. Malfatti, S. G. Tringe, C. R. Currie, and R. Kolter. 2017. Major changes in microbial diversity and community composition across gut sections of a juvenile Panchlora cockroach, PLoS One 12(5), e0177189. GLBRC
201710.1105/tpc.17.00338Gonzales-Vigil, E., C. A. Hefer, M. E. von Loessl, J. La Mantia, and S. D. Mansfield. 2017. Exploiting Natural Variation to Uncover an Alkene Biosynthetic Enzyme in Poplar, Plant Cell 29(8), 2000-2015. GLBRC
201710.1111/nph.14758Gou, J., C. Fu, S. Liu, C. Tang, S. Debnath, A. Flanagan, Y. Ge, Y. Tang, Q. Jiang, P. R. Larson, J. Wen, and Z. Y. Wang. 2017. The miR156-SPL4 module predominantly regulates aerial axillary bud formation and controls shoot architecture, New Phytol 216(3), 829-840. BESC
201710.1111/nph.14101Grabowski, P. P., J. Evans, C. Daum, S. Deshpande, K. W. Barry, M. Kennedy, G. Ramstein, S. M. Kaeppler, C. R. Buell, Y. Jiang, and M. D. Casler. 2017. Genome-wide associations with flowering time in switchgrass using exome-capture sequencing data, New Phytol 213(1), 154-169. .GLBRC
201710.1016/j.fuel.2016.12.064Groendyk, M., and D. Rothamer. 2017. Effect of increased fuel volatility on CDC operation in a light-duty CIDI engine, Fuel 194, 195-210. GLBRC
201710.1186/s13068-017-0757-5Gunawan, C., S. Xue, S. Pattathil, L. da Costa Sousa, B. E. Dale, and V. Balan. 2017. Comprehensive characterization of non-cellulosic recalcitrant cell wall carbohydrates in unhydrolyzed solids from AFEX-pretreated corn stover, Biotechnol Biofuels 10, 82. BESC GLBRC
201710.1146/annurev-ento-031616-035050.Gurr, G. M., S. D. Wratten, D. A. Landis, and M. You. 2017. Habitat Management to Suppress Pest Populations: Progress and Prospects, Annu Rev Entomol 62, 91-109. GLBRC
201710.1093/femsyr/fox019Haase, M. A. B., J. Kominek, Q. K. Langdon, C. P. Kurtzman, and C. T. Hittinger. 2017. Genome sequence and physiological analysis of Yamadazyma laniorum f.a. sp. nov. and a reevaluation of the apocryphal xylose fermentation of its sister species, Candida tenuis, FEMS Yeast Res 17(3). GLBRC
201710.1016/j.phytochem.2017.02.022Hansen, N. L., J. N. Nissen, and B. Hamberger. 2017. Two residues determine the product profile of the class II diterpene synthases TPS14 and TPS21 of Tripterygium wilfordii, Phytochemistry 138, 52-56. GLBRC
201710.1021/jacs.6b11895Haushalter, R. W., R. M. Phelan, K. M. Hoh, C. Su, G. Wang, E. E. Baidoo, and J. D. Keasling. 2017. Production of Odd-Carbon Dicarboxylic Acids in Escherichia coli Using an Engineered Biotin-Fatty Acid Biosynthetic Pathway, J Am Chem Soc 139(13), 4615-4618. JBEI
201710.1016/j.bbrc.2017.05.131He, H., J. Yan, X. Yu, Y. Liang, L. Fang, H. V. Scheller, and A. Zhang. 2017. The NADPH-oxidase AtRbohI plays a positive role in drought-stress response in Arabidopsis thaliana, Biochem Biophys Res Commun 491(3), 834-839. JBEI
201710.1016/j.ymben.2016.12.008He, L., Y. Xiu, J. A. Jones, E. E. K. Baidoo, J. D. Keasling, Y. J. Tang, and M. A. G. Koffas. 2017. Deciphering flux adjustments of engineered E. coli cells during fermentation with changing growth conditions, Metab Eng 39, 247-256. JBEI
201710.1039/c6lc01182aHeinemann, J., K. Deng, S. C. Shih, J. Gao, P. D. Adams, A. K. Singh, and T. R. Northen. 2017. On-chip integration of droplet microfluidics and nanostructure-initiator mass spectrometry for enzyme screening, Lab Chip 17(2), 323-331. JBEI
201710.1038/s41598-017-04609-5Hilley, J. L., B. D. Weers, S. K. Truong, R. F. McCormick, A. J. Mattison, B. A. McKinley, D. T. Morishige, and J. E. Mullet. 2017. Sorghum Dw2 Encodes a Protein Kinase Regulator of Stem Internode Length, Sci Rep 7(1), 4616. GLBRC
201710.1016/j.ymben.2017.06.011Hon, S., D. G. Olson, E. K. Holwerda, A. A. Lanahan, S. J. L. Murphy, M. I. Maloney, T. Zheng, B. Papanek, A. M. Guss, and L. R. Lynd. 2017. The ethanol pathway from Thermoanaerobacterium saccharolyticum improves ethanol production in Clostridium thermocellum, Metab Eng 42, 175-184. BESC
201710.1111/tpj.13743Hooper, C. M., T. J. Stevens, A. Saukkonen, I. R. Castleden, P. Singh, G. W. Mann, B. Fabre, J. Ito, M. J. Deery, K. S. Lilley, C. J. Petzold, A. H. Millar, J. L. Heazlewood, and H. T. Parsons. 2017. Multiple marker abundance profiling: combining selected reaction monitoring and data-dependent acquisition for rapid estimation of organelle abundance in subcellular samples, Plant J 92(6), 1202-1217. JBEI
201710.1016/j.ecolmodel.2017.06.007Izaurralde, R. C., W. B. McGill, J. R. Williams, C. D. Jones, R. P. Link, D. H. Manowitz, D. E. Schwab, X. Zhang, G. P. Robertson, and N. Millar. 2017. Simulating microbial denitrification with EPIC: Model description and evaluation, Ecological Modelling 359, 349-362. GLBRC
201710.2135/cropsci2017.04.0266Jakubowski, A. R., M. D. Casler, and R. D. Jackson. 2017. Legume Addition to Perennial Warm-Season Grass Swards Increases Harvested Biomass, Crop Science 57(6), 3343. GLBRC
201710.2135/cropsci2017.03.0193Jakubowski, A. R., R. D. Jackson, and M. D. Casler. 2017. Can Biomass Yield of Switchgrass be Increased without Increasing Nitrogen Requirements?, Crop Science 57(4), 2024. GLBRC
201710.2134/agronj2017.03.0129Jean, M., D. Pennington, M. Quigley, and K. Thelen. 2017. Improving Biomass and Ethanol Yield by Intercropping a Winter Cereal with Corn, Agronomy Journal 109(6), 2530. GLBRC
201710.1515/hf-2016-0112Jensen, A., Y. Cabrera, C.-W. Hsieh, J. Nielsen, J. Ralph, and C. Felby. 2017. 2D NMR characterization of wheat straw residual lignin after dilute acid pretreatment with different severities, Holzforschung 71(6). GLBRC
201710.1038/s41598-017-12901-7Jensen, H. M., T. Eng, V. Chubukov, R. A. Herbert, and A. Mukhopadhyay. 2017. Improving membrane protein expression and function using genomic edits, Sci Rep 7(1), 13030. JBEI
201710.1371/journal.pone.0173095Jensen, J. K., and C. G. Wilkerson. 2017. Brachypodium as an experimental system for the study of stem parenchyma biology in grasses, PLoS One 12(3), e0173095. GLBRC
201710.1002/bit.26229Jin, M., C. Sarks, B. D. Bals, N. Posawatz, C. Gunawan, B. E. Dale, and V. Balan. 2017. Toward high solids loading process for lignocellulosic biofuel production at a low cost, Biotechnol Bioeng 114(5), 980-989. GLBRC
201710.1002/bit.26302Jin, M., Y. Liu, L. da Costa Sousa, B. E. Dale, and V. Balan. 2017. Development of rapid bioconversion with integrated recycle technology for ethanol production from extractive ammonia pretreated corn stover, Biotechnol Bioeng 114(8), 1713-1720. GLBRC
201710.1186/s13068-017-0734-zJohnson, A. M., H. Kim, J. Ralph, and S. D. Mansfield. 2017. Natural acetylation impacts carbohydrate recovery during deconstruction of Populus trichocarpa wood, Biotechnol Biofuels 10, 48. GLBRC
201710.1186/s13068-017-0939-1Johnson, C. R., R. J. Millwood, Y. Tang, J. Gou, R. W. Sykes, G. B. Turner, M. F. Davis, Y. Sang, Z. Y. Wang, and C. N. Stewart, Jr. 2017. Field-grown miR156 transgenic switchgrass reproduction, yield, global gene expression analysis, and bioconfinement, Biotechnol Biofuels 10, 255. BESC
201710.1002/pld3.26Johnson, C. R., R. J. Millwood, Z.-Y. Wang, and C. N. Stewart. 2017. Light and temperature effects on miR156 transgenic switchgrass flowering: A simulated latitudinal study, Plant Direct 1(5), e00026. BESC
201710.1016/j.meteno.2017.05.002Johnson, C. W., P. E. Abraham, J. G. Linger, P. Khanna, R. L. Hettich, and G. T. Beckham. 2017. Eliminating a global regulator of carbon catabolite repression enhances the conversion of aromatic lignin monomers to muconate in Pseudomonas putida KT2440, Metab Eng Commun 5, 19-25. BESC
201710.1111/gcbb.12473Jones, C. D., X. Zhang, A. D. Reddy, G. P. Robertson, and R. C. Izaurralde. 2017. The greenhouse gas intensity and potential biofuel production capacity of maize stover harvest in the US Midwest, GCB Bioenergy 9(10), 1543-1554. GLBRC
201710.1111/gcbb.12473Joubert, W., J. Nance, S. Climer, D. Weighill, and D. Jacobson. 2017. Parallel accelerated custom correlation coefficient calculations for genomics applications, Parallel Computing. DOI.BESC
201710.1104/pp.17.00576Jun, S. Y., A. M. Walker, H. Kim, J. Ralph, W. Vermerris, S. E. Sattler, and C. Kang. 2017. The Enzyme Activity and Substrate Specificity of Two Major Cinnamyl Alcohol Dehydrogenases in Sorghum (Sorghum bicolor), SbCAD2 and SbCAD4, Plant Physiol 174(4), 2128-2145. GLBRC
201710.1016/j.ymben.2017.03.010Kang, A., C. W. Meadows, N. Canu, J. D. Keasling, and T. S. Lee. 2017. High-throughput enzyme screening platform for the IPP-bypass mevalonate pathway for isopentenol production, Metab Eng 41, 125-134. JBEI
201710.1104/pp.17.01172Karlen, S. D., R. A. Smith, H. Kim, D. Padmakshan, A. Bartuce, J. K. Mobley, H. C. A. Free, B. G. Smith, P. J. Harris, and J. Ralph. 2017. Highly Decorated Lignins in Leaf Tissues of the Canary Island Date Palm Phoenix canariensis, Plant Physiol 175(3), 1058-1067. GLBRC
201710.1186/s13068-017-0848-3Kebrom, T. H., B. McKinley, and J. E. Mullet. 2017. Dynamics of gene expression during development and expansion of vegetative stem internodes of bioenergy sorghum, Biotechnol Biofuels 10, 159. GLBRC
201710.1016/j.ymben.2017.11.004Kim, E. M., H. M. Woo, T. Tian, S. Yilmaz, P. Javidpour, J. D. Keasling, and T. S. Lee. 2017. Autonomous control of metabolic state by a quorum sensing (QS)-mediated regulator for bisabolene production in engineered E. coli, Metab Eng 44, 325-336. JBEI
201710.1021/acs.biomac.7b01223Kim, H., D. Padmakshan, Y. Li, J. Rencoret, R. D. Hatfield, and J. Ralph. 2017. Characterization and Elimination of Undesirable Protein Residues in Plant Cell Wall Materials for Enhancing Lignin Analysis by Solution-State Nuclear Magnetic Resonance Spectroscopy, Biomacromolecules 18(12), 4184-4195. GLBRC
201710.1039/c6gc02473dKim, K. H., B. A. Simmons, and S. Singh. 2017. Catalytic transfer hydrogenolysis of ionic liquid processed biorefinery lignin to phenolic compounds, Green Chemistry 19(1), 215-224. JBEI
201710.1002/cssc.201601515Kim, K. H., R. C. Brown, T. Daugaard, W. F. Tivol, M. Auer, B. Simmons, and S. Singh. 2017. Strategy for Extending the Stability of Bio-oil-Derived Phenolic Oligomers by Mild Hydrotreatment with Ionic-Liquid-Stabilized Nanoparticles, ChemSusChem 10(5), 884-893. JBEI
201710.1021/acssuschemeng.6b03102Kim, K. H., T. Dutta, E. D. Walter, N. G. Isern, J. R. Cort, B. A. Simmons, and S. Singh. 2017. Chemoselective Methylation of Phenolic Hydroxyl Group Prevents Quinone Methide Formation and Repolymerization During Lignin Depolymerization, ACS Sustainable Chemistry & Engineering 5(5), 3913-3919. JBEI
201710.1186/s13068-017-0784-2Kim, K. H., T. Dutta, J. Ralph, S. D. Mansfield, B. A. Simmons, and S. Singh. 2017. Impact of lignin polymer backbone esters on ionic liquid pretreatment of poplar, Biotechnol Biofuels 10, 101. GLBRC JBEI
201710.1007/s00425-017-2687-7.Kim, S. J., S. Zemelis-Durfee, C. Wilkerson, and F. Brandizzi. 2017. In Brachypodium a complex signaling is actuated to protect cells from proteotoxic stress and facilitate seed filling, Planta 246(1), 75-89. GLBRC
201710.1002/bit.26242Kim, S. K., D. Chung, M. E. Himmel, Y. J. Bomble, and J. Westpheling. 2017. Engineering the N-terminal end of CelA results in improved performance and growth of Caldicellulosiruptor bescii on crystalline cellulose, Biotechnol Bioeng 114(5), 945-950. BESC
201710.1007/s10295-017-1982-4Kim, S. K., D. Chung, M. E. Himmel, Y. J. Bomble, and J. Westpheling. 2017. Heterologous expression of a beta-D-glucosidase in Caldicellulosiruptor bescii has a surprisingly modest effect on the activity of the exoproteome and growth on crystalline cellulose, J Ind Microbiol Biotechnol 44(12), 1643-1651. BESC
201710.1002/bit.26366Kim, S. K., D. Chung, M. E. Himmel, Y. J. Bomble, and J. Westpheling. 2017. In vivo synergistic activity of a CAZyme cassette from Acidothermus cellulolyticus significantly improves the cellulolytic activity of the C. bescii exoproteome, Biotechnol Bioeng 114(11), 2474-2480. BESC
201710.1186/s13068-017-0750-zKim, S. K., J. Groom, D. Chung, J. Elkins, and J. Westpheling. 2017. Expression of a heat-stable NADPH-dependent alcohol dehydrogenase from Thermoanaerobacter pseudethanolicus 39E in Clostridium thermocellum 1313 results in increased hydroxymethylfurfural resistance, Biotechnol Biofuels 10, 66. BESC
201710.1111/1365-2664.12901Kim, T. N., A. F. Fox, B. D. Wills, T. D. Meehan, D. A. Landis, C. Gratton, and J. Firn. 2017. Harvesting biofuel grasslands has mixed effects on natural enemy communities and no effects on biocontrol services, Journal of Applied Ecology 54(6), 2011-2021. GLBRC
201710.1073/pnas.1619263114Kohler, A. C., M. J. L. Mills, P. D. Adams, B. A. Simmons, and K. L. Sale. 2017. Structure of aryl O-demethylase offers molecular insight into a catalytic tyrosine-dependent mechanism, Proc Natl Acad Sci U S A 114(16), E3205-E3214. JBEI
201710.1016/j.compchemeng.2017.02.024Kong, L., V. Avadiappan, K. Huang, and C. T. Maravelias. 2017. Simultaneous chemical process synthesis and heat integration with unclassified hot/cold process streams, Computers & Chemical Engineering 101, 210-225. GLBRC
201710.1021/acs.iecr.7b01689Kong, L., Y. Wu, and C. T. Maravelias. 2017. Simultaneous Utility and Heat Exchanger Area Targeting for Integrated Process Synthesis and Heat Integration, Industrial & Engineering Chemistry Research 56(41), 11847-11859. GLBRC
201710.1093/jxb/erx275Kong, Q., W. Ma, H. Yang, G. Ma, J. J. Mantyla, and C. Benning. 2017. The Arabidopsis WRINKLED1 transcription factor affects auxin homeostasis in roots, J Exp Bot 68(16), 4627-4634. GLBRC
201710.1038/ngeo2963Kravchenko, A. N., E. R. Toosi, A. K. Guber, N. E. Ostrom, J. Yu, K. Azeem, M. L. Rivers, and G. P. Robertson. 2017. Hotspots of soil N2O emission enhanced through water absorption by plant residue, Nature Geoscience 10(7), 496-500. GLBRC
201710.1186/s13068-017-0925-7Kruer-Zerhusen, N., M. Alahuhta, V. V. Lunin, M. E. Himmel, Y. J. Bomble, and D. B. Wilson. 2017. Structure of a Thermobifida fusca lytic polysaccharide monooxygenase and mutagenesis of key residues, Biotechnol Biofuels 10, 243. BESC
2017Lakshmanan, V., P. Ray, and K. D. Craven. 2017. Rhizosphere Sampling Protocols for Microbiome (16S/18S/ITS rRNA) Library Preparation and Enrichment for the Isolation of Drought Tolerance-Promoting Microbes. In Plant Stress Tolerance: Methods and Protocols, 2nd ed., 349-362. Ed. R. Sunkar. Springer.BESC
201710.1007/978-1-4939-7136-7_4Lakshmanan, V., P. Ray, and K. D. Craven. 2017. Toward a Resilient, Functional Microbiome: Drought Tolerance-Alleviating Microbes for Sustainable Agriculture, Methods Mol Biol 1631, 69-84. BESC
201710.1016/j.baae.2016.07.005Landis, D. A. 2017. Designing agricultural landscapes for biodiversity-based ecosystem services, Basic and Applied Ecology 18, 1-12. GLBRC
2017Lao, J., A. M. Smith-Moritz, J. C. Mortimer, and J. L. Heazlewood. 2017. Enrichment of the Plant Cytosolic Fraction. In Isolation of Plant Organelles and Structures: Methods and Protocols 213-232. Eds. N. L. Taylor, and A. H. Millar. Springer New York.JBEI
2017 10.1111/gcbb.12352LeDuc, S. D., X. Zhang, C. M. Clark, and R. C. Izaurralde. 2017. Cellulosic feedstock production on Conservation Reserve Program land: potential yields and environmental effects, GCB Bioenergy 9(2), 460-468. GLBRC
201710.1128/mBio.00513-17Lemmer, K. C., W. Zhang, S. J. Langer, A. C. Dohnalkova, D. Hu, R. A. Lemke, J. S. Piotrowski, G. Orr, D. R. Noguera, and T. J. Donohue. 2017. Mutations That Alter the Bacterial Cell Envelope Increase Lipid Production, MBio 8(3). GLBRC
201710.1126/science.aan6874Lenarcic, T., I. Albert, H. Bohm, V. Hodnik, K. Pirc, A. B. Zavec, M. Podobnik, D. Pahovnik, E. Zagar, R. Pruitt, P. Greimel, A. Yamaji-Hasegawa, T. Kobayashi, A. Zienkiewicz, J. Gomann, J. C. Mortimer, L. Fang, A. Mamode-Cassim, M. Deleu, L. Lins, C. Oecking, I. Feussner, S. Mongrand, G. Anderluh, and T. Nurnberger. 2017. Eudicot plant-specific sphingolipids determine host selectivity of microbial NLP cytolysins, Science 358(6369), 1431-1434. JBEI
201710.1007/s00253-017-8168-xLi, B., and J. D. Walton. 2017. Functional diversity for biomass deconstruction in family 5 subfamily 5 (GH5_5) of fungal endo-beta1,4-glucanases, Appl Microbiol Biotechnol 101(10), 4093-4101. GLBRC
201710.1105/tpc.17.00154Li, G., R. Jain, M. Chern, N. T. Pham, J. A. Martin, T. Wei, W. S. Schackwitz, A. M. Lipzen, P. Q. Duong, K. C. Jones, L. Jiang, D. Ruan, D. Bauer, Y. Peng, K. W. Barry, J. Schmutz, and P. C. Ronald. 2017. The Sequences of 1504 Mutants in the Model Rice Variety Kitaake Facilitate Rapid Functional Genomic Studies, Plant Cell 29(6), 1218-1231. JBEI
201710.1073/pnas.1618360114Li, H., D. J. Yelle, C. Li, M. Yang, J. Ke, R. Zhang, Y. Liu, N. Zhu, S. Liang, X. Mo, J. Ralph, C. R. Currie, and J. Mo. 2017. Lignocellulose pretreatment in a fungus-cultivating termite, Proc Natl Acad Sci U S A 114(18), 4709-4714. GLBRC
201710.1007/s12155-016-9798-zLi, M., D. L. Williams, M. Heckwolf, N. de Leon, S. Kaeppler, R. W. Sykes, and D. Hodge. 2017. Prediction of Cell Wall Properties and Response to Deconstruction Using Alkaline Pretreatment in Diverse Maize Genotypes Using Py-MBMS and NIR, BioEnergy Research 10(2), 329-343. BESC
201710.1186/s13068-016-0695-7Li, M., Y. Pu, C. G. Yoo, E. Gjersing, S. R. Decker, C. Doeppke, T. Shollenberger, T. J. Tschaplinski, N. L. Engle, R. W. Sykes, M. F. Davis, H. L. Baxter, M. Mazarei, C. Fu, R. A. Dixon, Z. Y. Wang, C. Neal Stewart, Jr., and A. J. Ragauskas. 2017. Study of traits and recalcitrance reduction of field-grown COMT down-regulated switchgrass, Biotechnol Biofuels 10, 12. BESC
201710.1002/slct.201700735Li, M., Y. Pu, T. J. Tschaplinski, and A. J. Ragauskas. 2017. 31P?NMR Characterization of Tricin and Its Structurally Similar Flavonoids, ChemistrySelect 2(12), 3557-3561. BESC
201710.1016/j.cell.2017.06.008Li, W., Z. Zhu, M. Chern, J. Yin, C. Yang, L. Ran, M. Cheng, M. He, K. Wang, J. Wang, X. Zhou, X. Zhu, Z. Chen, J. Wang, W. Zhao, B. Ma, P. Qin, W. Chen, Y. Wang, J. Liu, W. Wang, X. Wu, P. Li, J. Wang, L. Zhu, S. Li, and X. Chen. 2017. A Natural Allele of a Transcription Factor in Rice Confers Broad-Spectrum Blast Resistance, Cell 170(1), 114-126 e115. JBEI
201710.1074/jbc.M117.777417Li, Z., T. Mukherjee, K. Bowler, S. Namdari, Z. Snow, S. Prestridge, A. Carlton, and M. Bar-Peled. 2017. A four-gene operon in Bacillus cereus produces two rare spore-decorating sugars, J Biol Chem 292(18), 7636-7650. BESC
201710.1021/acssynbio.6b00295Liang, Y., S. Richardson, J. Yan, V. T. Benites, C. Cheng-Yue, T. Tran, J. Mortimer, A. Mukhopadhyay, J. D. Keasling, H. V. Scheller, and D. Loque. 2017. Endoribonuclease-Based Two-Component Repressor Systems for Tight Gene Expression Control in Plants, ACS Synth Biol 6(5), 806-816. JBEI
201710.3389/fpls.2017.00982Liu, S., C. Fu, J. Gou, L. Sun, D. Huhman, Y. Zhang, and Z. Y. Wang. 2017. Simultaneous Downregulation of MTHFR and COMT in Switchgrass Affects Plant Performance and Induces Lesion-Mimic Cell Death, Front Plant Sci 8, 982. BESC
201710.1016/j.ymben.2016.10.018Lo, J., D. G. Olson, S. J. Murphy, L. Tian, S. Hon, A. Lanahan, A. M. Guss, and L. R. Lynd. 2017. Engineering electron metabolism to increase ethanol production in Clostridium thermocellum, Metab Eng 39, 71-79. BESC
201710.1016/j.copbio.2017.03.008Lynd, L. R., X. Liang, M. J. Biddy, A. Allee, H. Cai, T. Foust, M. E. Himmel, M. S. Laser, M. Wang, and C. E. Wyman. 2017. Cellulosic ethanol: status and innovation, Curr Opin Biotechnol 45, 202-211. BESC
201710.1007/s11120-016-0281-7Ma, J. Y., W. Sun, N. K. Koteyeva, E. Voznesenskaya, S. S. Stutz, A. Gandin, A. M. Smith-Moritz, J. L. Heazlewood, and A. B. Cousins. 2017. Influence of light and nitrogen on the photosynthetic efficiency in the C4 plant Miscanthus x giganteus, Photosynth Res 131(1), 1-13. JBEI
201710.1186/s12864-017-3902-4MacMillan, C. P., H. Birke, A. Chuah, E. Brill, Y. Tsuji, J. Ralph, E. S. Dennis, D. Llewellyn, and F. A. Pettolino. 2017. Tissue and cell-specific transcriptomes in cotton reveal the subtleties of gene regulation underlying the diversity of plant secondary cell walls, BMC Genomics 18(1), 539. GLBRC
201710.1016/j.copbio.2016.11.006Martien, J. I., and D. Amador-Noguez. 2017. Recent applications of metabolomics to advance microbial biofuel production, Curr Opin Biotechnol 43, 118-126. GLBRC
201710.1016/j.sab.2017.10.008Martin, M. Z., D. C. Glasgow, T. J. Tschaplinski, G. A. Tuskan, L. E. Gunter, N. L. Engle, A. M. Wymore, and D. J. Weston. 2017. Correlating laser-induced breakdown spectroscopy with neutron activation analysis to determine the elemental concentration in the ionome of the Populus trichocarpa leaf, Spectrochimica Acta Part B: Atomic Spectroscopy 138, 46-53. BESC
201710.1073/pnas.1708124114McAndrew, R. P., N. Sathitsuksanoh, M. M. Mbughuni, R. A. Heins, J. H. Pereira, A. George, K. L. Sale, B. G. Fox, B. A. Simmons, and P. D. Adams. 2017. Reply to Kiser: Dioxygen binding in NOV1 crystal structures, Proc Natl Acad Sci U S A 114(30), E6029-E6030. JBEI
201710.1039/c6gc03515aMcClelland, D. J., A. H. Motagamwala, Y. Li, M. R. Rover, A. M. Wittrig, C. Wu, J. S. Buchanan, R. C. Brown, J. Ralph, J. A. Dumesic, and G. W. Huber. 2017. Functionality and molecular weight distribution of red oak lignin before and after pyrolysis and hydrogenation, Green Chemistry 19(5), 1378-1389. GLBRC
201710.1128/mBio.00644-17McDonald, B. R., and C. R. Currie. 2017. Lateral Gene Transfer Dynamics in the Ancient Bacterial Genus Streptomyces, MBio 8(3). GLBRC
201710.1002/bit.26296Mendez-Perez, D., J. Alonso-Gutierrez, Q. Hu, M. Molinas, E. E. K. Baidoo, G. Wang, L. J. G. Chan, P. D. Adams, C. J. Petzold, J. D. Keasling, and T. S. Lee. 2017. Production of jet fuel precursor monoterpenoids from engineered Escherichia coli, Biotechnol Bioeng 114(8), 1703-1712. JBEI
201710.19080/RAPSCI.2017.01.555551Meng, X., and A. Ragauskas. 2017. Pseudo-Lignin Formation during Dilute acid Pretreatment for Cellulosic Ethanol, Recent Advances in Petrochemical Science 1(1), 1-5. BESC
201710.1002/cssc.201601303Meng, X., Y. Pu, C. G. Yoo, M. Li, G. Bali, D. Y. Park, E. Gjersing, M. F. Davis, W. Muchero, G. A. Tuskan, T. J. Tschaplinski, and A. J. Ragauskas. 2017. An In-Depth Understanding of Biomass Recalcitrance Using Natural Poplar Variants as the Feedstock, ChemSusChem 10(1), 139-150. BESC
201710.1016/j.biombioe.2017.03.012Miesel, J. R., L. C. Jach-Smith, M. J. Renz, and R. D. Jackson. 2017. Distribution of switchgrass ( Panicum virgatum L.) aboveground biomass in response to nitrogen addition and across harvest dates, Biomass and Bioenergy 100, 74-83. GLBRC
201710.1002/jcc.25054Mills, M. J. L., K. L. Sale, B. A. Simmons, and P. L. A. Popelier. 2017. Rhorix: An interface between quantum chemical topology and the 3D graphics program blender, J Comput Chem 38(29), 2538-2552. JBEI
201710.1021/acssuschemeng.7b01424Mittal, A., R. Katahira, B. S. Donohoe, B. A. Black, S. Pattathil, J. M. Stringer, and G. T. Beckham. 2017. Alkaline Peroxide Delignification of Corn Stover, ACS Sustainable Chemistry & Engineering 5(7), 6310-6321. BESC
201710.1073/pnas.1620119114Mizrachi, E., L. Verbeke, N. Christie, A. C. Fierro, S. D. Mansfield, M. F. Davis, E. Gjersing, G. A. Tuskan, M. Van Montagu, Y. Van de Peer, K. Marchal, and A. A. Myburg. 2017. Network-based integration of systems genetics data reveals pathways associated with lignocellulosic biomass accumulation and processing, Proc Natl Acad Sci U S A 114(5), 1195-1200. BESC
201710.1111/pbi.12655Mnich, E., R. Vanholme, P. Oyarce, S. Liu, F. Lu, G. Goeminne, B. Jorgensen, M. S. Motawie, W. Boerjan, J. Ralph, P. Ulvskov, B. L. Moller, N. Bjarnholt, and J. Harholt. 2017. Degradation of lignin beta-aryl ether units in Arabidopsis thaliana expressing LigD, LigF and LigG from Sphingomonas paucimobilis SYK-6, Plant Biotechnol J 15(5), 581-593. GLBRC
201710.1186/s12934-017-0819-1Mohamed, E. T., S. Wang, R. M. Lennen, M. J. Herrgard, B. A. Simmons, S. W. Singer, and A. M. Feist. 2017. Generation of a platform strain for ionic liquid tolerance using adaptive laboratory evolution, Microb Cell Fact 16(1), 204. JBEI
201710.1021/acssuschemeng.7b00596Mohapatra, S., S. Pattathil, and H. Thatoi. 2017. Structural and Functional Characterization of Two Pennisetum sp. Biomass during Ultrasono-Assisted Alkali Pretreatment and Enzymatic Hydrolysis for Understanding the Mechanism of Targeted Delignification and Enhanced Saccharification, ACS Sustainable Chemistry & Engineering 5(8), 6486-6497. BESC
201710.1099/ijsem.0.002186Morais, C. G., T. M. Batista, J. Kominek, B. M. Borelli, C. Furtado, R. G. Moreira, G. R. Franco, L. H. Rosa, C. Fonseca, C. T. Hittinger, M. A. Lachance, and C. A. Rosa. 2017. Spathaspora boniae sp. nov., a D-xylose-fermenting species in the Candida albicans/Lodderomyces clade, Int J Syst Evol Microbiol 67(10), 3798-3805. GLBRC
201710.1021/acssynbio.7b00204Morrell, W. C., G. W. Birkel, M. Forrer, T. Lopez, T. W. H. Backman, M. Dussault, C. J. Petzold, E. E. K. Baidoo, Z. Costello, D. Ando, J. Alonso-Gutierrez, K. W. George, A. Mukhopadhyay, I. Vaino, J. D. Keasling, P. D. Adams, N. J. Hillson, and H. Garcia Martin. 2017. The Experiment Data Depot: A Web-Based Software Tool for Biological Experimental Data Storage, Sharing, and Visualization, ACS Synth Biol 6(12), 2248-2259. JBEI
201710.1007/978-1-4939-6722-3_16Mortimer, J. C. 2017. Structural Analysis of Cell Wall Polysaccharides Using PACE, Methods Mol Biol 1544, 223-231. JBEI
201710.1016/j.rser.2016.11.253Neupane, B., and J. Rubin. 2017. Implications of U.S. biofuels policy for sustainable transportation energy in Maine and the Northeast, Renewable and Sustainable Energy Reviews 70, 729-735. JBEI
201710.1021/acssuschemeng.7b02116Neupane, B., N. V. S. N. M. Konda, S. Singh, B. A. Simmons, and C. D. Scown. 2017. Life-Cycle Greenhouse Gas and Water Intensity of Cellulosic Biofuel Production Using Cholinium Lysinate Ionic Liquid Pretreatment, ACS Sustainable Chemistry & Engineering 5(11), 10176-10185. JBEI
201710.1016/j.renene.2016.05.009Ng, R. T. L., and C. T. Maravelias. 2017. Design of biofuel supply chains with variable regional depot and biorefinery locations, Renewable Energy 100, 90-102. GLBRC
201710.1016/j.apenergy.2017.08.161Ng, R. T. L., and C. T. Maravelias. 2017. Economic and energetic analysis of biofuel supply chains, Applied Energy 205, 1571-1582. GLBRC
201710.1073/pnas.1704652114Nguyen, T. Y., C. M. Cai, R. Kumar, and C. E. Wyman. 2017. Overcoming factors limiting high-solids fermentation of lignocellulosic biomass to ethanol, Proc Natl Acad Sci U S A 114(44), 11673-11678. BESC
201710.1016/j.plantsci.2017.01.014Novo, M., C. Silvar, F. Merino, T. Martinez-Cortes, F. Lu, J. Ralph, and F. Pomar. 2017. Deciphering the role of the phenylpropanoid metabolism in the tolerance of Capsicum annuum L. to Verticillium dahliae Kleb, Plant Sci 258, 12-20. GLBRC
201710.3791/55310Oates, L. G., H. W. Read, J. L. M. Gutknecht, D. S. Duncan, T. B. Balser, and R. D. Jackson. 2017. A Lipid Extraction and Analysis Method for Characterizing Soil Microbes in Experiments with Many Samples, J Vis Exp(125). GLBRC
201710.1021/acssynbio.6b00200Oberortner, E., J. F. Cheng, N. J. Hillson, and S. Deutsch. 2017. Streamlining the Design-to-Build Transition with Build-Optimization Software Tools, ACS Synth Biol 6(3), 485-496. JBEI
201710.1016/j.ymben.2016.11.011Olson, D. G., M. Horl, T. Fuhrer, J. Cui, J. Zhou, M. I. Maloney, D. Amador-Noguez, L. Tian, U. Sauer, and L. R. Lynd. 2017. Glycolysis without pyruvate kinase in Clostridium thermocellum, Metab Eng 39, 169-180. BESC
2017 10.1371/journal.pone.0186440Orellana, R., G. Chaput, L. M. Markillie, H. Mitchell, M. Gaffrey, G. Orr, and K. M. DeAngelis. 2017. Multi-time series RNA-seq analysis of Enterobacter lignolyticus SCF1 during growth in lignin-amended medium, PLoS One 12(10), e0186440. JBEI
201710.1007/s10533-017-0301-5Ostrom, N. E., and P. H. Ostrom. 2017. Mining the isotopic complexity of nitrous oxide: a review of challenges and opportunities, Biogeochemistry 132(3), 359-372. GLBRC
201710.1039/c6gc02637kPapa, G., J. Kirby, N. V. S. N. Murthy Konda, K. Tran, S. Singh, J. D. Keasling, G. F. Peter, and B. A. Simmons. 2017. Development of an integrated approach for a-pinene recovery and sugar production from loblolly pine using ionic liquids, Green Chemistry 19(4), 1117-1127. JBEI
201710.1016/j.biortech.2017.05.167.Papa, G., T. Feldman, K. L. Sale, F. Adani, S. Singh, and B. A. Simmons. 2017. Parametric study for the optimization of ionic liquid pretreatment of corn stover, Bioresour Technol 241, 627-637. JBEI
201710.1016/j.biortech.2017.05.001Parisutham, V., S. P. Chandran, A. Mukhopadhyay, S. K. Lee, and J. D. Keasling. 2017. Intracellular cellobiose metabolism and its applications in lignocellulose-based biorefineries, Bioresour Technol 239, 496-506. .JBEI
201710.1186/s12284-017-0166-1.Park, C. J., T. Wei, R. Sharma, and P. C. Ronald. 2017. Overexpression of Rice Auxilin-Like Protein, XB21, Induces Necrotic Lesions, up-Regulates Endocytosis-Related Genes, and Confers Enhanced Resistance to Xanthomonas oryzae pv. oryzae, Rice (N Y) 10(1), 27. JBEI
201710.1371/journal.pone.0179410.Park, J. J., E. Dempewolf, W. Zhang, and Z. Y. Wang. 2017. RNA-guided transcriptional activation via CRISPR/dCas9 mimics overexpression phenotypes in Arabidopsis, PLoS One 12(6), e0179410. BESC
201710.7554/eLife.23001.Pateraki, I., J. Andersen-Ranberg, N. B. Jensen, S. G. Wubshet, A. M. Heskes, V. Forman, B. Hallstrom, B. Hamberger, M. S. Motawia, C. E. Olsen, D. Staerk, J. Hansen, B. L. Moller, and B. Hamberger. 2017. Total biosynthesis of the cyclic AMP booster forskolin from Coleus forskohlii, Elife 6. GLBRC
201710.1016/j.biortech.2016.11.064.Perez-Pimienta, J. A., A. Vargas-Tah, K. M. Lopez-Ortega, Y. N. Medina-Lopez, J. A. Mendoza-Perez, S. Avila, S. Singh, B. A. Simmons, I. Loaces, and A. Martinez. 2017. Sequential enzymatic saccharification and fermentation of ionic liquid and organosolv pretreated agave bagasse for ethanol production, Bioresour Technol 225, 191-198. JBEI
201710.1186/s13068-017-0758-4Perez-Pimienta, J. A., N. Sathitsuksanoh, V. S. Thompson, K. Tran, T. Ponce-Noyola, V. Stavila, S. Singh, and B. A. Simmons. 2017. Ternary ionic liquid-water pretreatment systems of an agave bagasse and municipal solid waste blend, Biotechnol Biofuels 10, 72. JBEI
201710.1186/s13068-017-0763-7Peris, D., R. V. Moriarty, W. G. Alexander, E. Baker, K. Sylvester, M. Sardi, Q. K. Langdon, D. Libkind, Q. M. Wang, F. Y. Bai, J. B. Leducq, G. Charron, C. R. Landry, J. P. Sampaio, P. Goncalves, K. E. Hyma, J. C. Fay, T. K. Sato, and C. T. Hittinger. 2017. Hybridization and adaptive evolution of diverse Saccharomyces species for cellulosic biofuel production, Biotechnol Biofuels 10, 78. GLBRC
201710.1021/acssynbio.6b00202Phelan, R. M., D. Sachs, S. J. Petkiewicz, J. F. Barajas, J. M. Blake-Hedges, M. G. Thompson, A. Reider Apel, B. J. Rasor, L. Katz, and J. D. Keasling. 2017. Development of Next Generation Synthetic Biology Tools for Use in Streptomyces venezuelae, ACS Synth Biol 6(1), 159-166. JBEI
201710.1186/s13068-016-0697-5Poudel, S., R. J. Giannone, M. Rodriguez, Jr., B. Raman, M. Z. Martin, N. L. Engle, J. R. Mielenz, I. Nookaew, S. D. Brown, T. J. Tschaplinski, D. Ussery, and R. L. Hettich. 2017. Integrated omics analyses reveal the details of metabolic adaptation of Clostridium thermocellum to lignocellulose-derived growth inhibitors released during the deconstruction of switchgrass, Biotechnol Biofuels 10, 14. BESC
201710.1007/s10533-017-0346-5Proemse, B. C., A. E. Murray, C. Schallenberg, B. McKiernan, B. T. Glazer, S. A. Young, N. E. Ostrom, A. R. Bowie, M. E. Wieser, F. Kenig, P. T. Doran, and R. Edwards. 2017. Iron cycling in the anoxic cryo-ecosystem of Antarctic Lake Vida, Biogeochemistry 134(1-2), 17-27. GLBRC
201710.1111/nph.14609Pruitt, R. N., A. Joe, W. Zhang, W. Feng, V. Stewart, B. Schwessinger, J. R. Dinneny, and P. C. Ronald. 2017. A microbially derived tyrosine-sulfated peptide mimics a plant peptide hormone, New Phytol 215(2), 725-736. JBEI
201710.1021/acssuschemeng.7b02212Qureshi, A. S., J. Zhang, L. da Costa Sousa, and J. Bao. 2017. Antibacterial Peptide Secreted by Pediococcus acidilactici Enables Efficient Cellulosic Open l-Lactic Acid Fermentation, ACS Sustainable Chemistry & Engineering 5(10), 9254-9262. GLBRC
201710.3389/fpls.2017.00806Rao, X., and R. A. Dixon. 2017. Brassinosteroid Mediated Cell Wall Remodeling in Grasses under Abiotic Stress, Front Plant Sci 8, 806. BESC
201710.1073/pnas.1701894114Rautengarten, C., D. Birdseye, S. Pattathil, H. E. McFarlane, S. Saez-Aguayo, A. Orellana, S. Persson, M. G. Hahn, H. V. Scheller, J. L. Heazlewood, and B. Ebert. 2017. The elaborate route for UDP-arabinose delivery into the Golgi of plants, Proc Natl Acad Sci U S A 114(16), 4261-4266. JBEI
201710.1093/nar/gkw1023Reider Apel, A., L. d'Espaux, M. Wehrs, D. Sachs, R. A. Li, G. J. Tong, M. Garber, O. Nnadi, W. Zhuang, N. J. Hillson, J. D. Keasling, and A. Mukhopadhyay. 2017. A Cas9-based toolkit to program gene expression in Saccharomyces cerevisiae, Nucleic Acids Res 45(1), 496-508. JBEI
201710.1126/science.aal2324Robertson, G. P., S. K. Hamilton, B. L. Barham, B. E. Dale, R. C. Izaurralde, R. D. Jackson, D. A. Landis, S. M. Swinton, K. D. Thelen, and J. M. Tiedje. 2017. Cellulosic biofuel contributions to a sustainable energy future: Choices and outcomes, Science 356(6345). GLBRC
201710.1021/acssuschemeng.7b01818Rodriguez, A., D. Salvachúa, R. Katahira, B. A. Black, N. S. Cleveland, M. Reed, H. Smith, E. E. K. Baidoo, J. D. Keasling, B. A. Simmons, G. T. Beckham, and J. M. Gladden. 2017. Base-Catalyzed Depolymerization of Solid Lignin-Rich Streams Enables Microbial Conversion, ACS Sustainable Chemistry & Engineering 5(9), 8171-8180. JBEI
201710.1146/annurev-ento-031616-035444.Rosenheim, J. A., and C. Gratton. 2017. Ecoinformatics (Big Data) for Agricultural Entomology: Pitfalls, Progress, and Promise, Annu Rev Entomol 62, 399-417. GLBRC
201710.1016/j.ymben.2017.04.002Rydzak, T., D. Garcia, D. M. Stevenson, M. Sladek, D. M. Klingeman, E. K. Holwerda, D. Amador-Noguez, S. D. Brown, and A. M. Guss. 2017. Deletion of Type I glutamine synthetase deregulates nitrogen metabolism and increases ethanol production in Clostridium thermocellum, Metab Eng 41, 182-191. BESC
201710.1016/j.fuel.2017.01.070Sakai, S., and D. Rothamer. 2017. Effect of ethanol blending on particulate formation from premixed combustion in spark-ignition engines, Fuel 196, 154-168. GLBRC
201710.1104/pp.17.00920Saleme, M. L. S., I. Cesarino, L. Vargas, H. Kim, R. Vanholme, G. Goeminne, R. Van Acker, F. C. A. Fonseca, A. Pallidis, W. Voorend, J. N. Junior, D. Padmakshan, J. Van Doorsselaere, J. Ralph, and W. Boerjan. 2017. Silencing CAFFEOYL SHIKIMATE ESTERASE Affects Lignification and Improves Saccharification in Poplar, Plant Physiol 175(3), 1040-1057. GLBRC
201710.2134/agronj2016.08.0454Sanford, G. R., L. G. Oates, S. S. Roley, D. S. Duncan, R. D. Jackson, G. P. Robertson, and K. D. Thelen. 2017. Biomass Production a Stronger Driver of Cellulosic Ethanol Yield than Biomass Quality, Agronomy Journal 109(5), 1911. GLBRC
201710.1093/femsyr/fox042Sardi, M., and A. P. Gasch. 2017. Incorporating comparative genomics into the design-test-learn cycle of microbial strain engineering, FEMS Yeast Res 17(5). GLBRC
201710.1007/s10295-017-1949-5Sarks, C., M. Jin, V. Balan, and B. E. Dale. 2017. Fed-batch hydrolysate addition and cell separation by settling in high cell density lignocellulosic ethanol fermentations on AFEX corn stover in the Rapid Bioconversion with Integrated recycling Technology process, J Ind Microbiol Biotechnol 44(9), 1261-1272. GLBRC
201710.1038/nplants.2017.24Scheller, H. V. 2017. Plant cell wall: Never too much acetate, Nat Plants 3, 17024. JBEI
201710.1186/s13068-017-0965-zSchuerg, T., J. P. Prahl, R. Gabriel, S. Harth, F. Tachea, C. S. Chen, M. Miller, F. Masson, Q. He, S. Brown, M. Mirshiaghi, L. Liang, L. M. Tom, D. Tanjore, N. Sun, T. R. Pray, and S. W. Singer. 2017. Xylose induces cellulase production in Thermoascus aurantiacus, Biotechnol Biofuels 10, 271. JBEI
201710.1016/j.mib.2017.03.010Shade, A., M. A. Jacques, and M. Barret. 2017. Ecological patterns of seed microbiome diversity, transmission, and assembly, Curr Opin Microbiol 37, 15-22. GLBRC
201710.1038/s41559-017-0126Shen, X. X., C. T. Hittinger, and A. Rokas. 2017. Contentious relationships in phylogenomic studies can be driven by a handful of genes, Nat Ecol Evol 1(5), 126. GLBRC
201710.1002/bit.26180Shi, J., D. Wu, L. Zhang, B. A. Simmons, S. Singh, B. Yang, and C. E. Wyman. 2017. Dynamic changes of substrate reactivity and enzyme adsorption on partially hydrolyzed cellulose, Biotechnol Bioeng 114(3), 503-515. JBEI BESC
201710.1111/gbi.12200Shih, P. M., J. Hemp, L. M. Ward, N. J. Matzke, and W. W. Fischer. 2017. Crown group Oxyphotobacteria postdate the rise of oxygen, Geobiology 15(1), 19-29. JBEI
201710.1073/pnas.1710798114Shih, P. M., L. M. Ward, and W. W. Fischer. 2017. Evolution of the 3-hydroxypropionate bicycle and recent transfer of anoxygenic photosynthesis into the Chloroflexi, Proc Natl Acad Sci U S A 114(40), 10749-10754. JBEI
201710.3389/fbioe.2017.00031Shymansky, C. M., G. Wang, E. E. K. Baidoo, J. Gin, A. R. Apel, A. Mukhopadhyay, H. Garcia Martin, and J. D. Keasling. 2017. Flux-Enabled Exploration of the Role of Sip1 in Galactose Yeast Metabolism, Front Bioeng Biotechnol 5, 31. JBEI
201710.1038/srep42121Singh, R., J. Hu, M. R. Regner, J. W. Round, J. Ralph, J. N. Saddler, and L. D. Eltis. 2017. Enhanced delignification of steam-pretreated poplar by a bacterial laccase, Sci Rep 7, 42121. GLBRC
201710.1007/s00253-017-8506-zSitepu, I. R., L. A. Garay, L. Enriquez, R. Fry, J. H. Butler, J. M. Lopez, A. Kanti, S. A. Faulina, A. J. Nugroho, B. A. Simmons, S. W. Singer, C. W. Simmons, and K. Boundy-Mills. 2017. 1-Ethyl-3-methylimidazolium tolerance and intracellular lipid accumulation of 38 oleaginous yeast species, Appl Microbiol Biotechnol 101(23-24), 8621-8631. JBEI
201710.1186/s13068-017-0793-1Smith, R. A., C. L. Cass, M. Mazaheri, R. S. Sekhon, M. Heckwolf, H. Kaeppler, N. de Leon, S. D. Mansfield, S. M. Kaeppler, J. C. Sedbrook, S. D. Karlen, and J. Ralph. 2017. Suppression of CINNAMOYL-CoA REDUCTASE increases the level of monolignol ferulates incorporated into maize lignins, Biotechnol Biofuels 10, 109. GLBRC
201710.1104/pp.17.00434Smith, R. A., M. Schuetz, S. D. Karlen, D. Bird, N. Tokunaga, Y. Sato, S. D. Mansfield, J. Ralph, and A. L. Samuels. 2017. Defining the Diverse Cell Populations Contributing to Lignification in Arabidopsis Stems, Plant Physiology 174(2), 1028-1036. GLBRC
201710.1021/acssynbio.6b00240Soh, L. M. J., W. S. Mak, P. P. Lin, L. Mi, F. Y. Chen, R. Damoiseaux, J. B. Siegel, and J. C. Liao. 2017. Engineering a Thermostable Keto Acid Decarboxylase Using Directed Evolution and Computationally Directed Protein Design, ACS Synth Biol 6(4), 610-618. BESC
201710.1016/j.biocon.2016.12.008Spiesman, B. J., A. Bennett, R. Isaacs, and C. Gratton. 2017. Bumble bee colony growth and reproduction depend on local flower dominance and natural habitat area in the surrounding landscape, Biological Conservation 206, 217-223. GLBRC
201710.1016/j.biombioe.2017.07.007Sprunger, C. D., L. G. Oates, R. D. Jackson, and G. P. Robertson. 2017. Plant community composition influences fine root production and biomass allocation in perennial bioenergy cropping systems of the upper Midwest, USA, Biomass and Bioenergy 105, 248-258. GLBRC
201710.3791/54631Steffan, S. A., P. S. Dharampal, L. Diaz-Garcia, C. R. Currie, J. Zalapa, and C. T. Hittinger. 2017. Empirical, Metagenomic, and Computational Techniques Illuminate the Mechanisms by which Fungicides Compromise Bee Health, J Vis Exp(128). GLBRC
201710.1016/j.biortech.2016.11.092Stoklosa, R. J., A. Del Pilar Orjuela, L. da Costa Sousa, N. Uppugundla, D. L. Williams, B. E. Dale, D. B. Hodge, and V. Balan. 2017. Techno-economic comparison of centralized versus decentralized biorefineries for two alkaline pretreatment processes, Bioresour Technol 226, 9-17. GLBRC
201710.1016/j.copbio.2017.02.016Straub, C. T., B. M. Zeldes, G. J. Schut, M. W. Adams, and R. M. Kelly. 2017. Extremely thermophilic energy metabolisms: biotechnological prospects, Curr Opin Biotechnol 45, 104-112. BESC
201710.1186/s13068-017-0842-9Sun, J., J. Shi, N. Murthy Konda, D. Campos, D. Liu, S. Nemser, J. Shamshina, T. Dutta, P. Berton, G. Gurau, R. D. Rogers, B. A. Simmons, and S. Singh. 2017. Efficient dehydration and recovery of ionic liquid after lignocellulosic processing using pervaporation, Biotechnol Biofuels 10, 154. JBEI
201710.1039/c7gc01179bSun, J., N. V. S. N. M. Konda, R. Parthasarathi, T. Dutta, M. Valiev, F. Xu, B. A. Simmons, and S. Singh. 2017. One-pot integrated biofuel production using low-cost biocompatible protic ionic liquids, Green Chemistry 19(13), 3152-3163. JBEI
201710.1111/gcbb.12336Swinton, S. M., S. Tanner, B. L. Barham, D. F. Mooney, and T. Skevas. 2017. How willing are landowners to supply land for bioenergy crops in the Northern Great Lakes Region?, GCB Bioenergy 9(2), 414-428. GLBRC
201710.1111/tpj.13382Tartaglio, V., E. A. Rennie, R. Cahoon, G. Wang, E. Baidoo, J. C. Mortimer, E. B. Cahoon, and H. V. Scheller. 2017. Glycosylation of inositol phosphorylceramide sphingolipids is required for normal growth and reproduction in Arabidopsis, Plant J 89(2), 278-290. JBEI
201710.1002/bit.26374Thompson, R. A., and C. T. Trinh. 2017. Overflow metabolism and growth cessation in Clostridium thermocellum DSM1313 during high cellulose loading fermentations, Biotechnol Bioeng 114(11), 2592-2604. BESC
201710.1039/c7fd00158dTian, M., P. Kumar, S. T. P. Gupta, and J. L. Reed. 2017. Metabolic modeling for design of cell factories. In Systems Biology, 71-107 Eds. J. Nielsen, and S. Hohmann. Wiley-VCH Verlag GmbH & Co. KGaA.GLBRC
2017Tian, T., and T. S. Lee. 2017. Advanced Biodiesel and Biojet Fuels from Lignocellulosic Biomass. In Consequences of Microbial Interactions with Hydrocarbons, Oils, and Lipids: Production of Fuels and Chemicals, 1-25. Ed. S. Y. Lee. Cham: Springer International Publishing.JBEI
201710.1039/c7fd00158dTo, T. Q., K. Procter, B. A. Simmons, S. Subashchandrabose, and R. Atkin. 2017. Low cost ionic liquid-water mixtures for effective extraction of carbohydrate and lipid from algae, Faraday Discuss 206, 93-112. JBEI
201710.1016/j.fuel.2017.04.051To, T. Q., K. Shah, P. Tremain, B. A. Simmons, B. Moghtaderi, and R. Atkin. 2017. Treatment of lignite and thermal coal with low cost amino acid based ionic liquid-water mixtures, Fuel 202, 296-306. JBEI
201710.1002/cplu.201700138.Tolbert, A. K., C. G. Yoo, and A. J. Ragauskas. 2017. Understanding the Changes to Biomass Surface Characteristics after Ammonia and Organosolv Pretreatments by Using Time-of-Flight Secondary-Ion Mass Spectrometry (TOF-SIMS), ChemPlusChem 82(5), 686-690. BESC
201710.1021/acssuschemeng.6b01877Tolbert, A. K., J. M. Young, S. Jung, D. Chung, A. Passian, J. Westpheling, and A. J. Ragauskus. 2017. Surface Characterization of Populus during Caldicellulosiruptor bescii Growth by TOF-SIMS Analysis, ACS Sustainable Chemistry & Engineering 5(3), 2084-2089. BESC
201710.1002/ese3.144Tolbert, A., and A. J. Ragauskas. 2017. Advances in understanding the surface chemistry of lignocellulosic biomass via time-of-flight secondary ion mass spectrometry, Energy Science & Engineering 5(1), 5-20. BESC
201710.1007/s12155-017-9832-9Tornqvist, C.-E., B. Vaillancourt, J. Kim, C. R. Buell, S. M. Kaeppler, and M. D. Casler. 2017. Transcriptional Analysis of Flowering Time in Switchgrass, BioEnergy Research 10(3), 700-713. GLBRC
201710.1186/s13068-017-0751-yTran, T. N. T., R. J. Breuer, R. Avanasi Narasimhan, L. S. Parreiras, Y. Zhang, T. K. Sato, and T. P. Durrett. 2017. Metabolic engineering of Saccharomyces cerevisiae to produce a reduced viscosity oil from lignocellulose, Biotechnol Biofuels 10, 69. GLBRC
201710.3389/fpls.2017.00335Truong, S. K., R. F. McCormick, and J. E. Mullet. 2017. Bioenergy Sorghum Crop Model Predicts VPD-Limited Transpiration Traits Enhance Biomass Yield in Water-Limited Environments, Front Plant Sci 8, 335. GLBRC
201710.1371/journal.pone.0173094Tsai, A. Y., K. Chan, C. Y. Ho, T. Canam, R. Capron, E. R. Master, and K. Brautigam. 2017. Transgenic expression of fungal accessory hemicellulases in Arabidopsis thaliana triggers transcriptional patterns related to biotic stress and defense response, PLoS One 12(3), e0173094. JBEI
201710.1016/j.aca.2017.09.023Tuomivaara, S. T., P. Schliekelman, A. V. Nairn, K. W. Moremen, and W. S. York. 2017. RElative QUantitation Inferred by Evaluating Mixtures (REQUIEM), Anal Chim Acta 993, 22-37. BESC
201710.1111/pbi.12682Unda, F., H. Kim, C. Hefer, J. Ralph, and S. D. Mansfield. 2017. Altering carbon allocation in hybrid poplar (Populus alba x grandidentata) impacts cell wall growth and development, Plant Biotechnol J 15(7), 865-878. GLBRC
2017 10.1111/tpj.13628Urbanowicz, B. R., V. S. Bharadwaj, M. Alahuhta, M. J. Pena, V. V. Lunin, Y. J. Bomble, S. Wang, J. Y. Yang, S. T. Tuomivaara, M. E. Himmel, K. W. Moremen, W. S. York, and M. F. Crowley. 2017. Structural, mutagenic and in silico studies of xyloglucan fucosylation in Arabidopsis thaliana suggest a water-mediated mechanism, Plant J 91(6), 931-949. BESC
201710.3389/fmicb.2017.01272Utturkar, S. M., D. M. Klingeman, R. A. Hurt, Jr., and S. D. Brown. 2017. A Case Study into Microbial Genome Assembly Gap Sequences and Finishing Strategies, Front Microbiol 8, 1272. BESC
201710.1007/s12155-016-9810-7Valdez, Z. P., W. C. Hockaday, C. A. Masiello, M. E. Gallagher, and G. Philip Robertson. 2017. Soil Carbon and Nitrogen Responses to Nitrogen Fertilizer and Harvesting Rates in Switchgrass Cropping Systems, BioEnergy Research 10(2), 456-464. GLBRC
201710.1104/pp.17.00834Van Acker, R., A. Dejardin, S. Desmet, L. Hoengenaert, R. Vanholme, K. Morreel, F. Laurans, H. Kim, N. Santoro, C. Foster, G. Goeminne, F. Legee, C. Lapierre, G. Pilate, J. Ralph, and W. Boerjan. 2017. Different Routes for Conifer- and Sinapaldehyde and Higher Saccharification upon Deficiency in the Dehydrogenase CAD1, Plant Physiol 175(3), 1018-1039. .GLBRC
201710.1186/s13068-017-0917-7Verbeke, T. J., G. M. Garcia, and J. G. Elkins. 2017. The effect of switchgrass loadings on feedstock solubilization and biofuel production by Clostridium thermocellum, Biotechnol Biofuels 10, 233. BESC
201710.1038/srep43355Verbeke, T. J., R. J. Giannone, D. M. Klingeman, N. L. Engle, T. Rydzak, A. M. Guss, T. J. Tschaplinski, S. D. Brown, R. L. Hettich, and J. G. Elkins. 2017. Pentose sugars inhibit metabolism and increase expression of an AgrD-type cyclic pentapeptide in Clostridium thermocellum, Sci Rep 7, 43355. BESC
201710.3389/fpls.2017.01505Verhertbruggen, Y., J. L. Walker, F. Guillon, and H. V. Scheller. 2017. A Comparative Study of Sample Preparation for Staining and Immunodetection of Plant Cell Walls by Light Microscopy, Front Plant Sci 8, 1505. JBEI
201710.1002/wsbm.1391Voit, E. O. 2017. The best models of metabolism, Wiley Interdiscip Rev Syst Biol Med 9(6). BESC
201710.1186/s13068-017-0703-6Walker, J. A., S. Pattathil, L. F. Bergeman, E. T. Beebe, K. Deng, M. Mirzai, T. R. Northen, M. G. Hahn, and B. G. Fox. 2017. Determination of glycoside hydrolase specificities during hydrolysis of plant cell walls using glycome profiling, Biotechnol Biofuels 10, 31. GLBRC JBEI BESC
201710.1002/bit.26287.Wan, N., D. M. DeLorenzo, L. He, L. You, C. M. Immethun, G. Wang, E. E. K. Baidoo, W. Hollinshead, J. D. Keasling, T. S. Moon, and Y. J. Tang. 2017. Cyanobacterial carbon metabolism: Fluxome plasticity and oxygen dependence, Biotechnol Bioeng 114(7), 1593-1602. JBEI
201710.1105/tpc.17.00397Wang, K., J. E. Froehlich, A. Zienkiewicz, H. L. Hersh, and C. Benning. 2017. A Plastid Phosphatidylglycerol Lipase Contributes to the Export of Acyl Groups from Plastids for Seed Oil Biosynthesis, Plant Cell 29(7), 1678-1696. GLBRC
201710.1007/10_2016_46Weighill, D. A., and D. Jacobson. 2017. Network Metamodeling: Effect of Correlation Metric Choice on Phylogenomic and Transcriptomic Network Topology, Adv Biochem Eng Biotechnol 160, 143-183. BESC
201710.1107/S2053230X17004587Welner, D. H., A. Y. Tsai, A. M. DeGiovanni, H. V. Scheller, and P. D. Adams. 2017. X-ray diffraction analysis and in vitro characterization of the UAM2 protein from Oryza sativa, Acta Crystallogr F Struct Biol Commun 73(Pt 4), 241-245. JBEI
201710.1371/journal.pone.0177591Welner, D. H., D. Shin, G. P. Tomaleri, A. M. DeGiovanni, A. Y. Tsai, H. M. Tran, S. F. Hansen, D. T. Green, H. V. Scheller, and P. D. Adams. 2017. Plant cell wall glycosyltransferases: High-throughput recombinant expression screening and general requirements for these challenging enzymes, PLoS One 12(6), e0177591. JBEI
201710.1128/AEM.00444-17Williams-Rhaesa, A. M., F. L. Poole, 2nd, J. T. Dinsmore, G. L. Lipscomb, G. M. Rubinstein, I. M. Scott, J. M. Conway, L. L. Lee, P. A. Khatibi, R. M. Kelly, and M. W. W. Adams. 2017. Genome Stability in Engineered Strains of the Extremely Thermophilic Lignocellulose-Degrading Bacterium Caldicellulosiruptor bescii, Appl Environ Microbiol 83(14). BESC
201710.1186/s13068-017-0918-6Willis, J. D., J. N. Grant, M. Mazarei, L. M. Kline, C. S. Rempe, A. G. Collins, G. B. Turner, S. R. Decker, R. W. Sykes, M. F. Davis, N. Labbe, J. L. Jurat-Fuentes, and C. N. Stewart. 2017. The TcEG1 beetle (Tribolium castaneum) cellulase produced in transgenic switchgrass is active at alkaline pH and auto-hydrolyzes biomass for increased cellobiose release, Biotechnology for Biofuels 10(1), 230. BESC
201710.1128/AEM.02751-16Wilson, C. M., D. M. Klingeman, C. Schlachter, M. H. Syed, C. W. Wu, A. M. Guss, and S. D. Brown. 2017. LacI Transcriptional Regulatory Networks in Clostridium thermocellum DSM1313, Appl Environ Microbiol 83(5). BESC
201710.1039/c6re00227gWon, W., A. H. Motagamwala, J. A. Dumesic, and C. T. Maravelias. 2017. A co-solvent hydrolysis strategy for the production of biofuels: process synthesis and technoeconomic analysis, Reaction Chemistry & Engineering 2(3), 397-405. GLBRC
2017Wong, J., L. Rios-Solis, and J. D. Keasling. 2017. Microbial Production of Isoprenoids. In Consequences of Microbial Interactions with Hydrocarbons, Oils, and Lipids: Production of Fuels and Chemicals, 1-24. Ed. S. Y. Lee. Cham: Springer International Publishing.JBEI
201710.1128/genomeA.00300-17Woo, H. L., K. M. DeAngelis, H. Teshima, K. Davenport, H. Daligault, T. Erkkila, L. Goodwin, W. Gu, C. C. Lo, C. Munk, M. Scholz, Y. Xu, P. Chain, D. Bruce, C. Detter, R. Tapia, C. Han, B. A. Simmons, and T. C. Hazen. 2017. High-Quality Draft Genome Sequences of Four Lignocellulose-Degrading Bacteria Isolated from Puerto Rican Forest Soil: Gordonia sp., Paenibacillus sp., Variovorax sp., and Vogesella sp, Genome Announc 5(18). JBEI
201710.1104/pp.16.01178Woods, D. P., R. Bednarek, F. Bouche, S. P. Gordon, J. P. Vogel, D. F. Garvin, and R. M. Amasino. 2017. Genetic Architecture of Flowering-Time Variation in Brachypodium distachyon, Plant Physiol 173(1), 269-279. GLBRC
201710.1073/pnas.1700536114Woods, D. P., T. S. Ream, F. Bouche, J. Lee, N. Thrower, C. Wilkerson, and R. M. Amasino. 2017. Establishment of a vernalization requirement in Brachypodium distachyon requires REPRESSOR OF VERNALIZATION1, Proc Natl Acad Sci U S A 114(25), 6623-6628. GLBRC
201710.1038/s41598-017-02628-wWu, C. W., T. Spike, D. M. Klingeman, M. Rodriguez, V. R. Bremer, and S. D. Brown. 2017. Generation and Characterization of Acid Tolerant Fibrobacter succinogenes S85, Sci Rep 7(1), 2277. BESC
201710.1016/j.compchemeng.2016.10.007Wu, W., K. Yenkie, and C. T. Maravelias. 2017. A superstructure-based framework for bio-separation network synthesis, Computers & Chemical Engineering 96, 1-17. GLBRC
201710.1038/s41598-017-07895-1.Wu, W., T. Dutta, A. M. Varman, A. Eudes, B. Manalansan, D. Loque, and S. Singh. 2017. Lignin Valorization: Two Hybrid Biochemical Routes for the Conversion of Polymeric Lignin into Value-added Chemicals, Sci Rep 7(1), 8420. JBEI
2017 10.1021/acschembio.7b00388Wyche, T. P., R. F. R. Alvarenga, J. S. Piotrowski, M. N. Duster, S. R. Warrack, G. Cornilescu, T. J. De Wolfe, Y. Hou, D. R. Braun, G. A. Ellis, S. W. Simpkins, J. Nelson, C. L. Myers, J. Steele, H. Mori, N. Safdar, J. L. Markley, S. R. Rajski, and T. S. Bugni. 2017. Chemical Genomics, Structure Elucidation, and in Vivo Studies of the Marine-Derived Anticlostridial Ecteinamycin, ACS Chem Biol 12(9), 2287-2295. GLBRC
2017Wyman, C. E., and B. Yang. 2017. Combined Severity Factor for Predicting Sugar Recovery in Acid-Catalyzed Pretreatment Followed by Enzymatic Hydrolysis. In Hydrothermal Processing in Biorefinery, 161-180. Eds. H. Ruiz, M. Hedegaard Thomsen, and H. Trajano.BESC
2017Wyman, C. E., C. M. Cai, and R. Kumar. 2017. Ethanol from cellulosic biomass. In Encyclopedia of Sustainability Science and Technology. Ed. R. A. Meyers.BESC
2017 10.1104/pp.16.00095Xu, D., J. Shi, C. Rautengarten, L. Yang, X. Qian, M. Uzair, L. Zhu, Q. Luo, G. An, F. Wassmann, L. Schreiber, J. L. Heazlewood, H. V. Scheller, J. Hu, D. Zhang, and W. Liang. 2017. Defective Pollen Wall 2 (DPW2) Encodes an Acyl Transferase Required for Rice Pollen Development, Plant Physiol 173(1), 240-255. 10.1104/pp.16.00095.JBEI
201710.1186/s13068-017-0927-5Yaegashi, J., J. Kirby, M. Ito, J. Sun, T. Dutta, M. Mirsiaghi, E. R. Sundstrom, A. Rodriguez, E. Baidoo, D. Tanjore, T. Pray, K. Sale, S. Singh, J. D. Keasling, B. A. Simmons, S. W. Singer, J. K. Magnuson, A. P. Arkin, J. M. Skerker, and J. M. Gladden. 2017. Rhodosporidium toruloides: a new platform organism for conversion of lignocellulose into terpene biofuels and bioproducts, Biotechnol Biofuels 10, 241. JBEI
201710.1002/ehs2.1259Yang, Q., X. Zhang, M. Abraha, S. Del grosso, G. P. Robertson, and J. Chen. 2017. Enhancing the soil and water assessment tool model for simulating N2O emissions of three agricultural systems, Ecosystem Health and Sustainability 3(2), e01259. GLBRC
201710.1105/tpc.17.00182Yang, Y., A. Zienkiewicz, A. Lavell, and C. Benning. 2017. Coevolution of Domain Interactions in the Chloroplast TGD1, 2, 3 Lipid Transfer Complex Specific to Brassicaceae and Poaceae Plants, Plant Cell 29(6), 1500-1515. GLBRC
201710.1186/s13068-017-0760-xYang, Y., C. G. Yoo, H. B. Guo, W. Rottmann, K. A. Winkeler, C. M. Collins, L. E. Gunter, S. S. Jawdy, X. Yang, H. Guo, Y. Pu, A. J. Ragauskas, G. A. Tuskan, and J. G. Chen. 2017. Overexpression of a Domain of Unknown Function 266-containing protein results in high cellulose content, reduced recalcitrance, and enhanced plant growth in the bioenergy crop Populus, Biotechnol Biofuels 10, 74. BESC
201710.1186/s13068-017-0804-2Yenkie, K. M., W. Wu, and C. T. Maravelias. 2017. Synthesis and analysis of separation networks for the recovery of intracellular chemicals generated from microbial-based conversions, Biotechnol Biofuels 10, 119. GLBRC
201710.1126/sciadv.aao6741Yeung, L. Y., S. Li, I. E. Kohl, J. A. Haslun, N. E. Ostrom, H. Hu, T. P. Fischer, E. A. Schauble, and E. D. Young. 2017. Extreme enrichment in atmospheric (15)N(15)N, Sci Adv 3(11), eaao6741. GLBRC
201710.1039/c6gc03627aYoo, C. G., M. Li, X. Meng, Y. Pu, and A. J. Ragauskas. 2017. Effects of organosolv and ammonia pretreatments on lignin properties and its inhibition for enzymatic hydrolysis, Green Chemistry 19(8), 2006-2016. .BESC
201710.1016/j.cogsc.2017.03.003.Yoo, C. G., Y. Pu, and A. J. Ragauskas. 2017. Ionic liquids: Promising green solvents for lignocellulosic biomass utilization, Current Opinion in Green and Sustainable Chemistry 5, 5-11. BESC
201710.1039/c7gc02219kYoo, C. G., Y. Yang, Y. Pu, X. Meng, W. Muchero, K. L. Yee, O. A. Thompson, M. Rodriguez, G. Bali, N. L. Engle, E. Lindquist, V. Singan, J. Schmutz, S. P. DiFazio, T. J. Tschaplinski, G. A. Tuskan, J.-G. Chen, B. Davison, and A. J. Ragauskas. 2017. Insights of biomass recalcitrance in natural Populus trichocarpa variants for biomass conversion, Green Chemistry 19(22), 5467-5478. BESC
2017York, W. S., M. Allahyari, and D. Hogan. 2017. NMR Databases for Plant Cell Wall Biopolymers. In NMR in Glycoscience and Glycotechnology. Eds. K. Kato, and T. Peters. Royal Society of Chemistry.BESC
201710.1016/j.procbio.2016.11.002Yu, C., D. R. Harrold, J. T. Claypool, B. A. Simmons, S. W. Singer, C. W. Simmons, and J. S. VanderGheynst. 2017. Nitrogen amendment of green waste impacts microbial community, enzyme secretion and potential for lignocellulose decomposition, Process Biochemistry 52, 214-222. JBEI
201710.1021/acs.energyfuels.7b01567Yuan, X., L. He, S. Singh, B. A. Simmons, and G. Cheng. 2017. Effect of Ionic Liquid Pretreatment on the Porosity of Pine: Insights from Small-Angle Neutron Scattering, Nitrogen Adsorption Analysis, and X-ray Diffraction, Energy & Fuels 31(10), 10874-10879. JBEI
201710.1021/acssuschemeng.7b00480.Yuan, X., S. Singh, B. A. Simmons, and G. Cheng. 2017. Biomass Pretreatment Using Dilute Aqueous Ionic Liquid (IL) Solutions with Dynamically Varying IL Concentration and Its Impact on IL Recycling, ACS Sustainable Chemistry & Engineering 5(5), 4408-4413. JBEI
201710.1016/j.biortech.2017.02.014Yuan, X., Y. Duan, L. He, S. Singh, B. Simmons, and G. Cheng. 2017. Characterization of white poplar and eucalyptus after ionic liquid pretreatment as a function of biomass loading using X-ray diffraction and small angle neutron scattering, Bioresour Technol 232, 113-118. JBEI
201710.1002/cssc.201700101Yue, F., F. Lu, M. Regner, R. Sun, and J. Ralph. 2017. Lignin-Derived Thioacidolysis Dimers: Reevaluation, New Products, Authentication, and Quantification, ChemSusChem 10(5), 830-835. GLBRC
201710.1016/j.indcrop.2017.03.045Yue, F., R. Gao, J. S. Piotrowski, M. Kabbage, F. Lu, and J. Ralph. 2017. Scaled-up production of poacic acid, a plant-derived antifungal agent, Industrial Crops and Products 103, 240-243. GLBRC
201710.1021/acschembio.7b00714Yuzawa, S., C. B. Bailey, T. Fujii, R. Jocic, J. F. Barajas, V. T. Benites, E. E. K. Baidoo, Y. Chen, C. J. Petzold, L. Katz, and J. D. Keasling. 2017. Heterologous Gene Expression of N-Terminally Truncated Variants of LipPks1 Suggests a Functionally Critical Structural Motif in the N-terminus of Modular Polyketide Synthase, ACS Chem Biol 12(11), 2725-2729. JBEI
201710.1038/ja.2016.136Yuzawa, S., J. D. Keasling, and L. Katz. 2017. Bio-based production of fuels and industrial chemicals by repurposing antibiotic-producing type I modular polyketide synthases: opportunities and challenges, J Antibiot (Tokyo) 70(4), 378-385. JBEI
201710.1021/acssynbio.6b00176Yuzawa, S., K. Deng, G. Wang, E. E. Baidoo, T. R. Northen, P. D. Adams, L. Katz, and J. D. Keasling. 2017. Comprehensive in Vitro Analysis of Acyltransferase Domain Exchanges in Modular Polyketide Synthases and Its Application for Short-Chain Ketone Production, ACS Synth Biol 6(1), 139-147. JBEI
2017 10.1016/j.copbio.2017.03.004Zargar, A., C. B. Bailey, R. W. Haushalter, C. B. Eiben, L. Katz, and J. D. Keasling. 2017. Leveraging microbial biosynthetic pathways for the generation of 'drop-in' biofuels, Curr Opin Biotechnol 45, 156-163. JBEI
201710.1039/c6gc03379bZeng, J., M. J. L. Mills, B. A. Simmons, M. S. Kent, and K. L. Sale. 2017. Understanding factors controlling depolymerization and polymerization in catalytic degradation of ß-ether linked model lignin compounds by versatile peroxidase, Green Chemistry 19(9), 2145-2154. JBEI
2017Zeng, W., B. Ebert, H. T. Parsons, C. Rautengarten, A. Bacic, and J. L. Heazlewood. 2017. Enrichment of Golgi Membranes from Triticum aestivum (Wheat) Seedlings. In Isolation of Plant Organelles and Structures: Methods and Protocols, 131-150. Eds. N. L. Taylor, and A. H. Millar. Springer New York.JBEI
201710.1186/s13068-017-0953-3Zeng, Y., M. E. Himmel, and S. Y. Ding. 2017. Visualizing chemical functionality in plant cell walls, Biotechnol Biofuels 10, 263. GLBRC
201710.1016/j.soilbio.2017.04.019Zhang, B., C. R. Penton, C. Xue, J. F. Quensen, S. S. Roley, J. Guo, A. Garoutte, T. Zheng, and J. M. Tiedje. 2017. Soil depth and crop determinants of bacterial communities under ten biofuel cropping systems, Soil Biology and Biochemistry 112, 140-152. GLBRC
201710.1021/acssuschemeng.7b03084Zhang, J., C. Lei, G. Liu, Y. Bao, V. Balan, and J. Bao. 2017. In-Situ Vacuum Distillation of Ethanol Helps To Recycle Cellulase and Yeast during SSF of Delignified Corncob Residues, ACS Sustainable Chemistry & Engineering 5(12), 11676-11685. GLBRC
201710.1021/acssynbio.6b00372Zhang, J., J. F. Barajas, M. Burdu, G. Wang, E. E. Baidoo, and J. D. Keasling. 2017. Application of an Acyl-CoA Ligase from Streptomyces aizunensis for Lactam Biosynthesis, ACS Synth Biol 6(5), 884-890. JBEI
201710.1039/c7gc00944eZhao, W., L.-P. Xiao, G. Song, R.-C. Sun, L. He, S. Singh, B. A. Simmons, and G. Cheng. 2017. From lignin subunits to aggregates: insights into lignin solubilization, Green Chemistry 19(14), 3272-3281. JBEI
201710.1186/s13068-017-0898-6Zhivin, O., B. Dassa, S. Morais, S. M. Utturkar, S. D. Brown, B. Henrissat, R. Lamed, and E. A. Bayer. 2017. Unique organization and unprecedented diversity of the Bacteroides (Pseudobacteroides) cellulosolvens cellulosome system, Biotechnol Biofuels 10, 211. BESC
201710.1007/s10295-016-1896-6Zhou, J., X. Shao, D. G. Olson, S. J. Murphy, L. Tian, and L. R. Lynd. 2017. Determining the roles of the three alcohol dehydrogenases (AdhA, AdhB and AdhE) in Thermoanaerobacter ethanolicus during ethanol formation, J Ind Microbiol Biotechnol 44(4-5), 745-757. BESC
201710.1002/cssc.201701317Zhou, S., T. Runge, S. D. Karlen, J. Ralph, E. Gonzales-Vigil, and S. D. Mansfield. 2017. Chemical Pulping Advantages of Zip-lignin Hybrid Poplar, ChemSusChem 10(18), 3565-3573. GLBRC
201710.1186/s13068-016-0686-8Zienkiewicz, K., A. Zienkiewicz, E. Poliner, Z. Y. Du, K. Vollheyde, C. Herrfurth, S. Marmon, E. M. Farre, I. Feussner, and C. Benning. 2017. Nannochloropsis, a rich source of diacylglycerol acyltransferases for engineering of triacylglycerol content in different hosts, Biotechnol Biofuels 10, 8. GLBRC
201710.1128/AEM.00969-17Zurawski, J. V., P. A. Khatibi, H. O. Akinosho, C. T. Straub, S. H. Compton, J. M. Conway, L. L. Lee, A. J. Ragauskas, B. H. Davison, M. W. W. Adams, and R. M. Kelly. 2017. Bioavailability of Carbohydrate Content in Natural and Transgenic Switchgrasses for the Extreme Thermophile Caldicellulosiruptor bescii, Appl Environ Microbiol 83(17). BESC
201610.1007/s10021-016-9981-2Abraha, M., I. Gelfand, S. K. Hamilton, C. Shao, Y.-J. Su, G. P. Robertson, and J. Chen. 2016. Ecosystem Water-Use Efficiency of Annual Corn and Perennial Grasslands: Contributions from Land-Use History and Species Composition, Ecosystems 19(6), 1001-1012. GLBRC
201610.7726/ajbb.2016.1008Adkins, A., and K. Thelen. 2016. Switchgrass Ash Content Response to Harvest Timing and Two Harvest/Storage Methods of a Bioenergy Cropping System in the Great Lakes Region, American Journal of Biomass and Bioenergy. GLBRC
201610.1016/j.fgb.2015.11.002Alexander, W. G., D. Peris, B. T. Pfannenstiel, D. A. Opulente, M. Kuang, and C. T. Hittinger. 2016. Efficient engineering of marker-free synthetic allotetraploids of Saccharomyces, Fungal Genet Biol 89, 10-17. GLBRC
201610.1073/pnas.1517242113Alexander, W. G., J. H. Wisecaver, A. Rokas, and C. T. Hittinger. 2016. Horizontally acquired genes in early-diverging pathogenic fungi enable the use of host nucleosides and nucleotides, Proc Natl Acad Sci U S A 113(15), 4116-4121. GLBRC
201610.1016/j.cub.2016.08.021Amsbury, S., L. Hunt, N. Elhaddad, A. Baillie, M. Lundgren, Y. Verhertbruggen, H. V. Scheller, J. P. Knox, A. J. Fleming, and J. E. Gray. 2016. Stomatal Function Requires Pectin De-methyl-esterification of the Guard Cell Wall, Curr Biol 26(21), 2899-2906. JBEI
201610.1038/nenergy.2015.20Armstrong, R. C., C. Wolfram, K. P. de Jong, R. Gross, N. S. Lewis, B. Boardman, A. J. Ragauskas, K. Ehrhardt-Martinez, G. Crabtree, and M. V. Ramana. 2016. Deconstructing Biomass [part of The frontiers of energy], Nature Energy 1(1), 15020. BESC
201610.1038/nature18008Badalyan, A., and S. S. Stahl. 2016. Cooperative electrocatalytic alcohol oxidation with electron-proton-transfer mediators, Nature 535(7612), 406-410. GLBRC
201610.1098/rsos.150677Bahlai, C. A., and D. A. Landis. 2016. Predicting plant attractiveness to pollinators with passive crowdsourcing, R Soc Open Sci 3(6), 150677. GLBRC
201610.1016/j.biombioe.2016.08.013Bali, G., R. Khunsupat, H. Akinosho, R. S. Payyavula, R. Samuel, G. A. Tuskan, U. C. Kalluri, and A. J. Ragauskas. 2016. Characterization of cellulose structure of Populus plants modified in candidate cellulose biosynthesis genes, Biomass and Bioenergy 94, 146-154. BESC
201610.1039/c5gc01748cBansal, N., A. Bhalla, S. Pattathil, S. L. Adelman, M. G. Hahn, D. B. Hodge, and E. L. Hegg. 2016. Cell wall-associated transition metals improve alkaline-oxidative pretreatment in diverse hardwoods, Green Chemistry 18(5), 1405-1415. BESC
2016Barham, B. L., D. F. Mooney, and S. M. Swinton. 2016: Inconvenient truths about landowner (Un)willingness to grow dedicated bioenergy crops. Choices, 4 ed., Agricultural and Applied Economics Association.GLBRC
201610.1038/nplants.2016.50Barros, J., J. C. Serrani-Yarce, F. Chen, D. Baxter, B. J. Venables, and R. A. Dixon. 2016. Role of bifunctional ammonia-lyase in grass cell wall biosynthesis, Nat Plants 2(6), 16050. BESC
201610.1007/s10681-016-1632-3Baxter, H. L., L. W. Alexander, M. Mazarei, E. Haynes, G. B. Turner, R. W. Sykes, S. R. Decker, M. F. Davis, R. A. Dixon, Z.-Y. Wang, and C. Neal Stewart. 2016. Hybridization of downregulated-COMT transgenic switchgrass lines with field-selected switchgrass for improved biomass traits, Euphytica 209(2), 341-355. BESC
201610.1007/s12155-016-9751-1Baxter, H. L., M. Mazarei, C. Fu, Q. Cheng, G. B. Turner, R. W. Sykes, M. T. Windham, M. F. Davis, R. A. Dixon, Z.-Y. Wang, and C. N. Stewart. 2016. Time Course Field Analysis of COMT-Downregulated Switchgrass: Lignification, Recalcitrance, and Rust Susceptibility, BioEnergy Research 9(4), 1087-1100. BESC
201610.1016/j.copbio.2016.02.030Beckham, G. T., C. W. Johnson, E. M. Karp, D. Salvachua, and D. R. Vardon. 2016. Opportunities and challenges in biological lignin valorization, Curr Opin Biotechnol 42, 40-53. BESC
201610.1016/j.meteno.2016.07.001Beller, H. R., P. Zhou, T. N. M. Jewell, E. B. Goh, and J. D. Keasling. 2016. Enhanced fatty acid production in engineered chemolithoautotrophic bacteria using reduced sulfur compounds as energy sources, Metab Eng Commun 3, 211-215. JBEI
201610.1186/s12864-016-3244-7Bellora, N., M. Moline, M. David-Palma, M. A. Coelho, C. T. Hittinger, J. P. Sampaio, P. Goncalves, and D. Libkind. 2016. Comparative genomics provides new insights into the diversity, physiology, and sexuality of the only industrially exploited tremellomycete: Phaffia rhodozyma, BMC Genomics 17(1), 901. GLBRC
201610.1093/femsle/fnw091Beri, D., D. G. Olson, E. K. Holwerda, and L. R. Lynd. 2016. Nicotinamide cofactor ratios in engineered strains of Clostridium thermocellum and Thermoanaerobacterium saccharolyticum, FEMS Microbiol Lett 363(11). BESC
201610.1186/s13068-016-0683-yBewg, W. P., C. Poovaiah, W. Lan, J. Ralph, and H. D. Coleman. 2016. RNAi downregulation of three key lignin genes in sugarcane improves glucose release without reduction in sugar production, Biotechnol Biofuels 9, 270. GLBRC
201610.1016/j.biortech.2016.04.138Bhagia, S., A. Nunez, C. E. Wyman, and R. Kumar. 2016. Robustness of two-step acid hydrolysis procedure for composition analysis of poplar, Bioresour Technol 216, 1077-1082. BESC
201610.1186/s13068-016-0660-5Bhagia, S., H. Li, X. Gao, R. Kumar, and C. E. Wyman. 2016. Flowthrough pretreatment with very dilute acid provides insights into high lignin contribution to biomass recalcitrance, Biotechnol Biofuels 9, 245. BESC
201610.1186/s13068-016-0521-2Bhagia, S., W. Muchero, R. Kumar, G. A. Tuskan, and C. E. Wyman. 2016. Natural genetic variability reduces recalcitrance in poplar, Biotechnol Biofuels 9, 106. 10.1186/s13068-016-0521-2.BESC
201610.1186/s13068-016-0442-0Bhalla, A., N. Bansal, R. J. Stoklosa, M. Fountain, J. Ralph, D. B. Hodge, and E. L. Hegg. 2016. Effective alkaline metal-catalyzed oxidative delignification of hybrid poplar, Biotechnol Biofuels 9, 34. GLBRC
201610.1371/journal.pbio.1002475Book, A. J., G. R. Lewin, B. R. McDonald, T. E. Takasuka, E. Wendt-Pienkowski, D. T. Doering, S. Suh, K. F. Raffa, B. G. Fox, and C. R. Currie. 2016. Evolution of High Cellulolytic Activity in Symbiotic Streptomyces through Selection of Expanded Gene Content and Coordinated Gene Expression, PLoS Biol 14(6), e1002475. .GLBRC
201610.1126/science.aad8865Boyken, S. E., Z. Chen, B. Groves, R. A. Langan, G. Oberdorfer, A. Ford, J. M. Gilmore, C. Xu, F. DiMaio, J. H. Pereira, B. Sankaran, G. Seelig, P. H. Zwart, and D. Baker. 2016. De novo design of protein homo-oligomers with modular hydrogen-bond network-mediated specificity, Science 352(6286), 680-687. JBEI
201610.1021/acssynbio.6b00115Brown, M. E., A. Mukhopadhyay, and J. D. Keasling. 2016. Engineering Bacteria to Catabolize the Carbonaceous Component of Sarin: Teaching E. coli to Eat Isopropanol, ACS Synth Biol 5(12), 1485-1496. JBEI
201610.3389/fmicb.2016.01979Brumm, P. J., K. Gowda, F. T. Robb, and D. A. Mead. 2016. The Complete Genome Sequence of Hyperthermophile Dictyoglomus turgidum DSM 6724 Reveals a Specialized Carbohydrate Fermentor, Front Microbiol 7, 1979. GLBRC
201610.1016/j.cels.2016.04.004Brunk, E., K. W. George, J. Alonso-Gutierrez, M. Thompson, E. Baidoo, G. Wang, C. J. Petzold, D. McCloskey, J. Monk, L. Yang, E. J. O'Brien, T. S. Batth, H. G. Martin, A. Feist, P. D. Adams, J. D. Keasling, B. O. Palsson, and T. S. Lee. 2016. Characterizing Strain Variation in Engineered E. coli Using a Multi-Omics-Based Workflow, Cell Syst 2(5), 335-346. JBEI
201610.1111/pbi.12560Bryan, A. C., S. Jawdy, L. Gunter, E. Gjersing, R. Sykes, M. A. Hinchee, K. A. Winkeler, C. M. Collins, N. Engle, T. J. Tschaplinski, X. Yang, G. A. Tuskan, W. Muchero, and J. G. Chen. 2016. Knockdown of a laccase in Populus deltoides confers altered cell wall chemistry and increased sugar release, Plant Biotechnol J 14(10), 2010-2020. BESC
2016C., C., and J. L. Reed. 2016. Applications of constraint-based models for biochemical production. In Biotechnology for Biofuel Production and Optimization, 201-226. Elsevier.GLBRC
201610.1038/ncomms11989Cai, Y., K. Zhang, H. Kim, G. Hou, X. Zhang, H. Yang, H. Feng, L. Miller, J. Ralph, and C. J. Liu. 2016. Enhancing digestibility and ethanol yield of Populus wood via expression of an engineered monolignol 4-O-methyltransferase, Nat Commun 7, 11989. GLBRC
201610.3389/fpls.2016.00708Cass, C. L., A. A. Lavell, N. Santoro, C. E. Foster, S. D. Karlen, R. A. Smith, J. Ralph, D. F. Garvin, and J. C. Sedbrook. 2016. Cell Wall Composition and Biomass Recalcitrance Differences Within a Genotypically Diverse Set of Brachypodium distachyon Inbred Lines, Front Plant Sci 7, 708. GLBRC
201610.1007/s00253-015-7025-zCha, M., D. Chung, and J. Westpheling. 2016. Deletion of a gene cluster for [Ni-Fe] hydrogenase maturation in the anaerobic hyperthermophilic bacterium Caldicellulosiruptor bescii identifies its role in hydrogen metabolism, Appl Microbiol Biotechnol 100(4), 1823-1831. BESC
201610.1073/pnas.1601256113.Chai, M., C. Zhou, I. Molina, C. Fu, J. Nakashima, G. Li, W. Zhang, J. Park, Y. Tang, Q. Jiang, and Z. Y. Wang. 2016. A class II KNOX gene, KNOX4, controls seed physical dormancy, Proc Natl Acad Sci U S A 113(25), 6997-7002. BESC
201610.1186/s12284-016-0106-5Chandran, A. K. N., Y. H. Yoo, P. Cao, R. Sharma, M. Sharma, C. Dardick, P. C. Ronald, and K. H. Jung. 2016. Updated Rice Kinase Database RKD 2.0: enabling transcriptome and functional analysis of rice kinase genes, Rice (N Y) 9(1), 40. JBEI
201610.1002/prot.24965Chen, M., L. Bu, M. Alahuhta, R. Brunecky, Q. Xu, V. V. Lunin, J. W. Brady, M. F. Crowley, M. E. Himmel, and Y. J. Bomble. 2016. Strategies to reduce end-product inhibition in family 48 glycoside hydrolases, Proteins 84(3), 295-304. BESC
201610.1002/bit.25909Chen, M., M. E. Himmel, D. B. Wilson, and J. W. Brady. 2016. Simulation studies of substrate recognition by the exocellulase CelF from Clostridium cellulolyticum, Biotechnol Bioeng 113(7), 1433-1440. BESC
201610.1371/journal.pone.0167005Chen, S., S. M. Kaeppler, K. P. Vogel, and M. D. Casler. 2016. Selection Signatures in Four Lignin Genes from Switchgrass Populations Divergently Selected for In Vitro Dry Matter Digestibility, PLoS One 11(11), e0167005. GLBRC
201610.1039/c5gc02286jChen, W., D. J. McClelland, A. Azarpira, J. Ralph, Z. Luo, and G. W. Huber. 2016. Low temperature hydrogenation of pyrolytic lignin over Ru/TiO2: 2D HSQC and 13C NMR study of reactants and products, Green Chemistry 18(1), 271-281. GLBRC
201610.1371/journal.pgen.1006049Chern, M., Q. Xu, R. S. Bart, W. Bai, D. Ruan, W. H. Sze-To, P. E. Canlas, R. Jain, X. Chen, and P. C. Ronald. 2016. A Genetic Screen Identifies a Requirement for Cysteine-Rich-Receptor-Like Kinases in Rice NH1 (OsNPR1)-Mediated Immunity, PLoS Genet 12(5), e1006049. JBEI
201610.1038/npjsba.2016.9Chubukov, V., A. Mukhopadhyay, C. J. Petzold, J. D. Keasling, and H. G. Martin. 2016. Synthetic and systems biology for microbial production of commodity chemicals, NPJ Syst Biol Appl 2, 16009. JBEI
2016Chuck, C. J., M. McManus, M. J. Allen, and S. Singh. 2016. Feedstocks for Aviation Biofuels. In Biofuels for Aviation: Feedstocks, Technology and Implementation, 17-34. Ed. C. J. Chuck. Academic Press.JBEI
201610.1039/c6re00172fChundawat, S. P. S., C. D. Paavola, B. Raman, M. Nouailler, S. L. Chan, J. R. Mielenz, V. Receveur-Brechot, J. D. Trent, and B. E. Dale. 2016. Saccharification of thermochemically pretreated cellulosic biomass using native and engineered cellulosomal enzyme systems, Reaction Chemistry & Engineering 1(6), 616-628. GLBRC BESC
201610.2134/jeq2015.07.0377Collier, S. M., A. P. Dean, L. G. Oates, M. D. Ruark, and R. D. Jackson. 2016. Does Plant Biomass Manipulation in Static Chambers Affect Nitrous Oxide Emissions from Soils?, J Environ Qual 45(2), 751-756. GLBRC
201610.1074/jbc.M115.707810Conway, J. M., W. S. Pierce, J. H. Le, G. W. Harper, J. H. Wright, A. L. Tucker, J. V. Zurawski, L. L. Lee, S. E. Blumer-Schuette, and R. M. Kelly. 2016. Multidomain, Surface Layer-associated Glycoside Hydrolases Contribute to Plant Polysaccharide Degradation by Caldicellulosiruptor Species, J Biol Chem 291(13), 6732-6747. BESC
201610.1021/acs.biochem.5b01044Cornish, A. J., B. Ginovska, A. Thelen, J. C. da Silva, T. A. Soares, S. Raugei, M. Dupuis, W. J. Shaw, and E. L. Hegg. 2016. Single-Amino Acid Modifications Reveal Additional Controls on the Proton Pathway of [FeFe]-Hydrogenase, Biochemistry 55(22), 3165-3173. GLBRC
201610.1002/slct.201600733Corno, L., R. Pilu, K. Tran?, F. Tambone, S. Singh?, B. A. Simmons?, and F. Adani. 2016. Sugars Production for Green Chemistry from 2nd Generation Crop (Arundo donax L.): A Full Field Approach, ChemistrySelect 1(11), 2617-2623. JBEI
201610.1186/s13068-016-0513-2Costa, T. H., M. E. Vega-Sanchez, A. M. Milagres, H. V. Scheller, and A. Ferraz. 2016. Tissue-specific distribution of hemicelluloses in six different sugarcane hybrids as related to cell wall recalcitrance, Biotechnol Biofuels 9, 99. JBEI
201610.1007/s12155-016-9774-7Cronin, K. R., T. M. Runge, X. Zhang, R. C. Izaurralde, D. J. Reinemann, and J. C. Sinistore. 2016. Spatially Explicit Life Cycle Analysis of Cellulosic Ethanol Production Scenarios in Southwestern Michigan, BioEnergy Research 10(1), 13-25. GLBRC
201610.1016/j.geoderma.2016.07.020Cui, L., C. Liang, D. S. Duncan, X. Bao, H. Xie, H. He, K. Wickings, X. Zhang, and F. Chen. 2016. Impacts of vegetation type and climatic zone on neutral sugar distribution in natural forest soils, Geoderma 282, 139-146. GLBRC
201610.1039/c6gc00298fda Costa Sousa, L., M. Foston, V. Bokade, A. Azarpira, F. Lu, A. J. Ragauskas, J. Ralph, B. Dale, and V. Balan. 2016. Isolation and characterization of new lignin streams derived from extractive-ammonia (EA) pretreatment, Green Chemistry 18(15), 4205-4215. BESC GLBRC
201610.1039/c5ee03051jda Costa Sousa, L., M. Jin, S. P. S. Chundawat, V. Bokade, X. Tang, A. Azarpira, F. Lu, U. Avci, J. Humpula, N. Uppugundla, C. Gunawan, S. Pattathil, A. M. Cheh, N. Kothari, R. Kumar, J. Ralph, M. G. Hahn, C. E. Wyman, S. Singh, B. A. Simmons, B. E. Dale, and V. Balan. 2016. Next-generation ammonia pretreatment enhances cellulosic biofuel production, Energy & Environmental Science 9(4), 1215-1223. GLBRC
201610.1039/c5ee03051jda Costa Sousa, L., M. Jin, S. P. S. Chundawat, V. Bokade, X. Tang, A. Azarpira, F. Lu, U. Avci, J. Humpula, N. Uppugundla, C. Gunawan, S. Pattathil, A. M. Cheh, N. Kothari, R. Kumar, J. Ralph, M. G. Hahn, C. E. Wyman, S. Singh, B. A. Simmons, B. E. Dale, and V. Balan. 2016. Next-generation ammonia pretreatment enhances cellulosic biofuel production, Energy & Environmental Science 9(4), 1215-1223. JBEI GLBRC BESC
2016Davison, B. H., and J. Lievense. 2016: Commercializing Industrial Biotechnology - Technology Challenges and Opportunities. Chemical Engineering Progress, 35.BESC
201610.1021/acs.jproteome.5b00876de Michele, R., H. E. McFarlane, H. T. Parsons, M. J. Meents, J. Lao, S. M. Gonzalez Fernandez-Nino, C. J. Petzold, W. B. Frommer, A. L. Samuels, and J. L. Heazlewood. 2016. Free-Flow Electrophoresis of Plasma Membrane Vesicles Enriched by Two-Phase Partitioning Enhances the Quality of the Proteome from Arabidopsis Seedlings, J Proteome Res 15(3), 900-913. JBEI
201610.1186/s12934-016-0417-7Dickinson, Q., S. Bottoms, L. Hinchman, S. McIlwain, S. Li, C. L. Myers, C. Boone, J. J. Coon, A. Hebert, T. K. Sato, R. Landick, and J. S. Piotrowski. 2016. Mechanism of imidazolium ionic liquids toxicity in Saccharomyces cerevisiae and rational engineering of a tolerant, xylose-fermenting strain, Microb Cell Fact 15, 17. GLBRC
2016Ding, S.-Y. 2016. Nanoscale structure of biomass. In Reaction Pathways and Mechanisms in Thermocatalytic Biomass Conversion I, Green Chemistry and Sustainable Technology, 1-14. Eds. M. Schlaf, and Z. C. Zhang. Springer Singapore.GLBRC
201610.3389/fgene.2016.00006Dolatshahi, S., and E. O. Voit. 2016. Identification of Metabolic Pathway Systems, Front Genet 7, 6. BESC
201610.1186/s13068-016-0445-xDumitrache, A., H. Akinosho, M. Rodriguez, Jr., X. Meng, C. G. Yoo, J. Natzke, N. L. Engle, R. W. Sykes, T. J. Tschaplinski, W. Muchero, A. J. Ragauskas, B. H. Davison, and S. D. Brown. 2016. Consolidated bioprocessing of Populus using Clostridium (Ruminiclostridium) thermocellum: a case study on the impact of lignin composition and structure, Biotechnol Biofuels 9, 31. BESC
201610.1016/j.soilbio.2016.02.002Duncan, D. S., K. A. Jewell, G. Suen, and R. D. Jackson. 2016. Detection of short-term cropping system-induced changes to soil bacterial communities differs among four molecular characterization methods, Soil Biology and Biochemistry 96, 160-168. GLBRC
201610.1371/journal.pone.0151919Duran, B. E., D. S. Duncan, L. G. Oates, C. J. Kucharik, and R. D. Jackson. 2016. Nitrogen Fertilization Effects on Productivity and Nitrogen Loss in Three Grass-Based Perennial Bioenergy Cropping Systems, PLoS One 11(3), e0151919. GLBRC
2016Dutta, T., J. Shi, J. Sun, X. Zhang, G. Cheng, B. A. Simmons, and S. Singh. 2016. Ionic Liquid Pretreatment of Lignocellulosic Biomass for Biofuels and Chemicals. In Ionic Liquids in the Biorefinery Concept?: Challenges and Perspectives, 65-94.JBEI
2016Eckert, C., and C. Trinh. 2016. Biotechnology for Biofuel Production and Optimization. Elsevier, 572 pp.BESC
201610.1021/acs.biochem.6b00129Eng, C. H., S. Yuzawa, G. Wang, E. E. Baidoo, L. Katz, and J. D. Keasling. 2016. Alteration of Polyketide Stereochemistry from anti to syn by a Ketoreductase Domain Exchange in a Type I Modular Polyketide Synthase Subunit, Biochemistry 55(12), 1677-1680. JBEI
201610.1093/pcp/pcw016Eudes, A., J. H. Pereira, S. Yogiswara, G. Wang, V. Teixeira Benites, E. E. Baidoo, T. S. Lee, P. D. Adams, J. D. Keasling, and D. Loque. 2016. Exploiting the Substrate Promiscuity of Hydroxycinnamoyl-CoA:Shikimate Hydroxycinnamoyl Transferase to Reduce Lignin, Plant Cell Physiol 57(3), 568-579. JBEI
201610.1186/s12934-016-0593-5Eudes, A., M. Mouille, D. S. Robinson, V. T. Benites, G. Wang, L. Roux, Y. L. Tsai, E. E. Baidoo, T. Y. Chiu, J. L. Heazlewood, H. V. Scheller, A. Mukhopadhyay, J. D. Keasling, S. Deutsch, and D. Loque. 2016. Exploiting members of the BAHD acyltransferase family to synthesize multiple hydroxycinnamate and benzoate conjugates in yeast, Microb Cell Fact 15(1), 198. JBEI
201610.3389/fbioe.2016.00058Eudes, A., N. Zhao, N. Sathitsuksanoh, E. E. Baidoo, J. Lao, G. Wang, S. Yogiswara, T. S. Lee, S. Singh, J. C. Mortimer, J. D. Keasling, B. A. Simmons, and D. Loque. 2016. Expression of S-adenosylmethionine Hydrolase in Tissues Synthesizing Secondary Cell Walls Alters Specific Methylated Cell Wall Fractions and Improves Biomass Digestibility, Front Bioeng Biotechnol 4, 58. JBEI
201610.1105/tpc.16.00186Fang, L., T. Ishikawa, E. A. Rennie, G. M. Murawska, J. Lao, J. Yan, A. Y. Tsai, E. E. Baidoo, J. Xu, J. D. Keasling, T. Demura, M. Kawai-Yamada, H. V. Scheller, and J. C. Mortimer. 2016. Loss of Inositol Phosphorylceramide Sphingolipid Mannosylation Induces Plant Immune Responses and Reduces Cellulose Content in Arabidopsis, Plant Cell 28(12), 2991-3004. JBEI
201610.1016/j.fuel.2016.05.099Ferris, A. M., and D. A. Rothamer. 2016. Methodology for the experimental measurement of vapor-liquid equilibrium distillation curves using a modified ASTM D86 setup, Fuel 182, 467-479. GLBRC
201610.1039/c5gc02828kFoston, M., R. Samuel, J. He, and A. J. Ragauskas. 2016. A review of whole cell wall NMR by the direct-dissolution of biomass, Green Chemistry 18(3), 608-621. BESC
201610.1016/j.agee.2016.07.003Fox, A. F., T. N. Kim, C. A. Bahlai, J. M. Woltz, C. Gratton, and D. A. Landis. 2016. Cover crops have neutral effects on predator communities and biological control services in annual cellulosic bioenergy cropping systems, Agriculture, Ecosystems & Environment 232, 101-109. GLBRC
201610.1039/c6gc00642fFrederix, M., F. Mingardon, M. Hu, N. Sun, T. Pray, S. Singh, B. A. Simmons, J. D. Keasling, and A. Mukhopadhyay. 2016. Development of an E. coli strain for one-pot biofuel production from ionic liquid pretreated cellulose and switchgrass, Green Chemistry 18(15), 4189-4197. JBEI
201610.1021/acssynbio.6b00011Gach, P. C., S. C. Shih, J. Sustarich, J. D. Keasling, N. J. Hillson, P. D. Adams, and A. K. Singh. 2016. A Droplet Microfluidic Platform for Automating Genetic Engineering, ACS Synth Biol 5(5), 426-433. JBEI
201610.1111/pbi.12439Gallego-Giraldo, L., G. Shadle, H. Shen, J. Barros-Rios, S. Fresquet Corrales, H. Wang, and R. A. Dixon. 2016. Combining enhanced biomass density with reduced lignin level for improved forage quality, Plant Biotechnol J 14(3), 895-904. BESC
201610.1016/j.mimet.2016.10.018Garoutte, A., E. Cardenas, J. Tiedje, and A. Howe. 2016. Methodologies for probing the metatranscriptome of grassland soil, J Microbiol Methods 131, 122-129. GLBRC
201610.1002/fee.1258Geertsema, W., W. A. H. Rossing, D. A. Landis, F. J. J. A. Bianchi, P. C. J. van Rijn, J. H. J. Schaminée, T. Tscharntke, and W. van der Werf. 2016. Actionable knowledge for ecological intensification of agriculture, Frontiers in Ecology and the Environment 14(4), 209-216. GLBRC
201610.1111/gcb.13426Gelfand, I., I. Shcherbak, N. Millar, A. N. Kravchenko, and G. P. Robertson. 2016. Long-term nitrous oxide fluxes in annual and perennial agricultural and unmanaged ecosystems in the upper Midwest USA, Glob Chang Biol 22(11), 3594-3607. GLBRC
201610.3389/fbioe.2016.00076Ghosh, A., D. Ando, J. Gin, W. Runguphan, C. Denby, G. Wang, E. E. Baidoo, C. Shymansky, J. D. Keasling, and H. Garcia Martin. 2016. (13)C Metabolic Flux Analysis for Systematic Metabolic Engineering of S. cerevisiae for Overproduction of Fatty Acids, Front Bioeng Biotechnol 4, 76. JBEI
201610.1021/acssynbio.6b00121Ghosh, I. N., and R. Landick. 2016. OptSSeq: High-Throughput Sequencing Readout of Growth Enrichment Defines Optimal Gene Expression Elements for Homoethanologenesis, ACS Synth Biol 5(12), 1519-1534. GLBRC
201610.1016/j.meteno.2016.01.004Groom, J., D. Chung, D. G. Olson, L. R. Lynd, A. M. Guss, and J. Westpheling. 2016. Promiscuous plasmid replication in thermophiles: Use of a novel hyperthermophilic replicon for genetic manipulation of Clostridium thermocellum at its optimum growth temperature, Metab Eng Commun 3, 30-38. BESC
201610.1186/s13068-016-0446-9Guilliams, A., S. Pattathil, D. Willies, M. Richards, Y. Pu, S. Kandemkavil, and E. Wiswall. 2016. Physical and chemical differences between one-stage and two-stage hydrothermal pretreated hardwood substrates for use in cellulosic ethanol production, Biotechnol Biofuels 9, 30. BESC
201610.1128/AEM.02772-15.Guo, J., J. R. Cole, Q. Zhang, C. T. Brown, and J. M. Tiedje. 2016. Microbial Community Analysis with Ribosomal Gene Fragments from Shotgun Metagenomes, Appl Environ Microbiol 82(1), 157-166. GLBRC
201610.1107/S1600577516009024Gupta, S., J. Feng, L. J. Chan, C. J. Petzold, and C. Y. Ralston. 2016. Synchrotron X-ray footprinting as a method to visualize water in proteins, J Synchrotron Radiat 23(Pt 5), 1056-1069. JBEI
201610.1016/j.tibs.2016.04.006Gupta, V. K., C. P. Kubicek, J. G. Berrin, D. W. Wilson, M. Couturier, A. Berlin, E. X. F. Filho, and T. Ezeji. 2016. Fungal Enzymes for Bio-Products from Sustainable and Waste Biomass, Trends Biochem Sci 41(7), 633-645. BESC
201610.1111/tpj.13177Ha, C. M., L. Escamilla-Trevino, J. C. Yarce, H. Kim, J. Ralph, F. Chen, and R. A. Dixon. 2016. An essential role of caffeoyl shikimate esterase in monolignol biosynthesis in Medicago truncatula, Plant J 86(5), 363-375. GLBRC BESC
201610.1021/acssynbio.5b00153Hagen, A., S. Poust, T. Rond, J. L. Fortman, L. Katz, C. J. Petzold, and J. D. Keasling. 2016. Engineering a Polyketide Synthase for In Vitro Production of Adipic Acid, ACS Synth Biol 5(1), 21-27. JBEI
201610.1038/srep37453Han, J., J. Chen, Y. Miao, and S. Wan. 2016. Multiple Resource Use Efficiency (mRUE): A New Concept for Ecosystem Production, Sci Rep 6, 37453. GLBRC
201610.1007/978-1-4939-6463-5_8Hansen, S. F., B. Ebert, C. Rautengarten, and J. L. Heazlewood. 2016. Proteomic Characterization of Golgi Membranes Enriched from Arabidopsis Suspension Cell Cultures, Methods Mol Biol 1496, 91-109. JBEI
201610.2134/agronj2015.0167Hao, X., K. Thelen, and J. Gao. 2016. Spatial Variability in Biomass Yield of Switchgrass, Native Prairie, and Corn at Field Scale, Agronomy Journal 108(2), 548. GLBRC
201610.1371/journal.pone.0147310Harkenrider, M., R. Sharma, D. De Vleesschauwer, L. Tsao, X. Zhang, M. Chern, P. Canlas, S. Zuo, and P. C. Ronald. 2016. Overexpression of Rice Wall-Associated Kinase 25 (OsWAK25) Alters Resistance to Bacterial and Fungal Pathogens, PLoS One 11(1), e0147310. JBEI
201610.1002/biot.201600266Harman-Ware, A. E., C. Foster, R. M. Happs, C. Doeppke, K. Meunier, J. Gehan, F. Yue, F. Lu, and M. F. Davis. 2016. A thioacidolysis method tailored for higher-throughput quantitative analysis of lignin monomers, Biotechnol J 11(10), 1268-1273. BESC GLBRC
201610.1016/j.biombioe.2016.06.016Healey, A. L., J. S. Lupoi, D. J. Lee, R. W. Sykes, J. M. Guenther, K. Tran, S. R. Decker, S. Singh, B. A. Simmons, and R. J. Henry. 2016. Effect of aging on lignin content, composition and enzymatic saccharification in Corymbia hybrids and parental taxa between years 9 and 12, Biomass and Bioenergy 93, 50-59. BESC JBEI
201610.1074/jbc.M115.694307Helmich, K. E., J. H. Pereira, D. L. Gall, R. A. Heins, R. P. McAndrew, C. Bingman, K. Deng, K. C. Holland, D. R. Noguera, B. A. Simmons, K. L. Sale, J. Ralph, T. J. Donohue, P. D. Adams, and G. N. Phillips, Jr. 2016. Structural Basis of Stereospecificity in the Bacterial Enzymatic Cleavage of beta-Aryl Ether Bonds in Lignin, J Biol Chem 291(10), 5234-5246. GLBRC JBEI
201610.1007/s00253-016-7294-1Herring, C. D., P. G. Thorne, and L. R. Lynd. 2016. Clostridium thermocellum releases coumaric acid during degradation of untreated grasses by the action of an unknown enzyme, Appl Microbiol Biotechnol 100(6), 2907-2915. BESC
201610.1186/s13068-016-0536-8Herring, C. D., W. R. Kenealy, A. Joe Shaw, S. F. Covalla, D. G. Olson, J. Zhang, W. Ryan Sillers, V. Tsakraklides, J. S. Bardsley, S. R. Rogers, P. G. Thorne, J. P. Johnson, A. Foster, I. D. Shikhare, D. M. Klingeman, S. D. Brown, B. H. Davison, L. R. Lynd, and D. A. Hogsett. 2016. Strain and bioprocess improvement of a thermophilic anaerobe for the production of ethanol from wood, Biotechnol Biofuels 9, 125. BESC
201610.1021/acssynbio.6b00146Hillson, N. J., H. A. Plahar, J. Beal, and R. Prithviraj. 2016. Improving Synthetic Biology Communication: Recommended Practices for Visual Depiction and Digital Submission of Genetic Designs, ACS Synth Biol 5(6), 449-451. JBEI
201610.1128/mBio.01106-16Hiras, J., Y. W. Wu, K. Deng, C. D. Nicora, J. T. Aldrich, D. Frey, S. Kolinko, E. W. Robinson, J. M. Jacobs, P. D. Adams, T. R. Northen, B. A. Simmons, and S. W. Singer. 2016. Comparative Community Proteomics Demonstrates the Unexpected Importance of Actinobacterial Glycoside Hydrolase Family 12 Protein for Crystalline Cellulose Hydrolysis, MBio 7(4). JBEI
201610.1038/ismej.2015.158Hiras, J., Y. W. Wu, S. A. Eichorst, B. A. Simmons, and S. W. Singer. 2016. Refining the phylum Chlorobi by resolving the phylogeny and metabolic potential of the representative of a deeply branching, uncultivated lineage, ISME J 10(4), 833-845. JBEI
201610.1186/s13068-016-0630-yHollinshead, W. D., S. Rodriguez, H. G. Martin, G. Wang, E. E. Baidoo, K. L. Sale, J. D. Keasling, A. Mukhopadhyay, and Y. J. Tang. 2016. Examining Escherichia coli glycolytic pathways, catabolite repression, and metabolite channeling using Deltapfk mutants, Biotechnol Biofuels 9, 212. JBEI
201610.1016/j.meteno.2016.04.001Hon, S., A. A. Lanahan, L. Tian, R. J. Giannone, R. L. Hettich, D. G. Olson, and L. R. Lynd. 2016. Development of a plasmid-based expression system in Clostridium thermocellum and its use to screen heterologous expression of bifunctional alcohol dehydrogenases (adhEs), Metab Eng Commun 3, 120-129. BESC
201610.1126/science.aaf6206Horn, P. J., and C. Benning. 2016. The plant lipidome in human and environmental health, Science 353(6305), 1228-1232. GLBRC
201610.1111/tpj.13163Horn, P. J., J. Liu, J. C. Cocuron, K. McGlew, N. A. Thrower, M. Larson, C. Lu, A. P. Alonso, and J. Ohlrogge. 2016. Identification of multiple lipid genes with modifications in expression and sequence associated with the evolution of hydroxy fatty acid accumulation in Physaria fendleri, Plant J 86(4), 322-348. GLBRC
201610.1073/pnas.1600406113Huang, Y., Y. Wang, L. Tan, L. Sun, J. Petrosino, M. Z. Cui, F. Hao, and M. Zhang. 2016. Nanospherical arabinogalactan proteins are a key component of the high-strength adhesive secreted by English ivy, Proc Natl Acad Sci U S A 113(23), E3193-3202. BESC
201610.1371/journal.pone.0151087Javidpour, P., S. Deutsch, V. K. Mutalik, N. J. Hillson, C. J. Petzold, J. D. Keasling, and H. R. Beller. 2016. Investigation of Proposed Ladderane Biosynthetic Genes from Anammox Bacteria by Heterologous Expression in E. coli, PLoS One 11(3), e0151087. JBEI
201610.1111/gcbb.12289Jesus, E. d. C., C. Liang, J. F. Quensen, E. Susilawati, R. D. Jackson, T. C. Balser, and J. M. Tiedje. 2016. Influence of corn, switchgrass, and prairie cropping systems on soil microbial communities in the upper Midwest of the United States, GCB Bioenergy 8(2), 481-494. GLBRC
201610.1039/c6ra04443cJoshua, C. J., B. A. Simmons, and S. W. Singer. 2016. Ferricyanide-based analysis of aqueous lignin suspension revealed sequestration of water-soluble lignin moieties, RSC Advances 6(59), 54382-54393. JBEI
201610.3389/fpls.2016.01455Kalluri, U. C., R. S. Payyavula, J. L. Labbe, N. Engle, G. Bali, S. S. Jawdy, R. W. Sykes, M. Davis, A. Ragauskas, G. A. Tuskan, and T. J. Tschaplinski. 2016. Down-Regulation of KORRIGAN-Like Endo-beta-1,4-Glucanase Genes Impacts Carbon Partitioning, Mycorrhizal Colonization and Biomass Production in Populus, Front Plant Sci 7, 1455. BESC
2016Kang, A., and T. S. Lee. 2016. Secondary Metabolism for Isoprenoid-based Biofuels A2 In Biotechnology for Biofuel Production and Optimization, 35-71. Eds. C. Eckert, and C. Trinh. Elsevier.JBEI
201610.1016/j.ymben.2015.12.002Kang, A., K. W. George, G. Wang, E. Baidoo, J. D. Keasling, and T. S. Lee. 2016. Isopentenyl diphosphate (IPP)-bypass mevalonate pathways for isopentenol production, Metab Eng 34, 25-35. JBEI
201610.1093/jxb/erw292Kang, J. H., M. L. Campos, S. Zemelis-Durfee, J. M. Al-Haddad, A. D. Jones, F. W. Telewski, F. Brandizzi, and G. A. Howe. 2016. Molecular cloning of the tomato Hairless gene implicates actin dynamics in trichome-mediated defense and mechanical properties of stem tissue, J Exp Bot 67(18), 5313-5324. GLBRC
201610.1126/sciadv.1600393Karlen, S. D., C. Zhang, M. L. Peck, R. A. Smith, D. Padmakshan, K. E. Helmich, H. C. Free, S. Lee, B. G. Smith, F. Lu, J. C. Sedbrook, R. Sibout, J. H. Grabber, T. M. Runge, K. S. Mysore, P. J. Harris, L. E. Bartley, and J. Ralph. 2016. Monolignol ferulate conjugates are naturally incorporated into plant lignins, Sci Adv 2(10), e1600393. GLBRC
201610.1111/mec.13872Khadempour, L., K. E. Burnum-Johnson, E. S. Baker, C. D. Nicora, B. M. Webb-Robertson, R. A. White, 3rd, M. E. Monroe, E. L. Huang, R. D. Smith, and C. R. Currie. 2016. The fungal cultivar of leaf-cutter ants produces specific enzymes in response to different plant substrates, Mol Ecol 25(22), 5795-5805. GLBRC
201610.1093/glycob/cww044Kim, S. J., and F. Brandizzi. 2016. The plant secretory pathway for the trafficking of cell wall polysaccharides and glycoproteins, Glycobiology 26(9), 940-949. GLBRC
201610.1186/s13068-016-0588-9Kim, S. K., D. Chung, M. E. Himmel, Y. J. Bomble, and J. Westpheling. 2016. Heterologous expression of family 10 xylanases from Acidothermus cellulolyticus enhances the exoproteome of Caldicellulosiruptor bescii and growth on xylan substrates, Biotechnol Biofuels 9(1), 176. BESC
201610.1002/bbb.1712Kim, S., and B. E. Dale. 2016. A distributed cellulosic biorefinery system in the US Midwest based on corn stover, Biofuels, Bioproducts and Biorefining 10(6), 819-832. GLBRC
201610.1016/j.ymben.2016.10.017Kirby, J., K. L. Dietzel, G. Wichmann, R. Chan, E. Antipov, N. Moss, E. E. K. Baidoo, P. Jackson, S. P. Gaucher, S. Gottlieb, J. LaBarge, T. Mahatdejkul, K. M. Hawkins, S. Muley, J. D. Newman, P. Liu, J. D. Keasling, and L. Zhao. 2016. Engineering a functional 1-deoxy-D-xylulose 5-phosphate (DXP) pathway in Saccharomyces cerevisiae, Metab Eng 38, 494-503. JBEI
2016Konda, M., D. Loqué, and C. Scown. 2016. Towards Economically Sustainable Lignocellulosic Biorefineries. In Valorization of Lignocellulosic Biomass in a Biorefinery: From Logistics to Environmental and Performance Impact. Eds. R. Kumar, S. Singh, and V. Balan. Nova Science Publishers, Inc.JBEI
201610.1016/j.compchemeng.2016.02.013Kong, L., S. M. Sen, C. A. Henao, J. A. Dumesic, and C. T. Maravelias. 2016. A superstructure-based framework for simultaneous process synthesis, heat integration, and utility plant design, Computers & Chemical Engineering 91, 68-84. GLBRC
201610.1016/j.molp.2016.04.013Kuang, B., X. Zhao, C. Zhou, W. Zeng, J. Ren, B. Ebert, C. T. Beahan, X. Deng, Q. Zeng, G. Zhou, M. S. Doblin, J. L. Heazlewood, A. Bacic, X. Chen, and A. M. Wu. 2016. Role of UDP-Glucuronic Acid Decarboxylase in Xylan Biosynthesis in Arabidopsis, Mol Plant 9(8), 1119-1131. JBEI
201610.1128/AEM.03538-15Lacroix, C., K. Renner, E. Cole, E. W. Seabloom, E. T. Borer, and C. M. Malmstrom. 2016. Methodological Guidelines for Accurate Detection of Viruses in Wild Plant Species, Appl Environ Microbiol 82(6), 1966-1975. GLBRC
2016 10.1111/tpj.13315Lan, W., J. Rencoret, F. Lu, S. D. Karlen, B. G. Smith, P. J. Harris, J. C. Del Rio, and J. Ralph. 2016. Tricin-lignins: occurrence and quantitation of tricin in relation to phylogeny, Plant J 88(6), 1046-1057. GLBRC
201610.1104/pp.16.02012Lan, W., K. Morreel, F. Lu, J. Rencoret, J. Carlos Del Rio, W. Voorend, W. Vermerris, W. Boerjan, and J. Ralph. 2016. Maize Tricin-Oligolignol Metabolites and Their Implications for Monocot Lignification, Plant Physiol 171(2), 810-820. GLBRC
201610.1128/genomeA.00229-16Lancaster, W. A., S. M. Utturkar, F. L. Poole, D. M. Klingeman, D. A. Elias, M. W. Adams, and S. D. Brown. 2016. Near-Complete Genome Sequence of Clostridium paradoxum Strain JW-YL-7, Genome Announc 4(3). BESC
201610.1002/bit.25947Layton, D. S., and C. T. Trinh. 2016. Expanding the modular ester fermentative pathways for combinatorial biosynthesis of esters from volatile organic acids, Biotechnol Bioeng 113(8), 1764-1776. BESC
201610.1016/j.meteno.2016.08.001.Layton, D. S., and C. T. Trinh. 2016. Microbial synthesis of a branched-chain ester platform from organic waste carboxylates, Metab Eng Commun 3, 245-251. BESC
201610.1101/cshperspect.a023903Lechner, A., E. Brunk, and J. D. Keasling. 2016. The Need for Integrated Approaches in Metabolic Engineering, Cold Spring Harb Perspect Biol 8(11). JBEI
201610.1038/nmicrobiol.2015.3.Leducq, J. B., L. Nielly-Thibault, G. Charron, C. Eberlein, J. P. Verta, P. Samani, K. Sylvester, C. T. Hittinger, G. Bell, and C. R. Landry. 2016. Speciation driven by hybridization and chromosomal plasticity in a wild yeast, Nat Microbiol 1, 15003. GLBRC
201610.1371/journal.pone.0151840Lewin, G. R., A. L. Johnson, R. D. Soto, K. Perry, A. J. Book, H. A. Horn, A. A. Pinto-Tomas, and C. R. Currie. 2016. Cellulose-Enriched Microbial Communities from Leaf-Cutter Ant (Atta colombica) Refuse Dumps Vary in Taxonomic Composition and Degradation Ability, PLoS One 11(3), e0151840. GLBRC
201610.1146/annurev-micro-102215-095748.Lewin, G. R., C. Carlos, M. G. Chevrette, H. A. Horn, B. R. McDonald, R. J. Stankey, B. G. Fox, and C. R. Currie. 2016. Evolution and Ecology of Actinobacteria and Their Bioenergy Applications, Annu Rev Microbiol 70, 235-254. GLBRC
201610.1016/j.molp.2016.03.009.Li, G., M. Chern, R. Jain, J. A. Martin, W. S. Schackwitz, L. Jiang, M. E. Vega-Sanchez, A. M. Lipzen, K. W. Barry, J. Schmutz, and P. C. Ronald. 2016. Genome-Wide Sequencing of 41 Rice (Oryza sativa L.) Mutated Lines Reveals Diverse Mutations Induced by Fast-Neutron Irradiation, Mol Plant 9(7), 1078-1081. JBEI
201610.1007/s12155-016-9798-z.Li, M., D. L. Williams, M. Heckwolf, N. de Leon, S. Kaeppler, R. W. Sykes, and D. Hodge. 2016. Prediction of Cell Wall Properties and Response to Deconstruction Using Alkaline Pretreatment in Diverse Maize Genotypes Using Py-MBMS and NIR, BioEnergy Research 10(2), 329-343. GLBRC
201610.3389/fchem.2016.00045Li, M., Y. Pu, and A. J. Ragauskas. 2016. Current Understanding of the Correlation of Lignin Structure with Biomass Recalcitrance, Front Chem 4, 45. BESC
201610.1039/c5gc03062e.Li, M., Y. Pu, C. G. Yoo, and A. J. Ragauskas. 2016. The occurrence of tricin and its derivatives in plants, Green Chemistry 18(6), 1439-1454. BESC
201610.1074/jbc.M116.724708.Li, Z., S. Hwang, and M. Bar-Peled. 2016. Discovery of a Unique Extracellular Polysaccharide in Members of the Pathogenic Bacillus That Can Co-form with Spores, J Biol Chem 291(36), 19051-19067. BESC
201610.1016/j.soilbio.2015.11.020Liang, C., E. d. C. Jesus, D. S. Duncan, J. F. Quensen, R. D. Jackson, T. C. Balser, and J. M. Tiedje. 2016. Switchgrass rhizospheres stimulate microbial biomass but deplete microbial necromass in agricultural soils of the upper Midwest, USA, Soil Biology and Biochemistry 94, 173-180. GLBRC
201610.1016/j.soilbio.2016.08.002Liang, C., J. Kao-Kniffin, G. R. Sanford, K. Wickings, T. C. Balser, and R. D. Jackson. 2016. Microorganisms and their residues under restored perennial grassland communities of varying diversity, Soil Biology and Biochemistry 103, 192-200. GLBRC
201610.1038/nrmicro.2016.32.Liao, J. C., L. Mi, S. Pontrelli, and S. Luo. 2016. Fuelling the future: microbial engineering for the production of sustainable biofuels, Nat Rev Microbiol 14(5), 288-304. BESC
201610.1093/pcp/pcw125Lin, F., C. Manisseri, A. Fagerstrom, M. L. Peck, M. E. Vega-Sanchez, B. Williams, D. M. Chiniquy, P. Saha, S. Pattathil, B. Conlin, L. Zhu, M. G. Hahn, W. G. Willats, H. V. Scheller, P. C. Ronald, and L. E. Bartley. 2016. Cell Wall Composition and Candidate Biosynthesis Gene Expression During Rice Development, Plant Cell Physiol 57(10), 2058-2075. JBEI
201610.1186/s13036-016-0024-5Linshiz, G., E. Jensen, N. Stawski, C. Bi, N. Elsbree, H. Jiao, J. Kim, R. Mathies, J. D. Keasling, and N. J. Hillson. 2016. End-to-end automated microfluidic platform for synthetic biology: from design to functional analysis, J Biol Eng 10, 3. JBEI
201610.1128/AEM.00570-16.Lipscomb, G. L., J. M. Conway, S. E. Blumer-Schuette, R. M. Kelly, and M. W. W. Adams. 2016. A Highly Thermostable Kanamycin Resistance Marker Expands the Tool Kit for Genetic Manipulation of Caldicellulosiruptor bescii, Appl Environ Microbiol 82(14), 4421-4428. BESC
201610.1039/c6gc00657dLiszka, M. J., A. Kang, N. V. S. N. M. Konda, K. Tran, J. M. Gladden, S. Singh, J. D. Keasling, C. D. Scown, T. S. Lee, B. A. Simmons, and K. L. Sale. 2016. Switchable ionic liquids based on di-carboxylic acids for one-pot conversion of biomass to an advanced biofuel, Green Chemistry 18(14), 4012-4021. JBEI
201610.1016/j.copbio.2015.10.001Liu, W., and C. N. Stewart, Jr. 2016. Plant synthetic promoters and transcription factors, Curr Opin Biotechnol 37, 36-44. BESC
201610.1093/femsyr/fow044Lopes, M. R., C. G. Morais, J. Kominek, R. M. Cadete, M. A. Soares, A. P. Uetanabaro, C. Fonseca, M. A. Lachance, C. T. Hittinger, and C. A. Rosa. 2016. Genomic analysis and D-xylose fermentation of three novel Spathaspora species: Spathaspora girioi sp. nov., Spathaspora hagerdaliae f. a., sp. nov. and Spathaspora gorwiae f. a., sp. nov, FEMS Yeast Res 16(4). GLBRC
201610.1073/pnas.1607504113.Luo, D., R. Callari, B. Hamberger, S. G. Wubshet, M. T. Nielsen, J. Andersen-Ranberg, B. M. Hallstrom, F. Cozzi, H. Heider, B. Lindberg Moller, D. Staerk, and B. Hamberger. 2016. Oxidation and cyclization of casbene in the biosynthesis of Euphorbia factors from mature seeds of Euphorbia lathyris L, Proc Natl Acad Sci U S A 113(34), E5082-5089. GLBRC
201610.3389/fbioe.2016.00025Lupoi, J., B. Simmons, and R. Henry. 2016. Editorial: Biomass Modification, Characterization, and Process Monitoring Analytics to Support Biofuel and Biomaterial Production, Front Bioeng Biotechnol 4, 25. JBEI
2016Lynd, L. R., A. M. Guss, M. E. Himmel, D. Beri, C. Herring, E. K. Holwerda, S. J. Murphy, D. G. Olson, J. Paye, T. Rydzak, X. Shao, L. Tian, and R. Worthen. 2016. Advances in Consolidated bioprocessing using clostridium thermocellum and thermoanaerobacter saccharolyticum. In Industrial Biotechnology: Microorganisms, 365-394.BESC
201610.1111/tpj.13244Ma, W., Q. Kong, J. J. Mantyla, Y. Yang, J. B. Ohlrogge, and C. Benning. 2016. 14-3-3 protein mediates plant seed oil biosynthesis through interaction with AtWRI1, Plant J 88(2), 228-235. GLBRC
2016Manga, P., D. M. Klingeman, T. Y. Lu, T. L. Mehlhorn, D. A. Pelletier, L. J. Hauser, C. M. Wilson, and S. D. Brown. 2016. Replicates, Read Numbers, and Other Important Experimental Design Considerations for Microbial RNA-seq Identified Using Bacillus thuringiensis Datasets, Front Microbiol 7, 794. 10.3389/fmicb.2016.00794.BESC
201610.1073/pnas.1608917113McAndrew, R. P., N. Sathitsuksanoh, M. M. Mbughuni, R. A. Heins, J. H. Pereira, A. George, K. L. Sale, B. G. Fox, B. A. Simmons, and P. D. Adams. 2016. Structure and mechanism of NOV1, a resveratrol-cleaving dioxygenase, Proc Natl Acad Sci U S A 113(50), 14324-14329. GLBRC JBEI
201610.1104/pp.16.00948McCormick, R. F., S. K. Truong, and J. E. Mullet. 2016. 3D Sorghum Reconstructions from Depth Images Identify QTL Regulating Shoot Architecture, Plant Physiol 172(2), 823-834. GLBRC
201610.1002/ecs2.1426McDaniel, M. D., A. S. Grandy, L. K. Tiemann, and M. N. Weintraub. 2016. Eleven years of crop diversification alters decomposition dynamics of litter mixtures incubated with soil, Ecosphere 7(8), e01426. GLBRC
201610.1534/g3.116.029389McIlwain, S. J., D. Peris, M. Sardi, O. V. Moskvin, F. Zhan, K. S. Myers, N. M. Riley, A. Buzzell, L. S. Parreiras, I. M. Ong, R. Landick, J. J. Coon, A. P. Gasch, T. K. Sato, and C. T. Hittinger. 2016. Genome Sequence and Analysis of a Stress-Tolerant, Wild-Derived Strain of Saccharomyces cerevisiae Used in Biofuels Research, G3 (Bethesda) 6(6), 1757-1766. GLBRC
201610.1111/tpj.13269.McKinley, B., W. Rooney, C. Wilkerson, and J. Mullet. 2016. Dynamics of biomass partitioning, stem gene expression, cell wall biosynthesis, and sucrose accumulation during development of Sorghum bicolor, Plant J 88(4), 662-680. GLBRC
201610.1021/acssuschemeng.6b00603Meng, X., Q. Sun, M. Kosa, F. Huang, Y. Pu, and A. J. Ragauskas. 2016. Physicochemical Structural Changes of Poplar and Switchgrass during Biomass Pretreatment and Enzymatic Hydrolysis, ACS Sustainable Chemistry & Engineering 4(9), 4563-4572. BESC
201610.1186/s13568-016-0189-9Montella, S., V. Balan, L. da Costa Sousa, C. Gunawan, S. Giacobbe, O. Pepe, and V. Faraco. 2016. Saccharification of newspaper waste after ammonia fiber expansion or extractive ammonia, AMB Express 6(1), 18. GLBRC
201610.1021/jacs.6b03285Mostofian, B., C. M. Cai, M. D. Smith, L. Petridis, X. Cheng, C. E. Wyman, and J. C. Smith. 2016. Local Phase Separation of Co-solvents Enhances Pretreatment of Biomass for Bioenergy Applications, J Am Chem Soc 138(34), 10869-10878. BESC
201610.1039/c6gc02297aMotagamwala, A. H., W. Won, C. T. Maravelias, and J. A. Dumesic. 2016. An engineered solvent system for sugar production from lignocellulosic biomass using biomass derived ?-valerolactone, Green Chemistry 18(21), 5756-5763. GLBRC
201610.1016/j.copbio.2015.10.009Mottiar, Y., R. Vanholme, W. Boerjan, J. Ralph, and S. D. Mansfield. 2016. Designer lignins: harnessing the plasticity of lignification, Curr Opin Biotechnol 37, 190-200. GLBRC
201610.1016/j.carbon.2016.02.053Nar, M., H. R. Rizvi, R. A. Dixon, F. Chen, A. Kovalcik, and N. D'Souza. 2016. Superior plant based carbon fibers from electrospun poly-(caffeyl alcohol) lignin, Carbon 103, 372-383. BESC
201610.1128/AEM.02274-15Nelson, W. C., Y. Maezato, Y. W. Wu, M. F. Romine, and S. R. Lindemann. 2016. Identification and Resolution of Microdiversity through Metagenomic Sequencing of Parallel Consortia, Appl Environ Microbiol 82(1), 255-267. JBEI
201610.1039/c5gc01977jNguyen, T. Y., C. M. Cai, O. Osman, R. Kumar, and C. E. Wyman. 2016. CELF pretreatment of corn stover boosts ethanol titers and yields from high solids SSF with low enzyme loadings, Green Chemistry 18(6), 1581-1589. BESC
201610.1016/j.cell.2016.02.004Nielsen, J., and J. D. Keasling. 2016. Engineering Cellular Metabolism, Cell 164(6), 1185-1197. JBEI
201610.1016/j.agee.2016.09.008Oates, L. G., D. S. Duncan, G. R. Sanford, C. Liang, and R. D. Jackson. 2016. Bioenergy cropping systems that incorporate native grasses stimulate growth of plant-associated soil microbes in the absence of nitrogen fertilization, Agriculture, Ecosystems & Environment 233, 396-403. GLBRC
201610.1111/gcbb.12268Oates, L. G., D. S. Duncan, I. Gelfand, N. Millar, G. P. Robertson, and R. D. Jackson. 2016. Nitrous oxide emissions during establishment of eight alternative cellulosic bioenergy cropping systems in the North Central United States, GCB Bioenergy 8(3), 539-549. GLBRC
201610.1186/s13068-016-0657-0Ong, R. G., A. Higbee, S. Bottoms, Q. Dickinson, D. Xie, S. A. Smith, J. Serate, E. Pohlmann, A. D. Jones, J. J. Coon, T. K. Sato, G. R. Sanford, D. Eilert, L. G. Oates, J. S. Piotrowski, D. M. Bates, D. Cavalier, and Y. Zhang. 2016. Inhibition of microbial biofuel production in drought-stressed switchgrass hydrolysate, Biotechnol Biofuels 9, 237.GLBRC
201610.1007/s00253-016-7525-5Pace, S., S. J. Ceballos, D. Harrold, W. Stannard, B. A. Simmons, S. W. Singer, M. P. Thelen, and J. S. VanderGheynst. 2016. Enrichment of microbial communities tolerant to the ionic liquids tetrabutylphosphonium chloride and tributylethylphosphonium diethylphosphate, Appl Microbiol Biotechnol 100(12), 5639-5652. JBEI
201610.1007/s00299-016-2039-2Pandey, S. K., A. Nookaraju, T. Fujino, S. Pattathil, and C. P. Joshi. 2016. Virus-induced gene silencing (VIGS)-mediated functional characterization of two genes involved in lignocellulosic secondary cell wall formation, Plant Cell Rep 35(11), 2353-2367. BESC
201610.1111/pbi.12505Park, S. H., R. G. Ong, and M. Sticklen. 2016. Strategies for the production of cell wall-deconstructing enzymes in lignocellulosic biomass and their utilization for biofuel production, Plant Biotechnol J 14(6), 1329-1344. GLBRC
201610.1186/s13068-016-0561-7Parthasarathi, R., J. Sun, T. Dutta, N. Sun, S. Pattathil, N. V. Murthy Konda, A. G. Peralta, B. A. Simmons, and S. Singh. 2016. Activation of lignocellulosic biomass for higher sugar yields using aqueous ionic liquid at low severity process conditions, Biotechnol Biofuels 9, 160. JBEI BESC
2016Passian, A., R. H. Farahi, and B. H. Davison. 2016: Optonanomechanical spectroscopic imaging. Imaging and Microscopy.BESC
201610.3389/fpls.2016.00882Pattathil, S., M. W. Ingwers, O. L. Victoriano, S. Kandemkavil, M. A. McGuire, R. O. Teskey, and D. P. Aubrey. 2016. Cell Wall Ultrastructure of Stem Wood, Roots, and Needles of a Conifer Varies in Response to Moisture Availability, Front Plant Sci 7, 882. BESC
201610.1146/annurev-arplant-043015-112222Pauly, M., and K. Keegstra. 2016. Biosynthesis of the Plant Cell Wall Matrix Polysaccharide Xyloglucan, Annu Rev Plant Biol 67, 235-259. GLBRC
201610.1038/nature17174Paustian, K., J. Lehmann, S. Ogle, D. Reay, G. P. Robertson, and P. Smith. 2016. Climate-smart soils, Nature 532(7597), 49-57. GLBRC
201610.1186/s13068-015-0412-yPaye, J. M., A. Guseva, S. K. Hammer, E. Gjersing, M. F. Davis, B. H. Davison, J. Olstad, B. S. Donohoe, T. Y. Nguyen, C. E. Wyman, S. Pattathil, M. G. Hahn, and L. R. Lynd. 2016. Biological lignocellulose solubilization: comparative evaluation of biocatalysts and enhancement via cotreatment, Biotechnol Biofuels 9, 8. BESC
201610.1007/s00425-016-2527-1Pena, M. J., A. R. Kulkarni, J. Backe, M. Boyd, M. A. O'Neill, and W. S. York. 2016. Structural diversity of xylans in the cell walls of monocots, Planta 244(3), 589-606. BESC
201610.1074/jbc.M115.700427Pereira, J. H., R. A. Heins, D. L. Gall, R. P. McAndrew, K. Deng, K. C. Holland, T. J. Donohue, D. R. Noguera, B. A. Simmons, K. L. Sale, J. Ralph, and P. D. Adams. 2016. Structural and Biochemical Characterization of the Early and Late Enzymes in the Lignin beta-Aryl Ether Cleavage Pathway from Sphingobium sp. SYK-6, J Biol Chem 291(19), 10228-10238. JBEI GLBRC
201610.1016/j.biortech.2016.03.103.Perez-Pimienta, J. A., C. A. Flores-Gomez, H. A. Ruiz, N. Sathitsuksanoh, V. Balan, L. da Costa Sousa, B. E. Dale, S. Singh, and B. A. Simmons. 2016. Evaluation of agave bagasse recalcitrance using AFEX, autohydrolysis, and ionic liquid pretreatments, Bioresour Technol 211, 216-223. JBEI
201610.1016/j.biombioe.2016.05.001.Perez-Pimienta, J. A., H. M. Poggi-Varaldo, T. Ponce-Noyola, A. C. Ramos-Valdivia, J. A. Chavez-Carvayar, V. Stavila, and B. A. Simmons. 2016. Fractional pretreatment of raw and calcium oxalate-extracted agave bagasse using ionic liquid and alkaline hydrogen peroxide, Biomass and Bioenergy 91, 48-55. JBEI
2016Peris, D., Q. K. Langdon, R. V. Moriarty, K. Sylvester, M. Bontrager, G. Charron, J. B. Leducq, C. R. Landry, D. Libkind, and C. T. Hittinger. 2016. Complex Ancestries of Lager-Brewing Hybrids Were Shaped by Standing Variation in the Wild Yeast Saccharomyces eubayanus, PLoS Genet 12(7), e1006155. 10.1371/journal.pgen.1006155.GLBRC
201610.3389/fpls.2016.00055.Petrik, D. L., C. L. Cass, D. Padmakshan, C. E. Foster, J. P. Vogel, S. D. Karlen, J. Ralph, and J. C. Sedbrook. 2016. BdCESA7, BdCESA8, and BdPMT Utility Promoter Constructs for Targeted Expression to Secondary Cell-Wall-Forming Cells of Grasses, Front Plant Sci 7, 55. GLBRC
201610.1021/acssuschemeng.6b01803.Pingali, S. V., V. S. Urban, W. T. Heller, J. McGaughey, H. O’Neill, M. B. Foston, H. Li, C. E. Wyman, D. A. Myles, P. Langan, A. Ragauskas, B. Davison, and B. R. Evans. 2016. Understanding Multiscale Structural Changes During Dilute Acid Pretreatment of Switchgrass and Poplar, ACS Sustainable Chemistry & Engineering 5(1), 426-435. BESC
201610.1186/s13068-016-0559-1.Poovaiah, C. R., W. P. Bewg, W. Lan, J. Ralph, and H. D. Coleman. 2016. Sugarcane transgenics expressing MYB transcription factors show improved glucose release, Biotechnol Biofuels 9, 143. GLBRC
2016Pu, Y., X. Meng, C. G. Yoo, M. Li, and A. J. Ragauskas. 2016. Analytical methods for biomass characterization during pretreatment and bioconversion. In Valorization of lignocellulosic biomass in a biorefinery: from logistics to environmental and performance impact, 37-78. Ed. R. Kumar.BESC
201610.1534/g3.115.024950Ramstein, G. P., J. Evans, S. M. Kaeppler, R. B. Mitchell, K. P. Vogel, C. R. Buell, and M. D. Casler. 2016. Accuracy of Genomic Prediction in Switchgrass (Panicum virgatum L.) Improved by Accounting for Linkage Disequilibrium, G3 (Bethesda) 6(4), 1049-1062. GLBRC
201610.3389/fpls.2016.01525Rao, X., and R. A. Dixon. 2016. The Differences between NAD-ME and NADP-ME Subtypes of C4 Photosynthesis: More than Decarboxylating Enzymes, Front Plant Sci 7, 1525. BESC
201610.1093/jxb/erv553Rao, X., N. Lu, G. Li, J. Nakashima, Y. Tang, and R. A. Dixon. 2016. Comparative cell-specific transcriptomics reveals differentiation of C4 photosynthesis pathways in switchgrass and other C4 lineages, J Exp Bot 67(6), 1649-1662. BESC
201610.1038/ncomms12119Rautengarten, C., B. Ebert, L. Liu, S. Stonebloom, A. M. Smith-Moritz, M. Pauly, A. Orellana, H. V. Scheller, and J. L. Heazlewood. 2016. The Arabidopsis Golgi-localized GDP-L-fucose transporter is required for plant development, Nat Commun 7, 12119. JBEI
201610.1007/s11274-015-1970-7Ray, P., and K. D. Craven. 2016. Sebacina vermifera: a unique root symbiont with vast agronomic potential, World J Microbiol Biotechnol 32(1), 16. BESC
201610.1038/srep19512Reider Apel, A., M. Ouellet, H. Szmidt-Middleton, J. D. Keasling, and A. Mukhopadhyay. 2016. Evolved hexose transporter enhances xylose uptake and glucose/xylose co-utilization in Saccharomyces cerevisiae, Sci Rep 6, 19512. JBEI
201610.1016/j.fbr.2016.06.002Reilly, M. C., J. K. Magnuson, and S. E. Baker. 2016. Approaches to understanding protein hypersecretion in fungi, Fungal Biology Reviews 30(4), 145-151. JBEI
201610.1016/j.jaap.2016.07.016Rencoret, J., J. C. del Río, K. G. J. Nierop, A. Gutiérrez, and J. Ralph. 2016. Rapid Py-GC/MS assessment of the structural alterations of lignins in genetically modified plants, Journal of Analytical and Applied Pyrolysis 121, 155-164. GLBRC
201610.1073/pnas.1603941113Riley, R., S. Haridas, K. H. Wolfe, M. R. Lopes, C. T. Hittinger, M. Goker, A. A. Salamov, J. H. Wisecaver, T. M. Long, C. H. Calvey, A. L. Aerts, K. W. Barry, C. Choi, A. Clum, A. Y. Coughlan, S. Deshpande, A. P. Douglass, S. J. Hanson, H. P. Klenk, K. M. LaButti, A. Lapidus, E. A. Lindquist, A. M. Lipzen, J. P. Meier-Kolthoff, R. A. Ohm, R. P. Otillar, J. L. Pangilinan, Y. Peng, A. Rokas, C. A. Rosa, C. Scheuner, A. A. Sibirny, J. C. Slot, J. B. Stielow, H. Sun, C. P. Kurtzman, M. Blackwell, I. V. Grigoriev, and T. W. Jeffries. 2016. Comparative genomics of biotechnologically important yeasts, Proc Natl Acad Sci U S A 113(35), 9882-9887. GLBRC
201610.1002/ange.201510351Rinaldi, R., R. Jastrzebski, M. T. Clough, J. Ralph, M. Kennema, P. C. A. Bruijnincx, and B. M. Weckhuysen. 2016. Wege zur Verwertung von Lignin: Fortschritte in der Biotechnik, der Bioraffination und der Katalyse, Angewandte Chemie 128(29), 8296-8354. GLBRC
201610.1002/anie.201510351Rinaldi, R., R. Jastrzebski, M. T. Clough, J. Ralph, M. Kennema, P. C. Bruijnincx, and B. M. Weckhuysen. 2016. Paving the Way for Lignin Valorisation: Recent Advances in Bioengineering, Biorefining and Catalysis, Angew Chem Int Ed Engl 55(29), 8164-8215. GLBRC
201610.1016/j.jcat.2016.08.011Ro, I., C. Sener, T. M. Stadelman, M. R. Ball, J. M. Venegas, S. P. Burt, I. Hermans, J. A. Dumesic, and G. W. Huber. 2016. Measurement of intrinsic catalytic activity of Pt monometallic and Pt-MoO x interfacial sites over visible light enhanced PtMoO x /SiO 2 catalyst in reverse water gas shift reaction, Journal of Catalysis 344, 784-794. GLBRC
201610.1186/s12934-016-0447-1Rodriguez, S., C. M. Denby, T. Van Vu, E. E. Baidoo, G. Wang, and J. D. Keasling. 2016. ATP citrate lyase mediated cytosolic acetyl-CoA biosynthesis increases mevalonate production in Saccharomyces cerevisiae, Microb Cell Fact 15, 48. JBEI
201610.1088/1748-9326/11/6/064007Ruan, L., A. K. Bhardwaj, S. K. Hamilton, and G. P. Robertson. 2016. Nitrogen fertilization challenges the climate benefit of cellulosic biofuels, Environmental Research Letters 11(6), 064007. GLBRC
201610.1104/pp.16.00173S, M. W., S. J. Kim, L. Renna, C. A. F, D. S. T, and F. Brandizzi. 2016. Pectin Methylesterification Impacts the Relationship between Photosynthesis and Plant Growth, Plant Physiol 171(2), 833-848. GLBRC
201610.1007/s12155-016-9770-ySalazar, M. M., A. Grandis, S. Pattathil, J. L. Neto, E. L. O. Camargo, A. Alves, J. C. Rodrigues, F. Squina, J. P. F. Cairo, M. S. Buckeridge, M. G. Hahn, and G. A. G. Pereira. 2016. Eucalyptus Cell Wall Architecture: Clues for Lignocellulosic Biomass Deconstruction, BioEnergy Research 9(3), 969-979. BESC
201610.1016/j.agee.2015.10.018Sanford, G. R., L. G. Oates, P. Jasrotia, K. D. Thelen, G. P. Robertson, and R. D. Jackson. 2016. Comparative productivity of alternative cellulosic bioenergy cropping systems in the North Central USA, Agriculture, Ecosystems & Environment 216, 344-355. GLBRC
201610.1021/acs.jpcb.6b00789Sangha, A. K., L. Petridis, X. Cheng, and J. C. Smith. 2016. Relative Binding Affinities of Monolignols to Horseradish Peroxidase, J Phys Chem B 120(31), 7635-7640. BESC
201610.1128/AEM.01603-16Sardi, M., N. Rovinskiy, Y. Zhang, and A. P. Gasch. 2016. Leveraging Genetic-Background Effects in Saccharomyces cerevisiae To Improve Lignocellulosic Hydrolysate Tolerance, Appl Environ Microbiol 82(19), 5838-5849. GLBRC
201610.1016/j.biortech.2016.01.008Sarks, C., A. Higbee, J. Piotrowski, S. Xue, J. J. Coon, T. K. Sato, M. Jin, V. Balan, and B. E. Dale. 2016. Quantifying pretreatment degradation compounds in solution and accumulated by cells during solids and yeast recycling in the Rapid Bioconversion with Integrated recycling Technology process using AFEX corn stover, Bioresour Technol 205, 24-33. GLBRC
2016 10.1080/17597269.2015.1132368Sarks, C., B. D. Bals, J. Wynn, F. Teymouri, S. Schwegmann, K. Sanders, M. Jin, V. Balan, and B. E. Dale. 2016. Scaling up and benchmarking of ethanol production from pelletized pilot scale AFEX treated corn stover using Zymomonas mobilis 8b, Biofuels 7(3), 253-262. GLBRC
201610.1371/journal.pgen.1006372Sato, T. K., M. Tremaine, L. S. Parreiras, A. S. Hebert, K. S. Myers, A. J. Higbee, M. Sardi, S. J. McIlwain, I. M. Ong, R. J. Breuer, R. Avanasi Narasimhan, M. A. McGee, Q. Dickinson, A. La Reau, D. Xie, M. Tian, J. L. Reed, Y. Zhang, J. J. Coon, C. T. Hittinger, A. P. Gasch, and R. Landick. 2016. Directed Evolution Reveals Unexpected Epistatic Interactions That Alter Metabolic Regulation and Enable Anaerobic Xylose Use by Saccharomyces cerevisiae, PLoS Genet 12(10), e1006372. GLBRC
201610.1021/acscatal.6b00072Schwartz, T. J., S. D. Lyman, A. H. Motagamwala, M. A. Mellmer, and J. A. Dumesic. 2016. Selective Hydrogenation of Unsaturated Carbon-Carbon Bonds in Aromatic-Containing Platform Molecules, ACS Catalysis 6(3), 2047-2054. GLBRC
201610.1039/c5ib00232jSchwessinger, B., X. Li, T. L. Ellinghaus, L. J. Chan, T. Wei, A. Joe, N. Thomas, R. Pruitt, P. D. Adams, M. S. Chern, C. J. Petzold, C. C. Liu, and P. C. Ronald. 2016. A second-generation expression system for tyrosine-sulfated proteins and its application in crop protection, Integr Biol (Camb) 8(4), 542-545. JBEI
201610.3389/fpls.2016.00822Sekhon, R. S., M. W. Breitzman, R. R. Silva, N. Santoro, W. L. Rooney, N. de Leon, and S. M. Kaeppler. 2016. Stover Composition in Maize and Sorghum Reveals Remarkable Genetic Variation and Plasticity for Carbohydrate Accumulation, Front Plant Sci 7, 822. GLBRC
201610.1021/acscatal.5b02028.Sener, C., T. S. Wesley, A. C. Alba-Rubio, M. D. Kumbhalkar, S. H. Hakim, F. H. Ribeiro, J. T. Miller, and J. A. Dumesic. 2016. PtMo Bimetallic Catalysts Synthesized by Controlled Surface Reactions for Water Gas Shift, ACS Catalysis 6(2), 1334-1344. GLBRC
201610.1007/s12155-016-9733-3Serba, D. D., R. W. Sykes, E. L. Gjersing, S. R. Decker, G. Daverdin, K. M. Devos, E. C. Brummer, and M. C. Saha. 2016. Cell Wall Composition and Underlying QTL in an F1 Pseudo-Testcross Population of Switchgrass, BioEnergy Research 9(3), 836-850. BESC
201610.1186/s12864-016-3377-8Serba, D. D., S. R. Uppalapati, N. Krom, S. Mukherjee, Y. Tang, K. S. Mysore, and M. C. Saha. 2016. Transcriptome analysis in switchgrass discloses ecotype difference in photosynthetic efficiency, BMC Genomics 17(1), 1040. BESC
201610.1186/s13068-016-0514-1Shao, X., J. Zhou, D. G. Olson, and L. R. Lynd. 2016. A markerless gene deletion and integration system for Thermoanaerobacter ethanolicus, Biotechnol Biofuels 9, 100. BESC
201610.1534/g3.116.034744Shen, X. X., X. Zhou, J. Kominek, C. P. Kurtzman, C. T. Hittinger, and A. Rokas. 2016. Reconstructing the Backbone of the Saccharomycotina Yeast Phylogeny Using Genome-Scale Data, G3 (Bethesda) 6(12), 3927-3939. GLBRC
201610.1039/c6gc01193dShi, J., S. Pattathil, R. Parthasarathi, N. A. Anderson, J. I. Kim, S. Venketachalam, M. G. Hahn, C. Chapple, B. A. Simmons, and S. Singh. 2016. Impact of engineered lignin composition on biomass recalcitrance and ionic liquid pretreatment efficiency, Green Chemistry 18(18), 4884-4895. JBEI BESC
201610.1038/ncomms13215Shih, P. M., K. Vuu, N. Mansoori, L. Ayad, K. B. Louie, B. P. Bowen, T. R. Northen, and D. Loque. 2016. A robust gene-stacking method utilizing yeast assembly for plant synthetic biology, Nat Commun 7, 13215. JBEI
201610.1111/tpj.13176Shih, P. M., Y. Liang, and D. Loque. 2016. Biotechnology and synthetic biology approaches for metabolic engineering of bioenergy crops, Plant J 87(1), 103-117. JBEI
201610.1126/science.aaf7810Shuai, L., M. T. Amiri, Y. M. Questell-Santiago, F. Heroguel, Y. Li, H. Kim, R. Meilan, C. Chapple, J. Ralph, and J. S. Luterbacher. 2016. Formaldehyde stabilization facilitates lignin monomer production during biomass depolymerization, Science 354(6310), 329-333. GLBRC
201610.1002/cssc.201600195Shylesh, S., A. A. Gokhale, C. D. Scown, D. Kim, C. R. Ho, and A. T. Bell. 2016. From Sugars to Wheels: The Conversion of Ethanol to 1,3-Butadiene over Metal-Promoted Magnesia-Silicate Catalysts, ChemSusChem 9(12), 1462-1472. JBEI
201610.1016/j.apsoil.2016.04.018Simmons, C. W., B. Higgins, S. Staley, L. D. Joh, B. A. Simmons, S. W. Singer, J. J. Stapleton, and J. S. VanderGheynst. 2016. The role of organic matter amendment level on soil heating, organic acid accumulation, and development of bacterial communities in solarized soil, Applied Soil Ecology 106, 37-46. JBEI
201610.1105/tpc.15.00900Simpson, J. P., and J. B. Ohlrogge. 2016. A Novel Pathway for Triacylglycerol Biosynthesis Is Responsible for the Accumulation of Massive Quantities of Glycerolipids in the Surface Wax of Bayberry (Myrica pensylvanica) Fruit, Plant Cell 28(1), 248-264. GLBRC
201610.1016/j.bbalip.2016.01.022Simpson, J. P., N. Thrower, and J. B. Ohlrogge. 2016. How did nature engineer the highest surface lipid accumulation among plants? Exceptional expression of acyl-lipid-associated genes for the assembly of extracellular triacylglycerol by Bayberry (Myrica pensylvanica) fruits, Biochim Biophys Acta 1861(9 Pt B), 1243-1252. GLBRC
201610.1016/j.landusepol.2015.09.027Skevas, T., N. J. Hayden, S. M. Swinton, and F. Lupi. 2016. Landowner willingness to supply marginal land for bioenergy production, Land Use Policy 50, 507-517. GLBRC
201610.1111/gcbb.12320Skevas, T., S. M. Swinton, S. Tanner, G. Sanford, and K. D. Thelen. 2016. Investment risk in bioenergy crops, GCB Bioenergy 8(6), 1162-1177. GLBRC
201610.3791/54227Slininger, P. J., M. A. Shea-Andersh, S. R. Thompson, B. S. Dien, C. P. Kurtzman, L. D. Sousa, and V. Balan. 2016. Techniques for the Evolution of Robust Pentose-fermenting Yeast for Bioconversion of Lignocellulose to Ethanol, J Vis Exp(116). GLBRC
201610.1021/acs.jpcb.5b09770Smith, M. D., B. Mostofian, L. Petridis, X. Cheng, and J. C. Smith. 2016. Molecular Driving Forces behind the Tetrahydrofuran-Water Miscibility Gap, J Phys Chem B 120(4), 740-747. BESC
201610.1039/c5gc01952dSmith, M. D., B. Mostofian, X. Cheng, L. Petridis, C. M. Cai, C. E. Wyman, and J. C. Smith. 2016. Cosolvent pretreatment in cellulosic biofuel production: effect of tetrahydrofuran-water on lignin structure and dynamics, Green Chemistry 18(5), 1268-1277. BESC
201610.1039/c5cp07088kSmith, M. D., L. Petridis, X. Cheng, B. Mostofian, and J. C. Smith. 2016. Enhanced sampling simulation analysis of the structure of lignin in the THF-water miscibility gap, Phys Chem Chem Phys 18(9), 6394-6398. BESC
201610.1128/JB.01025-15Spero, M. A., J. R. Brickner, J. T. Mollet, T. Pisithkul, D. Amador-Noguez, and T. J. Donohue. 2016. Different Functions of Phylogenetically Distinct Bacterial Complex I Isozymes, J Bacteriol 198(8), 1268-1280. GLBRC
2016Spero, M. A., S. Imam, D. R. Noguera, and T. J. Donohue. 2016. Electron partitioning in anoxic phototrophic bacteria. In Cytochrome Complexes: Evolution, Structures, Energy Transduction, and Signaling, 679-700. Eds. W. A. Cramer, and T. Kallas. Springer Verlag.GLBRC
201610.1016/j.biombioe.2016.06.012Stahlheber, K. A., B. Watson, T. L. Dickson, R. Disney, and K. L. Gross. 2016. Balancing biofuel production and biodiversity: Harvesting frequency effects on production and community composition in planted tallgrass prairie, Biomass and Bioenergy 92, 98-105. GLBRC
201610.1038/nbt.3683Stefely, J. A., N. W. Kwiecien, E. C. Freiberger, A. L. Richards, A. Jochem, M. J. P. Rush, A. Ulbrich, K. P. Robinson, P. D. Hutchins, M. T. Veling, X. Guo, Z. A. Kemmerer, K. J. Connors, E. A. Trujillo, J. Sokol, H. Marx, M. S. Westphall, A. S. Hebert, D. J. Pagliarini, and J. J. Coon. 2016. Mitochondrial protein functions elucidated by multi-omic mass spectrometry profiling, Nat Biotechnol 34(11), 1191-1197. GLBRC
201610.3835/plantgenome2015.04.0025Stelpflug, S. C., R. S. Sekhon, B. Vaillancourt, C. N. Hirsch, C. R. Buell, N. de Leon, and S. M. Kaeppler. 2016. An Expanded Maize Gene Expression Atlas based on RNA Sequencing and its Use to Explore Root Development, Plant Genome 9(1). GLBRC
201610.1186/s12870-016-0780-x.Stonebloom, S., B. Ebert, G. Xiong, S. Pattathil, D. Birdseye, J. Lao, M. Pauly, M. G. Hahn, J. L. Heazlewood, and H. V. Scheller. 2016. A DUF-246 family glycosyltransferase-like gene affects male fertility and the biosynthesis of pectic arabinogalactans, BMC Plant Biol 16, 90. BESC JBEI
201610.1039/c6ee00913aSun, J., N. V. S. N. M. Konda, J. Shi, R. Parthasarathi, T. Dutta, F. Xu, C. D. Scown, B. A. Simmons, and S. Singh. 2016. CO2 enabled process integration for the production of cellulosic ethanol using bionic liquids, Energy & Environmental Science 9(9), 2822-2834. JBEI
201610.1039/c6gc02258hSun, J., T. Dutta, R. Parthasarathi, K. H. Kim, N. Tolic, R. K. Chu, N. G. Isern, J. R. Cort, B. A. Simmons, and S. Singh. 2016. Rapid room temperature solubilization and depolymerization of polymeric lignin at high loadings, Green Chemistry 18(22), 6012-6020. JBEI
201610.1002/bit.25690Sun, L., S. Singh, M. Joo, M. Vega-Sanchez, P. Ronald, B. A. Simmons, P. Adams, and M. Auer. 2016. Non-invasive imaging of cellulose microfibril orientation within plant cell walls by polarized Raman microspectroscopy, Biotechnol Bioeng 113(1), 82-90. JBEI
2016 10.1039/c6gc00977hSun, Q., R. Khunsupat, K. Akato, J. Tao, N. Labbé, N. C. Gallego, J. J. Bozell, T. G. Rials, G. A. Tuskan, T. J. Tschaplinski, A. K. Naskar, Y. Pu, and A. J. Ragauskas. 2016. A study of poplar organosolv lignin after melt rheology treatment as carbon fiber precursors, Green Chemistry 18(18), 5015-5024. BESC
201610.7717/peerj.2446Thomas, N. C., B. Schwessinger, F. Liu, H. Chen, T. Wei, Y. P. Nguyen, I. W. F. Shaker, and P. C. Ronald. 2016. XA21-specific induction of stress-related genes following Xanthomonas infection of detached rice leaves, PeerJ 4, e2446. JBEI
201610.1186/s13068-016-0607-xThompson, R. A., S. Dahal, S. Garcia, I. Nookaew, and C. T. Trinh. 2016. Exploring complex cellular phenotypes and model-guided strain design with a novel genome-scale metabolic model of Clostridium thermocellum DSM 1313 implementing an adjustable cellulosome, Biotechnol Biofuels 9(1), 194. BESC
201610.1186/s13068-016-0528-8Tian, L., B. Papanek, D. G. Olson, T. Rydzak, E. K. Holwerda, T. Zheng, J. Zhou, M. Maloney, N. Jiang, R. J. Giannone, R. L. Hettich, A. M. Guss, and L. R. Lynd. 2016. Simultaneous achievement of high ethanol yield and titer in Clostridium thermocellum, Biotechnol Biofuels 9, 116. BESC
201610.1128/AEM.02130-16Tian, L., J. Lo, X. Shao, T. Zheng, D. G. Olson, and L. R. Lynd. 2016. Ferredoxin:NAD+ Oxidoreductase of Thermoanaerobacterium saccharolyticum and Its Role in Ethanol Formation, Appl Environ Microbiol 82(24), 7134-7141. BESC
201610.1021/acs.energyfuels.6b00560Tolbert, A. K., T. Ma, U. C. Kalluri, and A. J. Ragauskas. 2016. Determining the Syringyl/Guaiacyl Lignin Ratio in the Vessel and Fiber Cell Walls of Transgenic Populus Plants, Energy & Fuels 30(7), 5716-5720. BESC
201610.1002/bit.25831Torr, K. M., K. T. Love, B. A. Simmons, and S. J. Hill. 2016. Structural features affecting the enzymatic digestibility of pine wood pretreated with ionic liquids, Biotechnol Bioeng 113(3), 540-549. JBEI
201610.1016/j.coche.2016.07.005Trinh, C. T., and B. Mendoza. 2016. Modular cell design for rapid, efficient strain engineering toward industrialization of biology, Current Opinion in Chemical Engineering 14, 18-25. BESC
201610.1016/j.biombioe.2015.12.004Tumbalam, P., K. D. Thelen, A. Adkins, B. Dale, V. Balan, C. Gunawan, and J. Gao. 2016. Corn stover ethanol yield as affected by grain yield, Bt trait, and environment, Biomass and Bioenergy 85, 119-125. GLBRC
201610.1080/15427528.2016.1189472Tumbalam, P., K. Hard, and K. D. Thelen. 2016. Integrating Winter Annual Cereal Rye or Triticale into a Corn Forage Biofuel Production System, Journal of Crop Improvement 30(5), 526-540. GLBRC
201610.1128/genomeA.01043-16Utturkar, S. M., E. A. Bayer, I. Borovok, R. Lamed, R. A. Hurt, M. L. Land, D. M. Klingeman, D. Elias, J. Zhou, M. Huntemann, A. Clum, M. Pillay, K. Palaniappan, N. Varghese, N. Mikhailova, D. Stamatis, T. B. Reddy, C. Y. Ngan, C. Daum, N. Shapiro, V. Markowitz, N. Ivanova, N. Kyrpides, T. Woyke, and S. D. Brown. 2016. Application of Long Sequence Reads To Improve Genomes for Clostridium thermocellum AD2, Clostridium thermocellum LQRI, and Pelosinus fermentans R7, Genome Announc 4(5). BESC
201610.1104/pp.15.01356Vandavasi, V. G., D. K. Putnam, Q. Zhang, L. Petridis, W. T. Heller, B. T. Nixon, C. H. Haigler, U. Kalluri, L. Coates, P. Langan, J. C. Smith, J. Meiler, and H. O'Neill. 2016. A Structural Study of CESA1 Catalytic Domain of Arabidopsis Cellulose Synthesis Complex: Evidence for CESA Trimers, Plant Physiol 170(1), 123-135. BESC
201610.1007/s10295-016-1797-8Vinay-Lara, E., S. Wang, L. Bai, E. Phrommao, J. R. Broadbent, and J. L. Steele. 2016. Lactobacillus casei as a biocatalyst for biofuel production, J Ind Microbiol Biotechnol 43(9), 1205-1213. GLBRC
201610.1104/pp.16.00845Walker, A. M., S. A. Sattler, M. Regner, J. P. Jones, J. Ralph, W. Vermerris, S. E. Sattler, and C. Kang. 2016. The Structure and Catalytic Mechanism of Sorghum bicolor Caffeoyl-CoA O-Methyltransferase, Plant Physiol 172(1), 78-92. GLBRC
201610.1016/j.bbrep.2016.08.009Warner, L., E. Gjersing, S. E. Follett, K. W. Elliott, S. V. Dzyuba, and K. Varga. 2016. The effects of high concentrations of ionic liquid on GB1 protein structure and dynamics probed by high-resolution magic-angle-spinning NMR spectroscopy, Biochem Biophys Rep 8, 75-80. BESC
201610.1111/mpp.12368Wei, T., M. Chern, F. Liu, and P. C. Ronald. 2016. Suppression of bacterial infection in rice by treatment with a sulfated peptide, Mol Plant Pathol 17(9), 1493-1498. JBEI
201610.7717/peerj.2507Wei, T., T. C. Chen, Y. T. Ho, and P. C. Ronald. 2016. Mutation of the rice XA21 predicted nuclear localization sequence does not affect resistance to Xanthomonas oryzae pv. oryzae, PeerJ 4, e2507. JBEI
201610.3390/insects7020023Wenninger, A., T. N. Kim, B. J. Spiesman, and C. Gratton. 2016. Contrasting Foraging Patterns: Testing Resource-Concentration and Dilution Effects with Pollinators and Seed Predators, Insects 7(2). GLBRC
201610.3389/fpls.2016.00675Willis, J. D., M. Mazarei, and C. N. Stewart, Jr. 2016. Transgenic Plant-Produced Hydrolytic Enzymes and the Potential of Insect Gut-Derived Hydrolases for Biofuels, Front Plant Sci 7, 675. BESC
2016Wilson, D. B. 2016. Microbial Diversity and Cellulase Production. In New and Future Developments in Microbial Biotechnology and Bioengineering. Ed. V. Gupta. Elsevier.BESC
201610.1093/molbev/msw073Wisecaver, J. H., W. G. Alexander, S. B. King, C. T. Hittinger, and A. Rokas. 2016. Dynamic Evolution of Nitric Oxide Detoxifying Flavohemoglobins, a Family of Single-Protein Metabolic Modules in Bacteria and Eukaryotes, Mol Biol Evol 33(8), 1979-1987. GLBRC
201610.1128/genomeA.01297-16Woo, H. L., K. B. O'Dell, S. Utturkar, K. R. McBride, M. Huntemann, A. Clum, M. Pillay, K. Palaniappan, N. Varghese, N. Mikhailova, D. Stamatis, T. B. Reddy, C. Y. Ngan, C. Daum, N. Shapiro, V. Markowitz, N. Ivanova, N. Kyrpides, T. Woyke, S. D. Brown, and T. C. Hazen. 2016. Near-Complete Genome Sequence of Thalassospira sp. Strain KO164 Isolated from a Lignin-Enriched Marine Sediment Microcosm, Genome Announc 4(6). BESC
201610.1104/pp.15.01279Woods, D. P., M. A. McKeown, Y. Dong, J. C. Preston, and R. M. Amasino. 2016. Evolution of VRN2/Ghd7-Like Genes in Vernalization-Mediated Repression of Grass Flowering, Plant Physiol 170(4), 2124-2135. GLBRC
201610.1002/aic.15300Wu, W., C. A. Henao, and C. T. Maravelias. 2016. A superstructure representation, generation, and modeling framework for chemical process synthesis, AIChE Journal 62(9), 3199-3214. GLBRC
201610.1371/journal.pone.0146983Wu, W., W. Tran, C. A. Taatjes, J. Alonso-Gutierrez, T. S. Lee, and J. M. Gladden. 2016. Rapid Discovery and Functional Characterization of Terpene Synthases from Four Endophytic Xylariaceae, PLoS One 11(2), e0146983. JBEI
201610.1093/bioinformatics/btv638Wu, Y. W., B. A. Simmons, and S. W. Singer. 2016. MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets, Bioinformatics 32(4), 605-607. JBEI
201610.1128/mSystems.00120-16Wu, Y. W., B. Higgins, C. Yu, A. P. Reddy, S. Ceballos, L. D. Joh, B. A. Simmons, S. W. Singer, and J. S. VanderGheynst. 2016. Ionic Liquids Impact the Bioenergy Feedstock-Degrading Microbiome and Transcription of Enzymes Relevant to Polysaccharide Hydrolysis, mSystems 1(6). JBEI
201610.3389/fpls.2016.00520Wuddineh, W. A., M. Mazarei, J. Y. Zhang, G. B. Turner, R. W. Sykes, S. R. Decker, M. F. Davis, M. K. Udvardi, and C. N. Stewart, Jr. 2016. Identification and Overexpression of a Knotted1-Like Transcription Factor in Switchgrass (Panicum virgatum L.) for Lignocellulosic Feedstock Improvement, Front Plant Sci 7, 520. BESC
201610.1073/pnas.1605482113Xiong, W., P. P. Lin, L. Magnusson, L. Warner, J. C. Liao, P. C. Maness, and K. J. Chou. 2016. CO2-fixing one-carbon metabolism in a cellulose-degrading bacterium Clostridium thermocellum, Proc Natl Acad Sci U S A 113(46), 13180-13185. BESC
201610.1039/c5ee02940fXu, F., J. Sun, N. V. S. N. M. Konda, J. Shi, T. Dutta, C. D. Scown, B. A. Simmons, and S. Singh. 2016. Transforming biomass conversion with ionic liquids: process intensification and the development of a high-gravity, one-pot process for the production of cellulosic ethanol, Energy & Environmental Science 9(3), 1042-1049. JBEI
201610.1126/sciadv.1501254Xu, Q., M. G. Resch, K. Podkaminer, S. Yang, J. O. Baker, B. S. Donohoe, C. Wilson, D. M. Klingeman, D. G. Olson, S. R. Decker, R. J. Giannone, R. L. Hettich, S. D. Brown, L. R. Lynd, E. A. Bayer, M. E. Himmel, and Y. J. Bomble. 2016. Dramatic performance of Clostridium thermocellum explained by its wide range of cellulase modalities, Sci Adv 2(2), e1501254. BESC
201610.1111/gcbb.12303Xue, C., C. R. Penton, B. Zhang, M. Zhao, D. E. Rothstein, D. J. Mladenoff, J. A. Forrester, Q. Shen, and J. M. Tiedje. 2016. Soil fungal and bacterial responses to conversion of open land to short-rotation woody biomass crops, GCB Bioenergy 8(4), 723-736. GLBRC
201610.1111/nph.13898Yang, J., E. Worley, Q. Ma, J. Li, I. Torres-Jerez, G. Li, P. X. Zhao, Y. Xu, Y. Tang, and M. Udvardi. 2016. Nitrogen remobilization and conservation, and underlying senescence-associated gene expression in the perennial switchgrass Panicum virgatum, New Phytol 211(1), 75-89. BESC
201610.1111/1751-7915.12408Yang, S., Q. Fei, Y. Zhang, L. M. Contreras, S. M. Utturkar, S. D. Brown, M. E. Himmel, and M. Zhang. 2016. Zymomonas mobilis as a model system for production of biofuels and biochemicals, Microb Biotechnol 9(6), 699-717. GLBRC BESC
201610.1038/srep20469Yang, Y., Y. Liang, X. Han, T. Y. Chiu, A. Ghosh, H. Chen, and M. Tang. 2016. The roles of arbuscular mycorrhizal fungi (AMF) in phytoremediation and tree-herb interactions in Pb contaminated soil, Sci Rep 6, 20469. JBEI
201610.1016/j.ijadhadh.2016.05.002Yelle, D. J., and J. Ralph. 2016. Characterizing phenol-formaldehyde adhesive cure chemistry within the wood cell wall, International Journal of Adhesion and Adhesives 70, 26-36. GLBRC
201610.1002/cssc.201600135Yoo, C. G., Y. Pu, M. Li, and A. J. Ragauskas. 2016. Elucidating Structural Characteristics of Biomass using Solution-State 2 D NMR with a Mixture of Deuterated Dimethylsulfoxide and Hexamethylphosphoramide, ChemSusChem 9(10), 1090-1095. BESC
201610.1007/s00253-016-7955-0Yu, C., B. A. Simmons, S. W. Singer, M. P. Thelen, and J. S. VanderGheynst. 2016. Ionic liquid-tolerant microorganisms and microbial communities for lignocellulose conversion to bioproducts, Appl Microbiol Biotechnol 100(24), 10237-10249. JBEI
201610.1021/acs.biomac.6b00256Yue, F., F. Lu, S. Ralph, and J. Ralph. 2016. Identification of 4-O-5-Units in Softwood Lignins via Definitive Lignin Models and NMR, Biomacromolecules 17(6), 1909-1920. GLBRC
201610.1038/ja.2016.64Yuzawa, S., J. D. Keasling, and L. Katz. 2016. Insights into polyketide biosynthesis gained from repurposing antibiotic-producing polyketide synthases to produce fuels and chemicals, J Antibiot (Tokyo) 69(7), 494-499. JBEI
201610.1038/srep31362Zargar, K., R. Saville, R. M. Phelan, S. G. Tringe, C. J. Petzold, J. D. Keasling, and H. R. Beller. 2016. In vitro Characterization of Phenylacetate Decarboxylase, a Novel Enzyme Catalyzing Toluene Biosynthesis in an Anaerobic Microbial Community, Sci Rep 6, 31362. JBEI
201610.1186/s13068-016-0669-9.Zeng, Y., J. M. Yarbrough, A. Mittal, M. P. Tucker, T. B. Vinzant, S. R. Decker, and M. E. Himmel. 2016. In situ label-free imaging of hemicellulose in plant cell walls using stimulated Raman scattering microscopy, Biotechnol Biofuels 9, 256. BESC
201610.1111/gcbb.12269.Zenone, T., D. Zona, I. Gelfand, B. Gielen, M. Camino-Serrano, and R. Ceulemans. 2016. CO2 uptake is offset by CH4 and N2O emissions in a poplar short-rotation coppice, GCB Bioenergy 8(3), 524-538. GLBRC
201610.1016/j.meteno.2015.11.001.Zhang, J., E. Kao, G. Wang, E. E. K. Baidoo, M. Chen, and J. D. Keasling. 2016. Metabolic engineering of Escherichia coli for the biosynthesis of 2-pyrrolidone, Metab Eng Commun 3, 1-7. JBEI
201610.1111/tpj.13233Zhang, M., X. Cao, Q. Jia, and J. Ohlrogge. 2016. FUSCA3 activates triacylglycerol accumulation in Arabidopsis seedlings and tobacco BY2 cells, Plant J 88(1), 95-107. GLBRC
201610.1039/c6ra00745gZhang, W., N. Sathitsuksanoh, B. A. Simmons, C. E. Frazier, J. R. Barone, and S. Renneckar. 2016. Revealing the thermal sensitivity of lignin during glycerol thermal processing through structural analysis, RSC Advances 6(36), 30234-30246. JBEI
201610.1155/2016/4130376Zhang, X., R. Jain, and G. Li. 2016. Roles of Rack1 Proteins in Fungal Pathogenesis, Biomed Res Int 2016, 4130376. JBEI
201610.1039/c6gc01813kZhao, W., B. Simmons, S. Singh, A. Ragauskas, and G. Cheng. 2016. From lignin association to nano-/micro-particle preparation: extracting higher value of lignin, Green Chemistry 18(21), 5693-5700. JBEI
201610.1128/JB.00542-16Zheng, T., D. G. Olson, S. J. Murphy, X. Shao, L. Tian, and L. R. Lynd. 2016. Both adhE and a separate NADPH-dependent alcohol dehydrogenase (adhA) are necessary for high ethanol production in Thermoanaerobacterium saccharolyticum, J Bacteriol. BESC
201610.1534/g3.116.034249Zhou, X., D. Peris, J. Kominek, C. P. Kurtzman, C. T. Hittinger, and A. Rokas. 2016. In Silico Whole Genome Sequencer and Analyzer (iWGS): a Computational Pipeline to Guide the Design and Analysis of de novo Genome Sequencing Studies, G3 (Bethesda) 6(11), 3655-3662. GLBRC
201610.1104/pp.16.00168Zhu, Y., J. Yan, W. Liu, L. Liu, Y. Sheng, Y. Sun, Y. Li, H. V. Scheller, M. Jiang, X. Hou, L. Ni, and A. Zhang. 2016. Phosphorylation of a NAC Transcription Factor by a Calcium/Calmodulin-Dependent Protein Kinase Regulates Abscisic Acid-Induced Antioxidant Defense in Maize, Plant Physiol 171(3), 1651-1664. JBEI
201610.1128/AEM.01298-16Zhu, Y., L. Han, K. L. Hefferon, N. R. Silvaggi, D. B. Wilson, and M. J. McBride. 2016. Periplasmic Cytophaga hutchinsonii Endoglucanases Are Required for Use of Crystalline Cellulose as the Sole Source of Carbon and Energy, Appl Environ Microbiol 82(15), 4835-4845. BESC
201610.1007/s12155-016-9713-7Ziebell, A., E. Gjersing, M. Hinchee, R. Katahira, R. W. Sykes, D. K. Johnson, and M. F. Davis. 2016. Downregulation of p-Coumaroyl Quinate/Shikimate 3'-Hydroxylase (C3'H) or Cinnamate-4-hydrolylase (C4H) in Eucalyptus urophylla?×?Eucalyptus grandis Leads to Increased Extractability, BioEnergy Research 9(2), 691-699. BESC
201610.1016/j.bbalip.2016.02.008Zienkiewicz, K., Z. Y. Du, W. Ma, K. Vollheyde, and C. Benning. 2016. Stress-induced neutral lipid biosynthesis in microalgae - Molecular, cellular and physiological insights, Biochim Biophys Acta 1861(9 Pt B), 1269-1281. GLBRC
201510.1111/gcbb.12239Abraha, M., J. Chen, H. Chu, T. Zenone, R. John, Y.-J. Su, S. K. Hamilton, and G. P. Robertson. 2015. Evapotranspiration of annual and perennial biofuel crops in a variable climate, GCB Bioenergy 7(6), 1344-1356. GLBRC
201510.1021/acs.jproteome.5b00823Abraham, P. E., X. Wang, P. Ranjan, I. Nookaew, B. Zhang, G. A. Tuskan, and R. L. Hettich. 2015. Integrating mRNA and Protein Sequencing Enables the Detection and Quantitative Profiling of Natural Protein Sequence Variants of Populus trichocarpa, J Proteome Res 14(12), 5318-5326. BESC
201510.1007/s10646-015-1543-4Akinosho, H., T. Rydzak, A. Borole, A. Ragauskas, and D. Close. 2015. Toxicological challenges to microbial bioethanol production and strategies for improved tolerance, Ecotoxicology 24(10), 2156-2174. BESC
201510.1107/S1399004715013760Alahuhta, M., L. E. Taylor, 2nd, R. Brunecky, D. W. Sammond, W. Michener, M. W. Adams, M. E. Himmel, Y. J. Bomble, and V. Lunin. 2015. The catalytic mechanism and unique low pH optimum of Caldicellulosiruptor bescii family 3 pectate lyase, Acta Crystallogr D Biol Crystallogr 71(Pt 9), 1946-1954. BESC
201510.1016/j.ymben.2014.11.011Alonso-Gutierrez, J., E. M. Kim, T. S. Batth, N. Cho, Q. Hu, L. J. G. Chan, C. J. Petzold, N. J. Hillson, P. D. Adams, J. D. Keasling, H. Garcia Martin, and T. S. Lee. 2015. Principal component analysis of proteomics (PCAP) as a tool to direct metabolic engineering, Metab Eng 28, 123-133. JBEI
201510.1105/tpc.15.00373Anderson, N. A., Y. Tobimatsu, P. N. Ciesielski, E. Ximenes, J. Ralph, B. S. Donohoe, M. Ladisch, and C. Chapple. 2015. Manipulation of Guaiacyl and Syringyl Monomer Biosynthesis in an Arabidopsis Cinnamyl Alcohol Dehydrogenase Mutant Results in Atypical Lignin Biosynthesis and Modified Cell Wall Structure, Plant Cell 27(8), 2195-2209. GLBRC
201510.1002/bit.25604Araya, F., E. Troncoso, R. T. Mendonca, and J. Freer. 2015. Condensed lignin structures and re-localization achieved at high severities in autohydrolysis of Eucalyptus globulus wood and their relationship with cellulose accessibility, Biotechnol Bioeng 112(9), 1783-1791. GLBRC
201510.1002/bbb.1524Archambault-Léger, V., Z. Losordo, and L. R. Lynd. 2015. Energy, sugar dilution, and economic analysis of hot water flow-through pre-treatment for producing biofuel from sugarcane residues, Biofuels, Bioproducts and Biorefining 9(1), 95-108. BESC
201510.1021/acs.est.5b02062Austin, S., W. S. Kontur, A. Ulbrich, J. Z. Oshlag, W. Zhang, A. Higbee, Y. Zhang, J. J. Coon, D. B. Hodge, T. J. Donohue, and D. R. Noguera. 2015. Metabolism of Multiple Aromatic Compounds in Corn Stover Hydrolysate by Rhodopseudomonas palustris, Environ Sci Technol 49(14), 8914-8922. GLBRC
201510.1371/journal.pone.0134752Aylward, F. O., L. Khadempour, D. M. Tremmel, B. R. McDonald, C. D. Nicora, S. Wu, R. J. Moore, D. J. Orton, M. E. Monroe, P. D. Piehowski, S. O. Purvine, R. D. Smith, M. S. Lipton, K. E. Burnum-Johnson, and C. R. Currie. 2015. Enrichment and Broad Representation of Plant Biomass-Degrading Enzymes in the Specialized Hyphal Swellings of Leucoagaricus gongylophorus, the Fungal Symbiont of Leaf-Cutter Ants, PLoS One 10(8), e0134752. GLBRC
201510.1093/molbev/msv168Baker, E., B. Wang, N. Bellora, D. Peris, A. B. Hulfachor, J. A. Koshalek, M. Adams, D. Libkind, and C. T. Hittinger. 2015. The Genome Sequence of Saccharomyces eubayanus and the Domestication of Lager-Brewing Yeasts, Mol Biol Evol 32(11), 2818-2831. GLBRC
201510.1128/genomeA.00074-15Baker, S. E., W. Schackwitz, A. Lipzen, J. Martin, S. Haridas, K. LaButti, I. V. Grigoriev, B. A. Simmons, and K. McCluskey. 2015. Draft Genome Sequence of Neurospora crassa Strain FGSC 73, Genome Announc 3(2). JBEI
201510.1002/cssc.201402752Bali, G., X. Meng, J. I. Deneff, Q. Sun, and A. J. Ragauskas. 2015. The effect of alkaline pretreatment methods on cellulose structure and accessibility, ChemSusChem 8(2), 275-279. BESC
2015Bandaru, V., C. Izaurralde, and K. Zhao. 2015. Biomass potential of switchgrass and miscanthus on the USA's marginal lands. In Sustainable Biofuels: An Ecological Assessment of Future Energy, 299-317. DeGruyter.GLBRC
201510.1016/j.chembiol.2015.06.022Barajas, J. F., R. M. Phelan, A. J. Schaub, J. T. Kliewer, P. J. Kelly, D. R. Jackson, R. Luo, J. D. Keasling, and S. C. Tsai. 2015. Comprehensive Structural and Biochemical Analysis of the Terminal Myxalamid Reductase Domain for the Engineered Production of Primary Alcohols, Chem Biol 22(8), 1018-1029. JBEI
201510.1007/s12155-014-9570-1Baxter, H. L., C. R. Poovaiah, K. L. Yee, M. Mazarei, M. Rodriguez, O. A. Thompson, H. Shen, G. B. Turner, S. R. Decker, R. W. Sykes, F. Chen, M. F. Davis, J. R. Mielenz, B. H. Davison, R. A. Dixon, and C. N. Stewart. 2015. Field Evaluation of Transgenic Switchgrass Plants Overexpressing PvMYB4 for Reduced Biomass Recalcitrance, BioEnergy Research 8(3), 910-921. BESC
201510.1186/s12711-015-0105-9Beissinger, T. M., G. J. Rosa, S. M. Kaeppler, D. Gianola, and N. de Leon. 2015. Defining window-boundaries for genomic analyses using smoothing spline techniques, Genet Sel Evol 47, 30. GLBRC
201510.1186/s13068-015-0267-2Bekiaris, G., J. Lindedam, C. Peltre, S. R. Decker, G. B. Turner, J. Magid, and S. Bruun. 2015. Rapid estimation of sugar release from winter wheat straw during bioethanol production using FTIR-photoacoustic spectroscopy, Biotechnol Biofuels 8, 85. BESC
201510.1039/c5np00068hBeller, H. R., T. S. Lee, and L. Katz. 2015. Natural products as biofuels and bio-based chemicals: fatty acids and isoprenoids, Nat Prod Rep 32(10), 1508-1526. JBEI
201510.1074/jbc.M114.623579Bianchetti, C. M., T. E. Takasuka, S. Deutsch, H. S. Udell, E. J. Yik, L. F. Bergeman, and B. G. Fox. 2015. Active site and laminarin binding in glycoside hydrolase family 55, J Biol Chem 290(19), 11819-11832. GLBRC
201510.1186/s40793-015-0100-3Billings, A. F., J. L. Fortney, T. C. Hazen, B. Simmons, K. W. Davenport, L. Goodwin, N. Ivanova, N. C. Kyrpides, K. Mavromatis, T. Woyke, and K. M. DeAngelis. 2015. Genome sequence and description of the anaerobic lignin-degrading bacterium Tolumonas lignolytica sp. nov, Stand Genomic Sci 10, 106. JBEI
201510.1186/s13068-015-0218-yBiswal, A. K., Z. Hao, S. Pattathil, X. Yang, K. Winkeler, C. Collins, S. S. Mohanty, E. A. Richardson, I. Gelineo-Albersheim, K. Hunt, D. Ryno, R. W. Sykes, G. B. Turner, A. Ziebell, E. Gjersing, W. Lukowitz, M. F. Davis, S. R. Decker, M. G. Hahn, and D. Mohnen. 2015. Downregulation of GAUT12 in Populus deltoides by RNA silencing results in reduced recalcitrance, increased growth and reduced xylan and pectin in a woody biofuel feedstock, Biotechnol Biofuels 8, 41. BESC
201510.1186/s13068-015-0204-4Biswas, R., T. Zheng, D. G. Olson, L. R. Lynd, and A. M. Guss. 2015. Elimination of hydrogenase active site assembly blocks H2 production and increases ethanol yield in Clostridium thermocellum, Biotechnol Biofuels 8, 20. BESC
201510.1074/jbc.M115.641480Blumer-Schuette, S. E., M. Alahuhta, J. M. Conway, L. L. Lee, J. V. Zurawski, R. J. Giannone, R. L. Hettich, V. V. Lunin, M. E. Himmel, and R. M. Kelly. 2015. Discrete and structurally unique proteins (tapirins) mediate attachment of extremely thermophilic Caldicellulosiruptor species to cellulose, J Biol Chem 290(17), 10645-10656. BESC
2015Brown, S. D., K. B. Sander, C.-W. Wu, and A. M. Guss. 2015. Clostridium thermocellum: Engineered for the Production of Bioethanol. In Direct Microbial Conversion of Biomass to Advanced Biofuels, 321-333. Ed. M. E. Himmel. Elsevier.BESC
201510.1186/s40793-015-0031-zBrumm, P. J., M. L. Land, and D. A. Mead. 2015. Complete genome sequence of Geobacillus thermoglucosidasius C56-YS93, a novel biomass degrader isolated from obsidian hot spring in Yellowstone National Park, Stand Genomic Sci 10, 73. GLBRC
201510.3389/fmicb.2015.00430Brumm, P. J., P. De Maayer, D. A. Mead, and D. A. Cowan. 2015. Genomic analysis of six new Geobacillus strains reveals highly conserved carbohydrate degradation architectures and strategies, Front Microbiol 6, 430. GLBRC
201510.1186/s40793-015-0075-0Brumm, P., M. L. Land, L. J. Hauser, C. D. Jeffries, Y. J. Chang, and D. A. Mead. 2015. Complete genome sequences of Geobacillus sp. Y412MC52, a xylan-degrading strain isolated from obsidian hot spring in Yellowstone National Park, Stand Genomic Sci 10, 81. GLBRC
201510.1007/s12155-015-9585-2Brumm, P., M. L. Land, L. J. Hauser, C. D. Jeffries, Y.-J. Chang, and D. A. Mead. 2015. Complete Genome Sequence of Geobacillus strain Y4.1MC1, a Novel CO-Utilizing Geobacillus thermoglucosidasius Strain Isolated from Bath Hot Spring in Yellowstone National Park, BioEnergy Research 8(3), 1039-1045. GLBRC
201510.1007/s12155-015-9584-3Bukhman, Y. V., N. W. DiPiazza, J. Piotrowski, J. Shao, A. G. W. Halstead, M. D. Bui, E. Xie, and T. K. Sato. 2015. Modeling Microbial Growth Curves with GCAT, BioEnergy Research 8(3), 1022-1030. GLBRC
201510.1021/acssuschemeng.5b00473Caes, B. R., R. E. Teixeira, K. G. Knapp, and R. T. Raines. 2015. Biomass to Furanics: Renewable Routes to Chemicals and Fuels, ACS Sustainable Chemistry & Engineering 3(11), 2591-2605. GLBRC
201510.1038/ngeo2553Campioli, M., S. Vicca, S. Luyssaert, J. Bilcke, E. Ceschia, F. S. Chapin Iii, P. Ciais, M. Fernández-Martínez, Y. Malhi, M. Obersteiner, D. Olefeldt, D. Papale, S. L. Piao, J. Peñuelas, P. F. Sullivan, X. Wang, T. Zenone, and I. A. Janssens. 2015. Biomass production efficiency controlled by management in temperate and boreal ecosystems, Nature Geoscience 8(11), 843-846. GLBRC
201510.1039/c4cp05004eCarmona, C., P. Langan, J. C. Smith, and L. Petridis. 2015. Why genetic modification of lignin leads to low-recalcitrance biomass, Phys Chem Chem Phys 17(1), 358-364. BESC
2015Carpita, N. S., J. Ralph, and M. McCann. 2015. The Cell Wall. In Biochemistry and Molecuar Biology of Plants, 2nd ed., 45-110. Eds. W. Gruissem, B. B. Buchanan, and R. L. Jones. Wiley.GLBRC
201510.1007/s12155-015-9580-7Casler, M. D., W. Vermerris, and R. A. Dixon. 2015. Replication Concepts for Bioenergy Research Experiments, BioEnergy Research 8(1), 1-16. BESC
201510.1093/jxb/erv269Cass, C. L., A. Peraldi, P. F. Dowd, Y. Mottiar, N. Santoro, S. D. Karlen, Y. V. Bukhman, C. E. Foster, N. Thrower, L. C. Bruno, O. V. Moskvin, E. T. Johnson, M. E. Willhoit, M. Phutane, J. Ralph, S. D. Mansfield, P. Nicholson, and J. C. Sedbrook. 2015. Effects of PHENYLALANINE AMMONIA LYASE (PAL) knockdown on cell wall composition, biomass digestibility, and biotic and abiotic stress responses in Brachypodium, J Exp Bot 66(14), 4317-4335. GLBRC
201510.1007/s12155-015-9674-2Chen, X., Q. Ma, X. Rao, Y. Tang, Y. Wang, G. Li, C. Zhang, X. Mao, R. A. Dixon, and Y. Xu. 2015. Genome-Scale Identification of Cell-Wall-Related Genes in Switchgrass through Comparative Genomics and Computational Analyses of Transcriptomic Data, BioEnergy Research 9(1), 172-180. BESC
201510.1039/c4ee03147dCheng, G., X. Zhang, B. Simmons, and S. Singh. 2015. Theory, practice and prospects of X-ray and neutron scattering for lignocellulosic biomass characterization: towards understanding biomass pretreatment, Energy & Environmental Science 8(2), 436-455. JBEI
201510.1042/BJ20150235Chiu, T. Y., J. Lao, B. Manalansan, D. Loque, S. J. Roux, and J. L. Heazlewood. 2015. Biochemical characterization of Arabidopsis APYRASE family reveals their roles in regulating endomembrane NDP/NMP homoeostasis, Biochem J 472(1), 43-54. JBEI
201510.1093/nar/gkv177Chou, W. C., Q. Ma, S. Yang, S. Cao, D. M. Klingeman, S. D. Brown, and Y. Xu. 2015. Analysis of strand-specific RNA-seq data using machine learning reveals the structures of transcription units in Clostridium thermocellum, Nucleic Acids Res 43(10), e67. BESC
201510.1128/AEM.01102-15Chubukov, V., F. Mingardon, W. Schackwitz, E. E. Baidoo, J. Alonso-Gutierrez, Q. Hu, T. S. Lee, J. D. Keasling, and A. Mukhopadhyay. 2015. Acute Limonene Toxicity in Escherichia coli Is Caused by Limonene Hydroperoxide and Alleviated by a Point Mutation in Alkyl Hydroperoxidase AhpC, Appl Environ Microbiol 81(14), 4690-4696. JBEI
201510.1186/s13068-015-0296-xChung, D., J. Young, M. Cha, R. Brunecky, Y. J. Bomble, M. E. Himmel, and J. Westpheling. 2015. Expression of the Acidothermus cellulolyticus E1 endoglucanase in Caldicellulosiruptor bescii enhances its ability to deconstruct crystalline cellulose, Biotechnol Biofuels 8, 113. BESC
201510.1371/journal.pone.0119508Chung, D., J. Young, Y. J. Bomble, T. A. Vander Wall, J. Groom, M. E. Himmel, and J. Westpheling. 2015. Homologous expression of the Caldicellulosiruptor bescii CelA reveals that the extracellular protein is glycosylated, PLoS One 10(3), e0119508. BESC
201510.1186/s13068-015-0346-4Chung, D., M. Cha, E. N. Snyder, J. G. Elkins, A. M. Guss, and J. Westpheling. 2015. Cellulosic ethanol production via consolidated bioprocessing at 75 degrees C by engineered Caldicellulosiruptor bescii, Biotechnol Biofuels 8, 163. BESC
201510.1186/s13068-015-0287-yChung, D., T. J. Verbeke, K. L. Cross, J. Westpheling, and J. G. Elkins. 2015. Expression of a heat-stable NADPH-dependent alcohol dehydrogenase in Caldicellulosiruptor bescii results in furan aldehyde detoxification, Biotechnol Biofuels 8, 102. BESC
201510.1093/molbev/msv112Clowers, K. J., J. Heilberger, J. S. Piotrowski, J. L. Will, and A. P. Gasch. 2015. Ecological and Genetic Barriers Differentiate Natural Populations of Saccharomyces cerevisiae, Mol Biol Evol 32(9), 2317-2327. GLBRC
201510.1111/mec.13439Clowers, K. J., J. L. Will, and A. P. Gasch. 2015. A unique ecological niche fosters hybridization of oak-tree and vineyard isolates of Saccharomyces cerevisiae, Mol Ecol 24(23), 5886-5898. GLBRC
201510.1128/genomeA.00444-15Coelho, M. A., J. M. Almeida, C. T. Hittinger, and P. Goncalves. 2015. Draft Genome Sequence of Sporidiobolus salmonicolor CBS 6832, a Red-Pigmented Basidiomycetous Yeast, Genome Announc 3(3). GLBRC
201510.1371/journal.pone.0125324Cornish, A. J., R. Green, K. Gartner, S. Mason, and E. L. Hegg. 2015. Characterization of Hydrogen Metabolism in the Multicellular Green Alga Volvox carteri, PLoS One 10(4), e0125324. GLBRC
201510.1186/s12918-015-0159-xCurrie, D. H., B. Raman, C. M. Gowen, T. J. Tschaplinski, M. L. Land, S. D. Brown, S. F. Covalla, D. M. Klingeman, Z. K. Yang, N. L. Engle, C. M. Johnson, M. Rodriguez, A. J. Shaw, W. R. Kenealy, L. R. Lynd, S. S. Fong, J. R. Mielenz, B. H. Davison, D. A. Hogsett, and C. D. Herring. 2015. Genome-scale resources for Thermoanaerobacterium saccharolyticum, BMC Syst Biol 9, 30. BESC
201510.1038/nature13995Cuskin, F., E. C. Lowe, M. J. Temple, Y. Zhu, E. Cameron, N. A. Pudlo, N. T. Porter, K. Urs, A. J. Thompson, A. Cartmell, A. Rogowski, B. S. Hamilton, R. Chen, T. J. Tolbert, K. Piens, D. Bracke, W. Vervecken, Z. Hakki, G. Speciale, J. L. Munoz-Munoz, A. Day, M. J. Pena, R. McLean, M. D. Suits, A. B. Boraston, T. Atherly, C. J. Ziemer, S. J. Williams, G. J. Davies, D. W. Abbott, E. C. Martens, and H. J. Gilbert. 2015. Human gut Bacteroidetes can utilize yeast mannan through a selfish mechanism, Nature 517(7533), 165-169. BESC
201510.1016/j.cbpa.2015.09.009d'Espaux, L., D. Mendez-Perez, R. Li, and J. D. Keasling. 2015. Synthetic biology for microbial production of lipid-based biofuels, Curr Opin Chem Biol 29, 58-65. JBEI
2015Dale, B. E., and M. Holtzapple. 2015. SBE Special Section: Lignocellulosic Biofuels - The Need for Biofuels, Chemical Engineering Progress Magazine 81, 57-69. DOI.GLBRC
2015 10.1128/genomeA.01022-15Dassa, B., S. Utturkar, R. A. Hurt, D. M. Klingeman, M. Keller, J. Xu, Y. H. Reddy, I. Borovok, I. Rozman Grinberg, R. Lamed, O. Zhivin, E. A. Bayer, and S. D. Brown. 2015. Near-Complete Genome Sequence of the Cellulolytic Bacterium Bacteroides (Pseudobacteroides) cellulosolvens ATCC 35603, Genome Announc 3(5). BESC
201510.1002/bbb.1549Davison, B. H., C. C. Brandt, A. M. Guss, U. C. Kalluri, A. V. Palumbo, R. L. Stouder, and E. G. Webb. 2015. The impact of biotechnological advances on the future of US bioenergy, Biofuels, Bioproducts and Biorefining 9(5), 454-467. BESC
201510.1016/j.copbio.2014.07.008de Rond, T., M. Danielewicz, and T. Northen. 2015. High throughput screening of enzyme activity with mass spectrometry imaging, Curr Opin Biotechnol 31, 1-9. JBEI
201510.1093/jxb/erv183De Souza, A. P., C. L. Alvim Kamei, A. F. Torres, S. Pattathil, M. G. Hahn, L. M. Trindade, and M. S. Buckeridge. 2015. How cell wall complexity influences saccharification efficiency in Miscanthus sinensis, J Exp Bot 66(14), 4351-4365. BESC
201510.3791/53163Decker, S. R., R. W. Sykes, G. B. Turner, J. S. Lupoi, C. Doepkke, M. P. Tucker, L. A. Schuster, K. Mazza, M. E. Himmel, M. F. Davis, and E. Gjersing. 2015. High-throughput Screening of Recalcitrance Variations in Lignocellulosic Biomass: Total Lignin, Lignin Monomers, and Enzymatic Sugar Release, J Vis Exp(103). BESC
2015Degreif, D., A. Bertl, J. Keasling, and I. Budin. 2015. A novel flocculation pathway mediated by ER membrane fluidity. In 27th International Conference on Yeast Genetics and Molecular Biology.JBEI
201510.1016/j.biombioe.2015.07.006del Río, J. C., A. G. Lino, J. L. Colodette, C. F. Lima, A. Gutiérrez, Á. T. Martínez, F. Lu, J. Ralph, and J. Rencoret. 2015. Differences in the chemical structure of the lignins from sugarcane bagasse and straw, Biomass and Bioenergy 81, 322-338. GLBRC
201510.1186/s13068-015-0373-1DeMartini, J. D., M. Foston, X. Meng, S. Jung, R. Kumar, A. J. Ragauskas, and C. E. Wyman. 2015. How chip size impacts steam pretreatment effectiveness for biological conversion of poplar wood into fermentable sugars, Biotechnol Biofuels 8, 209. BESC
201510.3389/fbioe.2015.00153Deng, K., J. M. Guenther, J. Gao, B. P. Bowen, H. Tran, V. Reyes-Ortiz, X. Cheng, N. Sathitsuksanoh, R. Heins, T. E. Takasuka, L. F. Bergeman, H. Geertz-Hansen, S. Deutsch, D. Loque, K. L. Sale, B. A. Simmons, P. D. Adams, A. K. Singh, B. G. Fox, and T. R. Northen. 2015. Development of a High Throughput Platform for Screening Glycoside Hydrolases Based on Oxime-NIMS, Front Bioeng Biotechnol 3, 153. JBEI
201510.3389/fbioe.2015.00165Deng, K., T. E. Takasuka, C. M. Bianchetti, L. F. Bergeman, P. D. Adams, T. R. Northen, and B. G. Fox. 2015. Use of Nanostructure-Initiator Mass Spectrometry to Deduce Selectivity of Reaction in Glycoside Hydrolases, Front Bioeng Biotechnol 3, 165. GLBRC JBEI
201510.1371/journal.pone.0135253Dickson, T. L., and K. L. Gross. 2015. Can the Results of Biodiversity-Ecosystem Productivity Studies Be Translated to Bioenergy Production?, PLoS One 10(9), e0135253. GLBRC
201510.1105/tpc.114.134643Dima, O., K. Morreel, B. Vanholme, H. Kim, J. Ralph, and W. Boerjan. 2015. Small glycosylated lignin oligomers are stored in Arabidopsis leaf vacuoles, Plant Cell 27(3), 695-710. GLBRC
201510.1039/c5ra09676fDolan, J. A., N. Sathitsuksanoh, K. Rodriguez, B. A. Simmons, C. E. Frazier, and S. Renneckar. 2015. Biocomposite adhesion without added resin: understanding the chemistry of the direct conversion of wood into adhesives, RSC Advances 5(82), 67267-67276. JBEI
201510.1016/j.cbpa.2015.08.014Donohoe, B. S., and M. G. Resch. 2015. Mechanisms employed by cellulase systems to gain access through the complex architecture of lignocellulosic substrates, Curr Opin Chem Biol 29, 100-107. BESC
201510.1105/tpc.114.133827Ebert, B., C. Rautengarten, X. Guo, G. Xiong, S. Stonebloom, A. M. Smith-Moritz, T. Herter, L. J. Chan, P. D. Adams, C. J. Petzold, M. Pauly, W. G. Willats, J. L. Heazlewood, and H. V. Scheller. 2015. Identification and Characterization of a Golgi-Localized UDP-Xylose Transporter Family from Arabidopsis, Plant Cell 27(4), 1218-1227. JBEI
201510.1093/aepp/ppu044Egbendewe-Mondzozo, A., S. M. Swinton, S. Kang, W. M. Post, J. C. Binfield, and W. Thompson. 2015. Bioenergy Supply and Environmental Impacts on Cropland: Insights from Multi-market Forecasts in a Great Lakes Subregional Bioeconomic Model, Applied Economic Perspectives and Policy 37(4), 602-618. GLBRC
201510.1111/pbi.12310Eudes, A., N. Sathitsuksanoh, E. E. Baidoo, A. George, Y. Liang, F. Yang, S. Singh, J. D. Keasling, B. A. Simmons, and D. Loque. 2015. Expression of a bacterial 3-dehydroshikimate dehydratase reduces lignin content and improves biomass saccharification efficiency, Plant Biotechnol J 13(9), 1241-1250. JBEI
201510.1371/journal.pone.0138972Eudes, A., V. Teixeira Benites, G. Wang, E. E. Baidoo, T. S. Lee, J. D. Keasling, and D. Loque. 2015. Precursor-Directed Combinatorial Biosynthesis of Cinnamoyl, Dihydrocinnamoyl, and Benzoyl Anthranilates in Saccharomyces cerevisiae, PLoS One 10(10), e0138972. JBEI
201510.1111/tpj.13041Evans, J., E. Crisovan, K. Barry, C. Daum, J. Jenkins, G. Kunde-Ramamoorthy, A. Nandety, C. Y. Ngan, B. Vaillancourt, C. L. Wei, J. Schmutz, S. M. Kaeppler, M. D. Casler, and C. R. Buell. 2015. Diversity and population structure of northern switchgrass as revealed through exome capture sequencing, Plant J 84(4), 800-815. GLBRC
201510.1186/s13068-015-0334-8Faraji, M., L. L. Fonseca, L. Escamilla-Trevino, R. A. Dixon, and E. O. Voit. 2015. Computational inference of the structure and regulation of the lignin pathway in Panicum virgatum, Biotechnol Biofuels 8, 151. BESC
201510.1007/s00122-014-2451-3Foerster, J. M., T. Beissinger, N. de Leon, and S. Kaeppler. 2015. Large effect QTL explain natural phenotypic variation for the developmental timing of vegetative phase change in maize (Zea mays L.), Theor Appl Genet 128(3), 529-538. GLBRC
201510.3389/fpls.2015.00674Ford, K. L., W. Zeng, J. L. Heazlewood, and A. Bacic. 2015. Characterization of protein N-glycosylation by tandem mass spectrometry using complementary fragmentation techniques, Front Plant Sci 6, 674. JBEI
201510.1016/j.biortech.2015.08.065Foston, M., H. L. Trajano, R. Samuel, C. E. Wyman, J. He, and A. J. Ragauskas. 2015. Recalcitrance and structural analysis by water-only flowthrough pretreatment of (13)C enriched corn stover stem, Bioresour Technol 197, 128-136. BESC
201510.1002/bbb.1559Fulton, L. M., L. R. Lynd, A. Körner, N. Greene, and L. R. Tonachel. 2015. The need for biofuels as part of a low carbon energy future, Biofuels, Bioproducts and Biorefining 9(5), 476-483. BESC
201510.1039/c5ra01503kGardner, J. L., W. He, C. Li, J. Wong, K. L. Sale, B. A. Simmons, S. Singh, and D. Tanjore. 2015. Calorimetric evaluation indicates that lignin conversion to advanced biofuels is vital to improving energy yields, RSC Advances 5(63), 51092-51101. JBEI
2015Gelfand, I., and P. Robertson. 2015. Mitigation of greenhouse gases in agricultural ecosystems. In The Ecology of Agricultural Landscapes: Long-Term Research on the Path to Sustainability, 419-458. Oxford University Press.GLBRC
201510.1016/j.agee.2015.07.005Gelfand, I., M. Cui, J. Tang, and G. P. Robertson. 2015. Short-term drought response of N 2 O and CO 2 emissions from mesic agricultural soils in the US Midwest, Agriculture, Ecosystems & Environment 212, 127-133. GLBRC
201510.1039/c4gc01208aGeorge, A., A. Brandt, K. Tran, S. M. S. N. S. Zahari, D. Klein-Marcuschamer, N. Sun, N. Sathitsuksanoh, J. Shi, V. Stavila, R. Parthasarathi, S. Singh, B. M. Holmes, T. Welton, B. A. Simmons, and J. P. Hallett. 2015. Design of low-cost ionic liquids for lignocellulosic biomass pretreatment, Green Chemistry 17(3), 1728-1734. JBEI
2015George, K. W., J. Alonso-Gutierrez, J. D. Keasling, and T. S. Lee. 2015. Isoprenoid Drugs, Biofuels, and Chemicals-Artemisinin, Farnesene, and Beyond. In Biotechnology of Isoprenoids. Advances in Biochemical Engineering/Biotechnology. Eds. J. Schrader, and J. Bohlmann. Springer.JBEI
201510.1038/srep11128George, K. W., M. G. Thompson, A. Kang, E. Baidoo, G. Wang, L. J. Chan, P. D. Adams, C. J. Petzold, J. D. Keasling, and T. S. Lee. 2015. Metabolic engineering for the high-yield production of isoprenoid-based C(5) alcohols in E. coli, Sci Rep 5, 11128. JBEI
201510.3389/fbioe.2015.00044.Gonzalez Fernandez-Nino, S. M., A. M. Smith-Moritz, L. J. Chan, P. D. Adams, J. L. Heazlewood, and C. J. Petzold. 2015. Standard flow liquid chromatography for shotgun proteomics in bioenergy research, Front Bioeng Biotechnol 3, 44. JBEI
201510.1093/nar/gkv655Gonzalez, T. L., Y. Liang, B. N. Nguyen, B. J. Staskawicz, D. Loque, and M. C. Hammond. 2015. Tight regulation of plant immune responses by combining promoter and suicide exon elements, Nucleic Acids Res 43(14), 7152-7161. JBEI
201510.1007/s12155-015-9605-2Grabber, J. H., N. Santoro, C. E. Foster, S. Elumalai, J. Ralph, and X. Pan. 2015. Incorporation of Flavonoid Derivatives or Pentagalloyl Glucose into Lignin Enhances Cell Wall Saccharification Following Mild Alkaline or Acidic Pretreatments, BioEnergy Research 8(3), 1391-1400. GLBRC
201510.2134/agronj15.0066Gratton, C., M. Casler, R. Groves, and T. N. Kim. 2015. Insecticide Applications have Minor Effects on Switchgrass Biomass Yield, Agronomy Journal 107(6), 2031. GLBRC
201510.4271/2015-01-0952Groendyk, M. A., and D. Rothamer. 2015. Effects of Fuel Physical Properties on Auto-Ignition Characteristics in a Heavy Duty Compression Ignition Engine, SAE International Journal of Fuels and Lubricants 8(1), 200-213. GLBRC
201510.1073/pnas.1512240112Gupta, S., M. Guttman, R. L. Leverenz, K. Zhumadilova, E. G. Pawlowski, C. J. Petzold, K. K. Lee, C. Y. Ralston, and C. A. Kerfeld. 2015. Local and global structural drivers for the photoactivation of the orange carotenoid protein, Proc Natl Acad Sci U S A 112(41), E5567-5574. JBEI
201510.1371/journal.pone.0134964Guzzo de Carli Poelking, V., A. Giordano, M. E. Ricci-Silva, T. C. Rhys Williams, D. Alves Pecanha, M. Contin Ventrella, J. Rencoret, J. Ralph, M. H. Pereira Barbosa, and M. Loureiro. 2015. Analysis of a Modern Hybrid and an Ancient Sugarcane Implicates a Complex Interplay of Factors in Affecting Recalcitrance to Cellulosic Ethanol Production, PLoS One 10(8), e0134964. GLBRC
201510.1534/g3.115.017665Haase, N. J., T. Beissinger, C. N. Hirsch, B. Vaillancourt, S. Deshpande, K. Barry, C. R. Buell, S. M. Kaeppler, and N. de Leon. 2015. Shared Genomic Regions Between Derivatives of a Large Segregating Population of Maize Identified Using Bulked Segregant Analysis Sequencing and Traditional Linkage Analysis, G3 (Bethesda) 5(8), 1593-1602. GLBRC
201510.1088/1748-9326/10/6/064015Hamilton, S. K., M. Z. Hussain, A. K. Bhardwaj, B. Basso, and G. P. Robertson. 2015. Comparative water use by maize, perennial crops, restored prairie, and poplar trees in the US Midwest, Environmental Research Letters 10(6), 064015. GLBRC
201510.1016/j.biortech.2015.01.135Han, J., J. S. Luterbacher, D. M. Alonso, J. A. Dumesic, and C. T. Maravelias. 2015. A lignocellulosic ethanol strategy via nonenzymatic sugar production: process synthesis and analysis, Bioresour Technol 182, 258-266. GLBRC
201510.1016/j.compchemeng.2015.04.007Han, J., S. Murat Sen, J. S. Luterbacher, D. M. Alonso, J. A. Dumesic, and C. T. Maravelias. 2015. Process systems engineering studies for the synthesis of catalytic biomass-to-fuels strategies, Computers & Chemical Engineering 81, 57-69. GLBRC
201510.1016/j.ymben.2015.04.003Haushalter, R. W., D. Groff, S. Deutsch, L. The, T. A. Chavkin, S. F. Brunner, L. Katz, and J. D. Keasling. 2015. Development of an orthogonal fatty acid biosynthesis system in E. coli for oleochemical production, Metab Eng 30, 1-6. JBEI
201510.3389/fbioe.2015.00190Healey, A. L., D. J. Lee, A. Furtado, B. A. Simmons, and R. J. Henry. 2015. Efficient Eucalypt Cell Wall Deconstruction and Conversion for Sustainable Lignocellulosic Biofuels, Front Bioeng Biotechnol 3, 190. JBEI
201510.1186/s13007-015-0070-xHeckwolf, S., M. Heckwolf, S. M. Kaeppler, N. de Leon, and E. P. Spalding. 2015. Image analysis of anatomical traits in stalk transections of maize and other grasses, Plant Methods 11, 26. GLBRC
201510.1128/AEM.01689-15Henningsen, B. M., S. Hon, S. F. Covalla, C. Sonu, D. A. Argyros, T. F. Barrett, E. Wiswall, A. C. Froehlich, and R. M. Zelle. 2015. Increasing anaerobic acetate consumption and ethanol yields in Saccharomyces cerevisiae with NADPH-specific alcohol dehydrogenase, Appl Environ Microbiol 81(23), 8108-8117. BESC
201510.1016/j.gde.2015.10.008Hittinger, C. T., A. Rokas, F. Y. Bai, T. Boekhout, P. Goncalves, T. W. Jeffries, J. Kominek, M. A. Lachance, D. Libkind, C. A. Rosa, J. P. Sampaio, and C. P. Kurtzman. 2015. Genomics and the making of yeast biodiversity, Curr Opin Genet Dev 35, 100-109. GLBRC
201510.3389/fbioe.2015.00182Hoang, N. V., A. Furtado, F. C. Botha, B. A. Simmons, and R. J. Henry. 2015. Potential for Genetic Improvement of Sugarcane as a Source of Biomass for Biofuels, Front Bioeng Biotechnol 3, 182. JBEI
2015Hobdey, S. E., B. S. Donohoe, R. Brunecky, M. Himmel, and Y. J. Bomble. 2015. New Insights into Microbial Strategies for Biomass Conversion. In Direct Microbial Conversion of Biomass to Advanced Biofuels, 111-127. Ed. M. E. Himmel. Elsevier.BESC
201510.7554/eLife.05462Hose, J., C. M. Yong, M. Sardi, Z. Wang, M. A. Newton, and A. P. Gasch. 2015. Dosage compensation can buffer copy-number variation in wild yeast, Elife 4. GLBRC
201510.1111/1462-2920.13020Hudson, C. M., E. Kirton, M. I. Hutchinson, J. L. Redfern, B. Simmons, E. Ackerman, S. Singh, K. P. Williams, D. O. Natvig, and A. J. Powell. 2015. Lignin-modifying processes in the rhizosphere of arid land grasses, Environ Microbiol 17(12), 4965-4978. JBEI
201510.1007/s11120-014-0061-1Imam, S., C. M. Fitzgerald, E. M. Cook, T. J. Donohue, and D. R. Noguera. 2015. Quantifying the effects of light intensity on bioproduction and maintenance energy during photosynthetic growth of Rhodobacter sphaeroides, Photosynth Res 123(2), 167-182. GLBRC
201510.1371/journal.pcbi.1004103Imam, S., D. R. Noguera, and T. J. Donohue. 2015. An integrated approach to reconstructing genome-scale transcriptional regulatory networks, PLoS Comput Biol 11(2), e1004103. GLBRC
201510.1128/mBio.02461-14Imam, S., D. R. Noguera, and T. J. Donohue. 2015. CceR and AkgR regulate central carbon and energy metabolism in alphaproteobacteria, MBio 6(1). GLBRC
201510.1016/j.agee.2015.02.006Jach-Smith, L. C., and R. D. Jackson. 2015. Nitrogen conservation decreases with fertilizer addition in two perennial grass cropping systems for bioenergy, Agriculture, Ecosystems & Environment 204, 62-71. GLBRC
201510.1021/acs.orglett.5b01527Johnson, R. E., T. de Rond, V. N. Lindsay, J. D. Keasling, and R. Sarpong. 2015. Synthesis of Cycloprodigiosin Identifies the Natural Isolate as a Scalemic Mixture, Org Lett 17(14), 3474-3477. JBEI
201510.1371/journal.pone.0139195Joyce, B. L., V. D. Zheljazkov, R. Sykes, C. L. Cantrell, C. Hamilton, D. G. Mann, M. Rodriguez, J. R. Mielenz, T. Astatkie, and C. N. Stewart, Jr. 2015. Ethanol and High-Value Terpene Co-Production from Lignocellulosic Biomass of Cymbopogon flexuosus and Cymbopogon martinii, PLoS One 10(10), e0139195. BESC
201510.1186/s12284-015-0060-7Jung, K. H., P. Cao, R. Sharma, R. Jain, and P. C. Ronald. 2015. Phylogenomics databases for facilitating functional genomics in rice, Rice (N Y) 8(1), 60. JBEI
201510.1016/j.soilbio.2015.09.005Kallenbach, C. M., A. S. Grandy, S. D. Frey, and A. F. Diefendorf. 2015. Microbial physiology and necromass regulate agricultural soil carbon accumulation, Soil Biology and Biochemistry 91, 279-290. GLBRC
201510.1111/gcbb.12218Kallenbach, C. M., and A. Stuart Grandy. 2015. Land-use legacies regulate decomposition dynamics following bioenergy crop conversion, GCB Bioenergy 7(6), 1232-1244. GLBRC
201510.3390/bioengineering2040184Kang, A., and T. S. Lee. 2015. Converting Sugars to Biofuels: Ethanol and Beyond, Bioengineering (Basel) 2(4), 184-203. JBEI
201510.1080/17597269.2014.996729.Keller, M., A. Loder, M. Basen, J. Izquierdo, R. M. Kelly, and M. W. W. Adams. 2015. Production of lignofuels and electrofuels by extremely thermophilic microbes, Biofuels 5(5), 499-515. BESC
201510.1039/c5gc01083gKent, M. S., I. C. Avina, N. Rader, M. L. Busse, A. George, N. Sathitsuksanoh, E. Baidoo, J. Timlin, N. H. Giron, M. C. Celina, L. E. Martin, R. Polsky, V. H. Chavez, D. L. Huber, J. D. Keasling, S. Singh, B. A. Simmons, and K. L. Sale. 2015. Assay for lignin breakdown based on lignin films: insights into the Fenton reaction with insoluble lignin, Green Chemistry 17(10), 4830-4845. JBEI
201510.1186/s12870-015-0586-2Kilaru, A., X. Cao, P. B. Dabbs, H. J. Sung, M. M. Rahman, N. Thrower, G. Zynda, R. Podicheti, E. Ibarra-Laclette, L. Herrera-Estrella, K. Mockaitis, and J. B. Ohlrogge. 2015. Oil biosynthesis in a basal angiosperm: transcriptome analysis of Persea Americana mesocarp, BMC Plant Biol 15, 203. GLBRC
201510.1111/tpj.12802Kim, S. J., M. A. Held, S. Zemelis, C. Wilkerson, and F. Brandizzi. 2015. CGR2 and CGR3 have critical overlapping roles in pectin methylesterification and plant growth in Arabidopsis thaliana, Plant J 82(2), 208-220. GLBRC
201510.1111/tpj.12748Kim, S. J., S. Zemelis, K. Keegstra, and F. Brandizzi. 2015. The cytoplasmic localization of the catalytic site of CSLF6 supports a channeling model for the biosynthesis of mixed-linkage glucan, Plant J 81(4), 537-547. GLBRC
201510.1002/bbb.1554Kim, S., and B. E. Dale. 2015. All biomass is local: The cost, volume produced, and global warming impact of cellulosic biofuels depend strongly on logistics and local conditions, Biofuels, Bioproducts and Biorefining 9(4), 422-434. GLBRC
201510.1016/j.biombioe.2015.01.018Kim, S., and B. E. Dale. 2015. Comparing alternative cellulosic biomass biorefining systems: Centralized versus distributed processing systems, Biomass and Bioenergy 74, 135-147. GLBRC
201510.1128/AEM.02920-14Kirby, J., M. Nishimoto, R. W. Chow, E. E. Baidoo, G. Wang, J. Martin, W. Schackwitz, R. Chan, J. L. Fortman, and J. D. Keasling. 2015. Enhancing Terpene yield from sugars via novel routes to 1-deoxy-d-xylulose 5-phosphate, Appl Environ Microbiol 81(1), 130-138. JBEI
201510.1002/aic.14755Klein-Marcuschamer, D., and H. W. Blanch. 2015. Renewable fuels from biomass: Technical hurdles and economic assessment of biological routes, AIChE Journal 61(9), 2689-2701. JBEI
201510.1007/s12155-015-9594-1Konda, N. V. S. N. M., S. Singh, B. A. Simmons, and D. Klein-Marcuschamer. 2015. An Investigation on the Economic Feasibility of Macroalgae as a Potential Feedstock for Biorefineries, BioEnergy Research 8(3), 1046-1056. JBEI
201510.1104/pp.114.255943Kong, Y., M. J. Pena, L. Renna, U. Avci, S. Pattathil, S. T. Tuomivaara, X. Li, W. D. Reiter, F. Brandizzi, M. G. Hahn, A. G. Darvill, W. S. York, and M. A. O'Neill. 2015. Galactose-depleted xyloglucan is dysfunctional and leads to dwarfism in Arabidopsis, Plant Physiology 167(4), 1296-1306. GLBRC
201510.2136/sssaj2014.08.0325Kravchenko, A. N., and G. P. Robertson. 2015. Statistical Challenges in Analyses of Chamber-Based Soil CO2 and N2O Emissions Data, Soil Science Society of America Journal 79(1), 200. GLBRC
2015Kruer-Zerhusen, N., and D. B. Wilson. 2015. Bacterial AA10 Lytic Polysaccharide Monooxygenases Enhance the Hydrolytic Degradation of Recalcitrant Substrates. In Direct Microbial Conversion of Biomass to Advanced Biofuels, 111-127. Ed. M. E. Himmel. Elsevier.BESC
201510.1016/j.renene.2014.11.070Kumagai, A., L. Wu, S. Iwamoto, S.-H. Lee, T. Endo, M. Rodriguez, and J. R. Mielenz. 2015. Improvement of enzymatic saccharification of Populus and switchgrass by combined pretreatment with steam and wet disk milling, Renewable Energy 76, 782-789. BESC
201510.1104/pp.114.253757Lan, W., F. Lu, M. Regner, Y. Zhu, J. Rencoret, S. A. Ralph, U. I. Zakai, K. Morreel, W. Boerjan, and J. Ralph. 2015. Tricin, a flavonoid monomer in monocot lignification, Plant Physiol 167(4), 1284-1295. GLBRC
201510.1007/s10142-015-0433-4Land, M., L. Hauser, S. R. Jun, I. Nookaew, M. R. Leuze, T. H. Ahn, T. Karpinets, O. Lund, G. Kora, T. Wassenaar, S. Poudel, and D. W. Ussery. 2015. Insights from 20 years of bacterial genome sequencing, Funct Integr Genomics 15(2), 141-161. BESC
201510.1128/EC.00022-15Langner, T., M. Ozturk, S. Hartmann, S. Cord-Landwehr, B. Moerschbacher, J. D. Walton, and V. Gohre. 2015. Chitinases Are Essential for Cell Separation in Ustilago maydis, Eukaryot Cell 14(9), 846-857. GLBRC
201510.1002/pmic.201400487Lao, J., M. K. Sharma, R. Sharma, S. M. Fernandez-Nino, J. Schmutz, P. C. Ronald, J. L. Heazlewood, and B. Schwessinger. 2015. Proteome profile of the endomembrane of developing coleoptiles from switchgrass (Panicum virgatum), Proteomics 15(13), 2286-2290. JBEI
201510.1093/jxb/erv096Lara-Chavez, A., S. Lowman, S. Kim, Y. Tang, J. Zhang, M. Udvardi, J. Nowak, B. Flinn, and C. Mei. 2015. Global gene expression profiling of two switchgrass cultivars following inoculation with Burkholderia phytofirmans strain PsJN, J Exp Bot 66(14), 4337-4350. BESC
201510.1128/genomeA.00440-15Lee, L. L., J. A. Izquierdo, S. E. Blumer-Schuette, J. V. Zurawski, J. M. Conway, R. W. Cottingham, M. Huntemann, A. Copeland, I. M. Chen, N. Kyrpides, V. Markowitz, K. Palaniappan, N. Ivanova, N. Mikhailova, G. Ovchinnikova, E. Andersen, A. Pati, D. Stamatis, T. B. Reddy, N. Shapiro, H. P. Nordberg, M. N. Cantor, S. X. Hua, T. Woyke, and R. M. Kelly. 2015. Complete Genome Sequences of Caldicellulosiruptor sp. Strain Rt8.B8, Caldicellulosiruptor sp. Strain Wai35.B1, and Thermoanaerobacter cellulolyticus, Genome Announc 3(3). BESC
201510.1093/nar/gkv253Lee, T., T. Oh, S. Yang, J. Shin, S. Hwang, C. Y. Kim, H. Kim, H. Shim, J. E. Shim, P. C. Ronald, and I. Lee. 2015. RiceNet v2: an improved network prioritization server for rice genes, Nucleic Acids Res 43(W1), W122-127. JBEI
201510.1128/JB.02510-14Lemmer, K. C., A. C. Dohnalkova, D. R. Noguera, and T. J. Donohue. 2015. Oxygen-dependent regulation of bacterial lipid production, J Bacteriol 197(9), 1649-1658. GLBRC
201510.1126/science.aaa7234Leverenz, R. L., M. Sutter, A. Wilson, S. Gupta, A. Thurotte, C. Bourcier de Carbon, C. J. Petzold, C. Ralston, F. Perreau, D. Kirilovsky, and C. A. Kerfeld. 2015. PHOTOSYNTHESIS. A 12 A carotenoid translocation in a photoswitch associated with cyanobacterial photoprotection, Science 348(6242), 1463-1466. JBEI
201510.1007/s12155-015-9587-0Li, C., D. Tanjore, W. He, J. Wong, J. L. Gardner, V. S. Thompson, N. A. Yancey, K. L. Sale, B. A. Simmons, and S. Singh. 2015. Scale-Up of Ionic Liquid-Based Fractionation of Single and Mixed Feedstocks, BioEnergy Research 8(3), 982-991. JBEI
201510.1093/jxb/erv016Li, M., M. Heckwolf, J. D. Crowe, D. L. Williams, T. D. Magee, S. M. Kaeppler, N. de Leon, and D. B. Hodge. 2015. Cell-wall properties contributing to improved deconstruction by alkaline pre-treatment and enzymatic hydrolysis in diverse maize (Zea mays L.) lines, J Exp Bot 66(14), 4305-4315. GLBRC
201510.1186/s13068-015-0300-5Li, Z., N. Bansal, A. Azarpira, A. Bhalla, C. H. Chen, J. Ralph, E. L. Hegg, and D. B. Hodge. 2015. Chemical and structural changes associated with Cu-catalyzed alkaline-oxidative delignification of hybrid poplar, Biotechnol Biofuels 8, 123. GLBRC
201510.1074/jbc.M114.612747Li, Z., S. Hwang, J. Ericson, K. Bowler, and M. Bar-Peled. 2015. Pen and Pal are nucleotide-sugar dehydratases that convert UDP-GlcNAc to UDP-6-deoxy-D-GlcNAc-5,6-ene and then to UDP-4-keto-6-deoxy-L-AltNAc for CMP-pseudaminic acid synthesis in Bacillus thuringiensis, J Biol Chem 290(2), 691-704. BESC
201510.1890/14-0570.1Liere, H., T. N. Kim, B. P. Werling, T. D. Meehan, D. A. Landis, and C. Gratton. 2015. Trophic cascades in agricultural landscapes: indirect effects of landscape composition on crop yield, Ecological Applications 25(3), 652-661. GLBRC
201510.1186/s12864-015-2230-9Lin, K. H., B. Y. Liao, H. W. Chang, S. W. Huang, T. Y. Chang, C. Y. Yang, Y. B. Wang, Y. T. Lin, Y. W. Wu, S. L. Tang, and H. T. Yu. 2015. Metabolic characteristics of dominant microbes and key rare species from an acidic hot spring in Taiwan revealed by metagenomics, BMC Genomics 16, 1029. JBEI
201510.1016/j.ymben.2015.07.001Lin, P. P., L. Mi, A. H. Morioka, K. M. Yoshino, S. Konishi, S. C. Xu, B. A. Papanek, L. A. Riley, A. M. Guss, and J. C. Liao. 2015. Consolidated bioprocessing of cellulose to isobutanol using Clostridium thermocellum, Metab Eng 31, 44-52. BESC
201510.1128/JB.00420-15Lin, T. Y., T. M. Santos, W. S. Kontur, T. J. Donohue, and D. B. Weibel. 2015. A Cardiolipin-Deficient Mutant of Rhodobacter sphaeroides Has an Altered Cell Shape and Is Impaired in Biofilm Formation, J Bacteriol 197(21), 3446-3455. GLBRC
201510.1007/s10533-015-0132-1Lin, Y., J. Y. King, S. D. Karlen, and J. Ralph. 2015. Using 2D NMR spectroscopy to assess effects of UV radiation on cell wall chemistry during litter decomposition, Biogeochemistry 125(3), 427-436. GLBRC
201510.1111/pbi.12325Liu, J., A. Rice, K. McGlew, V. Shaw, H. Park, T. Clemente, M. Pollard, J. Ohlrogge, and T. P. Durrett. 2015. Metabolic engineering of oilseed crops to produce high levels of novel acetyl glyceride oils with reduced viscosity, freezing point and calorific value, Plant Biotechnol J 13(6), 858-865. GLBRC
201510.1016/j.indcrop.2014.11.019Liu, J., H. Tjellström, K. McGlew, V. Shaw, A. Rice, J. Simpson, D. Kosma, W. Ma, W. Yang, M. Strawsine, E. Cahoon, T. P. Durrett, and J. Ohlrogge. 2015. Field production, purification and analysis of high-oleic acetyl-triacylglycerols from transgenic Camelina sativa, Industrial Crops and Products 65, 259-268. GLBRC
201510.1016/j.tplants.2015.02.004Liu, W., and C. N. Stewart, Jr. 2015. Plant synthetic biology, Trends Plant Sci 20(5), 309-317. BESC
201510.1002/cssc.201501122Liu, Y., M. A. Mellmer, D. M. Alonso, and J. A. Dumesic. 2015. Effects of Water on the Copper-Catalyzed Conversion of Hydroxymethylfurfural in Tetrahydrofuran, ChemSusChem 8(23), 3983-3986. GLBRC
201510.1128/JB.00347-15Lo, J., T. Zheng, D. G. Olson, N. Ruppertsberger, S. A. Tripathi, L. Tian, A. M. Guss, and L. R. Lynd. 2015. Deletion of nfnAB in Thermoanaerobacterium saccharolyticum and Its Effect on Metabolism, J Bacteriol 197(18), 2920-2929. BESC
201510.1128/JB.02450-14Lo, J., T. Zheng, S. Hon, D. G. Olson, and L. R. Lynd. 2015. The bifunctional alcohol and aldehyde dehydrogenase gene, adhE, is necessary for ethanol production in Clostridium thermocellum and Thermoanaerobacterium saccharolyticum, J Bacteriol 197(8), 1386-1393. BESC
201510.1016/j.copbio.2014.12.019Long, M. R., W. K. Ong, and J. L. Reed. 2015. Computational methods in metabolic engineering for strain design, Curr Opin Biotechnol 34, 135-141. GLBRC
201510.1016/j.pbi.2015.05.018Loque, D., H. V. Scheller, and M. Pauly. 2015. Engineering of plant cell walls for enhanced biofuel production, Curr Opin Plant Biol 25, 151-161. JBEI
201510.1007/s12155-015-9583-4.Lu, F., S. D. Karlen, M. Regner, H. Kim, S. A. Ralph, R.-C. Sun, K.-i. Kuroda, M. A. Augustin, R. Mawson, H. Sabarez, T. Singh, G. Jimenez-Monteon, S. Zakaria, S. Hill, P. J. Harris, W. Boerjan, C. G. Wilkerson, S. D. Mansfield, and J. Ralph. 2015. Naturally p-Hydroxybenzoylated Lignins in Palms, BioEnergy Research 8(3), 934-952. GLBRC
201510.1093/jxb/eru401Lund, C. H., J. R. Bromley, A. Stenbaek, R. E. Rasmussen, H. V. Scheller, and Y. Sakuragi. 2015. A reversible Renilla luciferase protein complementation assay for rapid identification of protein-protein interactions reveals the existence of an interaction network involved in xyloglucan biosynthesis in the plant Golgi apparatus, J Exp Bot 66(1), 85-97. JBEI
201510.1007/s12155-015-9578-1Lupoi, J. S., A. Healey, S. Singh, R. Sykes, M. Davis, D. J. Lee, M. Shepherd, B. A. Simmons, and R. J. Henry. 2015. High-Throughput Prediction of Acacia and Eucalypt Lignin Syringyl/Guaiacyl Content Using FT-Raman Spectroscopy and Partial Least Squares Modeling, BioEnergy Research 8(3), 953-963. JBEI BESC
201510.1186/s13068-015-0279-yLupoi, J. S., A. Smith-Moritz, S. Singh, R. McQualter, H. V. Scheller, B. A. Simmons, and R. J. Henry. 2015. Localization of polyhydroxybutyrate in sugarcane using Fourier-transform infrared microspectroscopy and multivariate imaging, Biotechnol Biofuels 8, 98. JBEI
201510.1016/j.rser.2015.04.091Lupoi, J. S., S. Singh, R. Parthasarathi, B. A. Simmons, and R. J. Henry. 2015. Recent innovations in analytical methods for the qualitative and quantitative assessment of lignin, Renewable and Sustainable Energy Reviews 49, 871-906. JBEI
201510.1039/c5ee01322dLuterbacher, J. S., A. Azarpira, A. H. Motagamwala, F. Lu, J. Ralph, and J. A. Dumesic. 2015. Lignin monomer production integrated into the ?-valerolactone sugar platform, Energy & Environmental Science 8(9), 2657-2663. GLBRC
201510.1002/cssc.201403418Luterbacher, J. S., D. M. Alonso, J. M. Rand, Y. M. Questell-Santiago, J. H. Yeap, B. F. Pfleger, and J. A. Dumesic. 2015. Solvent-enabled nonenyzmatic sugar production from biomass for chemical and biological upgrading, ChemSusChem 8(8), 1317-1322. GLBRC
201510.1111/tpj.12933Ma, W., Q. Kong, M. Grix, J. J. Mantyla, Y. Yang, C. Benning, and J. B. Ohlrogge. 2015. Deletion of a C-terminal intrinsically disordered region of WRINKLED1 affects its stability and enhances oil accumulation in Arabidopsis, Plant J 83(5), 864-874. GLBRC
201510.1186/s12859-015-0805-8Mao, X., Q. Ma, B. Liu, X. Chen, H. Zhang, and Y. Xu. 2015. Revisiting operons: an analysis of the landscape of transcriptional units in E. coli, BMC Bioinformatics 16, 356. .BESC
201510.1371/journal.pcbi.1004363Martin, H. G., V. S. Kumar, D. Weaver, A. Ghosh, V. Chubukov, A. Mukhopadhyay, A. Arkin, and J. D. Keasling. 2015. A Method to Constrain Genome-Scale Models with 13C Labeling Data, PLoS Comput Biol 11(9), e1004363. 10.1371/journal.pcbi.1004363.JBEI
201510.1534/g3.115.017012McCormick, R. F., S. K. Truong, and J. E. Mullet. 2015. RIG: Recalibration and interrelation of genomic sequence data with the GATK, G3 (Bethesda) 5(4), 655-665. GLBRC
201510.1007/s00299-014-1710-8McGlew, K., V. Shaw, M. Zhang, R. J. Kim, W. Yang, B. Shorrosh, M. C. Suh, and J. Ohlrogge. 2015. An annotated database of Arabidopsis mutants of acyl lipid metabolism, Plant Cell Rep 34(4), 519-532. GLBRC
201510.1074/jbc.M115.664847McLean, R., J. K. Hobbs, M. D. Suits, S. T. Tuomivaara, D. R. Jones, A. B. Boraston, and D. W. Abbott. 2015. Functional Analyses of Resurrected and Contemporary Enzymes Illuminate an Evolutionary Path for the Emergence of Exolysis in Polysaccharide Lyase Family 2, Journal of Biological Chemistry 290(35), 21231-21243. BESC
201510.1007/s00253-015-6610-5Mearls, E. B., D. G. Olson, C. D. Herring, and L. R. Lynd. 2015. Development of a regulatable plasmid-based gene expression system for Clostridium thermocellum, Appl Microbiol Biotechnol 99(18), 7589-7599. BESC
201510.1088/1748-9326/10/11/114001Meehan, T. D., and C. Gratton. 2015. A consistent positive association between landscape simplification and insecticide use across the Midwestern US from 1997 through 2012, Environmental Research Letters 10(11), 114001. GLBRC
201510.1021/acs.est.5b01691Meier, P. J., K. R. Cronin, E. A. Frost, T. M. Runge, B. E. Dale, D. J. Reinemann, and J. Detlor. 2015. Potential for Electrified Vehicles to Contribute to U.S. Petroleum and Climate Goals and Implications for Advanced Biofuels, Environ Sci Technol 49(14), 8277-8286. GLBRC
201510.1021/acscatal.5b00274Mellmer, M. A., J. M. R. Gallo, D. Martin Alonso, and J. A. Dumesic. 2015. Selective Production of Levulinic Acid from Furfuryl Alcohol in THF Solvent Systems over H-ZSM-5, ACS Catalysis 5(6), 3354-3359. GLBRC
201510.1039/c5gc00689aMeng, X., T. Wells, Q. Sun, F. Huang, and A. Ragauskas. 2015. Insights into the effect of dilute acid, hot water or alkaline pretreatment on the cellulose accessible surface area and the overall porosity of Populus, Green Chemistry 17(8), 4239-4246. BESC
201510.1186/s13068-015-0261-8Mielenz, J. R., M. Rodriguez, Jr., O. A. Thompson, X. Yang, and H. Yin. 2015. Development of Agave as a dedicated biomass source: production of biofuels from whole plants, Biotechnol Biofuels 8, 79. BESC
2015Millar, N., and P. Robertson. 2015. Nitrogen transfers and transformations in row-crop ecosystems. In The Ecology of Agricultural Landscapes: Long-Term Research on the Path to Sustainability, 289-342. Oxford University Press.GLBRC
201510.1002/bit.25511Mingardon, F., C. Clement, K. Hirano, M. Nhan, E. G. Luning, A. Chanal, and A. Mukhopadhyay. 2015. Improving olefin tolerance and production in E. coli using native and evolved AcrB, Biotechnol Bioeng 112(5), 879-888. JBEI
2015Morais, S., M. E. Himmel, and E. A. Bayer. 2015. New Paradigms for Engineering Plant Cell Wall Degrading Enzymes. In Direct Microbial Conversion of Biomass to Advanced Biofuels, 129-149. Ed. M. E. Himmel. Elsevier.BESC
201510.1016/j.jes.2015.03.009Morrell-Falvey, J. L., J. G. Elkins, and Z. W. Wang. 2015. Determination of the cellulase activity distribution in Clostridium thermocellum and Caldicellulosiruptor obsidiansis cultures using a fluorescent substrate, J Environ Sci (China) 34, 212-218. BESC
201510.1111/tpj.12898Mortimer, J. C., N. Faria-Blanc, X. Yu, T. Tryfona, M. Sorieul, Y. Z. Ng, Z. Zhang, K. Stott, N. Anders, and P. Dupree. 2015. An unusual xylan in Arabidopsis primary cell walls is synthesised by GUX3, IRX9L, IRX10L and IRX14, Plant J 83(3), 413-426. JBEI
201510.1080/21628130.2015.1010923Moskvin, O. V., S. McIlwain, and I. M. Ong. 2015. CAMDA 2014: Making sense of RNA-Seq data: From low-level processing to functional analysis, Systems Biomedicine 2(2), 31-40. GLBRC
201510.1186/s12864-015-1215-zMuchero, W., J. Guo, S. P. DiFazio, J. G. Chen, P. Ranjan, G. T. Slavov, L. E. Gunter, S. Jawdy, A. C. Bryan, R. Sykes, A. Ziebell, J. Klapste, I. Porth, O. Skyba, F. Unda, Y. A. El-Kassaby, C. J. Douglas, S. D. Mansfield, J. Martin, W. Schackwitz, L. M. Evans, O. Czarnecki, and G. A. Tuskan. 2015. High-resolution genetic mapping of allelic variants associated with cell wall chemistry in Populus, BMC Genomics 16, 24. BESC
201510.1016/j.tim.2015.04.008Mukhopadhyay, A. 2015. Tolerance engineering in bacteria for the production of advanced biofuels and chemicals, Trends Microbiol 23(8), 498-508. JBEI
201510.1128/mBio.00076-15Murfin, K. E., M. M. Lee, J. L. Klassen, B. R. McDonald, B. Larget, S. Forst, S. P. Stock, C. R. Currie, and H. Goodrich-Blair. 2015. Xenorhabdus bovienii Strain Diversity Impacts Coevolution and Symbiotic Maintenance with Steinernema spp. Nematode Hosts, MBio 6(3), e00076. GLBRC
201510.1016/j.ymeth.2015.05.022Myers, K. S., D. M. Park, N. A. Beauchene, and P. J. Kiley. 2015. Defining bacterial regulons using ChIP-seq, Methods 86, 80-88. GLBRC
201510.3389/fpls.2015.00550Nafisi, M., M. Stranne, L. Fimognari, S. Atwell, H. J. Martens, P. R. Pedas, S. F. Hansen, C. Nawrath, H. V. Scheller, D. J. Kliebenstein, and Y. Sakuragi. 2015. Acetylation of cell wall is required for structural integrity of the leaf surface and exerts a global impact on plant stress responses, Front Plant Sci 6, 550. JBEI
201510.1038/srep16039Narula, C. K., Z. Li, E. M. Casbeer, R. A. Geiger, M. Moses-Debusk, M. Keller, M. V. Buchanan, and B. H. Davison. 2015. Heterobimetallic Zeolite, InV-ZSM-5, Enables Efficient Conversion of Biomass Derived Ethanol to Renewable Hydrocarbons, Sci Rep 5, 16039. BESC
201510.1021/acs.iecr.5b03677Ng, R. T. L., and C. T. Maravelias. 2015. Design of Cellulosic Ethanol Supply Chains with Regional Depots, Industrial & Engineering Chemistry Research 55(12), 3420-3432. GLBRC
2015 10.1002/cssc.201403045Nguyen, T. Y., C. M. Cai, R. Kumar, and C. E. Wyman. 2015. Co-solvent pretreatment reduces costly enzyme requirements for high sugar and ethanol yields from lignocellulosic biomass, ChemSusChem 8(10), 1716-1725. BESC
201510.1128/genomeA.00402-15O'Dell, K. B., H. L. Woo, S. Utturkar, D. Klingeman, S. D. Brown, and T. C. Hazen. 2015. Genome Sequence of Halomonas sp. Strain KO116, an Ionic Liquid-Tolerant Marine Bacterium Isolated from a Lignin-Enriched Seawater Microcosm, Genome Announc 3(3). BESC
2015Ohlrogge, J., J. Browse, and C. Somerville. 2015. Lipids. In Biochemistry and Molecular Biology of Plants, 2nd ed., 336-400. Eds. W. Gruissem, B. B. Buchanan, and R. L. Jones. Wiley.GLBRC
201510.1016/j.meteno.2015.03.002Olson, D. G., M. Maloney, A. A. Lanahan, S. Hon, L. J. Hauser, and L. R. Lynd. 2015. Identifying promoters for gene expression in Clostridium thermocellum, Metabolic Engineering Communications 2, 23-29. BESC
201510.1016/j.copbio.2015.02.006Olson, D. G., R. Sparling, and L. R. Lynd. 2015. Ethanol production by engineered thermophiles, Curr Opin Biotechnol 33, 130-141. BESC
201510.1016/j.biortech.2015.01.121Papa, G., S. Rodriguez, A. George, A. Schievano, V. Orzi, K. L. Sale, S. Singh, F. Adani, and B. A. Simmons. 2015. Comparison of different pretreatments for the production of bioethanol and biomethane from corn stover and switchgrass, Bioresour Technol 183, 101-110. JBEI
201510.1016/j.ymben.2015.09.002Papanek, B., R. Biswas, T. Rydzak, and A. M. Guss. 2015. Elimination of metabolic pathways to all traditional fermentation products increases ethanol yields in Clostridium thermocellum, Metab Eng 32, 49-54. BESC
201510.1525/abt.2015.77.4.2Parker, J. M., E. X. de los Santos, and C. W. Anderson. 2015. Learning Progressions & Climate Change, The American Biology Teacher 77(4), 232-238. GLBRC
201510.3389/fpls.2015.00301Parsons, H. T., and J. L. Heazlewood. 2015. Beyond the Western front: targeted proteomics and organelle abundance profiling, Front Plant Sci 6, 301. JBEI
201510.1021/acs.jpcb.5b02680Parthasarathi, R., K. Balamurugan, J. Shi, V. Subramanian, B. A. Simmons, and S. Singh. 2015. Theoretical Insights into the Role of Water in the Dissolution of Cellulose Using IL/Water Mixed Solvent Systems, J Phys Chem B 119(45), 14339-14349. JBEI
201510.22443/rms.inf.1.127Passian, A., R. Farahi, and B. Davison. 2015. Exploring the nano-world of plant cells with hybrid photonicmechanical forces, infocus Magazine, 4-9. BESC
201510.1111/nph.13532Patron, N. J., D. Orzaez, S. Marillonnet, H. Warzecha, C. Matthewman, M. Youles, O. Raitskin, A. Leveau, G. Farre, C. Rogers, A. Smith, J. Hibberd, A. A. Webb, J. Locke, S. Schornack, J. Ajioka, D. C. Baulcombe, C. Zipfel, S. Kamoun, J. D. Jones, H. Kuhn, S. Robatzek, H. P. Van Esse, D. Sanders, G. Oldroyd, C. Martin, R. Field, S. O'Connor, S. Fox, B. Wulff, B. Miller, A. Breakspear, G. Radhakrishnan, P. M. Delaux, D. Loque, A. Granell, A. Tissier, P. Shih, T. P. Brutnell, W. P. Quick, H. Rischer, P. D. Fraser, A. Aharoni, C. Raines, P. F. South, J. M. Ane, B. R. Hamberger, J. Langdale, J. Stougaard, H. Bouwmeester, M. Udvardi, J. A. Murray, V. Ntoukakis, P. Schafer, K. Denby, K. J. Edwards, A. Osbourn, and J. Haseloff. 2015. Standards for plant synthetic biology: a common syntax for exchange of DNA parts, New Phytol 208(1), 13-19. JBEI
201510.1093/jxb/erv107Pattathil, S., M. G. Hahn, B. E. Dale, and S. P. Chundawat. 2015. Insights into plant cell wall structure, architecture, and integrity using glycome profiling of native and AFEXTM-pre-treated biomass, J Exp Bot 66(14), 4279-4294. BESC GLBRC
201510.3389/fbioe.2015.00173Pattathil, S., U. Avci, T. Zhang, C. L. Cardenas, and M. G. Hahn. 2015. Immunological Approaches to Biomass Characterization and Utilization, Front Bioeng Biotechnol 3, 173. BESC
201510.1016/j.biombioe.2015.02.026Perez-Pimienta, J. A., M. G. Lopez-Ortega, J. A. Chavez-Carvayar, P. Varanasi, V. Stavila, G. Cheng, S. Singh, and B. A. Simmons. 2015. Characterization of agave bagasse as a function of ionic liquid pretreatment, Biomass and Bioenergy 75, 180-188. JBEI
201510.3389/fbioe.2015.00135Petzold, C. J., L. J. Chan, M. Nhan, and P. D. Adams. 2015. Analytics for Metabolic Engineering, Front Bioeng Biotechnol 3, 135. JBEI
201510.1021/sb5002517Phelan, R. M., O. N. Sekurova, J. D. Keasling, and S. B. Zotchev. 2015. Engineering terpene biosynthesis in Streptomyces for production of the advanced biofuel precursor bisabolene, ACS Synth Biol 4(4), 393-399. JBEI
201510.1073/pnas.1410400112Piotrowski, J. S., H. Okada, F. Lu, S. C. Li, L. Hinchman, A. Ranjan, D. L. Smith, A. J. Higbee, A. Ulbrich, J. J. Coon, R. Deshpande, Y. V. Bukhman, S. McIlwain, I. M. Ong, C. L. Myers, C. Boone, R. Landick, J. Ralph, M. Kabbage, and Y. Ohya. 2015. Plant-derived antifungal agent poacic acid targets beta-1,3-glucan, Proc Natl Acad Sci U S A 112(12), E1490-1497. GLBRC
201510.1007/978-1-4939-2269-7_23Piotrowski, J. S., S. W. Simpkins, S. C. Li, R. Deshpande, S. J. McIlwain, I. M. Ong, C. L. Myers, C. Boone, and R. J. Andersen. 2015. Chemical genomic profiling via barcode sequencing to predict compound mode of action, Methods Mol Biol 1263, 299-318. GLBRC
201510.1128/AEM.01324-15Pisithkul, T., T. B. Jacobson, T. J. O'Brien, D. M. Stevenson, and D. Amador-Noguez. 2015. Phenolic Amides Are Potent Inhibitors of De Novo Nucleotide Biosynthesis, Appl Environ Microbiol 81(17), 5761-5772. GLBRC
201510.1016/j.phytochem.2015.07.021Pollard, M., D. Delamarter, T. M. Martin, and Y. Shachar-Hill. 2015. Lipid labeling from acetate or glycerol in cultured embryos of Camelina sativa seeds: A tale of two substrates, Phytochemistry 118, 192-203. GLBRC
201510.1016/j.phytochem.2015.07.022Pollard, M., T. M. Martin, and Y. Shachar-Hill. 2015. Lipid analysis of developing Camelina sativa seeds and cultured embryos, Phytochemistry 118, 23-32. GLBRC
201510.1002/biot.201400499Poovaiah, C. R., M. Mazarei, S. R. Decker, G. B. Turner, R. W. Sykes, M. F. Davis, and C. N. Stewart, Jr. 2015. Transgenic switchgrass (Panicum virgatum L.) biomass is increased by overexpression of switchgrass sucrose synthase (PvSUS1), Biotechnol J 10(4), 552-563. BESC
201510.1002/cbic.201500228Poust, S., J. Piety, A. Bar-Even, C. Louw, D. Baker, J. D. Keasling, and J. B. Siegel. 2015. Mechanistic Analysis of an Engineered Enzyme that Catalyzes the Formose Reaction, Chembiochem 16(13), 1950-1954. JBEI
201510.1002/anie.201410124Poust, S., R. M. Phelan, K. Deng, L. Katz, C. J. Petzold, and J. D. Keasling. 2015. Divergent mechanistic routes for the formation of gem-dimethyl groups in the biosynthesis of complex polyketides, Angew Chem Int Ed Engl 54(8), 2370-2373. 10.1002/anie.201410124.JBEI
201510.1126/sciadv.1500245Pruitt, R. N., B. Schwessinger, A. Joe, N. Thomas, F. Liu, M. Albert, M. R. Robinson, L. J. Chan, D. D. Luu, H. Chen, O. Bahar, A. Daudi, D. De Vleesschauwer, D. Caddell, W. Zhang, X. Zhao, X. Li, J. L. Heazlewood, D. Ruan, D. Majumder, M. Chern, H. Kalbacher, S. Midha, P. B. Patil, R. V. Sonti, C. J. Petzold, C. C. Liu, J. S. Brodbelt, G. Felix, and P. C. Ronald. 2015. The rice immune receptor XA21 recognizes a tyrosine-sulfated protein from a Gram-negative bacterium, Sci Adv 1(6), e1500245. .JBEI
201510.1007/s12155-015-9655-5Pu, Y., F. Hu, F. Huang, and A. J. Ragauskas. 2015. Lignin Structural Alterations in Thermochemical Pretreatments with Limited Delignification, BioEnergy Research 8(3), 992-1003. BESC
201510.1371/journal.pbio.1002310Quinn, J. Y., R. S. Cox, 3rd, A. Adler, J. Beal, S. Bhatia, Y. Cai, J. Chen, K. Clancy, M. Galdzicki, N. J. Hillson, N. Le Novere, A. J. Maheshwari, J. A. McLaughlin, C. J. Myers, U. P, M. Pocock, C. Rodriguez, L. Soldatova, G. B. Stan, N. Swainston, A. Wipat, and H. M. Sauro. 2015. SBOL Visual: A Graphical Language for Genetic Designs, PLoS Biol 13(12), e1002310. JBEI
201510.1371/journal.pone.0118515Rachid, C. T., F. C. Balieiro, E. S. Fonseca, R. S. Peixoto, G. M. Chaer, J. M. Tiedje, and A. S. Rosado. 2015. Intercropped silviculture systems, a key to achieving soil fungal community management in eucalyptus plantations, PLoS One 10(2), e0118515. GLBRC
201510.1021/jacs.5b09672Rafiee, M., K. C. Miles, and S. S. Stahl. 2015. Electrocatalytic Alcohol Oxidation with TEMPO and Bicyclic Nitroxyl Derivatives: Driving Force Trumps Steric Effects, J Am Chem Soc 137(46), 14751-14757. GLBRC
201510.1007/s12155-015-9636-8Ray, P., T. Ishiga, S. R. Decker, G. B. Turner, and K. D. Craven. 2015. A Novel Delivery System for the Root Symbiotic Fungus, Sebacina vermifera, and Consequent Biomass Enhancement of Low Lignin COMT Switchgrass Lines, BioEnergy Research 8(3), 922-933. BESC
201510.1128/genomeA.00797-15Rooney, E. A., K. T. Rowe, A. Guseva, M. Huntemann, J. K. Han, A. Chen, N. C. Kyrpides, K. Mavromatis, V. M. Markowitz, K. Palaniappan, N. Ivanova, A. Pati, K. Liolios, H. P. Nordberg, M. N. Cantor, S. X. Hua, N. Shapiro, T. Woyke, L. R. Lynd, and J. A. Izquierdo. 2015. Draft Genome Sequence of the Cellulolytic and Xylanolytic Thermophile Clostridium clariflavum Strain 4-2a, Genome Announc 3(4). BESC
201510.1016/j.pbi.2015.05.016Ruberti, C., S. J. Kim, G. Stefano, and F. Brandizzi. 2015. Unfolded protein response in plants: one master, many questions, Curr Opin Plant Biol 27, 59-66. GLBRC
2015Russ, R. S., S. Wangen, D. L. Nye, R. B. Shapiro, W. Strinz, and M. Ferris. 2015. Fields of Fuel: Using a video game to support reasoning about sustainablity, The Science Teacher 82(3), 49-54.
201510.1007/s10295-015-1644-3Rydzak, T., L. R. Lynd, and A. M. Guss. 2015. Elimination of formate production in Clostridium thermocellum, J Ind Microbiol Biotechnol 42(9), 1263-1272. BESC
201510.1016/j.febslet.2015.08.026Sand, A., E. K. Holwerda, N. M. Ruppertsberger, M. Maloney, D. G. Olson, Y. Nataf, I. Borovok, A. L. Sonenshein, E. A. Bayer, R. Lamed, L. R. Lynd, and Y. Shoham. 2015. Three cellulosomal xylanase genes in Clostridium thermocellum are regulated by both vegetative SigA (sigma(A)) and alternative SigI6 (sigma(I6)) factors, FEBS Lett 589(20 Pt B), 3133-3140. BESC
201510.1186/s13068-015-0394-9Sander, K., C. M. Wilson, M. Rodriguez, Jr., D. M. Klingeman, T. Rydzak, B. H. Davison, and S. D. Brown. 2015. Clostridium thermocellum DSM 1313 transcriptional responses to redox perturbation, Biotechnol Biofuels 8, 211. BESC
201510.1007/s12155-015-9643-9Sathitsuksanoh, N., M. Sawant, Q. Truong, J. Tan, C. G. Canlas, N. Sun, W. Zhang, S. Renneckar, T. Prasomsri, J. Shi, Ö. Çetinkol, S. Singh, B. A. Simmons, and A. George. 2015. How Alkyl Chain Length of Alcohols Affects Lignin Fractionation and Ionic Liquid Recycle During Lignocellulose Pretreatment, BioEnergy Research 8(3), 973-981. JBEI
201510.1105/tpc.15.00379Sawake, S., N. Tajima, J. C. Mortimer, J. Lao, T. Ishikawa, X. Yu, Y. Yamanashi, Y. Yoshimi, M. Kawai-Yamada, P. Dupree, Y. Tsumuraya, and T. Kotake. 2015. KONJAC1 and 2 Are Key Factors for GDP-Mannose Generation and Affect l-Ascorbic Acid and Glucomannan Biosynthesis in Arabidopsis, Plant Cell 27(12), 3397-3409. JBEI
201510.1128/genomeA.00607-15Schicklberger, M., N. Shapiro, D. Loque, T. Woyke, and R. Chakraborty. 2015. Draft Genome Sequence of Raoultella terrigena R1Gly, a Diazotrophic Endophyte, Genome Announc 3(3). JBEI
201510.1371/journal.ppat.1004809Schwessinger, B., O. Bahar, N. Thomas, N. Holton, V. Nekrasov, D. Ruan, P. E. Canlas, A. Daudi, C. J. Petzold, V. R. Singan, R. Kuo, M. Chovatia, C. Daum, J. L. Heazlewood, C. Zipfel, and P. C. Ronald. 2015. Transgenic expression of the dicotyledonous pattern recognition receptor EFR in rice leads to ligand-dependent activation of defense responses, PLoS Pathog 11(3), e1004809. JBEI
201510.1128/AEM.01634-15Scott, I. M., G. M. Rubinstein, G. L. Lipscomb, M. Basen, G. J. Schut, A. M. Rhaesa, W. A. Lancaster, F. L. Poole, 2nd, R. M. Kelly, and M. W. Adams. 2015. A New Class of Tungsten-Containing Oxidoreductase in Caldicellulosiruptor, a Genus of Plant Biomass-Degrading Thermophilic Bacteria, Appl Environ Microbiol 81(20), 7339-7347. BESC
201510.1186/s13068-015-0275-2Scullin, C., A. G. Cruz, Y. D. Chuang, B. A. Simmons, D. Loque, and S. Singh. 2015. Restricting lignin and enhancing sugar deposition in secondary cell walls enhances monomeric sugar release after low temperature ionic liquid pretreatment, Biotechnol Biofuels 8, 95. JBEI
201510.1016/j.biortech.2014.09.105.Scullin, C., V. Stavila, A. Skarstad, J. D. Keasling, B. A. Simmons, and S. Singh. 2015. Optimization of renewable pinene production from the conversion of macroalgae Saccharina latissima, Bioresour Technol 184, 415-420. JBEI
201510.1186/s13068-015-0356-2Serate, J., D. Xie, E. Pohlmann, C. Donald, Jr., M. Shabani, L. Hinchman, A. Higbee, M. McGee, A. La Reau, G. E. Klinger, S. Li, C. L. Myers, C. Boone, D. M. Bates, D. Cavalier, D. Eilert, L. G. Oates, G. Sanford, T. K. Sato, B. Dale, R. Landick, J. Piotrowski, R. G. Ong, and Y. Zhang. 2015. Controlling microbial contamination during hydrolysis of AFEX-pretreated corn stover and switchgrass: effects on hydrolysate composition, microbial response and fermentation, Biotechnol Biofuels 8, 180. GLBRC
201510.3835/plantgenome2014.10.0075Serba, D. D., S. R. Uppalapati, S. Mukherjee, N. Krom, Y. Tang, K. S. Mysore, and M. C. Saha. 2015. Transcriptome Profiling of Rust Resistance in Switchgrass Using RNA-Seq Analysis, The Plant Genome 8(2), 0. BESC
201510.1007/s12155-015-9667-1Sharma, M. K., R. Sharma, P. Cao, M. Harkenrider, J. Jenkins, J. Grimwood, J. Zhang, M. K. Udvardi, J. Schmutz, and P. C. Ronald. 2015. Targeted Switchgrass BAC Library Screening and Sequence Analysis Identifies Predicted Biomass and Stress Response-Related Genes, BioEnergy Research 9(1), 109-122. JBEI
201510.1186/s13068-015-0257-4Shaw, A. J., B. B. Miller, S. R. Rogers, W. R. Kenealy, A. Meola, A. Bhandiwad, W. R. Sillers, I. Shikhare, D. A. Hogsett, and C. D. Herring. 2015. Anaerobic detoxification of acetic acid in a thermophilic ethanologen, Biotechnol Biofuels 8, 75. 10.1186/s13068-015-0257-4.BESC
201510.1007/s12155-015-9588-zShi, J., K. W. George, N. Sun, W. He, C. Li, V. Stavila, J. D. Keasling, B. A. Simmons, T. S. Lee, and S. Singh. 2015. Impact of Pretreatment Technologies on Saccharification and Isopentenol Fermentation of Mixed Lignocellulosic Feedstocks, BioEnergy Research 8(3), 1004-1013. JBEI
201510.1021/acssynbio.5b00062Shih, S. C., G. Goyal, P. W. Kim, N. Koutsoubelis, J. D. Keasling, P. D. Adams, N. J. Hillson, and A. K. Singh. 2015. A Versatile Microfluidic Device for Automating Synthetic Biology, ACS Synth Biol 4(10), 1151-1164. JBEI
201510.1039/c4lc00794hShih, S. C., P. C. Gach, J. Sustarich, B. A. Simmons, P. D. Adams, S. Singh, and A. K. Singh. 2015. A droplet-to-digital (D2D) microfluidic device for single cell assays, Lab Chip 15(1), 225-236. JBEI
201510.1073/pnas.1500545112Siegel, J. B., A. L. Smith, S. Poust, A. J. Wargacki, A. Bar-Even, C. Louw, B. W. Shen, C. B. Eiben, H. M. Tran, E. Noor, J. L. Gallaher, J. Bale, Y. Yoshikuni, M. H. Gelb, J. D. Keasling, B. L. Stoddard, M. E. Lidstrom, and D. Baker. 2015. Computational protein design enables a novel one-carbon assimilation pathway, Proc Natl Acad Sci U S A 112(12), 3704-3709. JBEI
201510.3389/fenrg.2014.00062Singh, S., G. Cheng, N. Sathitsuksanoh, D. Wu, P. Varanasi, A. George, V. Balan, X. Gao, R. Kumar, B. E. Dale, C. E. Wyman, and B. A. Simmons. 2015. Comparison of Different Biomass Pretreatment Techniques and Their Impact on Chemistry and Structure, Frontiers in Energy Research 2. BESC JBEI GLBRC
201510.1007/s12155-015-9611-4Sinistore, J. C., D. J. Reinemann, R. C. Izaurralde, K. R. Cronin, P. J. Meier, T. M. Runge, and X. Zhang. 2015. Life Cycle Assessment of Switchgrass Cellulosic Ethanol Production in the Wisconsin and Michigan Agricultural Contexts, BioEnergy Research 8(3), 897-909. GLBRC
201510.1007/s12155-015-9660-8Slater, S. C., B. A. Simmons, T. S. Rogers, M. F. Phillips, K. Nordahl, and B. H. Davison. 2015. The DOE Bioenergy Research Centers: History, Operations, and Scientific Output, BioEnergy Research 8(3), 881-896. BESC GLBRC JBEI
201510.1186/s13068-015-0239-6Slininger, P. J., M. A. Shea-Andersh, S. R. Thompson, B. S. Dien, C. P. Kurtzman, V. Balan, L. da Costa Sousa, N. Uppugundla, B. E. Dale, and M. A. Cotta. 2015. Evolved strains of Scheffersomyces stipitis achieving high ethanol productivity on acid- and base-pretreated biomass hydrolyzate at high solids loading, Biotechnol Biofuels 8, 60. GLBRC
201510.1104/pp.15.00815Smith, R. A., E. Gonzales-Vigil, S. D. Karlen, J. Y. Park, F. Lu, C. G. Wilkerson, L. Samuels, J. Ralph, and S. D. Mansfield. 2015. Engineering Monolignol p-Coumarate Conjugates into Poplar and Arabidopsis Lignins, Plant Physiol 169(4), 2992-3001. GLBRC
201510.3389/fpls.2015.00628Smith-Moritz, A. M., Z. Hao, S. G. Fernandez-Nino, J. U. Fangel, Y. Verhertbruggen, H. Y. Holman, W. G. Willats, P. C. Ronald, H. V. Scheller, J. L. Heazlewood, and M. E. Vega-Sanchez. 2015. Structural characterization of a mixed-linkage glucan deficient mutant reveals alteration in cellulose microfibril orientation in rice coleoptile mesophyll cell walls, Front Plant Sci 6, 628. JBEI
201510.1128/mBio.00389-15Spero, M. A., F. O. Aylward, C. R. Currie, and T. J. Donohue. 2015. Phylogenomic analysis and predicted physiological role of the proton-translocating NADH:quinone oxidoreductase (complex I) across bacteria, MBio 6(2). GLBRC
201510.1186/s13068-015-0403-zSrivastava, A. C., F. Chen, T. Ray, S. Pattathil, M. J. Pena, U. Avci, H. Li, D. V. Huhman, J. Backe, B. Urbanowicz, J. S. Miller, M. Bedair, C. E. Wyman, L. W. Sumner, W. S. York, M. G. Hahn, R. A. Dixon, E. B. Blancaflor, and Y. Tang. 2015. Loss of function of folylpolyglutamate synthetase 1 reduces lignin content and improves cell wall digestibility in Arabidopsis, Biotechnol Biofuels 8, 224. BESC
201510.1021/acscatal.5b02061Stavila, V., R. Parthasarathi, R. W. Davis, F. El Gabaly, K. L. Sale, B. A. Simmons, S. Singh, and M. D. Allendorf. 2015. MOF-Based Catalysts for Selective Hydrogenolysis of Carbon-Oxygen Ether Bonds, ACS Catalysis 6(1), 55-59. JBEI
201510.1002/bit.25445Su, Y. K., L. B. Willis, and T. W. Jeffries. 2015. Effects of aeration on growth, ethanol and polyol accumulation by Spathaspora passalidarum NRRL Y-27907 and Scheffersomyces stipitis NRRL Y-7124, Biotechnol Bioeng 112(3), 457-469. GLBRC
201510.1016/j.biortech.2015.02.087Sun, N., F. Xu, N. Sathitsuksanoh, V. S. Thompson, K. Cafferty, C. Li, D. Tanjore, A. Narani, T. R. Pray, B. A. Simmons, and S. Singh. 2015. Blending municipal solid waste with corn stover for sugar production using ionic liquid process, Bioresour Technol 186, 200-206. JBEI
201510.1021/acssuschemeng.5b00426Sun, Q., Y. Pu, X. Meng, T. Wells, and A. J. Ragauskas. 2015. Structural Transformation of Isolated Poplar and Switchgrass Lignins during Dilute Acid Treatment, ACS Sustainable Chemistry & Engineering 3(9), 2203-2210. BESC
201510.1007/s12155-015-9610-5Sykes, R. W., E. L. Gjersing, C. L. Doeppke, and M. F. Davis. 2015. High-Throughput Method for Determining the Sugar Content in Biomass with Pyrolysis Molecular Beam Mass Spectrometry, BioEnergy Research 8(3), 964-972. BESC
201510.1186/s13068-015-0316-xSykes, R. W., E. L. Gjersing, K. Foutz, W. H. Rottmann, S. A. Kuhn, C. E. Foster, A. Ziebell, G. B. Turner, S. R. Decker, M. A. Hinchee, and M. F. Davis. 2015. Down-regulation of p-coumaroyl quinate/shikimate 3'-hydroxylase (C3'H) and cinnamate 4-hydroxylase (C4H) genes in the lignin biosynthetic pathway of Eucalyptus urophylla x E. grandis leads to improved sugar release, Biotechnol Biofuels 8, 128. BESC
201510.1007/s12155-015-9680-4Sykes, V. R., F. L. Allen, J. R. Mielenz, C. N. Stewart, M. T. Windham, C. Y. Hamilton, M. Rodriguez, and K. L. Yee. 2015. Reduction of Ethanol Yield from Switchgrass Infected with Rust Caused by Puccinia emaculata, BioEnergy Research 9(1), 239-247. BESC
201510.1093/femsyr/fov002Sylvester, K., Q. M. Wang, B. James, R. Mendez, A. B. Hulfachor, and C. T. Hittinger. 2015. Temperature and host preferences drive the diversification of Saccharomyces and other yeasts: a survey and the discovery of eight new yeast species, FEMS Yeast Res 15(3). GLBRC
2015Takasumi, J. L., and J. C. Liao. 2015. Outlook for the Production of Butanol from Cellulolytic Strains of Clostridia. In Direct Microbial Conversion of Biomass to Advanced Biofuels, 291-306. Ed. M. E. Himmel. Elsevier.BESC
201510.1186/s13068-014-0179-6Tang, X., L. da Costa Sousa, M. Jin, S. P. Chundawat, C. K. Chambliss, M. W. Lau, Z. Xiao, B. E. Dale, and V. Balan. 2015. Designer synthetic media for studying microbial-catalyzed biofuel production, Biotechnol Biofuels 8(1), 1. GLBRC
201510.1007/s12155-014-9573-yTanger, P., M. E. Vega-Sánchez, M. Fleming, K. Tran, S. Singh, J. B. Abrahamson, C. E. Jahn, N. Santoro, E. B. Naredo, M. Baraoidan, J. M. C. Danku, D. E. Salt, K. L. McNally, B. A. Simmons, P. C. Ronald, H. Leung, D. R. Bush, J. K. McKay, and J. E. Leach. 2015. Cell Wall Composition and Bioenergy Potential of Rice Straw Tissues Are Influenced by Environment, Tissue Type, and Genotype, BioEnergy Research 8(3), 1165-1182. JBEI GLBRC
201510.1038/nnano.2015.168Tetard, L., A. Passian, R. H. Farahi, T. Thundat, and B. H. Davison. 2015. Opto-nanomechanical spectroscopic material characterization, Nat Nanotechnol 10(10), 870-877. BESC
201510.1016/j.ymben.2015.10.004.Thompson, R. A., D. S. Layton, A. M. Guss, D. G. Olson, L. R. Lynd, and C. T. Trinh. 2015. Elucidating central metabolic redox obstacles hindering ethanol production in Clostridium thermocellum, Metab Eng 32, 207-219. BESC
201510.1111/ele.12453Tiemann, L. K., A. S. Grandy, E. E. Atkinson, E. Marin-Spiotta, and M. D. McDaniel. 2015. Crop rotational diversity enhances belowground communities and functions in an agroecosystem, Ecol Lett 18(8), 761-771. GLBRC
201510.1111/gcbb.12126Tiemann, L. K., and A. S. Grandy. 2015. Mechanisms of soil carbon accrual and storage in bioenergy cropping systems, GCB Bioenergy 7(2), 161-174. GLBRC
201510.1093/jxb/eru500Tjellstrom, H., M. Strawsine, and J. B. Ohlrogge. 2015. Tracking synthesis and turnover of triacylglycerol in leaves, J Exp Bot 66(5), 1453-1461. GLBRC
201510.1016/j.biortech.2014.11.090Trajano, H. L., S. Pattathil, B. A. Tomkins, T. J. Tschaplinski, M. G. Hahn, G. J. Van Berkel, and C. E. Wyman. 2015. Xylan hydrolysis in Populus trichocarpa x P. deltoides and model substrates during hydrothermal pretreatment, Bioresour Technol 179, 202-210. BESC
201510.1111/pbi.12319Trumbo, J. L., B. Zhang, and C. N. Stewart, Jr. 2015. Manipulating microRNAs for improved biomass and biofuels from plant feedstocks, Plant Biotechnol J 13(3), 337-354. BESC
201510.1534/genetics.115.178608Truong, S. K., R. F. McCormick, W. L. Rooney, and J. E. Mullet. 2015. Harnessing Genetic Variation in Leaf Angle to Increase Productivity of Sorghum bicolor, Genetics 201(3), 1229-1238. GLBRC
201510.1111/tpj.12917Tsai, C. H., K. Zienkiewicz, C. L. Amstutz, B. G. Brink, J. Warakanont, R. Roston, and C. Benning. 2015. Dynamics of protein and polar lipid recruitment during lipid droplet assembly in Chlamydomonas reinhardtii, Plant J 83(4), 650-660. GLBRC
201510.1111/pbi.12316Tsuji, Y., R. Vanholme, Y. Tobimatsu, Y. Ishikawa, C. E. Foster, N. Kamimura, S. Hishiyama, S. Hashimoto, A. Shino, H. Hara, K. Sato-Izawa, P. Oyarce, G. Goeminne, K. Morreel, J. Kikuchi, T. Takano, M. Fukuda, Y. Katayama, W. Boerjan, J. Ralph, E. Masai, and S. Kajita. 2015. Introduction of chemically labile substructures into Arabidopsis lignin through the use of LigD, the Calpha-dehydrogenase from Sphingobium sp. strain SYK-6, Plant Biotechnol J 13(6), 821-832. GLBRC
201510.1021/sc500731cUnderkofler, K. A., R. E. Teixeira, S. A. Pietsch, K. G. Knapp, and R. T. Raines. 2015. Separation of Lignin from Corn Stover Hydrolysate with Quantitative Recovery of Ionic Liquid, ACS Sustain Chem Eng 3(4), 606-613. GLBRC
201510.1038/sdata.2015.14Utturkar, S. M., D. M. Klingeman, J. M. Bruno-Barcena, M. S. Chinn, A. M. Grunden, M. Kopke, and S. D. Brown. 2015. Sequence data for Clostridium autoethanogenum using three generations of sequencing technologies, Sci Data 2, 150014. BESC
201510.1111/pbi.12326Vega-Sanchez, M. E., D. Loque, J. Lao, M. Catena, Y. Verhertbruggen, T. Herter, F. Yang, J. Harholt, B. Ebert, E. E. Baidoo, J. D. Keasling, H. V. Scheller, J. L. Heazlewood, and P. C. Ronald. 2015. Engineering temporal accumulation of a low recalcitrance polysaccharide leads to increased C6 sugar content in plant cell walls, Plant Biotechnol J 13(7), 903-914. JBEI
201510.1016/j.molp.2014.11.017Velasquez, S. M., M. M. Ricardi, C. P. Poulsen, A. Oikawa, A. Dilokpimol, A. Halim, S. Mangano, S. P. Denita Juarez, E. Marzol, J. D. Salgado Salter, J. G. Dorosz, C. Borassi, S. R. Moller, R. Buono, Y. Ohsawa, K. Matsuoka, M. S. Otegui, H. V. Scheller, N. Geshi, B. L. Petersen, N. D. Iusem, and J. M. Estevez. 2015. Complex regulation of prolyl-4-hydroxylases impacts root hair expansion, Mol Plant 8(5), 734-746. JBEI
201510.1007/s00248-014-0500-8Vishnivetskaya, T. A., S. D. Hamilton-Brehm, M. Podar, J. J. Mosher, A. V. Palumbo, T. J. Phelps, M. Keller, and J. G. Elkins. 2015. Community analysis of plant biomass-degrading microorganisms from Obsidian Pool, Yellowstone National Park, Microb Ecol 69(2), 333-345. BESC
201510.1104/pp.15.00851Voiniciuc, C., M. H. Schmidt, A. Berger, B. Yang, B. Ebert, H. V. Scheller, H. M. North, B. Usadel, and M. Gunl. 2015. MUCILAGE-RELATED10 Produces Galactoglucomannan That Maintains Pectin and Cellulose Architecture in Arabidopsis Seed Mucilage, Plant Physiol 169(1), 403-420. JBEI
201510.1073/pnas.1411926112Wagner, A., Y. Tobimatsu, L. Phillips, H. Flint, B. Geddes, F. Lu, and J. Ralph. 2015. Syringyl lignin production in conifers: Proof of concept in a Pine tracheary element system, Proc Natl Acad Sci U S A 112(19), 6218-6223. GLBRC
201510.1186/s13068-015-0402-0Walker, J. A., T. E. Takasuka, K. Deng, C. M. Bianchetti, H. S. Udell, B. M. Prom, H. Kim, P. D. Adams, T. R. Northen, and B. G. Fox. 2015. Multifunctional cellulase catalysis targeted by fusion to different carbohydrate-binding modules, Biotechnol Biofuels 8, 220. 10.1186/s13068-015-0402-0.GLBRC JBEI
201510.1073/pnas.1504828112Walley, J., Y. Xiao, J. Z. Wang, E. E. Baidoo, J. D. Keasling, Z. Shen, S. P. Briggs, and K. Dehesh. 2015. Plastid-produced interorgannellar stress signal MEcPP potentiates induction of the unfolded protein response in endoplasmic reticulum, Proc Natl Acad Sci U S A 112(19), 6212-6217. JBEI
201510.1186/s40168-015-0093-6Wang, Q., J. A. Fish, M. Gilman, Y. Sun, C. T. Brown, J. M. Tiedje, and J. R. Cole. 2015. Xander: employing a novel method for efficient gene-targeted metagenomic assembly, Microbiome 3, 32. GLBRC
201510.1002/bit.25323Weaver, L. J., M. M. Sousa, G. Wang, E. Baidoo, C. J. Petzold, and J. D. Keasling. 2015. A kinetic-based approach to understanding heterologous mevalonate pathway function in E. coli, Biotechnol Bioeng 112(1), 111-119. JBEI
201510.1371/journal.pcbi.1004079Weighill, D. A., and D. A. Jacobson. 2015. 3-way networks: application of hypergraphs for modelling increased complexity in comparative genomics, PLoS Comput Biol 11(3), e1004079. BESC
201510.1002/jssc.201500551Wenz, C., C. Barbas, A. Lopez-Gonzalvez, A. Garcia, F. Benavente, V. Sanz-Nebot, T. Blanc, G. Freckleton, P. Britz-McKibbin, M. Shanmuganathan, F. de l'Escaille, J. Far, R. Haselberg, S. Huang, C. Huhn, M. Pattky, D. Michels, S. Mou, F. Yang, C. Neusuess, N. Tromsdorf, E. E. K. Baidoo, J. D. Keasling, and S. S. Park. 2015. Interlaboratory study to evaluate the robustness of capillary electrophoresis-mass spectrometry for peptide mapping, J Sep Sci 38(18), 3262-3270. JBEI
201510.5194/gmdd-8-2011-2015Wieder, W. R., A. S. Grandy, C. M. Kallenbach, P. G. Taylor, and G. B. Bonan. 2015. Representing life in the Earth system with soil microbial functional traits in the MIMICS model, Geoscientific Model Development Discussions 8(2), 2011-2052. GLBRC
2015Wilson, D. B. 2015. Processive Cellulases. In Direct Microbial Conversion of Biomass to Advanced Biofuels, 91-110. Ed. M. E. Himmel. Elsevier.BESC
2015Woods, D. P., and R. M. Amasino. 2015. Dissecting the control of flowering time in grasses using Brachypodium distachyon. In Genetics and Genomics of Brachypodium, 259-273. Ed. J. P. Vogel. Springer International Publishing.GLBRC
201510.1007/s12155-015-9600-7Wu, Y.-W., C. Joshua, S. A. Eichorst, J. M. Gladden, B. A. Simmons, and S. W. Singer. 2015. Genomic Analysis of Xylose Metabolism in Members of the Deinoccocus-Thermus Phylum from Thermophilic Biomass-Deconstructing Bacterial Consortia, BioEnergy Research 8(3), 1031-1038. JBEI
201510.3389/fbioe.2015.00101Wuddineh, W. A., M. Mazarei, G. B. Turner, R. W. Sykes, S. R. Decker, M. F. Davis, and C. N. Stewart, Jr. 2015. Identification and Molecular Characterization of the Switchgrass AP2/ERF Transcription Factor Superfamily, and Overexpression of PvERF001 for Improvement of Biomass Characteristics for Biofuel, Front Bioeng Biotechnol 3, 101. BESC
201510.1111/pbi.12287Wuddineh, W. A., M. Mazarei, J. Zhang, C. R. Poovaiah, D. G. Mann, A. Ziebell, R. W. Sykes, M. F. Davis, M. K. Udvardi, and C. N. Stewart, Jr. 2015. Identification and overexpression of gibberellin 2-oxidase (GA2ox) in switchgrass (Panicum virgatum L.) for improved plant architecture and reduced biomass recalcitrance, Plant Biotechnol J 13(5), 636-647. BESC
201510.1002/bbb.1582Wyman, C. E., and A. J. Ragauskas. 2015. Lignin Bioproducts to Enable Biofuels, Biofuels, Bioproducts and Biorefining 9(5), 447-449. BESC
2015Wyman, C. E., and B. E. Dale. 2015. Producing biofuels via the sugar platform, Chemical Engineering Progress Magazine 111, 45-57. DOI.GLBRC
2015Wyman, C., and B. Dale. 2015. Producing biofuels via the sugar platform. Vol. 111, 45-57 pp.BESC
201510.1186/s13068-015-0378-9Xue, S., N. Uppugundla, M. J. Bowman, D. Cavalier, L. Da Costa Sousa, E. D. B, and V. Balan. 2015. Sugar loss and enzyme inhibition due to oligosaccharide accumulation during high solids-loading enzymatic hydrolysis, Biotechnol Biofuels 8, 195. GLBRC
201510.1104/pp.15.01236Yang, Y., J. Munz, C. Cass, A. Zienkiewicz, Q. Kong, W. Ma, Sanjaya, J. Sedbrook, and C. Benning. 2015. Ectopic Expression of WRINKLED1 Affects Fatty Acid Homeostasis in Brachypodium distachyon Vegetative Tissues, Plant Physiol 169(3), 1836-1847. GLBRC
201510.1371/journal.pone.0145726Yang, Y., X. Han, Y. Liang, A. Ghosh, J. Chen, and M. Tang. 2015. The Combined Effects of Arbuscular Mycorrhizal Fungi (AMF) and Lead (Pb) Stress on Pb Accumulation, Plant Growth Parameters, Photosynthesis, and Antioxidant Enzymes in Robinia pseudoacacia L, PLoS One 10(12), e0145726. JBEI
201510.1016/j.soilbio.2015.03.018Yang, Y., Y. Song, H. V. Scheller, A. Ghosh, Y. Ban, H. Chen, and M. Tang. 2015. Community structure of arbuscular mycorrhizal fungi associated with Robinia pseudoacacia in uncontaminated and heavy metal contaminated soils, Soil Biology and Biochemistry 86, 146-158. JBEI
201510.1021/acs.biochem.5b00638Yao, J., H. Guo, M. Chaiprasongsuk, N. Zhao, F. Chen, X. Yang, and H. Guo. 2015. Substrate-Assisted Catalysis in the Reaction Catalyzed by Salicylic Acid Binding Protein 2 (SABP2), a Potential Mechanism of Substrate Discrimination for Some Promiscuous Enzymes, Biochemistry 54(34), 5366-5375. BESC
2015Yarbrough, J. M., A. Mittal, Y. J. Bomble, J. Olstad, E. J. Wolfrum, S. E. Hobdey, M. E. Himmel, and T. B. Vinzant. 2015. Influence of Particle Size on Direct Microbial Conversion of Hot Water Pretreated Poplar by Clostridium thermocellum. In Direct Microbial Conversion of Biomass to Advanced Biofuels, 307-319. Ed. M. E. Himmel. Elsevier.BESC
201510.1007/s12155-015-9659-1Yee, K. L., M. Rodriguez, C. Y. Hamilton, S. D. Hamilton-Brehm, O. A. Thompson, J. G. Elkins, B. H. Davison, and J. R. Mielenz. 2015. Fermentation of Dilute Acid Pretreated Populus by Clostridium thermocellum, Caldicellulosiruptor bescii, and Caldicellulosiruptor obsidiansis, BioEnergy Research 8(3), 1014-1021. BESC
201510.1007/s12155-015-9662-6Yoo, C. G., H. Kim, F. Lu, A. Azarpira, X. Pan, K. K. Oh, J. S. Kim, J. Ralph, and T. H. Kim. 2015. Understanding the Physicochemical Characteristics and the Improved Enzymatic Saccharification of Corn Stover Pretreated with Aqueous and Gaseous Ammonia, BioEnergy Research 9(1), 67-76. GLBRC
201510.1186/s13068-015-0392-yYu, C., A. P. Reddy, C. W. Simmons, B. A. Simmons, S. W. Singer, and J. S. VanderGheynst. 2015. Preservation of microbial communities enriched on lignocellulose under thermophilic and high-solid conditions, Biotechnol Biofuels 8, 206. JBEI
201510.1093/nar/gkv738Yu, M., L. Ji, D. A. Neumann, D. H. Chung, J. Groom, J. Westpheling, C. He, and R. J. Schmitz. 2015. Base-resolution detection of N4-methylcytosine in genomic DNA using 4mC-Tet-assisted-bisulfite- sequencing, Nucleic Acids Res 43(21), e148. BESC
201510.3389/fmicb.2015.01209Zeldes, B. M., M. W. Keller, A. J. Loder, C. T. Straub, M. W. Adams, and R. M. Kelly. 2015. Extremely thermophilic microorganisms as metabolic engineering platforms for production of fuels and industrial chemicals, Front Microbiol 6, 1209. BESC
201510.1186/s13068-015-0312-1Zeng, Y., S. Zhao, H. Wei, M. P. Tucker, M. E. Himmel, N. S. Mosier, R. Meilan, and S. Y. Ding. 2015. In situ micro-spectroscopic investigation of lignin in poplar cell walls pretreated by maleic acid, Biotechnol Biofuels 8, 126. BESC
201510.1128/AEM.00111-15Zhang, B., C. R. Penton, C. Xue, Q. Wang, T. Zheng, and J. M. Tiedje. 2015. Evaluation of the Ion Torrent Personal Genome Machine for Gene-Targeted Studies Using Amplicons of the Nitrogenase Gene nifH, Appl Environ Microbiol 81(13), 4536-4545. GLBRC
201510.1007/s10570-015-0588-0Zhang, L., Z. Lu, L. Velarde, L. Fu, Y. Pu, S.-Y. Ding, A. J. Ragauskas, H.-F. Wang, and B. Yang. 2015. Vibrational spectral signatures of crystalline cellulose using high resolution broadband sum frequency generation vibrational spectroscopy (HR-BB-SFG-VS), Cellulose 22(3), 1469-1484. BESC
201510.1016/j.envsoft.2014.10.005Zhang, X., R. C. Izaurralde, D. H. Manowitz, R. Sahajpal, T. O. West, A. M. Thomson, M. Xu, K. Zhao, S. D. LeDuc, and J. R. Williams. 2015. Regional scale cropland carbon budgets: Evaluating a geospatial agricultural modeling system using inventory data, Environmental Modelling & Software 63, 199-216. GLBRC
201510.1016/j.phytochem.2014.07.008Zhao, Q., Y. Zeng, Y. Yin, Y. Pu, L. A. Jackson, N. L. Engle, M. Z. Martin, T. J. Tschaplinski, S. Y. Ding, A. J. Ragauskas, and R. A. Dixon. 2015. Pinoresinol reductase 1 impacts lignin distribution during secondary cell wall biosynthesis in Arabidopsis, Phytochemistry 112, 170-178. BESC
201510.1128/JB.00232-15Zheng, T., D. G. Olson, L. Tian, Y. J. Bomble, M. E. Himmel, J. Lo, S. Hon, A. J. Shaw, J. P. van Dijken, and L. R. Lynd. 2015. Cofactor Specificity of the Bifunctional Alcohol and Aldehyde Dehydrogenase (AdhE) in Wild-Type and Mutant Clostridium thermocellum and Thermoanaerobacterium saccharolyticum, J Bacteriol 197(15), 2610-2619. BESC
201510.1186/s13068-015-0304-1Zhou, J., D. G. Olson, A. A. Lanahan, L. Tian, S. J. Murphy, J. Lo, and L. R. Lynd. 2015. Physiological roles of pyruvate ferredoxin oxidoreductase and pyruvate formate-lyase in Thermoanaerobacterium saccharolyticum JW/SL-YS485, Biotechnol Biofuels 8, 138. BESC
201510.1128/AEM.01622-15Zurawski, J. V., J. M. Conway, L. L. Lee, H. J. Simpson, J. A. Izquierdo, S. Blumer-Schuette, I. Nookaew, M. W. Adams, and R. M. Kelly. 2015. Comparative Analysis of Extremely Thermophilic Caldicellulosiruptor Species Reveals Common and Unique Cellular Strategies for Plant Biomass Utilization, Appl Environ Microbiol 81(20), 7159-7170. BESC
201410.3389/fchem.2014.00066Akinosho, H., K. Yee, D. Close, and A. Ragauskas. 2014. The emergence of Clostridium thermocellum as a high utility candidate for consolidated bioprocessing applications, Front Chem 2, 66. BESC
201410.1534/genetics.114.170118.Alexander, W. G., D. T. Doering, and C. T. Hittinger. 2014. High-efficiency genome editing and allele replacement in prototrophic and wild strains of Saccharomyces, Genetics 198(3), 859-866. GLBRC
201410.1038/ncomms5044Almeida, P., C. Goncalves, S. Teixeira, D. Libkind, M. Bontrager, I. Masneuf-Pomarede, W. Albertin, P. Durrens, D. J. Sherman, P. Marullo, C. T. Hittinger, P. Goncalves, and J. P. Sampaio. 2014. A Gondwanan imprint on global diversity and domestication of wine and cider yeast Saccharomyces uvarum, Nat Commun 5, 4044. GLBRC
201410.1016/j.biortech.2014.01.035Archambault-Leger, V., and L. R. Lynd. 2014. Fluid mechanics relevant to flow through pretreatment of cellulosic biomass, Bioresour Technol 157, 278-283. BESC
201410.1002/cssc.201402087Archambault-Leger, V., X. Shao, and L. R. Lynd. 2014. Simulated performance of reactor configurations for hot-water pretreatment of sugarcane bagasse, ChemSusChem 7(9), 2721-2727. BESC
201410.1016/j.carbpol.2013.06.007Atalla, R. S., M. F. Crowley, M. E. Himmel, and R. H. Atalla. 2014. Irreversible transformations of native celluloses, upon exposure to elevated temperatures, Carbohydr Polym 100, 2-8. BESC
201410.1128/mBio.02077-14Aylward, F. O., G. Suen, P. H. Biedermann, A. S. Adams, J. J. Scott, S. A. Malfatti, T. Glavina del Rio, S. G. Tringe, M. Poulsen, K. F. Raffa, K. D. Klepzig, and C. R. Currie. 2014. Convergent bacterial microbiotas in the fungal agricultural systems of insects, MBio 5(6), e02077. GLBRC
201410.1128/AEM.02091-14Bahulikar, R. A., I. Torres-Jerez, E. Worley, K. Craven, and M. K. Udvardi. 2014. Diversity of nitrogen-fixing bacteria associated with switchgrass in the native tallgrass prairie of northern Oklahoma, Appl Environ Microbiol 80(18), 5636-5643. BESC
201410.1155/2014/463074Balan, V. 2014. Current challenges in commercially producing biofuels from lignocellulosic biomass, ISRN Biotechnol 2014, 463074. GLBRC
201410.1002/bit.25022Bals, B. D., C. Gunawan, J. Moore, F. Teymouri, and B. E. Dale. 2014. Enzymatic hydrolysis of pelletized AFEX-treated corn stover at high solid loadings, Biotechnol Bioeng 111(2), 264-271. GLBRC
201410.1016/j.biortech.2013.11.024Basen, M., A. M. Rhaesa, I. Kataeva, C. J. Prybol, I. M. Scott, F. L. Poole, and M. W. Adams. 2014. Degradation of high loads of crystalline cellulose and of unpretreated plant biomass by the thermophilic bacterium Caldicellulosiruptor bescii, Bioresour Technol 152, 384-392. BESC
201410.1073/pnas.1413789111Basen, M., G. J. Schut, D. M. Nguyen, G. L. Lipscomb, R. A. Benn, C. J. Prybol, B. J. Vaccaro, F. L. Poole, 2nd, R. M. Kelly, and M. W. Adams. 2014. Single gene insertion drives bioalcohol production by a thermophilic archaeon, Proc Natl Acad Sci U S A 111(49), 17618-17623. BESC
201410.1073/pnas.1318511111Bates, P. D., S. R. Johnson, X. Cao, J. Li, J. W. Nam, J. G. Jaworski, J. B. Ohlrogge, and J. Browse. 2014. Fatty acid synthesis is inhibited by inefficient utilization of unusual fatty acids for glycerolipid assembly, Proc Natl Acad Sci U S A 111(3), 1204-1209. GLBRC
201410.1016/j.ymben.2014.08.004Batth, T. S., P. Singh, V. R. Ramakrishnan, M. M. L. Sousa, L. J. G. Chan, H. M. Tran, E. G. Luning, E. H. Y. Pan, K. M. Vuu, J. D. Keasling, P. D. Adams, and C. J. Petzold. 2014. A targeted proteomics toolkit for high-throughput absolute quantification of Escherichia coli proteins, Metab Eng 26, 48-56. JBEI
201410.4155/bfs.13.56Baxter, H. L., and C. N. Stewart. 2014. Effects of altered lignin biosynthesis on phenylpropanoid metabolism and plant stress, Biofuels 4(6), 635-650. BESC
201410.1111/pbi.12195Baxter, H. L., M. Mazarei, N. Labbe, L. M. Kline, Q. Cheng, M. T. Windham, D. G. Mann, C. Fu, A. Ziebell, R. W. Sykes, M. Rodriguez, Jr., M. F. Davis, J. R. Mielenz, R. A. Dixon, Z. Y. Wang, and C. N. Stewart, Jr. 2014. Two-year field analysis of reduced recalcitrance transgenic switchgrass, Plant Biotechnol J 12(7), 914-924. BESC
201410.1534/genetics.113.160655Beissinger, T. M., C. N. Hirsch, B. Vaillancourt, S. Deshpande, K. Barry, C. R. Buell, S. M. Kaeppler, D. Gianola, and N. de Leon. 2014. A genome-wide scan for evidence of selection in a maize population under long-term artificial selection for ear number, Genetics 196(3), 829-840. GLBRC
201410.1016/j.agee.2014.04.016Bennett, A. B., and R. Isaacs. 2014. Landscape composition influences pollinators and pollination services in perennial biofuel plantings, Agriculture, Ecosystems & Environment 193, 1-8. GLBRC
201410.1371/journal.pone.0110676Bennett, A. B., T. D. Meehan, C. Gratton, and R. Isaacs. 2014. Modeling pollinator community response to contrasting bioenergy scenarios, PLoS One 9(11), e110676. GLBRC
201410.1111/1574-6968.12332Bergmann, J. C., O. Y. Costa, J. M. Gladden, S. Singer, R. Heins, P. D'Haeseleer, B. A. Simmons, and B. F. Quirino. 2014. Discovery of two novel beta-glucosidases from an Amazon soil metagenomic library, FEMS Microbiol Lett 351(2), 147-155. JBEI
201410.1016/j.biortech.2014.03.112Bhalla, A., K. M. Bischoff, N. Uppugundla, V. Balan, and R. K. Sani. 2014. Novel thermostable endo-xylanase cloned and expressed from bacterium Geobacillus sp. WSUCF1, Bioresour Technol 165, 314-318. GLBRC
201410.1016/j.ymben.2013.10.012Bhandiwad, A., A. J. Shaw, A. Guss, A. Guseva, H. Bahl, and L. R. Lynd. 2014. Metabolic engineering of Thermoanaerobacterium saccharolyticum for n-butanol production, Metab Eng 21, 17-25. BESC
201410.1186/1754-6834-7-11Biswal, A. K., K. Soeno, M. L. Gandla, P. Immerzeel, S. Pattathil, J. Lucenius, R. Serimaa, M. G. Hahn, T. Moritz, L. J. Jonsson, M. Israelsson-Nordstrom, and E. J. Mellerowicz. 2014. Aspen pectate lyase PtxtPL1-27 mobilizes matrix polysaccharides from woody tissues and improves saccharification yield, Biotechnol Biofuels 7(1), 11. BESC
2014Biswas, R., A. Persad, and V. S. Bisaria. 2014. Production of Cellulolytic Enzymes. In Bioprocessing of Renewable Resources to Commodity Bioproducts, 105-132. Eds. V. S. Bisaria, and A. Kondo.BESC
201410.1371/journal.pone.0086389Biswas, R., S. Prabhu, L. R. Lynd, and A. M. Guss. 2014. Increase in ethanol yield via elimination of lactate production in an ethanol-tolerant mutant of Clostridium thermocellum, PLoS One 9(2), e86389. BESC
201410.1111/1574-6976.12044Blumer-Schuette, S. E., S. D. Brown, K. B. Sander, E. A. Bayer, I. Kataeva, J. V. Zurawski, J. M. Conway, M. W. Adams, and R. M. Kelly. 2014. Thermophilic lignocellulose deconstruction, FEMS Microbiol Rev 38(3), 393-448. BESC
201410.1038/nature13084Bonawitz, N. D., J. I. Kim, Y. Tobimatsu, P. N. Ciesielski, N. A. Anderson, E. Ximenes, J. Maeda, J. Ralph, B. S. Donohoe, M. Ladisch, and C. Chapple. 2014. Disruption of Mediator rescues the stunted growth of a lignin-deficient Arabidopsis mutant, Nature 509(7500), 376-380. GLBRC
201410.1128/AEM.01133-14Book, A. J., G. R. Lewin, B. R. McDonald, T. E. Takasuka, D. T. Doering, A. S. Adams, J. A. Blodgett, J. Clardy, K. F. Raffa, B. G. Fox, and C. R. Currie. 2014. Cellulolytic Streptomyces strains associated with herbivorous insects share a phylogenetically linked capacity to degrade lignocellulose, Appl Environ Microbiol 80(15), 4692-4701. GLBRC
201410.1186/1754-6834-7-109Book, A. J., R. M. Yennamalli, T. E. Takasuka, C. R. Currie, G. N. Phillips, Jr., and B. G. Fox. 2014. Evolution of substrate specificity in bacterial AA10 lytic polysaccharide monooxygenases, Biotechnol Biofuels 7, 109. GLBRC
201410.1186/1754-6834-7-40Brown, S. D., S. Nagaraju, S. Utturkar, S. De Tissera, S. Segovia, W. Mitchell, M. L. Land, A. Dassanayake, and M. Kopke. 2014. Comparison of single-molecule sequencing and hybrid approaches for finishing the genome of Clostridium autoethanogenum and analysis of CRISPR systems in industrial relevant Clostridia, Biotechnol Biofuels 7, 40. BESC
201410.4155/bfs.13.44Brumm, P. J. 2014. Bacterial genomes: what they teach us about cellulose degradation, Biofuels 4(6), 669-681. GLBRC
2014Brunecky, R., B. S. Donohoe, M. H. Selig, H. Wei, M. Resch, and M. E. Himmel. 2014. Basic Biological Research Relevant to Feestock Conversion. In Compendium of Bioenergy Plants: Corn, 33-69. Eds. S. Goldman, and C. Kole. CRC Press.BESC
201410.1126/science.1251701.Brunecky, R., M. Alahuhta, Q. Xu, B. S. Donohoe, M. F. Crowley, I. A. Kataeva, S. J. Yang, M. G. Resch, M. W. Adams, V. V. Lunin, M. E. Himmel, and Y. J. Bomble. 2014. Response to Comment on Revealing nature's cellulase diversity: the digestion mechanism of Caldicellulosiruptor bescii CelA, Science 344(6184), 578. BESC
201410.3389/fpls.2014.00732Brunner, A. M., L. M. Evans, C. Y. Hsu, and X. Sheng. 2014. Vernalization and the chilling requirement to exit bud dormancy: shared or separate regulation?, Front Plant Sci 5, 732. BESC
201410.1007/s00294-014-0427-0Calvey, C. H., L. B. Willis, and T. W. Jeffries. 2014. An optimized transformation protocol for Lipomyces starkeyi, Curr Genet 60(3), 223-230. GLBRC
201410.1074/jbc.M114.583286Cao, H., J. D. Walton, P. Brumm, and G. N. Phillips, Jr. 2014. Structure and substrate specificity of a eukaryotic fucosidase from Fusarium graminearum, J Biol Chem 289(37), 25624-25638. GLBRC
201410.1186/s12862-014-0207-yChai, J., G. Kora, T. H. Ahn, D. Hyatt, and C. Pan. 2014. Functional phylogenomics analysis of bacteria and archaea using consistent genome annotation with UniFam, BMC Evol Biol 14, 207. BESC
201410.1007/978-1-62703-782-2_4Chandrasekaran, A., and A. K. Singh. 2014. One-pot, microscale cell-free enzyme expression and screening, Methods Mol Biol 1118, 55-69. JBEI
201410.1128/genomeA.00777-14Chauhan, A., A. Smartt, J. Wang, S. Utturkar, A. Frank, M. Bi, J. Liu, D. Williams, T. Xu, M. Eldridge, A. Arreaza, A. Rogers, H. C. Gonzalez, A. C. Layton, H. L. Baxter, M. Mazarei, J. M. DeBruyn, C. N. Stewart, Jr., S. D. Brown, L. J. Hauser, and G. S. Sayler. 2014. Integrated metagenomics and metatranscriptomics analyses of root-associated soil from transgenic switchgrass, Genome Announc 2(4). BESC
2014Chen, J., R. John, G. Sun, S. McNulty, A. Normets, J. Xiao, M. G. Turner, and J. F. Franklin. 2014. Carbon fluxes and storages in forests and landscapes. In Forest Landscapes and Global Change: Challenges for Research and Management, 139-166. Eds. J. C. Azevedo, A. Perera, and M. A. Pinto. Springer.GLBRC
201410.1021/jp408767jChen, M., M. Kostylev, Y. J. Bomble, M. F. Crowley, M. E. Himmel, D. B. Wilson, and J. W. Brady. 2014. Experimental and modeling studies of an unusual water-filled pore structure with possible mechanistic implications in family 48 cellulases, J Phys Chem B 118(9), 2306-2315. BESC
201410.1093/mp/ssu003Chen, X., S. Zuo, B. Schwessinger, M. Chern, P. E. Canlas, D. Ruan, X. Zhou, J. Wang, A. Daudi, C. J. Petzold, J. L. Heazlewood, and P. C. Ronald. 2014. An XA21-associated kinase (OsSERK2) regulates immunity mediated by the XA21 and XA3 immune receptors, Mol Plant 7(5), 874-892. JBEI
201410.3303/CET1437053Chiaramonti, D., F. Martelli, V. Balan, and S. Kumar. 2014. Industrial initiatives towards lignocellulosic biofuel deployment: an assessment in US and EU, Chemical Engineering Transactions 37, 313-318. GLBRC
201410.3835/plantgenome2013.12.0041Childs, K. L., A. Nandety, C. N. Hirsch, E. Góngora-Castillo, J. Schmutz, S. M. Kaeppler, M. D. Casler, and C. R. Buell. 2014. Generation of Transcript Assemblies and Identification of Single Nucleotide Polymorphisms from Seven Lowland and Upland Cultivars of Switchgrass, The Plant Genome 7(2), 0. GLBRC
201410.4155/bfs.13.36Christopherson, M. R., and G. Suen. 2014. Nature’s bioreactor: the rumen as a model for biofuel production, Biofuels 4(5), 511-521. GLBRC
201410.1073/pnas.1402210111Chung, D., M. Cha, A. M. Guss, and J. Westpheling. 2014. Direct conversion of plant biomass to ethanol by engineered Caldicellulosiruptor bescii, Proc Natl Acad Sci U S A 111(24), 8931-8936. BESC
201410.1186/s13068-014-0147-1Chung, D., S. Pattathil, A. K. Biswal, M. G. Hahn, D. Mohnen, and J. Westpheling. 2014. Deletion of a gene cluster encoding pectin degrading enzymes in Caldicellulosiruptor bescii reveals an important role for pectin in plant biomass recalcitrance, Biotechnol Biofuels 7(1), 147. BESC
201410.1186/s13068-014-0165-zClarkson, S. M., S. D. Hamilton-Brehm, R. J. Giannone, N. L. Engle, T. J. Tschaplinski, R. L. Hettich, and J. G. Elkins. 2014. A comparative multidimensional LC-MS proteomic analysis reveals mechanisms for furan aldehyde detoxification in Thermoanaerobacter pseudethanolicus 39E, Biotechnol Biofuels 7(1), 165. BESC
201410.4161/rna.28306Cole, J. R., and J. M. Tiedje. 2014. History and impact of RDP: a legacy from Carl Woese to microbiology, RNA Biol 11(3), 239-243. GLBRC
201410.1093/nar/gkt1244Cole, J. R., Q. Wang, J. A. Fish, B. Chai, D. M. McGarrell, Y. Sun, C. T. Brown, A. Porras-Alfaro, C. R. Kuske, and J. M. Tiedje. 2014. Ribosomal Database Project: data and tools for high throughput rRNA analysis, Nucleic Acids Res 42(Database issue), D633-642. GLBRC
201410.3791/52110Collier, S. M., M. D. Ruark, L. G. Oates, W. E. Jokela, and C. J. Dell. 2014. Measurement of greenhouse gas flux from agricultural soils using static chambers, J Vis Exp(90), e52110. GLBRC
201410.1002/bbb.1488Cox, K., M. Renouf, A. Dargan, C. Turner, and D. Klein-Marcuschamer. 2014. Environmental life cycle assessment (LCA) of aviation biofuel from microalgae,Pongamia pinnata, and sugarcane molasses, Biofuels, Bioproducts and Biorefining 8(4), 579-593. JBEI
201410.1128/AEM.00998-14Currie, D. H., A. M. Guss, C. D. Herring, R. J. Giannone, C. M. Johnson, P. K. Lankford, S. D. Brown, R. L. Hettich, and L. R. Lynd. 2014. Profile of secreted hydrolases, associated proteins, and SlpA in Thermoanaerobacterium saccharolyticum during the degradation of hemicellulose, Appl Environ Microbiol 80(16), 5001-5011. BESC
2014Dale, B. 2014: Sobering numbers. Resource Magazine, 25.GLBRC
201410.1002/bbb.1504Dale, B. E., and R. G. Ong. 2014. Design, implementation, and evaluation of sustainable bioenergy production systems, Biofuels, Bioproducts and Biorefining 8(4), 487-503. GLBRC
201410.1111/jiec.12151Dale, B. E., and S. Kim. 2014. Can the Predictions of Consequential Life Cycle Assessment Be Tested in the Real World? Comment on “Using Attributional Life Cycle Assessment to Estimate Climate-Change Mitigation...”, Journal of Industrial Ecology 18(3), 466-467. GLBRC
201410.1021/es5025433Dale, B. E., J. E. Anderson, R. C. Brown, S. Csonka, V. H. Dale, G. Herwick, R. D. Jackson, N. Jordan, S. Kaffka, K. L. Kline, L. R. Lynd, C. Malmstrom, R. G. Ong, T. L. Richard, C. Taylor, and M. Q. Wang. 2014. Take a closer look: biofuels can support environmental, economic and social goals, Environ Sci Technol 48(13), 7200-7203. GLBRC
201410.1007/s12155-014-9508-7Daverdin, G., B. A. Bahri, X. Wu, D. D. Serba, C. Tobias, M. C. Saha, and K. M. Devos. 2014. Comparative Relationships and Chromosome Evolution in Switchgrass (Panicum virgatum) and Its Genomic Model, Foxtail Millet (Setaria italica), BioEnergy Research 8(1), 137-151. BESC
201410.1021/cb5000289Deng, K., T. E. Takasuka, R. Heins, X. Cheng, L. F. Bergeman, J. Shi, R. Aschenbrener, S. Deutsch, S. Singh, K. L. Sale, B. A. Simmons, P. D. Adams, A. K. Singh, B. G. Fox, and T. R. Northen. 2014. Rapid kinetic characterization of glycosyl hydrolases based on oxime derivatization and nanostructure-initiator mass spectrometry (NIMS), ACS Chem Biol 9(7), 1470-1479. GLBRC JBEI
201410.1007/s10570-014-0181-yDiehl, B. G., H. D. Watts, J. D. Kubicki, M. R. Regner, J. Ralph, and N. R. Brown. 2014. Towards lignin-protein crosslinking: amino acid adducts of a lignin model quinone methide, Cellulose 21(3), 1395-1407. GLBRC
201410.4155/bfs.13.11Donohue, T. 2014. Interview with Professor Timothy Donohue, Biofuels 4(3), 255-258. GLBRC
201410.1371/journal.pone.0100836Dougherty, M. J., H. M. Tran, V. Stavila, B. Knierim, A. George, M. Auer, P. D. Adams, and M. Z. Hadi. 2014. Cellulosic biomass pretreatment and sugar yields as a function of biomass particle size, PLoS One 9(6), e100836. JBEI
201410.1021/pr400788eDykstra, A. B., L. St Brice, M. Rodriguez, Jr., B. Raman, J. Izquierdo, K. D. Cook, L. R. Lynd, and R. L. Hettich. 2014. Development of a multipoint quantitation method to simultaneously measure enzymatic and structural components of the Clostridium thermocellum cellulosome protein complex, J Proteome Res 13(2), 692-701. BESC
201410.1007/s10295-013-1394-zEdwards, M. C., T. Williams, S. Pattathil, M. G. Hahn, and J. Doran-Peterson. 2014. Replacing a suite of commercial pectinases with a single enzyme, pectate lyase B, in Saccharomyces cerevisiae fermentations of cull peaches, J Ind Microbiol Biotechnol 41(4), 679-686. BESC
201410.1128/AEM.02795-14Eichorst, S. A., C. Joshua, N. Sathitsuksanoh, S. Singh, B. A. Simmons, and S. W. Singer. 2014. Substrate-Specific Development of Thermophilic Bacterial Consortia by Using Chemically Pretreated Switchgrass, Appl Environ Microbiol 80(23), 7423-7432. JBEI
201410.1007/s11103-013-0152-yEscamilla-Trevino, L. L., H. Shen, T. Hernandez, Y. Yin, Y. Xu, and R. A. Dixon. 2014. Early lignin pathway enzymes and routes to chlorogenic acid in switchgrass (Panicum virgatum L.), Plant Mol Biol 84(4-5), 565-576. BESC
2014walkEstavillo, G. M., Y. Verhertbruggen, B. J. Pogson, J. L. Heazlewood, H. V. Scheller, and J. Ito. 2014. Isolation of the plant cytosolic fraction for proteomic analysis. In Plant Proteomics: Methods and Protocols 453-467. Ed. K. Jorrin-Novo. Humana Press.JBEI
201410.1016/j.copbio.2014.01.002Eudes, A., Y. Liang, P. Mitra, and D. Loque. 2014. Lignin bioengineering, Curr Opin Biotechnol 26, 189-198. JBEI
201410.1111/tpj.12601Evans, J., J. Kim, K. L. Childs, B. Vaillancourt, E. Crisovan, A. Nandety, D. J. Gerhardt, T. A. Richmond, J. A. Jeddeloh, S. M. Kaeppler, M. D. Casler, and C. R. Buell. 2014. Nucleotide polymorphism and copy number variant detection using exome capture and next-generation sequencing in the polyploid grass Panicum virgatum, Plant J 79(6), 993-1008. GLBRC
201410.1038/ng.3075Evans, L. M., G. T. Slavov, E. Rodgers-Melnick, J. Martin, P. Ranjan, W. Muchero, A. M. Brunner, W. Schackwitz, L. Gunter, J. G. Chen, G. A. Tuskan, and S. P. DiFazio. 2014. Population genomics of Populus trichocarpa identifies signatures of selection and adaptive trait associations, Nat Genet 46(10), 1089-1096. BESC
201410.1128/mBio.01932-14Foo, J. L., H. M. Jensen, R. H. Dahl, K. George, J. D. Keasling, T. S. Lee, S. Leong, and A. Mukhopadhyay. 2014. Improving microbial biogasoline production in Escherichia coli using tolerance engineering, MBio 5(6), e01932. JBEI
201410.1371/journal.pone.0101115Frederix, M., K. Hutter, J. Leu, T. S. Batth, W. J. Turner, T. L. Ruegg, H. W. Blanch, B. A. Simmons, P. D. Adams, J. D. Keasling, M. P. Thelen, M. J. Dunlop, C. J. Petzold, and A. Mukhopadhyay. 2014. Development of a native Escherichia coli induction system for ionic liquid tolerance, PLoS One 9(7), e101115. JBEI
201410.1111/pbi.12300Furtado, A., J. S. Lupoi, N. V. Hoang, A. Healey, S. Singh, B. A. Simmons, and R. J. Henry. 2014. Modifying plants for biofuel and biomaterial production, Plant Biotechnol J 12(9), 1246-1258. JBEI
201410.1038/nbt.2891Galdzicki, M., K. P. Clancy, E. Oberortner, M. Pocock, J. Y. Quinn, C. A. Rodriguez, N. Roehner, M. L. Wilson, L. Adam, J. C. Anderson, B. A. Bartley, J. Beal, D. Chandran, J. Chen, D. Densmore, D. Endy, R. Grunberg, J. Hallinan, N. J. Hillson, J. D. Johnson, A. Kuchinsky, M. Lux, G. Misirli, J. Peccoud, H. A. Plahar, E. Sirin, G. B. Stan, A. Villalobos, A. Wipat, J. H. Gennari, C. J. Myers, and H. M. Sauro. 2014. The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology, Nat Biotechnol 32(6), 545-550. JBEI
201410.1074/jbc.M113.536250Gall, D. L., H. Kim, F. Lu, T. J. Donohue, D. R. Noguera, and J. Ralph. 2014. Stereochemical features of glutathione-dependent enzymes in the Sphingobium sp. strain SYK-6 beta-aryl etherase pathway, J Biol Chem 289(12), 8656-8667. GLBRC
201410.1021/es503886dGall, D. L., J. Ralph, T. J. Donohue, and D. R. Noguera. 2014. A group of sequence-related sphingomonad enzymes catalyzes cleavage of beta-aryl ether linkages in lignin beta-guaiacyl and beta-syringyl ether dimers, Environ Sci Technol 48(20), 12454-12463. GLBRC
201410.1186/s13068-014-0175-xGao, D., C. Haarmeyer, V. Balan, T. A. Whitehead, B. E. Dale, and S. P. Chundawat. 2014. Lignin triggers irreversible cellulase loss during pretreated lignocellulosic biomass saccharification, Biotechnol Biofuels 7(1), 175. GLBRC
201410.1002/bit.25174Gao, X., R. Kumar, and C. E. Wyman. 2014. Fast hemicellulose quantification via a simple one-step acid hydrolysis, Biotechnol Bioeng 111(6), 1088-1096. BESC
201410.1186/1754-6834-7-71Gao, X., R. Kumar, S. Singh, B. A. Simmons, V. Balan, B. E. Dale, and C. E. Wyman. 2014. Comparison of enzymatic reactivity of corn stover solids prepared by dilute acid, AFEX, and ionic liquid pretreatments, Biotechnol Biofuels 7, 71. JBEI BESC GLBRC
201410.1371/journal.pone.0087112Garcia, D. E., and J. D. Keasling. 2014. Kinetics of phosphomevalonate kinase from Saccharomyces cerevisiae, PLoS One 9(1), e87112. JBEI
201410.1111/mmi.12821Gardner, J. G., L. Crouch, A. Labourel, Z. Forsberg, Y. V. Bukhman, G. Vaaje-Kolstad, H. J. Gilbert, and D. H. Keating. 2014. Systems biology defines the biological significance of redox-active proteins during cellulose degradation in an aerobic bacterium, Mol Microbiol. GLBRC
201410.1128/AEM.01604-14Gaskell, J., A. Marty, M. Mozuch, P. J. Kersten, S. Splinter BonDurant, G. Sabat, A. Azarpira, J. Ralph, O. Skyba, S. D. Mansfield, R. A. Blanchette, and D. Cullen. 2014. Influence of Populus genotype on gene expression by the wood decay fungus Phanerochaete chrysosporium, Appl Environ Microbiol 80(18), 5828-5835. GLBRC
201410.1007/s10533-014-0061-4Gelfand, I., and G. Philip Robertson. 2014. A reassessment of the contribution of soybean biological nitrogen fixation to reactive N in the environment, Biogeochemistry 123(1-2), 175-184. GLBRC
201410.1002/bit.25226George, K. W., A. Chen, A. Jain, T. S. Batth, E. E. Baidoo, G. Wang, P. D. Adams, C. J. Petzold, J. D. Keasling, and T. S. Lee. 2014. Correlation analysis of targeted proteins and metabolites to assess and engineer microbial isopentenol production, Biotechnol Bioeng 111(8), 1648-1658. JBEI
201410.1371/journal.pcbi.1003827Ghosh, A., J. Nilmeier, D. Weaver, P. D. Adams, J. D. Keasling, A. Mukhopadhyay, C. J. Petzold, and H. G. Martin. 2014. A peptide-based method for 13C Metabolic Flux Analysis in microbial communities, PLoS Comput Biol 10(9), e1003827. JBEI
201410.2134/agronj2013.0270Gilmanov, T. G., J. M. Baker, C. J. Bernacchi, D. P. Billesbach, G. G. Burba, S. Castro, J. Chen, W. Eugster, M. L. Fischer, J. A. Gamon, M. T. Gebremedhin, A. J. Glenn, T. J. Griffis, J. L. Hatfield, M. W. Heuer, D. M. Howard, M. Y. Leclerc, H. W. Loescher, O. Marloie, T. P. Meyers, A. Olioso, R. L. Phillips, J. H. Prueger, R. H. Skinner, A. E. Suyker, M. Tenuta, and B. K. Wylie. 2014. Productivity and Carbon Dioxide Exchange of Leguminous Crops: Estimates from Flux Tower Measurements, Agronomy Journal 106(2), 545. GLBRC
201410.1186/1754-6834-7-15Gladden, J. M., J. I. Park, J. Bergmann, V. Reyes-Ortiz, P. D'Haeseleer, B. F. Quirino, K. L. Sale, B. A. Simmons, and S. W. Singer. 2014. Discovery and characterization of ionic liquid-tolerant thermophilic cellulases from a switchgrass-adapted microbial community, Biotechnol Biofuels 7(1), 15. JBEI
201410.1016/j.ymben.2014.09.003Goh, E. B., E. E. K. Baidoo, H. Burd, T. S. Lee, J. D. Keasling, and H. R. Beller. 2014. Substantial improvements in methyl ketone production in E. coli and insights on the pathway from in vitro studies, Metab Eng 26, 67-76. JBEI
201410.1002/bbb.1438Golberg, A., E. Vitkin, G. Linshiz, S. A. Khan, N. J. Hillson, Z. Yakhini, and M. L. Yarmush. 2014. Proposed design of distributed macroalgal biorefineries: thermodynamics, bioconversion technology, and sustainability implications for developing economies, Biofuels, Bioproducts and Biorefining 8(1), 67-82. JBEI
201410.1371/journal.pone.0086341Golberg, A., G. Linshiz, I. Kravets, N. Stawski, N. J. Hillson, M. L. Yarmush, R. S. Marks, and T. Konry. 2014. Cloud-enabled microscopy and droplet microfluidic platform for specific detection of Escherichia coli in water, PLoS One 9(1), e86341. JBEI
201410.1186/s12870-014-0344-xGondolf, V. M., R. Stoppel, B. Ebert, C. Rautengarten, A. J. Liwanag, D. Loque, and H. V. Scheller. 2014. A gene stacking approach leads to engineered plants with highly increased galactan levels in Arabidopsis, BMC Plant Biol 14, 344. JBEI
201410.1104/pp.114.241729Green, A. R., K. M. Lewis, J. T. Barr, J. P. Jones, F. Lu, J. Ralph, W. Vermerris, S. E. Sattler, and C. Kang. 2014. Determination of the Structure and Catalytic Mechanism of Sorghum bicolor Caffeic Acid O-Methyltransferase and the Structural Impact of Three brown midrib12 Mutations, Plant Physiol 165(4), 1440-1456. GLBRC
2014Greenler, J., L. Nye, and T. Tangen. 2014. Cellulose breakdown, The Science Teacher 81, 3-11. DOI.GLBRC
201410.4155/bfs.09.8Gregg, J. S., and R. C. Izaurralde. 2014. Effect of crop residue harvest on long-term crop yield, soil erosion and nutrient balance: trade-offs for a sustainable bioenergy feedstock, Biofuels 1(1), 69-83. GLBRC
201410.1186/s13068-014-0132-8Groom, J., D. Chung, J. Young, and J. Westpheling. 2014. Heterologous complementation of a pyrF deletion in Caldicellulosiruptor hydrothermalis generates a new host for the analysis of biomass deconstruction, Biotechnol Biofuels 7(1), 132. BESC
201410.1073/pnas.1401853111Haft, R. J., D. H. Keating, T. Schwaegler, M. S. Schwalbach, J. Vinokur, M. Tremaine, J. M. Peters, M. V. Kotlajich, E. L. Pohlmann, I. M. Ong, J. A. Grass, P. J. Kiley, and R. Landick. 2014. Correcting direct effects of ethanol on translation and transcription machinery confers ethanol tolerance in bacteria, Proc Natl Acad Sci U S A 111(25), E2576-2585. GLBRC
201410.1021/bi500951cHagen, A., S. Poust, T. de Rond, S. Yuzawa, L. Katz, P. D. Adams, C. J. Petzold, and J. D. Keasling. 2014. In vitro analysis of carboxyacyl substrate tolerance in the loading and first extension modules of borrelidin polyketide synthase, Biochemistry 53(38), 5975-5977. JBEI
201410.1021/sb400142bHaitjema, C. H., J. T. Boock, A. Natarajan, M. A. Dominguez, J. G. Gardner, D. H. Keating, S. T. Withers, and M. P. DeLisa. 2014. Universal genetic assay for engineering extracellular protein expression, ACS Synth Biol 3(2), 74-82. GLBRC
201410.1039/c3gc41511bHan, J., S. M. Sen, D. M. Alonso, J. A. Dumesic, and C. T. Maravelias. 2014. A strategy for the simultaneous catalytic conversion of hemicellulose and cellulose from lignocellulosic biomass to liquid transportation fuels, Green Chem. 16(2), 653-661. GLBRC
201410.3109/10409238.2014.889651Hao, Z., and D. Mohnen. 2014. A review of xylan and lignin biosynthesis: foundation for studying Arabidopsis irregular xylem mutants with pleiotropic phenotypes, Crit Rev Biochem Mol Biol 49(3), 212-241. BESC
201410.3389/fpls.2014.00357Hao, Z., U. Avci, L. Tan, X. Zhu, J. Glushka, S. Pattathil, S. Eberhard, T. Sholes, G. E. Rothstein, W. Lukowitz, R. Orlando, M. G. Hahn, and D. Mohnen. 2014. Loss of Arabidopsis GAUT12/IRX8 causes anther indehiscence and leads to reduced G lignin associated with altered matrix polysaccharide deposition, Front Plant Sci 5, 357. BESC
201410.1016/j.ymben.2014.09.002Haushalter, R. W., W. Kim, T. A. Chavkin, L. The, M. E. Garber, M. Nhan, P. D. Adams, C. J. Petzold, L. Katz, and J. D. Keasling. 2014. Production of anteiso-branched fatty acids in Escherichia coli; next generation biofuels with improved cold-flow properties, Metab Eng 26, 111-118. JBEI
201410.2134/agronj2013.0410Hedtcke, J. L., G. R. Sanford, K. E. Hadley, and K. D. Thelen. 2014. Maximizing Land Use during Switchgrass Establishment in the North Central United States, Agronomy Journal 106(2), 596. GLBRC
201410.1021/cb500244vHeins, R. A., X. Cheng, S. Nath, K. Deng, B. P. Bowen, D. C. Chivian, S. Datta, G. D. Friedland, P. D'Haeseleer, D. Wu, M. Tran-Gyamfi, C. S. Scullin, S. Singh, W. Shi, M. G. Hamilton, M. L. Bendall, A. Sczyrba, J. Thompson, T. Feldman, J. M. Guenther, J. M. Gladden, J. F. Cheng, P. D. Adams, E. M. Rubin, B. A. Simmons, K. L. Sale, T. R. Northen, and S. Deutsch. 2014. Phylogenomically guided identification of industrially relevant GH1 beta-glucosidases through DNA synthesis and nanostructure-initiator mass spectrometry, ACS Chem Biol 9(9), 2082-2091. JBEI
2014Held, M. A., L. Danhof, and F. Brandizzi. 2014. Identifying protein-protein interactions in Arabidopsis by co-immunoprecipitation of GFP-tagged proteins and proteomic detection. In Fluorescent Proteins. Ed. J. A. Rothnagel. Humana Press.GLBRC
201410.1371/journal.pone.0115775Herzberger, A. J., D. S. Duncan, and R. D. Jackson. 2014. Bouncing back: plant-associated soil microbes respond rapidly to prairie establishment, PLoS One 9(12), e115775. GLBRC
2014Hillson, N. J. 2014. j5 DNA assembly design automation In DNA Cloning and Assembly Methods, 245-269. Ed. S. Valla. Humana Press.JBEI
201410.4155/bfs.09.25Himmel, M. E., Q. Xu, Y. Luo, S.-Y. Ding, R. Lamed, and E. A. Bayer. 2014. Microbial enzyme systems for biomass conversion: emerging paradigms, Biofuels 1(2), 323-341. BESC
201410.1093/bfgp/elt051Hirsch, C. D., J. Evans, C. R. Buell, and C. N. Hirsch. 2014. Reduced representation approaches to interrogate genome diversity in large repetitive plant genomes, Brief Funct Genomics 13(4), 257-267. GLBRC
201410.1105/tpc.113.119982Hirsch, C. N., J. M. Foerster, J. M. Johnson, R. S. Sekhon, G. Muttoni, B. Vaillancourt, F. Penagaricano, E. Lindquist, M. A. Pedraza, K. Barry, N. de Leon, S. M. Kaeppler, and C. R. Buell. 2014. Insights into the maize pan-genome and pan-transcriptome, Plant Cell 26(1), 121-135. GLBRC
201410.1186/s13068-014-0155-1Holwerda, E. K., P. G. Thorne, D. G. Olson, D. Amador-Noguez, N. L. Engle, T. J. Tschaplinski, J. P. van Dijken, and L. R. Lynd. 2014. The exometabolome of Clostridium thermocellum reveals overflow metabolism at high cellulose loading, Biotechnol Biofuels 7(1), 155. BESC
201410.1073/pnas.1402564111Howe, A. C., J. K. Jansson, S. A. Malfatti, S. G. Tringe, J. M. Tiedje, and C. T. Brown. 2014. Tackling soil diversity with the assembly of large, complex metagenomes, Proc Natl Acad Sci U S A 111(13), 4904-4909. GLBRC
201410.1039/c3ra42841aHu, F., and A. Ragauskas. 2014. Suppression of pseudo-lignin formation under dilute acid pretreatment conditions, RSC Adv. 4(9), 4317-4323. BESC
201410.1111/1758-2229.12163Huang, E. L., F. O. Aylward, Y. M. Kim, B. J. Webb-Robertson, C. D. Nicora, Z. Hu, T. O. Metz, M. S. Lipton, R. D. Smith, C. R. Currie, and K. E. Burnum-Johnson. 2014. The fungus gardens of leaf-cutter ants undergo a distinct physiological transition during biomass degradation, Environ Microbiol Rep 6(4), 389-395. GLBRC
201410.1016/j.biortech.2013.10.082Humpula, J. F., N. Uppugundla, R. Vismeh, L. Sousa, S. P. Chundawat, A. D. Jones, V. Balan, B. E. Dale, and A. M. Cheh. 2014. Probing the nature of AFEX-pretreated corn stover derived decomposition products that inhibit cellulase activity, Bioresour Technol 152, 38-45. GLBRC
201410.1074/jbc.M114.614917Hwang, S., Z. Li, Y. Bar-Peled, A. Aronov, J. Ericson, and M. Bar-Peled. 2014. The biosynthesis of UDP-d-FucNAc-4N-(2)-oxoglutarate (UDP-Yelosamine) in Bacillus cereus ATCC 14579: Pat and Pyl, an aminotransferase and an ATP-dependent Grasp protein that ligates 2-oxoglutarate to UDP-4-amino-sugars, J Biol Chem 289(51), 35620-35632. BESC
201410.1371/journal.pgen.1004837Imam, S., D. R. Noguera, and T. J. Donohue. 2014. Global analysis of photosynthesis transcriptional regulatory networks, PLoS Genet 10(12), e1004837. GLBRC
201410.3389/fpls.2014.00021Ito, J., H. T. Parsons, and J. L. Heazlewood. 2014. The Arabidopsis cytosolic proteome: the metabolic heart of the cell, Front Plant Sci 5, 21. JBEI
201410.1016/j.ab.2013.11.026Ito, J., T. Herter, E. E. Baidoo, J. Lao, M. E. Vega-Sanchez, A. Michelle Smith-Moritz, P. D. Adams, J. D. Keasling, B. Usadel, C. J. Petzold, and J. L. Heazlewood. 2014. Analysis of plant nucleotide sugars by hydrophilic interaction liquid chromatography and tandem mass spectrometry, Anal Biochem 448, 14-22. JBEI
201410.1186/s13068-014-0136-4Izquierdo, J. A., S. Pattathil, A. Guseva, M. G. Hahn, and L. R. Lynd. 2014. Comparative analysis of the ability of Clostridium clariflavum strains and Clostridium thermocellum to utilize hemicellulose and unpretreated plant material, Biotechnol Biofuels 7(1), 136. BESC
201410.1186/1754-6834-7-52Jabbour, D., E. R. Angelos, A. Mukhopadhyay, A. Womboldt, M. S. Borrusch, and J. D. Walton. 2014. Factors contributing to the recalcitrance of herbaceous dicotyledons (forbs) to enzymatic deconstruction, Biotechnol Biofuels 7(1), 52. GLBRC
201410.1128/AEM.03194-13Javidpour, P., J. H. Pereira, E. B. Goh, R. P. McAndrew, S. M. Ma, G. D. Friedland, J. D. Keasling, S. R. Chhabra, P. D. Adams, and H. R. Beller. 2014. Biochemical and structural studies of NADH-dependent FabG used to increase the bacterial production of fatty acids under anaerobic conditions, Appl Environ Microbiol 80(2), 497-505. JBEI
201410.1111/tpj.12641Jensen, J. K., N. R. Johnson, and C. G. Wilkerson. 2014. Arabidopsis thaliana IRX10 and two related proteins from psyllium and Physcomitrella patens are xylan xylosyltransferases, Plant J 80(2), 207-215. GLBRC
201410.1111/pbi.12283Kalluri, U. C., H. Yin, X. Yang, and B. H. Davison. 2014. Systems and synthetic biology approaches to alter plant cell walls and reduce biomass recalcitrance, Plant Biotechnol J 12(9), 1207-1216. BESC
2014 10.1074/jbc.M114.587766Karkehabadi, S., K. E. Helmich, T. Kaper, H. Hansson, N. E. Mikkelsen, M. Gudmundsson, K. Piens, M. Fujdala, G. Banerjee, J. S. Scott-Craig, J. D. Walton, G. N. Phillips, Jr., and M. Sandgren. 2014. Biochemical characterization and crystal structures of a fungal family 3 beta-glucosidase, Cel3A from Hypocrea jecorina, J Biol Chem 289(45), 31624-31637. GLBRC
201410.1094/MPMI-12-13-0368-RKarpinets, T. V., B. H. Park, M. H. Syed, M. G. Klotz, and E. C. Uberbacher. 2014. Metabolic environments and genomic features associated with pathogenic and mutualistic interactions between bacteria and plants, Mol Plant Microbe Interact 27(7), 664-677. BESC
201410.4155/bfs.09.11Kausch, A. P., J. Hague, M. Oliver, Y. Li, H. Daniell, P. Mascia, L. S. Watrud, and C. N. Stewart. 2014. Transgenic perennial biofuel feedstocks and strategies for bioconfinement, Biofuels 1(1), 163-176. BESC
201410.3389/fmicb.2014.00402Keating, D. H., Y. Zhang, I. M. Ong, S. McIlwain, E. H. Morales, J. A. Grass, M. Tremaine, W. Bothfeld, A. Higbee, A. Ulbrich, A. J. Balloon, M. S. Westphall, J. Aldrich, M. S. Lipton, J. Kim, O. V. Moskvin, Y. V. Bukhman, J. J. Coon, P. J. Kiley, D. M. Bates, and R. Landick. 2014. Aromatic inhibitors derived from ammonia-pretreated lignocellulose hinder bacterial ethanologenesis by activating regulatory circuits controlling inhibitor efflux and detoxification, Front Microbiol 5, 402. GLBRC
2014 10.4155/bfs.12.87Keegstra, K. 2014. Interview with Professor Kenneth Keegstra, Biofuels 4(2), 147-150. GLBRC
2014 10.1016/j.biombioe.2014.03.032Kelkar, S., Z. Li, J. Bovee, K. D. Thelen, R. M. Kriegel, and C. M. Saffron. 2014. Pyrolysis of North-American grass species: Effect of feedstock composition and taxonomy on pyrolysis products, Biomass and Bioenergy 64, 152-161. GLBRC
201410.2134/agronj2013.0397Kells, B. J., and S. M. Swinton. 2014. Profitability of Cellulosic Biomass Production in the Northern Great Lakes Region, Agronomy Journal 106(2), 397. GLBRC
201410.1039/c3ra46338aKim, H., and J. Ralph. 2014. A gel-state 2D-NMR method for plant cell wall profiling and analysis: a model study with the amorphous cellulose and xylan from ball-milled cotton linters, RSC Adv. 4(15), 7549-7560. GLBRC
201410.1016/j.copbio.2014.02.009Kim, J., and J. L. Reed. 2014. Refining metabolic models and accounting for regulatory effects, Curr Opin Biotechnol 29, 34-38. GLBRC
201410.1093/pcp/pct197Kim, S. J., and F. Brandizzi. 2014. The plant secretory pathway: an essential factory for building the plant cell wall, Plant Cell Physiol 55(4), 687-693. GLBRC
201410.1007/s12155-013-9399-zKim, S., B. E. Dale, and P. Keck. 2014. Energy Requirements and Greenhouse Gas Emissions of Maize Production in the USA, BioEnergy Research 7(2), 753-764. GLBRC
201410.1016/j.biombioe.2014.09.015Kim, S., B. E. Dale, R. Heijungs, A. Azapagic, T. Darlington, and D. Kahlbaum. 2014. Indirect land use change and biofuels: Mathematical analysis reveals a fundamental flaw in the regulatory approach, Biomass and Bioenergy 71, 408-412. GLBRC
201410.1007/s11103-013-0154-9Kim, W. C., I. B. Reca, Y. Kim, S. Park, M. F. Thomashow, K. Keegstra, and K. H. Han. 2014. Transcription factors that directly regulate the expression of CSLA9 encoding mannan synthase in Arabidopsis thaliana, Plant Mol Biol 84(4-5), 577-587. GLBRC
201410.1007/s00299-013-1531-1King, Z. R., A. L. Bray, P. R. Lafayette, and W. A. Parrott. 2014. Biolistic transformation of elite genotypes of switchgrass (Panicum virgatum L.), Plant Cell Rep 33(2), 313-322. BESC
201410.1128/AEM.02155-14Kirby, J., M. Nishimoto, R. W. Chow, V. N. Pasumarthi, R. Chan, L. J. Chan, C. J. Petzold, and J. D. Keasling. 2014. Use of nonionic surfactants for improvement of terpene production in Saccharomyces cerevisiae, Appl Environ Microbiol 80(21), 6685-6693. JBEI
201410.1186/1754-6834-7-86Konda, N. M., J. Shi, S. Singh, H. W. Blanch, B. A. Simmons, and D. Klein-Marcuschamer. 2014. Understanding cost drivers and economic potential of two variants of ionic liquid pretreatment for cellulosic biofuel production, Biotechnol Biofuels 7, 86. JBEI
201410.1128/AEM.02706-13Kostylev, M., and D. Wilson. 2014. A distinct model of synergism between a processive endocellulase (TfCel9A) and an exocellulase (TfCel48A) from Thermobifida fusca, Appl Environ Microbiol 80(1), 339-344. BESC
201410.4155/bfs.11.150Kostylev, M., and D. Wilson. 2014. Synergistic interactions in cellulose hydrolysis, Biofuels 3(1), 61-70. BESC
201410.1002/bit.25139Kostylev, M., M. Alahuhta, M. Chen, R. Brunecky, M. E. Himmel, V. V. Lunin, J. Brady, and D. B. Wilson. 2014. Cel48A from Thermobifida fusca: structure and site directed mutagenesis of key residues, Biotechnol Bioeng 111(4), 664-673. BESC
201410.1016/j.biortech.2014.03.110Kumagai, A., S. Kawamura, S. H. Lee, T. Endo, M. Rodriguez, Jr., and J. R. Mielenz. 2014. Simultaneous saccharification and fermentation and a consolidated bioprocessing for Hinoki cypress and Eucalyptus after fibrillation by steam and subsequent wet-disk milling, Bioresour Technol 162, 89-95. BESC
201410.1002/bit.25218Kumar, R., and C. E. Wyman. 2014. Strong cellulase inhibition by Mannan polysaccharides in cellulose conversion to sugars, Biotechnol Bioeng 111(7), 1341-1353. BESC
201410.1016/j.str.2014.05.007Kung, Y., R. P. McAndrew, X. Xie, C. C. Liu, J. H. Pereira, P. D. Adams, and J. D. Keasling. 2014. Constructing tailored isoprenoid products by structure-guided modification of geranylgeranyl reductase, Structure 22(7), 1028-1036. JBEI
2014Kwit, C., M. Nageswara-Rao, and C. N. Stewart Jr. 2014. Switchgrass (Panicum virgatum L.) as a bioenergy crop: advantages, concerns, and future prospects. In Compendium of Bioenergy Plants: Switchgrass,, 403-420. Eds. H. Luo, Y. Wu, and C. Kole. CRC Press.BESC
201410.1371/journal.pbio.1001920Kyrpides, N. C., P. Hugenholtz, J. A. Eisen, T. Woyke, M. Goker, C. T. Parker, R. Amann, B. J. Beck, P. S. Chain, J. Chun, R. R. Colwell, A. Danchin, P. Dawyndt, T. Dedeurwaerdere, E. F. DeLong, J. C. Detter, P. De Vos, T. J. Donohue, X. Z. Dong, D. S. Ehrlich, C. Fraser, R. Gibbs, J. Gilbert, P. Gilna, F. O. Glockner, J. K. Jansson, J. D. Keasling, R. Knight, D. Labeda, A. Lapidus, J. S. Lee, W. J. Li, J. Ma, V. Markowitz, E. R. Moore, M. Morrison, F. Meyer, K. E. Nelson, M. Ohkuma, C. A. Ouzounis, N. Pace, J. Parkhill, N. Qin, R. Rossello-Mora, J. Sikorski, D. Smith, M. Sogin, R. Stevens, U. Stingl, K. Suzuki, D. Taylor, J. M. Tiedje, B. Tindall, M. Wagner, G. Weinstock, J. Weissenbach, O. White, J. Wang, L. Zhang, Y. G. Zhou, D. Field, W. B. Whitman, G. M. Garrity, and H. P. Klenk. 2014. Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains, PLoS Biol 12(8), e1001920. BESC
201410.1186/1944-3277-9-20Land, M. L., D. Hyatt, S. R. Jun, G. H. Kora, L. J. Hauser, O. Lukjancenko, and D. W. Ussery. 2014. Quality scores for 32,000 genomes, Stand Genomic Sci 9, 20. BESC
201410.1111/tpj.12577Lao, J., A. Oikawa, J. R. Bromley, P. McInerney, A. Suttangkakul, A. M. Smith-Moritz, H. Plahar, T. Y. Chiu, S. M. Gonzalez Fernandez-Nino, B. Ebert, F. Yang, K. M. Christiansen, S. F. Hansen, S. Stonebloom, P. D. Adams, P. C. Ronald, N. J. Hillson, M. Z. Hadi, M. E. Vega-Sanchez, D. Loque, H. V. Scheller, and J. L. Heazlewood. 2014. The plant glycosyltransferase clone collection for functional genomics, Plant J 79(3), 517-529. JBEI
201410.1098/rspb.2013.2472Leducq, J. B., G. Charron, P. Samani, A. K. Dube, K. Sylvester, B. James, P. Almeida, J. P. Sampaio, C. T. Hittinger, G. Bell, and C. R. Landry. 2014. Local climatic adaptation in a widespread microorganism, Proc Biol Sci 281(1777), 20132472. GLBRC
2014 10.1371/journal.pone.0105689Lee, S., J. T. Geller, T. Torok, C. H. Wu, M. Singer, F. C. Reid, D. R. Tarjan, T. C. Hazen, A. P. Arkin, and N. J. Hillson. 2014. Characterization of wastewater treatment plant microbial communities and the effects of carbon sources on diversity in laboratory models, PLoS One 9(8), e105689. JBEI
201410.1016/j.soilbio.2013.11.012Lee, Z. M., and T. M. Schmidt. 2014. Bacterial growth efficiency varies in soils under different land management practices, Soil Biology and Biochemistry 69, 282-290. GLBRC
201410.1073/pnas.1405520111Lemke, R. A., A. C. Peterson, E. C. Ziegelhoffer, M. S. Westphall, H. Tjellstrom, J. J. Coon, and T. J. Donohue. 2014. Synthesis and scavenging role of furan fatty acids, Proc Natl Acad Sci U S A 111(33), E3450-3457. GLBRC
201410.1128/mBio.01105-14Lennon, C. W., K. C. Lemmer, J. L. Irons, M. I. Sellman, T. J. Donohue, R. L. Gourse, and W. Ross. 2014. A Rhodobacter sphaeroides protein mechanistically similar to Escherichia coli DksA regulates photosynthetic growth, MBio 5(3), e01105-01114. GLBRC
201410.1534/genetics.114.167429Lewis, J. A., A. T. Broman, J. Will, and A. P. Gasch. 2014. Genetic architecture of ethanol-responsive transcriptome variation in Saccharomyces cerevisiae strains, Genetics 198(1), 369-382. GLBRC
201410.1186/1754-6834-7-50Li, H., S. Pattathil, M. B. Foston, S. Y. Ding, R. Kumar, X. Gao, A. Mittal, J. M. Yarbrough, M. E. Himmel, A. J. Ragauskas, M. G. Hahn, and C. E. Wyman. 2014. Agave proves to be a low recalcitrant lignocellulosic feedstock for biofuels production on semi-arid lands, Biotechnol Biofuels 7, 50. BESC
201410.1002/bit.25108Li, H., Y. Pu, R. Kumar, A. J. Ragauskas, and C. E. Wyman. 2014. Investigation of lignin deposition on cellulose during hydrothermal pretreatment, its effect on cellulose hydrolysis, and underlying mechanisms, Biotechnol Bioeng 111(3), 485-492. BESC
201410.1039/c4ra00824cLi, M., S. Pattathil, M. G. Hahn, and D. B. Hodge. 2014. Identification of features associated with plant cell wall recalcitrance to pretreatment by alkaline hydrogen peroxide in diverse bioenergy feedstocks using glycome profiling, RSC Adv. 4(33), 17282-17292. BESC
201410.1186/1754-6834-7-25Li, Y., T. Xu, T. J. Tschaplinski, N. L. Engle, Y. Yang, D. E. Graham, Z. He, and J. Zhou. 2014. Improvement of cellulose catabolism in Clostridium cellulolyticum by sporulation abolishment and carbon alleviation, Biotechnol Biofuels 7(1), 25. BESC
201410.1039/c3gc42303dLi, Z., S. Kelkar, L. Raycraft, M. Garedew, J. E. Jackson, D. J. Miller, and C. M. Saffron. 2014. A mild approach for bio-oil stabilization and upgrading: electrocatalytic hydrogenation using ruthenium supported on activated carbon cloth, Green Chem. 16(2), 844-852. GLBRC
201410.1016/j.pep.2014.02.013Lim, S., S. P. Chundawat, and B. G. Fox. 2014. Expression, purification and characterization of a functional carbohydrate-binding module from Streptomyces sp. SirexAA-E, Protein Expr Purif 98, 1-9. GLBRC
201410.1016/j.ymben.2014.03.006Lin, P. P., K. S. Rabe, J. L. Takasumi, M. Kadisch, F. H. Arnold, and J. C. Liao. 2014. Isobutanol production at elevated temperatures in thermophilic Geobacillus thermoglucosidasius, Metab Eng 24, 1-8. BESC
201410.1016/j.biombioe.2014.03.006Lindedam, J., S. Bruun, H. Jørgensen, S. R. Decker, G. B. Turner, J. D. DeMartini, C. E. Wyman, and C. Felby. 2014. Evaluation of high throughput screening methods in picking up differences between cultivars of lignocellulosic biomass for ethanol production, Biomass and Bioenergy 66, 261-267. BESC
201410.1021/sb4001728Linshiz, G., N. Stawski, G. Goyal, C. Bi, S. Poust, M. Sharma, V. Mutalik, J. D. Keasling, and N. J. Hillson. 2014. PR-PR: cross-platform laboratory automation system, ACS Synth Biol 3(8), 515-524. JBEI
201410.1186/s12866-014-0215-5Linville, J. L., M. Rodriguez, Jr., S. D. Brown, J. R. Mielenz, and C. D. Cox. 2014. Transcriptomic analysis of Clostridium thermocellum Populus hydrolysate-tolerant mutant strain shows increased cellular efficiency in response to Populus hydrolysate compared to the wild type strain, BMC Microbiol 14, 215. BESC
201410.1186/1754-6834-7-48Liu, T., D. L. Williams, S. Pattathil, M. Li, M. G. Hahn, and D. B. Hodge. 2014. Coupling alkaline pre-extraction with alkaline-oxidative post-treatment of corn stover to enhance enzymatic hydrolysis and fermentability, Biotechnol Biofuels 7(1), 48. BESC
2014Lu, F., and J. Ralph. 2014. The DFRC (Derivatization Followed by Reductive Cleavage) method and its applications for lignin characterization. In Lignin: Structural Analysis, Applications in Biomaterials, and Ecological Significance, 27-66. Nova Science Publishers.GLBRC
2014Lu, F., Ed. 2014: Lignin: structural analysis, applications in biomaterials, and ecological significance.GLBRC
201410.1186/1754-6834-7-93Lupoi, J. S., S. Singh, M. Davis, D. J. Lee, M. Shepherd, B. A. Simmons, and R. J. Henry. 2014. 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, Biotechnol Biofuels 7, 93. BESC
201410.1039/c4gc01160kLuterbacher, J. S., D. Martin Alonso, and J. A. Dumesic. 2014. Targeted chemical upgrading of lignocellulosic biomass to platform molecules, Green Chem. 16(12), 4816-4838. GLBRC
201410.1126/science.1246748Luterbacher, J. S., J. M. Rand, D. M. Alonso, J. Han, J. T. Youngquist, C. T. Maravelias, B. F. Pfleger, and J. A. Dumesic. 2014. Nonenzymatic sugar production from biomass using biomass-derived gamma-valerolactone, Science 343(6168), 277-280. GLBRC
201410.1093/nar/gku315Ma, Q., H. Zhang, X. Mao, C. Zhou, B. Liu, X. Chen, and Y. Xu. 2014. DMINDA: an integrated web server for DNA motif identification and analyses, Nucleic Acids Res 42(Web Server issue), W12-19. BESC
201410.1007/s11427-014-4734-yMa, Q., X. Chen, C. Liu, X. Mao, H. Zhang, F. Ji, C. Wu, and Y. Xu. 2014. Understanding the commonalities and differences in genomic organizations across closely related bacteria from an energy perspective, Sci China Life Sci 57(11), 1121-1130. BESC
201410.1021/jp501619yMac Dowell, N., F. Llovell, N. Sun, J. P. Hallett, A. George, P. A. Hunt, T. Welton, B. A. Simmons, and L. F. Vega. 2014. New experimental density data and soft-SAFT models of alkylimidazolium ([C(n)C(1)im](+)) chloride (Cl(-)), methylsulfate ([MeSO(4)](-)), and dimethylphosphate ([Me(2)PO(4)](-)) based ionic liquids, J Phys Chem B 118(23), 6206-6221. JBEI
2014 10.1016/j.fuel.2013.10.024Mack, J. H., V. H. Rapp, M. Broeckelmann, T. S. Lee, and R. W. Dibble. 2014. Investigation of biofuels from microorganism metabolism for use as anti-knock additives, Fuel 117, 939-943. JBEI
201410.1039/c3gc42424cMandalika, A., L. Qin, T. K. Sato, and T. Runge. 2014. Integrated biorefinery model based on production of furans using open-ended high yield processes, Green Chem. 16(5), 2480-2489. GLBRC
201410.1093/nar/gkt1048Mao, X., Q. Ma, C. Zhou, X. Chen, H. Zhang, J. Yang, F. Mao, W. Lai, and Y. Xu. 2014. DOOR 2.0: presenting operons and their functions through dynamic and integrated views, Nucleic Acids Res 42(Database issue), D654-659. BESC
201410.1038/srep04519Martin, J. A., N. V. Johnson, S. M. Gross, J. Schnable, X. Meng, M. Wang, D. Coleman-Derr, E. Lindquist, C. L. Wei, S. Kaeppler, F. Chen, and Z. Wang. 2014. A near complete snapshot of the Zea mays seedling transcriptome revealed from ultra-deep sequencing, Sci Rep 4, 4519. GLBRC
201410.1107/S1399004714021178McAndrew, R., R. N. Pruitt, S. G. Kamita, J. H. Pereira, D. Majumdar, B. D. Hammock, P. D. Adams, and P. C. Ronald. 2014. Structure of the OsSERK2 leucine-rich repeat extracellular domain, Acta Crystallogr D Biol Crystallogr 70(Pt 11), 3080-3086. JBEI
201410.1155/2014/287430McInerney, P., P. Adams, and M. Z. Hadi. 2014. Error Rate Comparison during Polymerase Chain Reaction by DNA Polymerase, Mol Biol Int 2014, 287430. JBEI
201410.1016/j.anaerobe.2014.06.004.Mearls, E. B., and L. R. Lynd. 2014. The identification of four histidine kinases that influence sporulation in Clostridium thermocellum, Anaerobe 28, 109-119. BESC
201410.1002/anie.201408359Mellmer, M. A., C. Sener, J. M. Gallo, J. S. Luterbacher, D. M. Alonso, and J. A. Dumesic. 2014. Solvent effects in acid-catalyzed biomass conversion reactions, Angew Chem Int Ed Engl 53(44), 11872-11875. GLBRC
201410.1039/c4gc01768dMellmer, M. A., D. Martin Alonso, J. S. Luterbacher, J. M. R. Gallo, and J. A. Dumesic. 2014. Effects of ?-valerolactone in hydrolysis of lignocellulosic biomass to monosaccharides, Green Chem. 16(11), 4659-4662. GLBRC
201410.1016/j.copbio.2014.01.014Meng, X., and A. J. Ragauskas. 2014. Recent advances in understanding the role of cellulose accessibility in enzymatic hydrolysis of lignocellulosic substrates, Curr Opin Biotechnol 27, 150-158. BESC
201410.1093/aepp/ppu033Mooney, D. F., B. L. Barham, and C. Lian. 2014. Inelastic and Fragmented Farm Supply Response for Second-generation Bioenergy Feedstocks: Ex Ante Survey Evidence from Wisconsin, Applied Economic Perspectives and Policy 37(2), 287-310. GLBRC
201410.1021/jp502889cMostofian, B., X. Cheng, and J. C. Smith. 2014. Replica-exchange molecular dynamics simulations of cellulose solvated in water and in the ionic liquid 1-butyl-3-methylimidazolium chloride, J Phys Chem B 118(38), 11037-11049. BESC
2014Muchero, W., J. Labbé, P. Ranjan, S. DiFazio, and G. A. Tuskan. 2014. Genome Resequencing in Populus: Revealing Large-Scale Genome Variation and Implications on Specialized-Trait Genomics. In Challenges and Opportunities for the World's Forests in the 21st Century Forestry Sciences, 587-595. Ed. T. Fenning. Springer.BESC
201410.1093/jxb/eru229Mullet, J., D. Morishige, R. McCormick, S. Truong, J. Hilley, B. McKinley, R. Anderson, S. N. Olson, and W. Rooney. 2014. Energy sorghum--a genetic model for the design of C4 grass bioenergy crops, J Exp Bot 65(13), 3479-3489. GLBRC
201410.1038/nature13308Myburg, A. A., D. Grattapaglia, G. A. Tuskan, U. Hellsten, R. D. Hayes, J. Grimwood, J. Jenkins, E. Lindquist, H. Tice, D. Bauer, D. M. Goodstein, I. Dubchak, A. Poliakov, E. Mizrachi, A. R. Kullan, S. G. Hussey, D. Pinard, K. van der Merwe, P. Singh, I. van Jaarsveld, O. B. Silva-Junior, R. C. Togawa, M. R. Pappas, D. A. Faria, C. P. Sansaloni, C. D. Petroli, X. Yang, P. Ranjan, T. J. Tschaplinski, C. Y. Ye, T. Li, L. Sterck, K. Vanneste, F. Murat, M. Soler, H. S. Clemente, N. Saidi, H. Cassan-Wang, C. Dunand, C. A. Hefer, E. Bornberg-Bauer, A. R. Kersting, K. Vining, V. Amarasinghe, M. Ranik, S. Naithani, J. Elser, A. E. Boyd, A. Liston, J. W. Spatafora, P. Dharmwardhana, R. Raja, C. Sullivan, E. Romanel, M. Alves-Ferreira, C. Kulheim, W. Foley, V. Carocha, J. Paiva, D. Kudrna, S. H. Brommonschenkel, G. Pasquali, M. Byrne, P. Rigault, J. Tibbits, A. Spokevicius, R. C. Jones, D. A. Steane, R. E. Vaillancourt, B. M. Potts, F. Joubert, K. Barry, G. J. Pappas, S. H. Strauss, P. Jaiswal, J. Grima-Pettenati, J. Salse, Y. Van de Peer, D. S. Rokhsar, and J. Schmutz. 2014. The genome of Eucalyptus grandis, Nature 510(7505), 356-362. BESC
201410.1016/j.ymben.2014.05.006.Myung, S., J. Rollin, C. You, F. Sun, S. Chandrayan, M. W. Adams, and Y. H. Zhang. 2014. In vitro metabolic engineering of hydrogen production at theoretical yield from sucrose, Metab Eng 24, 70-77. BESC
201410.1007/s10457-014-9728-zNageswara-Rao, M., M. Hanson, S. Agarwal, C. N. Stewart, and C. Kwit. 2014. Genetic diversity analysis of switchgrass (Panicum virgatum L.) populations using microsatellites and chloroplast sequences, Agroforestry Systems 88(5), 823-834. BESC
201410.1105/tpc.114.125260Niculaes, C., K. Morreel, H. Kim, F. Lu, L. S. McKee, B. Ivens, J. Haustraete, B. Vanholme, R. D. Rycke, M. Hertzberg, J. Fromm, V. Bulone, A. Polle, J. Ralph, and W. Boerjan. 2014. Phenylcoumaran benzylic ether reductase prevents accumulation of compounds formed under oxidative conditions in poplar xylem, Plant Cell 26(9), 3775-3791. GLBRC
201410.1038/nchembio.1519Nielsen, J., M. Fussenegger, J. Keasling, S. Y. Lee, J. C. Liao, K. Prather, and B. Palsson. 2014. Engineering synergy in biotechnology, Nat Chem Biol 10(5), 319-322. JBEI
201410.1007/s00253-013-5361-4Nowroozi, F. F., E. E. Baidoo, S. Ermakov, A. M. Redding-Johanson, T. S. Batth, C. J. Petzold, and J. D. Keasling. 2014. Metabolic pathway optimization using ribosome binding site variants and combinatorial gene assembly, Appl Microbiol Biotechnol 98(4), 1567-1581. JBEI
2014Ogle, S. M., P. R. Adler, F. J. Breidt, S. Del Grosso, J. Derner, A. Franzluebbers, M. Liebig, B. Linquist, G. P. Robertson, M. Schoeneberger, J. Six, C. van Kessel, R. Venterea, and T. O. West. 2014. Quantifying greenhouse sources and sinks in cropland and grazing land systems. In Quantifying Greenhouse Gas Fluxes in Agriculture and Forestry: Methods for Entity-Scale Inventory, Technical Bulletin Number 1939, 3-1-3-142. Eds. M. Eve, D. Pape, M. Flugge, R. Steele, D. Man, M. Riley-Gilbert, and S. Biggar. Office of the Chief Economist, U.S. Department of Agriculture.GLBRC
201410.1016/j.biortech.2014.02.016Oleskowicz-Popiel, P., D. Klein-Marcuschamer, B. A. Simmons, and H. W. Blanch. 2014. Lignocellulosic ethanol production without enzymes--technoeconomic analysis of ionic liquid pretreatment followed by acidolysis, Bioresour Technol 158, 294-299. JBEI
2014Ong, R. G., S. P. S. Chundawat, D. B. Hodge, S. Keskar, and B. E. Dale. 2014. Linking plant biology and pretreatment: Understanding the structure and organization of the plant cell wall and interactions with cellulosic biofuel production. In Plants and Bioenergy, 231-253. Eds. M. C. McCann, M. S. Buckeridge, and N. S. Carpita. Springer.GLBRC
201410.2134/jeq2014.02.0077Osterholz, W. R., C. J. Kucharik, J. L. Hedtcke, and J. L. Posner. 2014. Seasonal nitrous oxide and methane fluxes from grain- and forage-based production systems in wisconsin, USA, J Environ Qual 43(6), 1833-1843. GLBRC
201410.1111/gcbb.12069Palmer, M. M., J. A. Forrester, D. E. Rothstein, and D. J. Mladenoff. 2014. Conversion of open lands to short-rotation woody biomass crops: site variability affects nitrogen cycling and N2O fluxes in the US Northern Lake States, GCB Bioenergy 6(4), 450-464. GLBRC
201410.1371/journal.pone.0107499Parreiras, L. S., R. J. Breuer, R. Avanasi Narasimhan, A. J. Higbee, A. La Reau, M. Tremaine, L. Qin, L. B. Willis, B. D. Bice, B. L. Bonfert, R. C. Pinhancos, A. J. Balloon, N. Uppugundla, T. Liu, C. Li, D. Tanjore, I. M. Ong, H. Li, E. L. Pohlmann, J. Serate, S. T. Withers, B. A. Simmons, D. B. Hodge, M. S. Westphall, J. J. Coon, B. E. Dale, V. Balan, D. H. Keating, Y. Zhang, R. Landick, A. P. Gasch, and T. K. Sato. 2014. 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 9(9), e107499. JBEI GLBRC
2014Parsons, H. T., S. M. Gonzalez Fernandez-Nino, and J. L. Heazlewood. 2014. Separation of the plant golgi apparatus and endoplasmic reticulum by free-flow electrophoresis. In Plant Proteomics: Methods and Protocols, 527-539. Ed. K. Jorrin-Novo. Humana Press.JBEI
201410.1186/s12870-014-0265-8Payyavula, R. S., T. J. Tschaplinski, S. S. Jawdy, R. W. Sykes, G. A. Tuskan, and U. C. Kalluri. 2014. Metabolic profiling reveals altered sugar and secondary metabolism in response to UGPase overexpression in Populus, BMC Plant Biol 14, 265. BESC
201410.1007/s12155-014-9410-3Penning, B. W., R. W. Sykes, N. C. Babcock, C. K. Dugard, J. F. Klimek, D. Gamblin, M. Davis, T. R. Filley, N. S. Mosier, C. F. Weil, M. C. McCann, and N. C. Carpita. 2014. Validation of PyMBMS as a High-throughput Screen for Lignin Abundance in Lignocellulosic Biomass of Grasses, BioEnergy Research 7(3), 899-908. BESC
201410.1111/mec.12702Peris, D., K. Sylvester, D. Libkind, P. Goncalves, J. P. Sampaio, W. G. Alexander, and C. T. Hittinger. 2014. Population structure and reticulate evolution of Saccharomyces eubayanus and its lager-brewing hybrids, Mol Ecol 23(8), 2031-2045. GLBRC
201410.1021/ac5014767Peterson, A. C., J. P. Hauschild, S. T. Quarmby, D. Krumwiede, O. Lange, R. A. Lemke, F. Grosse-Coosmann, S. Horning, T. J. Donohue, M. S. Westphall, J. J. Coon, and J. Griep-Raming. 2014. Development of a GC/Quadrupole-Orbitrap mass spectrometer, part I: design and characterization, Anal Chem 86(20), 10036-10043. GLBRC
201410.1111/tpj.12420Petrik, D. L., S. D. Karlen, C. L. Cass, D. Padmakshan, F. Lu, S. Liu, P. Le Bris, S. Antelme, N. Santoro, C. G. Wilkerson, R. Sibout, C. Lapierre, J. Ralph, and J. C. Sedbrook. 2014. p-Coumaroyl-CoA:monolignol transferase (PMT) acts specifically in the lignin biosynthetic pathway in Brachypodium distachyon, Plant J 77(5), 713-726. GLBRC
201410.3389/fmicb.2014.00090.Piotrowski, J. S., Y. Zhang, D. M. Bates, D. H. Keating, T. K. Sato, I. M. Ong, and R. Landick. 2014. Death by a thousand cuts: the challenges and diverse landscape of lignocellulosic hydrolysate inhibitors, Front Microbiol 5, 90. GLBRC
201410.1111/pbi.12225Poovaiah, C. R., M. Nageswara-Rao, J. R. Soneji, H. L. Baxter, and C. N. Stewart, Jr. 2014. Altered lignin biosynthesis using biotechnology to improve lignocellulosic biofuel feedstocks, Plant Biotechnol J 12(9), 1163-1173. BESC
201410.1016/j.copbio.2014.04.011Poust, S., A. Hagen, L. Katz, and J. D. Keasling. 2014. Narrowing the gap between the promise and reality of polyketide synthases as a synthetic biology platform, Curr Opin Biotechnol 30, 32-39. JBEI
201410.3791/51381Pradhan Mitra, P., and D. Loque. 2014. Histochemical staining of Arabidopsis thaliana secondary cell wall elements, J Vis Exp(87). JBEI
2014Pryor, S. C., D. Scavia, C. Downer, M. Gaden, L. Iverson, R. Nordstrom, J. Patz, and P. Robertson. 2014. Midwest. In Climate Change Impacts in the United States: The Third National Climate Assessment, 418-440. U.S. Global Change Research Program.GLBRC
201410.1128/genomeA.00790-14Pyne, M. E., S. Utturkar, S. D. Brown, M. Moo-Young, D. A. Chung, and C. P. Chou. 2014. Improved Draft Genome Sequence of Clostridium pasteurianum Strain ATCC 6013 (DSM 525) Using a Hybrid Next-Generation Sequencing Approach, Genome Announc 2(4). BESC
201410.1126/science.1246843Ragauskas, A. J., G. T. Beckham, M. J. Biddy, R. Chandra, F. Chen, M. F. Davis, B. H. Davison, R. A. Dixon, P. Gilna, M. Keller, P. Langan, A. K. Naskar, J. N. Saddler, T. J. Tschaplinski, G. A. Tuskan, and C. E. Wyman. 2014. Lignin valorization: improving lignin processing in the biorefinery, Science 344(6185), 1246843. BESC
201410.1038/nature13867Rahimi, A., A. Ulbrich, J. J. Coon, and S. S. Stahl. 2014. Formic-acid-induced depolymerization of oxidized lignin to aromatics, Nature 515(7526), 249-252. GLBRC
201410.1073/pnas.1406073111Rautengarten, C., B. Ebert, I. Moreno, H. Temple, T. Herter, B. Link, D. Donas-Cofre, A. Moreno, S. Saez-Aguayo, F. Blanco, J. C. Mortimer, A. Schultink, W. D. Reiter, P. Dupree, M. Pauly, J. L. Heazlewood, H. V. Scheller, and A. Orellana. 2014. The Golgi localized bifunctional UDP-rhamnose/UDP-galactose transporter family of Arabidopsis, Proc Natl Acad Sci U S A 111(31), 11563-11568. JBEI
201410.1104/pp.113.232678Ream, T. S., D. P. Woods, C. J. Schwartz, C. P. Sanabria, J. A. Mahoy, E. M. Walters, H. F. Kaeppler, and R. M. Amasino. 2014. Interaction of photoperiod and vernalization determines flowering time of Brachypodium distachyon, Plant Physiol 164(2), 694-709. GLBRC
201410.1016/j.biortech.2013.12.051Reed, P. T., J. A. Izquierdo, and L. R. Lynd. 2014. Cellulose fermentation by Clostridium thermocellum and a mixed consortium in an automated repetitive batch reactor, Bioresour Technol 155, 50-56. BESC
201410.1371/journal.pone.0105014Ren, Y., S. F. Hansen, B. Ebert, J. Lau, and H. V. Scheller. 2014. 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 9(8), e105014. JBEI
201410.1016/j.copbio.2013.11.013Rennie, E. A., and H. V. Scheller. 2014. Xylan biosynthesis, Curr Opin Biotechnol 26, 100-107. JBEI
201410.1105/tpc.114.129171Rennie, E. A., B. Ebert, G. P. Miles, R. E. Cahoon, K. M. Christiansen, S. Stonebloom, H. Khatab, D. Twell, C. J. Petzold, P. D. Adams, P. Dupree, J. L. Heazlewood, E. B. Cahoon, and H. V. Scheller. 2014. Identification of a sphingolipid alpha-glucuronosyltransferase that is essential for pollen function in Arabidopsis, Plant Cell 26(8), 3314-3325. JBEI
201410.1111/nph.12757Reyes-Hernandez, B. J., A. C. Srivastava, Y. Ugartechea-Chirino, S. Shishkova, P. A. Ramos-Parra, V. Lira-Ruan, R. I. Diaz de la Garza, G. Dong, J. C. Moon, E. B. Blancaflor, and J. G. Dubrovsky. 2014. The root indeterminacy-to-determinacy developmental switch is operated through a folate-dependent pathway in Arabidopsis thaliana, New Phytol 202(4), 1223-1236. BESC
201410.1063/1.4874715Rhee, M., P. Liu, R. J. Meagher, Y. K. Light, and A. K. Singh. 2014. Versatile on-demand droplet generation for controlled encapsulation, Biomicrofluidics 8(3), 034112. JBEI
201410.1073/pnas.1400592111Riley, R., A. A. Salamov, D. W. Brown, L. G. Nagy, D. Floudas, B. W. Held, A. Levasseur, V. Lombard, E. Morin, R. Otillar, E. A. Lindquist, H. Sun, K. M. LaButti, J. Schmutz, D. Jabbour, H. Luo, S. E. Baker, A. G. Pisabarro, J. D. Walton, R. A. Blanchette, B. Henrissat, F. Martin, D. Cullen, D. S. Hibbett, and I. V. Grigoriev. 2014. Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi, Proc Natl Acad Sci U S A 111(27), 9923-9928. GLBRC
201410.1038/nclimate2402Robertson, G. P., P. R. Grace, R. C. Izaurralde, W. P. Parton, and X. Zhang. 2014. CO2 emissions from crop residue-derived biofuels, Nature Climate Change 4(11), 933-934. GLBRC
2014Robertson, P. 2014. Soil greenhouse gas emissions and their mitigation. In The Encyclopedia of Agriculture and Food Systems, 185-196. Academic Press.GLBRC
2014Robinson, W. 2014. Farming for Fuels, Dimensions 16(2), 46-48. DOI.BESC
201410.1038/nprot.2014.132Rodriguez, S., J. Kirby, C. M. Denby, and J. D. Keasling. 2014. Production and quantification of sesquiterpenes in Saccharomyces cerevisiae, including extraction, detection and quantification of terpene products and key related metabolites, Nat Protoc 9(8), 1980-1996. JBEI
201410.1371/journal.pbio.1001878Ronald, P. C. 2014. Lab to farm: applying research on plant genetics and genomics to crop improvement, PLoS Biol 12(6), e1001878. JBEI
201410.1021/jp507811dRotavera, B., J. Zador, O. Welz, L. Sheps, A. M. Scheer, J. D. Savee, M. Akbar Ali, T. S. Lee, B. A. Simmons, D. L. Osborn, A. Violi, and C. A. Taatjes. 2014. Photoionization mass spectrometric measurements of initial reaction pathways in low-temperature oxidation of 2,5-dimethylhexane, J Phys Chem A 118(44), 10188-10200. JBEI
201410.1038/ncomms4490Ruegg, T. L., E. M. Kim, B. A. Simmons, J. D. Keasling, S. W. Singer, T. S. Lee, and M. P. Thelen. 2014. An auto-inducible mechanism for ionic liquid resistance in microbial biofuel production, Nat Commun 5, 3490. JBEI
201410.1016/j.ymben.2013.07.003Runguphan, W., and J. D. Keasling. 2014. Metabolic engineering of Saccharomyces cerevisiae for production of fatty acid-derived biofuels and chemicals, Metab Eng 21, 103-113. JBEI
201410.1016/j.compag.2014.08.005Sahajpal, R., X. Zhang, R. C. Izaurralde, I. Gelfand, and G. C. Hurtt. 2014. Identifying representative crop rotation patterns and grassland loss in the US Western Corn Belt, Computers and Electronics in Agriculture 108, 173-182. GLBRC
201410.4155/bfs.09.17Samuel, R., Y. Pu, M. Foston, and A. J. Ragauskas. 2014. Solid-state NMR characterization of switchgrass cellulose after dilute acid pretreatment, Biofuels 1(1), 85-90. BESC
201410.3389/fenrg.2013.00014Samuel, R., Y. Pu, N. Jiang, C. Fu, Z.-Y. Wang, and A. Ragauskas. 2014. Structural Characterization of Lignin in Wild-Type versus COMT Down-Regulated Switchgrass, Frontiers in Energy Research 1. BESC
201410.1021/jp411998tSangha, A. K., B. H. Davison, R. F. Standaert, M. F. Davis, J. C. Smith, and J. M. Parks. 2014. Chemical factors that control lignin polymerization, J Phys Chem B 118(1), 164-170. BESC
201410.1186/1754-6834-7-73Sarks, C., M. Jin, T. K. Sato, V. Balan, and B. E. Dale. 2014. Studying the rapid bioconversion of lignocellulosic sugars into ethanol using high cell density fermentations with cell recycle, Biotechnol Biofuels 7, 73. GLBRC
201410.1021/sb4001382Sarria, S., B. Wong, H. Garcia Martin, J. D. Keasling, and P. Peralta-Yahya. 2014. Microbial synthesis of pinene, ACS Synth Biol 3(7), 466-475. JBEI
201410.1039/c3gc42295jSathitsuksanoh, N., K. M. Holtman, D. J. Yelle, T. Morgan, V. Stavila, J. Pelton, H. Blanch, B. A. Simmons, and A. George. 2014. Lignin fate and characterization during ionic liquid biomass pretreatment for renewable chemicals and fuels production, Green Chem. 16(3), 1236-1247. JBEI
201410.1128/AEM.01885-13Sato, T. K., T. Liu, L. S. Parreiras, D. L. Williams, D. J. Wohlbach, B. D. Bice, I. M. Ong, R. J. Breuer, L. Qin, D. Busalacchi, S. Deshpande, C. Daum, A. P. Gasch, and D. B. Hodge. 2014. Harnessing genetic diversity in Saccharomyces cerevisiae for fermentation of xylose in hydrolysates of alkaline hydrogen peroxide-pretreated biomass, Appl Environ Microbiol 80(2), 540-554. GLBRC
201410.1104/pp.114.245597Schuetz, M., A. Benske, R. A. Smith, Y. Watanabe, Y. Tobimatsu, J. Ralph, T. Demura, B. Ellis, and A. L. Samuels. 2014. Laccases direct lignification in the discrete secondary cell wall domains of protoxylem, Plant Physiol 166(2), 798-807. GLBRC
201410.1104/pp.114.235424Sekhon, R. S., C. N. Hirsch, K. L. Childs, M. W. Breitzman, P. Kell, S. Duvick, E. P. Spalding, C. R. Buell, N. de Leon, and S. M. Kaeppler. 2014. Phenotypic and Transcriptional Analysis of Divergently Selected Maize Populations Reveals the Role of Developmental Timing in Seed Size Determination, Plant Physiol 165(2), 658-669. GLBRC
201410.1007/s12155-014-9523-8Serba, D. D., G. Daverdin, J. H. Bouton, K. M. Devos, E. C. Brummer, and M. C. Saha. 2014. Quantitative Trait Loci (QTL) Underlying Biomass Yield and Plant Height in Switchgrass, BioEnergy Research 8(1), 307-324. BESC
201410.2136/sssaj2013.05.0181Shcherbak, I., and G. P. Robertson. 2014. Determining the Diffusivity of Nitrous Oxide in Soil using In Situ Tracers, Soil Science Society of America Journal 78(1), 79. GLBRC
201410.1073/pnas.1322434111Shcherbak, I., N. Millar, and G. P. Robertson. 2014. Global metaanalysis of the nonlinear response of soil nitrous oxide (N2O) emissions to fertilizer nitrogen, Proc Natl Acad Sci U S A 111(25), 9199-9204. GLBRC
201410.4155/bfs.11.136Shepherd, M., J. Bartle, D. J. Lee, J. Brawner, D. Bush, P. Turnbull, P. Macdonel, T. R. Brown, B. Simmons, and R. Henry. 2014. Eucalypts as a biofuel feedstock, Biofuels 2(6), 639-657. JBEI
201410.1039/c4gc00373jShi, J., K. Balamurugan, R. Parthasarathi, N. Sathitsuksanoh, S. Zhang, V. Stavila, V. Subramanian, B. A. Simmons, and S. Singh. 2014. Understanding the role of water during ionic liquid pretreatment of lignocellulose: co-solvent or anti-solvent?, Green Chem. 16(8), 3830-3840. JBEI
201410.4155/bfs.12.82Shi, J., V. S. Thompson, N. A. Yancey, V. Stavila, B. A. Simmons, and S. Singh. 2014. Impact of mixed feedstocks and feedstock densification on ionic liquid pretreatment efficiency, Biofuels 4(1), 63-72. JBEI
201410.1128/genomeA.00054-14Shields-Menard, S. A., S. D. Brown, D. M. Klingeman, K. Indest, D. Hancock, J. J. Wewalwela, W. T. French, and J. R. Donaldson. 2014. Draft Genome Sequence of Rhodococcus rhodochrous Strain ATCC 21198, Genome Announc 2(1). BESC
201410.4155/bfs.11.117Simmons, B. 2014. Rethinking renewable energy in Japan, Biofuels 2(4), 365-367. JBEI
201410.4155/bfs.10.75Simmons, B. A. 2014. Opportunities and challenges in advanced biofuel production: the importance of synthetic biology and combustion science, Biofuels 2(1), 5-7. JBEI
201410.1111/jam.12609Simmons, C. W., A. P. Reddy, B. A. Simmons, S. W. Singer, and J. S. VanderGheynst. 2014. Effect of inoculum source on the enrichment of microbial communities on two lignocellulosic bioenergy crops under thermophilic and high-solids conditions, J Appl Microbiol 117(4), 1025-1034. JBEI
201410.1002/btpr.1859Simmons, C. W., A. P. Reddy, J. S. Vandergheynst, B. A. Simmons, and S. W. Singer. 2014. Bacillus coagulans tolerance to 1-ethyl-3-methylimidazolium-based ionic liquids in aqueous and solid-state thermophilic culture, Biotechnol Prog 30(2), 311-316. JBEI
201410.1186/s13068-014-0180-0Simmons, C. W., A. P. Reddy, P. D'Haeseleer, J. Khudyakov, K. Billis, A. Pati, B. A. Simmons, S. W. Singer, M. P. Thelen, and J. S. VanderGheynst. 2014. Metatranscriptomic analysis of lignocellulolytic microbial communities involved in high-solids decomposition of rice straw, Biotechnol Biofuels 7(1), 495. JBEI
201410.1016/j.apsoil.2013.08.014Simmons, C. W., J. T. Claypool, M. N. Marshall, L. K. Jabusch, A. P. Reddy, B. A. Simmons, S. W. Singer, J. J. Stapleton, and J. S. VanderGheynst. 2014. Characterization of bacterial communities in solarized soil amended with lignocellulosic organic matter, Applied Soil Ecology 73, 97-104. JBEI
201410.1111/1567-1364.12224Sitepu, I. R., S. Shi, B. A. Simmons, S. W. Singer, K. Boundy-Mills, and C. W. Simmons. 2014. Yeast tolerance to the ionic liquid 1-ethyl-3-methylimidazolium acetate, FEMS Yeast Res 14(8), 1286-1294. JBEI
201410.1016/j.ecolecon.2014.07.027Skevas, T., S. M. Swinton, T. D. Meehan, T. N. Kim, C. Gratton, and A. Egbendewe-Mondzozo. 2014. Integrating agricultural pest biocontrol into forecasts of energy biomass production, Ecological Economics 106, 195-203. GLBRC
201410.1073/pnas.1405685111Socha, A. M., R. Parthasarathi, J. Shi, S. Pattathil, D. Whyte, M. Bergeron, A. George, K. Tran, V. Stavila, S. Venkatachalam, M. G. Hahn, B. A. Simmons, and S. Singh. 2014. Efficient biomass pretreatment using ionic liquids derived from lignin and hemicellulose, Proc Natl Acad Sci U S A 111(35), E3587-3595. JBEI BESC
201410.1039/c3gc42401dSun, N., R. Parthasarathi, A. M. Socha, J. Shi, S. Zhang, V. Stavila, K. L. Sale, B. A. Simmons, and S. Singh. 2014. Understanding pretreatment efficacy of four cholinium and imidazolium ionic liquids by chemistry and computation, Green Chem. 16(5), 2546-2557. JBEI
201410.1007/s10570-014-0303-6Sun, Q., M. Foston, D. Sawada, S. V. Pingali, H. M. O’Neill, H. Li, C. E. Wyman, P. Langan, Y. Pu, and A. J. Ragauskas. 2014. Comparison of changes in cellulose ultrastructure during different pretreatments of poplar, Cellulose 21(4), 2419-2431. BESC
201410.1186/s13068-014-0150-6Sun, Q., M. Foston, X. Meng, D. Sawada, S. V. Pingali, H. M. O'Neill, H. Li, C. E. Wyman, P. Langan, A. J. Ragauskas, and R. Kumar. 2014. Effect of lignin content on changes occurring in poplar cellulose ultrastructure during dilute acid pretreatment, Biotechnol Biofuels 7(1), 150. BESC
2014 10.1104/pp.114.245548Sundin, L., R. Vanholme, J. Geerinck, G. Goeminne, R. Hofer, H. Kim, J. Ralph, and W. Boerjan. 2014. Mutation of the inducible ARABIDOPSIS THALIANA CYTOCHROME P450 REDUCTASE2 alters lignin composition and improves saccharification, Plant Physiol 166(4), 1956-1971. GLBRC
201410.1016/j.agee.2014.03.006Syswerda, S. P., and G. P. Robertson. 2014. Ecosystem services along a management gradient in Michigan (USA) cropping systems, Agriculture, Ecosystems & Environment 189, 28-35. GLBRC
201410.1002/prot.24491Takasuka, T. E., C. M. Bianchetti, Y. Tobimatsu, L. F. Bergeman, J. Ralph, and B. G. Fox. 2014. Structure-guided analysis of catalytic specificity of the abundantly secreted chitosanase SACTE_5457 from Streptomyces sp. SirexAA-E, Proteins 82(7), 1245-1257. GLBRC
2014Takasuka, T. E., J. A. Walker, L. F. Bergeman, K. A. V. Meulen, S.-i. Makino, N. L. Elsen, and B. G. Fox. 2014. Cell-free translation of biofuels enzymes. In Cell-Free Protein Synthesis: Methods and Protocols, 71-95. Humana Press Inc.GLBRC
201410.1371/journal.pone.0094166Takasuka, T. E., J. F. Acheson, C. M. Bianchetti, B. M. Prom, L. F. Bergeman, A. J. Book, C. R. Currie, and B. G. Fox. 2014. Biochemical properties and atomic resolution structure of a proteolytically processed beta-mannanase from cellulolytic Streptomyces sp. SirexAA-E, PLoS One 9(4), e94166. GLBRC
201410.1371/journal.pone.0115906Tan, L., Y. Pu, S. Pattathil, U. Avci, J. Qian, A. Arter, L. Chen, M. G. Hahn, A. J. Ragauskas, and M. J. Kieliszewski. 2014. Changes in cell wall properties coincide with overexpression of extensin fusion proteins in suspension cultured tobacco cells, PLoS One 9(12), e115906. BESC
201410.1039/c4cc04692gTobimatsu, Y., D. Van de Wouwer, E. Allen, R. Kumpf, B. Vanholme, W. Boerjan, and J. Ralph. 2014. A click chemistry strategy for visualization of plant cell wall lignification, Chem Commun (Camb) 50(82), 12262-12265. GLBRC
201410.1002/bbb.1500Tolbert, A., H. Akinosho, R. Khunsupat, A. K. Naskar, and A. J. Ragauskas. 2014. Characterization and analysis of the molecular weight of lignin for biorefining studies, Biofuels, Bioproducts and Biorefining 8(6), 836-856. BESC
201410.1534/g3.114.012468Truong, S. K., R. F. McCormick, D. T. Morishige, and J. E. Mullet. 2014. Resolution of genetic map expansion caused by excess heterozygosity in plant recombinant inbred populations, G3 (Bethesda) 4(10), 1963-1969. GLBRC
201410.1021/ac500270qUlbrich, A., D. J. Bailey, M. S. Westphall, and J. J. Coon. 2014. Organic acid quantitation by NeuCode methylamidation, Anal Chem 86(9), 4402-4408. GLBRC
201410.1186/1754-6834-7-72.Uppugundla, N., L. da Costa Sousa, S. P. Chundawat, X. Yu, B. Simmons, S. Singh, X. Gao, R. Kumar, C. E. Wyman, B. E. Dale, and V. Balan. 2014. A comparative study of ethanol production using dilute acid, ionic liquid and AFEX pretreated corn stover, Biotechnol Biofuels 7, 72. JBEI BESC GLBRC
201410.1111/tpj.12643Urbanowicz, B. R., M. J. Pena, H. A. Moniz, K. W. Moremen, and W. S. York. 2014. Two Arabidopsis proteins synthesize acetylated xylan in vitro, Plant J 80(2), 197-206. BESC
201410.1073/pnas.1321673111Van Acker, R., J. C. Leple, D. Aerts, V. Storme, G. Goeminne, B. Ivens, F. Legee, C. Lapierre, K. Piens, M. C. Van Montagu, N. Santoro, C. E. Foster, J. Ralph, W. Soetaert, G. Pilate, and W. Boerjan. 2014. Improved saccharification and ethanol yield from field-grown transgenic poplar deficient in cinnamoyl-CoA reductase, Proc Natl Acad Sci U S A 111(2), 845-850. GLBRC
201410.1104/pp.113.233742Vanholme, B., R. Vanholme, H. Turumtay, G. Goeminne, I. Cesarino, F. Goubet, K. Morreel, J. Rencoret, V. Bulone, C. Hooijmaijers, R. De Rycke, G. Gheysen, J. Ralph, M. De Block, F. Meulewaeter, and W. Boerjan. 2014. Accumulation of N-acetylglucosamine oligomers in the plant cell wall affects plant architecture in a dose-dependent and conditional manner, Plant Physiol 165(1), 290-308. GLBRC
201410.1371/journal.pone.0110785Vinay-Lara, E., J. J. Hamilton, B. Stahl, J. R. Broadbent, J. L. Reed, and J. L. Steele. 2014. Genome-scale reconstruction of metabolic networks of Lactobacillus casei ATCC 334 and 12A, PLoS One 9(11), e110785. GLBRC
201410.1073/pnas.1309492111Werling, B. P., T. L. Dickson, R. Isaacs, H. Gaines, C. Gratton, K. L. Gross, H. Liere, C. M. Malmstrom, T. D. Meehan, L. Ruan, B. A. Robertson, G. P. Robertson, T. M. Schmidt, A. C. Schrotenboer, T. K. Teal, J. K. Wilson, and D. A. Landis. 2014. Perennial grasslands enhance biodiversity and multiple ecosystem services in bioenergy landscapes, Proc Natl Acad Sci U S A 111(4), 1652-1657. GLBRC
201410.5194/bg-11-3899-2014Wieder, W. R., A. S. Grandy, C. M. Kallenbach, and G. B. Bonan. 2014. Integrating microbial physiology and physio-chemical principles in soils with the MIcrobial-MIneral Carbon Stabilization (MIMICS) model, Biogeosciences 11(14), 3899-3917. GLBRC
201410.1126/science.1250161Wilkerson, C. G., S. D. Mansfield, F. Lu, S. Withers, J. Y. Park, S. D. Karlen, E. Gonzales-Vigil, D. Padmakshan, F. Unda, J. Rencoret, and J. Ralph. 2014. Monolignol ferulate transferase introduces chemically labile linkages into the lignin backbone, Science 344(6179), 90-93. GLBRC
201410.1007/s10295-014-1509-1Winger, A. M., J. L. Heazlewood, L. J. Chan, C. J. Petzold, K. Permaul, and S. Singh. 2014. Secretome analysis of the thermophilic xylanase hyper-producer Thermomyces lanuginosus SSBP cultivated on corn cobs, J Ind Microbiol Biotechnol 41(11), 1687-1696. JBEI
201410.1093/gbe/evu199Wohlbach, D. J., N. Rovinskiy, J. A. Lewis, M. Sardi, W. S. Schackwitz, J. A. Martin, S. Deshpande, C. G. Daum, A. Lipzen, T. K. Sato, and A. P. Gasch. 2014. Comparative Genomics of Saccharomyces cerevisiae Natural Isolates for Bioenergy Production, Genome Biology and Evolution 6(9), 2557-2566. GLBRC
201410.1186/1944-3277-9-19Woo, H. L., N. R. Ballor, T. C. Hazen, J. L. Fortney, B. Simmons, K. W. Davenport, L. Goodwin, N. Ivanova, N. C. Kyrpides, K. Mavromatis, T. Woyke, J. Jansson, J. Kimbrel, and K. M. DeAngelis. 2014. Complete genome sequence of the lignin-degrading bacterium Klebsiella sp. strain BRL6-2, Stand Genomic Sci 9, 19. JBEI
201410.1128/genomeA.00637-14Woo, H. L., S. Utturkar, D. Klingeman, B. A. Simmons, K. M. DeAngelis, S. D. Brown, and T. C. Hazen. 2014. Draft Genome Sequence of the Lignin-Degrading Burkholderia sp. Strain LIG30, Isolated from Wet Tropical Forest Soil, Genome Announc 2(3). JBEI BESC
201410.1016/j.syapm.2013.10.001.Woo, H. L., T. C. Hazen, B. A. Simmons, and K. M. DeAngelis. 2014. Enzyme activities of aerobic lignocellulolytic bacteria isolated from wet tropical forest soils, Syst Appl Microbiol 37(1), 60-67. JBEI
201410.3389/fpls.2014.00099Woods, D. P., T. S. Ream, and R. M. Amasino. 2014. Memory of the vernalized state in plants including the model grass Brachypodium distachyon, Front Plant Sci 5, 99. GLBRC
201410.1534/genetics.114.166785Woods, D. P., T. S. Ream, G. Minevich, O. Hobert, and R. M. Amasino. 2014. PHYTOCHROME C is an essential light receptor for photoperiodic flowering in the temperate grass, Brachypodium distachyon, Genetics 198(1), 397-408. GLBRC
201410.1186/2049-2618-2-26Wu, Y. W., Y. H. Tang, S. G. Tringe, B. A. Simmons, and S. W. Singer. 2014. MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm, Microbiome 2, 26. JBEI
201410.1002/anie.201405990Wyche, T. P., J. S. Piotrowski, Y. Hou, D. Braun, R. Deshpande, S. McIlwain, I. M. Ong, C. L. Myers, I. A. Guzei, W. M. Westler, D. R. Andes, and T. S. Bugni. 2014. Forazoline A: marine-derived polyketide with antifungal in vivo efficacy, Angew Chem Int Ed Engl 53(43), 11583-11586. GLBRC
201410.1016/j.indcrop.2014.05.023.Xiang, Z., J. Watson, Y. Tobimatsu, and T. Runge. 2014. Film-forming polymers from distillers’ grains: structural and material properties, Industrial Crops and Products 59, 282-289. GLBRC
201410.1007/s10570-014-0379-zXiang, Z., R. Anthony, Y. Tobimatsu, and T. Runge. 2014. Emulsifying properties of an arabinoxylan-protein gum from distillers’ grains and the co-production of animal feed, Cellulose 21(5), 3623-3635. GLBRC
2014 10.3389/fpls.2014.00388Xiao, L., H. Wei, M. E. Himmel, H. Jameel, and S. S. Kelley. 2014. NIR and Py-mbms coupled with multivariate data analysis as a high-throughput biomass characterization technique: a review, Front Plant Sci 5, 388. BESC
201410.1111/pbi.12142Xie, F., C. N. Stewart, Jr., F. A. Taki, Q. He, H. Liu, and B. Zhang. 2014. High-throughput deep sequencing shows that microRNAs play important roles in switchgrass responses to drought and salinity stress, Plant Biotechnol J 12(3), 354-366. BESC
201410.4155/bfs.11.116Yang, B., Z. Dai, S.-Y. Ding, and C. E. Wyman. 2014. Enzymatic hydrolysis of cellulosic biomass, Biofuels 2(4), 421-449. BESC
201410.1105/tpc.114.133769Yang, J., E. Worley, and M. Udvardi. 2014. A NAP-AAO3 regulatory module promotes chlorophyll degradation via ABA biosynthesis in Arabidopsis leaves, Plant Cell 26(12), 4862-4874. BESC
201410.1007/s12155-014-9566-xYang, J., E. Worley, I. Torres-Jerez, R. Miller, M. Wang, C. Fu, Z.-Y. Wang, Y. Tang, and M. Udvardi. 2014. PvNAC1 and PvNAC2 Are Associated with Leaf Senescence and Nitrogen Use Efficiency in Switchgrass, BioEnergy Research 8(2), 868-880. BESC
201410.1016/j.cois.2014.06.004Yang, L. H., and C. Gratton. 2014. Insects as drivers of ecosystem processes, Current Opinion in Insect Science 2, 26-32. GLBRC
201410.3389/fmicb.2014.00246Yang, S., C. Pan, G. B. Hurst, L. Dice, B. H. Davison, and S. D. Brown. 2014. Elucidation of Zymomonas mobilis physiology and stress responses by quantitative proteomics and transcriptomics, Front Microbiol 5, 246. BESC
201410.1186/s13068-014-0140-8Yang, S., M. A. Franden, S. D. Brown, Y. C. Chou, P. T. Pienkos, and M. Zhang. 2014. Insights into acetate toxicity in Zymomonas mobilis 8b using different substrates, Biotechnol Biofuels 7(1), 140. BESC
201410.1371/journal.pone.0109885Ye, Z., Y. Zheng, B. Li, M. S. Borrusch, R. Storms, and J. D. Walton. 2014. Enhancement of synthetic Trichoderma-based enzyme mixtures for biomass conversion with an alternative family 5 glycosyl hydrolase from Sporotrichum thermophile, PLoS One 9(10), e109885. GLBRC
201410.1186/1754-6834-7-75Yee, K. L., M. Rodriguez, Jr., O. A. Thompson, C. Fu, Z. Y. Wang, B. H. Davison, and J. R. Mielenz. 2014. Consolidated bioprocessing of transgenic switchgrass by an engineered and evolved Clostridium thermocellum strain, Biotechnol Biofuels 7, 75. BESC
201410.1128/AEM.02111-14Yelle, D. J., A. N. Kapich, C. J. Houtman, F. Lu, V. I. Timokhin, R. C. Fort, Jr., J. Ralph, and K. E. Hammel. 2014. A highly diastereoselective oxidant contributes to Ligninolysis by the white rot basidiomycete Ceriporiopsis subvermispora, Appl Environ Microbiol 80(24), 7536-7544. GLBRC
201410.1080/07352689.2014.870417Yin, H., C. J. Chen, J. Yang, D. J. Weston, J.-G. Chen, W. Muchero, N. Ye, T. J. Tschaplinski, S. D. Wullschleger, Z.-M. Cheng, G. A. Tuskan, and X. Yang. 2014. Functional Genomics of Drought Tolerance in Bioenergy Crops, Critical Reviews in Plant Sciences 33(2-3), 205-224. BESC
201410.1007/978-1-62703-764-8_13You, C., and Y. H. Zhang. 2014. Simple cloning and DNA assembly in Escherichia coli by prolonged overlap extension PCR, Methods Mol Biol 1116, 183-192. BESC
201410.1186/s13068-014-0142-6Young, J., D. Chung, Y. J. Bomble, M. E. Himmel, and J. Westpheling. 2014. Deletion of Caldicellulosiruptor bescii CelA reveals its crucial role in the deconstruction of lignocellulosic biomass, Biotechnol Biofuels 7(1), 142. BESC
201410.4155/bfs.11.135Yuan, J. S., X. Wang, and C. N. Stewart. 2014. Biomass feedstock: diversity as a solution, Biofuels 2(5), 491-493. BESC
201410.4155/bfs.11.130Yuan, J. S., Y. Qu, S. Li, and C. N. Stewart. 2014. US-China collaborative biofuel research: towards a global solution for petroleum replacement, Biofuels 2(5), 487-489. BESC
201410.1038/ja.2013.110Yuzawa, S., C. H. Eng, L. Katz, and J. D. Keasling. 2014. Enzyme analysis of the polyketide synthase leads to the discovery of a novel analog of the antibiotic alpha-lipomycin, J Antibiot (Tokyo) 67(2), 199-201. JBEI
201410.1039/c4an01300jZaharov, V. V., R. H. Farahi, P. J. Snyder, B. H. Davison, and A. Passian. 2014. Karhunen-Loeve treatment to remove noise and facilitate data analysis in sensing, spectroscopy and other applications, Analyst 139(22), 5927-5935. BESC
201410.1016/j.copbio.2013.09.008Zeng, Y., S. Zhao, S. Yang, and S. Y. Ding. 2014. Lignin plays a negative role in the biochemical process for producing lignocellulosic biofuels, Curr Opin Biotechnol 27, 38-45. BESC
201410.1016/j.scitotenv.2014.01.099Zhang, X., R. Sahajpal, D. H. Manowitz, K. Zhao, S. D. Leduc, M. Xu, W. Xiong, A. Zhang, R. C. Izaurralde, A. M. Thomson, T. O. West, and W. M. Post. 2014. Multi-scale geospatial agroecosystem modeling: a case study on the influence of soil data resolution on carbon budget estimates, Sci Total Environ 479-480, 138-150. GLBRC
201410.1146/annurev-phyto-082712-102237Zhao, Q., and R. A. Dixon. 2014. Altering the cell wall and its impact on plant disease: from forage to bioenergy, Annu Rev Phytopathol 52, 69-91. BESC
201410.1371/journal.pone.0098844Zhou, C., F. Mao, Y. Yin, J. Huang, J. P. Gogarten, and Y. Xu. 2014. AST: an automated sequence-sampling method for improving the taxonomic diversity of gene phylogenetic trees, PLoS One 9(6), e98844. BESC
201410.1105/tpc.114.123885Zhou, C., L. Han, G. Li, M. Chai, C. Fu, X. Cheng, J. Wen, Y. Tang, and Z. Y. Wang. 2014. STM/BP-Like KNOXI Is Uncoupled from ARP in the Regulation of Compound Leaf Development in Medicago truncatula, Plant Cell 26(4), 1464-1479. BESC
201410.1007/s12155-014-9486-9.Zhou, C., Q. Ma, X. Mao, B. Liu, Y. Yin, and Y. Xu. 2014. New Insights into Clostridia Through Comparative Analyses of Their 40 Genomes, BioEnergy Research 7(4), 1481-1492. BESC
201410.1111/jipb.12290Zuo, S., X. Zhou, M. Chen, S. Zhang, B. Schwessinger, D. Ruan, C. Yuan, J. Wang, X. Chen, and P. C. Ronald. 2014. OsSERK1 regulates rice development but not immunity to Xanthomonas oryzae pv. oryzae or Magnaporthe oryzae, J Integr Plant Biol 56(12), 1179-1192. JBEI
2014Zurawski, J. V., S. E. Blumer-Schuette, J. M. Conway, and R. M. Kelly. 2014. The Extremely Thermophilic Genus Caldicellulosiruptor: Physiological and Genomic Characteristics for Complex Carbohydrate Conversion to Molecular Hydrogen. In Microbial BioEnergy: Hydrogen Production, 177-195. Eds. D. Zannoni, and R. De Philippis. Springer Netherlands.BESC
201410.4155/bfs.09.5Çetinkol, Ö. P., D. C. Dibble, G. Cheng, M. S. Kent, B. Knierim, M. Auer, D. E. Wemmer, J. G. Pelton, Y. B. Melnichenko, J. Ralph, B. A. Simmons, and B. M. Holmes. 2014. Understanding the impact of ionic liquid pretreatment on eucalyptus, Biofuels 1(1), 33-46. JBEI GLBRC
201310.1074/mcp.M112.022996Abraham, P., R. J. Giannone, R. M. Adams, U. Kalluri, G. A. Tuskan, and R. L. Hettich. 2013. Putting the pieces together: high-performance LC-MS/MS provides network-, pathway-, and protein-level perspectives in Populus, Mol Cell Proteomics 12(1), 106-119. BESC
201310.1021/pr400192rAbraham, P., R. M. Adams, G. A. Tuskan, and R. L. Hettich. 2013. Moving away from the reference genome: evaluating a peptide sequencing tagging approach for single amino acid polymorphism identifications in the genus Populus, J Proteome Res 12(8), 3642-3651. BESC
201310.1128/AEM.00068-13Adams, A. S., F. O. Aylward, S. M. Adams, N. Erbilgin, B. H. Aukema, C. R. Currie, G. Suen, and K. F. Raffa. 2013. Mountain pine beetles colonizing historical and naive host trees are associated with a bacterial community highly enriched in genes contributing to terpene metabolism, Appl Environ Microbiol 79(11), 3468-3475. GLBRC
201310.1016/j.ces.2012.12.023Agnew, D. E., and B. F. Pfleger. 2013. Synthetic biology strategies for synthesizing polyhydroxyalkanoates from unrelated carbon sources, Chemical Engineering Science 103, 58-67. GLBRC
201310.1107/S0907444912050512Alahuhta, M., R. Brunecky, P. Chandrayan, I. Kataeva, M. W. Adams, M. E. Himmel, and V. V. Lunin. 2013. The structure and mode of action of Caldicellulosiruptor bescii family 3 pectate lyase in biomass deconstruction, Acta Crystallogr D Biol Crystallogr 69(Pt 4), 534-539. BESC
201310.1107/S1744309113030005Alahuhta, M., W. S. Adney, M. E. Himmel, and V. V. Lunin. 2013. Structure of Acidothermus cellulolyticus family 74 glycoside hydrolase at 1.82 A resolution, Acta Crystallogr Sect F Struct Biol Cryst Commun 69(Pt 12), 1335-1338. BESC
201310.1007/s10658-013-0317-1Alexander, H. M., K. E. Mauck, A. E. Whitfield, K. A. Garrett, and C. M. Malmstrom. 2013. Plant-virus interactions and the agro-ecological interface, European Journal of Plant Pathology 138(3), 529-547. GLBRC
201310.1039/c2cy20689gAlonso, D. M., J. M. R. Gallo, M. A. Mellmer, S. G. Wettstein, and J. A. Dumesic. 2013. Direct conversion of cellulose to levulinic acid and gamma-valerolactone using solid acid catalysts, Catal. Sci. Technol. 3(4), 927-931. GLBRC
201310.1039/c3gc37065hAlonso, D. M., S. G. Wettstein, and J. A. Dumesic. 2013. Gamma-valerolactone, a sustainable platform molecule derived from lignocellulosic biomass, Green Chemistry 15(3), 584. GLBRC
201310.1039/c2ee23617fAlonso, D. M., S. G. Wettstein, M. A. Mellmer, E. I. Gurbuz, and J. A. Dumesic. 2013. Integrated conversion of hemicellulose and cellulose from lignocellulosic biomass, Energy Environ. Sci. 6(1), 76-80. GLBRC
201310.1016/j.ymben.2013.05.004Alonso-Gutierrez, J., R. Chan, T. S. Batth, P. D. Adams, J. D. Keasling, C. J. Petzold, and T. S. Lee. 2013. Metabolic engineering of Escherichia coli for limonene and perillyl alcohol production, Metab Eng 19, 33-41. JBEI
201310.1017/s1742170512000385Asbjornsen, H., V. Hernandez-Santana, M. Liebman, J. Bayala, J. Chen, M. Helmers, C. K. Ong, and L. A. Schulte. 2013. Targeting perennial vegetation in agricultural landscapes for enhancing ecosystem services, Renewable Agriculture and Food Systems 29(02), 101-125. GLBRC
201310.1146/annurev-arplant-042811-105534Atmodjo, M. A., Z. Hao, and D. Mohnen. 2013. Evolving views of pectin biosynthesis, Annu Rev Plant Biol 64, 747-779. BESC
201310.1128/AEM.00518-13Aylward, F. O., B. R. McDonald, S. M. Adams, A. Valenzuela, R. A. Schmidt, L. A. Goodwin, T. Woyke, C. R. Currie, G. Suen, and M. Poulsen. 2013. Comparison of 26 sphingomonad genomes reveals diverse environmental adaptations and biodegradative capabilities, Appl Environ Microbiol 79(12), 3724-3733. GLBRC
201310.1128/genomeA.00238-12Aylward, F. O., D. M. Tremmel, D. C. Bruce, P. Chain, A. Chen, K. Walston Davenport, C. Detter, C. S. Han, J. Han, M. Huntemann, N. N. Ivanova, N. C. Kyrpides, V. Markowitz, K. Mavrommatis, M. Nolan, I. Pagani, A. Pati, S. Pitluck, S. Deshpande, L. Goodwin, T. Woyke, and C. R. Currie. 2013. Complete Genome of Enterobacteriaceae Bacterium Strain FGI 57, a Strain Associated with Leaf-Cutter Ant Fungus Gardens, Genome Announc 1(1). GLBRC
201310.1128/genomeA.00239-12Aylward, F. O., D. M. Tremmel, G. J. Starrett, D. C. Bruce, P. Chain, A. Chen, K. W. Davenport, C. Detter, C. S. Han, J. Han, M. Huntemann, N. N. Ivanova, N. C. Kyrpides, V. Markowitz, K. Mavrommatis, M. Nolan, I. Pagani, A. Pati, S. Pitluck, H. Teshima, S. Deshpande, L. Goodwin, T. Woyke, and C. R. Currie. 2013. Complete Genome of Serratia sp. Strain FGI 94, a Strain Associated with Leaf-Cutter Ant Fungus Gardens, Genome Announc 1(2), e0023912. GLBRC
201310.1128/AEM.03833-12Aylward, F. O., K. E. Burnum-Johnson, S. G. Tringe, C. Teiling, D. M. Tremmel, J. A. Moeller, J. J. Scott, K. W. Barry, P. D. Piehowski, C. D. Nicora, S. A. Malfatti, M. E. Monroe, S. O. Purvine, L. A. Goodwin, R. D. Smith, G. M. Weinstock, N. M. Gerardo, G. Suen, M. S. Lipton, and C. R. Currie. 2013. Leucoagaricus gongylophorus produces diverse enzymes for the degradation of recalcitrant plant polymers in leaf-cutter ant fungus gardens, Appl Environ Microbiol 79(12), 3770-3778. GLBRC
201310.1007/s12155-013-9348-xAzarpira, A., J. Ralph, and F. Lu. 2013. Catalytic Alkaline Oxidation of Lignin and its Model Compounds: a Pathway to Aromatic Biochemicals, BioEnergy Research 7(1), 78-86. GLBRC
201310.1002/bbb.1436Balan, V., D. Chiaramonti, and S. Kumar. 2013. Review of US and EU initiatives toward development, demonstration, and commercialization of lignocellulosic biofuels, Biofuels, Bioproducts and Biorefining 7(6), 732-759. GLBRC
201310.2134/jeq2013.05.0171Bandaru, V., R. C. Izaurralde, D. Manowitz, R. Link, X. Zhang, and W. M. Post. 2013. Soil carbon change and net energy associated with biofuel production on marginal lands: a regional modeling perspective, J Environ Qual 42(6), 1802-1814. GLBRC
201310.1104/pp.112.208694Bartley, L. E., M. L. Peck, S. R. Kim, B. Ebert, C. Manisseri, D. M. Chiniquy, R. Sykes, L. Gao, C. Rautengarten, M. E. Vega-Sanchez, P. I. Benke, P. E. Canlas, P. Cao, S. Brewer, F. Lin, W. L. Smith, X. Zhang, J. D. Keasling, R. E. Jentoff, S. B. Foster, J. Zhou, A. Ziebell, G. An, H. V. Scheller, and P. C. Ronald. 2013. Overexpression of a BAHD acyltransferase, OsAt10, alters rice cell wall hydroxycinnamic acid content and saccharification, Plant Physiol 161(4), 1615-1633. JBEI BESC
201310.1016/j.pbi.2013.02.015Bates, P. D., S. Stymne, and J. Ohlrogge. 2013. Biochemical pathways in seed oil synthesis, Curr Opin Plant Biol 16(3), 358-364. GLBRC
201310.1534/genetics.112.147710Beissinger, T. M., C. N. Hirsch, R. S. Sekhon, J. M. Foerster, J. M. Johnson, G. Muttoni, B. Vaillancourt, C. R. Buell, S. M. Kaeppler, and N. de Leon. 2013. Marker density and read depth for genotyping populations using genotyping-by-sequencing, Genetics 193(4), 1073-1081. GLBRC
201310.4236/aim.2013.31007Bhandiwad, A., A. Guseva, and L. Lynd. 2013. Metabolic Engineering of Thermoanaerobacterium thermosaccharolyticum for Increased n-Butanol Production, Advances in Microbiology 03(01), 46-51. BESC
201310.1186/1475-2859-12-107Bi, C., P. Su, J. Muller, Y. C. Yeh, S. R. Chhabra, H. R. Beller, S. W. Singer, and N. J. Hillson. 2013. Development of a broad-host synthetic biology toolbox for Ralstonia eutropha and its application to engineering hydrocarbon biofuel production, Microb Cell Fact 12, 107. JBEI
201310.1074/jbc.M113.475848Bianchetti, C. M., C. H. Harmann, T. E. Takasuka, G. L. Hura, K. Dyer, and B. G. Fox. 2013. Fusion of dioxygenase and lignin-binding domains in a novel secreted enzyme from cellulolytic Streptomyces sp. SirexAA-E, J Biol Chem 288(25), 18574-18587. GLBRC
201310.1016/j.jmb.2013.05.030Bianchetti, C. M., P. Brumm, R. W. Smith, K. Dyer, G. L. Hura, T. J. Rutkoski, and G. N. Phillips, Jr. 2013. Structure, dynamics, and specificity of endoglucanase D from Clostridium cellulovorans, J Mol Biol 425(22), 4267-4285. GLBRC
201310.1128/JB.02210-12Bokinsky, G., E. E. Baidoo, S. Akella, H. Burd, D. Weaver, J. Alonso-Gutierrez, H. Garcia-Martin, T. S. Lee, and J. D. Keasling. 2013. HipA-triggered growth arrest and beta-lactam tolerance in Escherichia coli are mediated by RelA-dependent ppGpp synthesis, J Bacteriol 195(14), 3173-3182. JBEI
201310.1128/genomeA.00323-13Brown, S. D., D. M. Klingeman, C. M. Johnson, A. Clum, A. Aerts, A. Salamov, A. Sharma, M. Zane, K. Barry, I. V. Grigoriev, B. H. Davison, L. R. Lynd, P. Gilna, H. Hau, D. A. Hogsett, and A. C. Froehlich. 2013. Genome Sequences of Industrially Relevant Saccharomyces cerevisiae Strain M3707, Isolated from a Sample of Distillers Yeast and Four Haploid Derivatives, Genome Announc 1(3). BESC
201310.1126/science.1244273Brunecky, R., M. Alahuhta, Q. Xu, B. S. Donohoe, M. F. Crowley, I. A. Kataeva, S. J. Yang, M. G. Resch, M. W. Adams, V. V. Lunin, M. E. Himmel, and Y. J. Bomble. 2013. Revealing nature's cellulase diversity: the digestion mechanism of Caldicellulosiruptor bescii CelA, Science 342(6165), 1513-1516. BESC
201310.1039/C2SC21403BCaes, B. R., M. J. Palte, and R. T. Raines. 2013. Organocatalytic Conversion of Cellulose into a Platform Chemical, Chem Sci 4(1), 196-199. GLBRC
201310.1002/cssc.201300267Caes, B. R., T. R. Van Oosbree, F. Lu, J. Ralph, C. T. Maravelias, and R. T. Raines. 2013. Simulated moving bed chromatography: separation and recovery of sugars and ionic liquid from biomass hydrolysates, ChemSusChem 6(11), 2083-2089. GLBRC
201310.3389/fpls.2013.00501Carroll, A. W., H. J. Joshi, and J. L. Heazlewood. 2013. Managing the green proteomes for the next decade of plant research, Front Plant Sci 4, 501. JBEI
2013Casler, M. D. 2013. Switchgrass breeding, genetics, and genomics. In Switchgrass, 29-52. Springer-Verlag.GLBRC
201310.1186/1754-6834-6-85Cha, M., D. Chung, J. G. Elkins, A. M. Guss, and J. Westpheling. 2013. Metabolic engineering of Caldicellulosiruptor bescii yields increased hydrogen production from lignocellulosic biomass, Biotechnol Biofuels 6(1), 85. BESC
201310.1007/s10295-013-1345-8Cha, M., H. Wang, D. Chung, J. L. Bennetzen, and J. Westpheling. 2013. Isolation and bioinformatic analysis of a novel transposable element, ISCbe4, from the hyperthermophilic bacterium, Caldicellulosiruptor bescii, J Ind Microbiol Biotechnol 40(12), 1443-1448. BESC
201310.1039/c3cc39155h.Chandrasekaran, A., K. Deng, C. Y. Koh, T. Takasuka, L. F. Bergeman, B. G. Fox, P. D. Adams, and A. K. Singh. 2013. A universal flow cytometry assay for screening carbohydrate-active enzymes using glycan microspheres, Chem Commun (Camb) 49(48), 5441-5443. GLBRC JBEI
201310.1039/c3lc41418cChang, C., J. Sustarich, R. Bharadwaj, A. Chandrasekaran, P. D. Adams, and A. K. Singh. 2013. Droplet-based microfluidic platform for heterogeneous enzymatic assays, Lab on a Chip 13(9), 1817-1822. JBEI
201310.1111/tpj.12012Chen, F., Y. Tobimatsu, L. Jackson, J. Nakashima, J. Ralph, and R. A. Dixon. 2013. Novel seed coat lignins in the Cactaceae: structure, distribution and implications for the evolution of lignin diversity, Plant J 73(2), 201-211. GLBRC BESC
201310.1016/j.ymben.2013.04.006Chen, X., A. P. Alonso, and Y. Shachar-Hill. 2013. Dynamic metabolic flux analysis of plant cell wall synthesis, Metab Eng 18, 78-85. GLBRC
201310.1093/mp/sss135Chen, X., M. E. Vega-Sanchez, Y. Verhertbruggen, D. Chiniquy, P. E. Canlas, A. Fagerstrom, L. Prak, U. Christensen, A. Oikawa, M. Chern, S. Zuo, F. Lin, M. Auer, W. G. Willats, L. Bartley, J. Harholt, H. V. Scheller, and P. C. Ronald. 2013. Inactivation of OsIRX10 leads to decreased xylan content in rice culm cell walls and improved biomass saccharification, Mol Plant 6(2), 570-573. JBEI
201310.1371/journal.pone.0079725Chen, Z., J. H. Pereira, H. Liu, H. M. Tran, N. S. Hsu, D. Dibble, S. Singh, P. D. Adams, R. Sapra, M. Z. Hadi, B. A. Simmons, and K. L. Sale. 2013. Improved activity of a thermophilic cellulase, Cel5A, from Thermotoga maritima on ionic liquid pretreated switchgrass, PLoS One 8(11), e79725. JBEI
201310.3389/fmicb.2013.00365Cheng, X., J. Hiras, K. Deng, B. Bowen, B. A. Simmons, P. D. Adams, S. W. Singer, and T. R. Northen. 2013. High throughput nanostructure-initiator mass spectrometry screening of microbial growth conditions for maximal beta-glucosidase production, Front Microbiol 4, 365. JBEI
201310.3389/fpls.2013.00083Chiniquy, D., P. Varanasi, T. Oh, J. Harholt, J. Katnelson, S. Singh, M. Auer, B. Simmons, P. D. Adams, H. V. Scheller, and P. C. Ronald. 2013. Three Novel Rice Genes Closely Related to the Arabidopsis IRX9, IRX9L, and IRX14 Genes and Their Roles in Xylan Biosynthesis, Front Plant Sci 4, 83. JBEI
201310.1093/nar/gks1202Chivian, D., P. S. Dehal, K. Keller, and A. P. Arkin. 2013. MetaMicrobesOnline: phylogenomic analysis of microbial communities, Nucleic Acids Res 41(Database issue), D648-654. JBEI
201310.1038/ncomms3595Chou, H. H., and J. D. Keasling. 2013. Programming adaptive control to evolve increased metabolite production, Nat Commun 4, 2595. JBEI
201310.1371/journal.pone.0053954Christopherson, M. R., G. Suen, S. Bramhacharya, K. A. Jewell, F. O. Aylward, D. Mead, and P. J. Brumm. 2013. The genome sequences of Cellulomonas fimi and Cellvibrio gilvus reveal the cellulolytic strategies of two facultative anaerobes, transfer of Cellvibrio gilvus to the genus Cellulomonas, and proposal of Cellulomonas gilvus sp. nov, PLoS One 8(1), e53954. GLBRC
2013Chundawat, S. P. S., B. Bals, T. Campbell, L. Sousa, D. Gao, M. Jin, P. Eranki, R. Garlock, F. Teymour, V. Balan, and B. E. Dale. 2013. Primer on ammonia fiber expansion pretreatment. In Aqueous Pretreatment of Plant Biomass for Biological and Chemical Conversion to Fuels and Chemicals, 169-200. Ed. C. E. Wyman.GLBRC
201310.1371/journal.pcbi.1003246Chung, D., D. Park, K. Myers, J. Grass, P. Kiley, R. Landick, and S. Keles. 2013. dPeak: high resolution identification of transcription factor binding sites from PET and SET ChIP-Seq data, PLoS Comput Biol 9(10), e1003246. GLBRC
201310.1007/s10295-013-1244-zChung, D., J. Farkas, and J. Westpheling. 2013. Detection of a novel active transposable element in Caldicellulosiruptor hydrothermalis and a new search for elements in this genus, J Ind Microbiol Biotechnol 40(5), 517-521. BESC
201310.1186/1754-6834-6-82Chung, D., J. Farkas, and J. Westpheling. 2013. Overcoming restriction as a barrier to DNA transformation in Caldicellulosiruptor species results in efficient marker replacement, Biotechnol Biofuels 6(1), 82. BESC
201310.1371/journal.pone.0062881Chung, D., M. Cha, J. Farkas, and J. Westpheling. 2013. Construction of a stable replicating shuttle vector for Caldicellulosiruptor species: use for extending genetic methodologies to other members of this genus, PLoS One 8(5), e62881. BESC
201310.1002/biot.201200316Cotten, C., and J. L. Reed. 2013. Constraint-based strain design using continuous modifications (CosMos) of flux bounds finds new strategies for metabolic engineering, Biotechnol J 8(5), 595-604. GLBRC
201310.1186/1471-2105-14-32Cotten, C., and J. L. Reed. 2013. Mechanistic analysis of multi-omics datasets to generate kinetic parameters for constraint-based metabolic models, BMC Bioinformatics 14, 32. GLBRC
2013 10.1186/1754-6834-6-52Cruz, A. G., C. Scullin, C. Mu, G. Cheng, V. Stavila, P. Varanasi, D. Xu, J. Mentel, Y. D. Chuang, B. A. Simmons, and S. Singh. 2013. Impact of high biomass loading on ionic liquid pretreatment, Biotechnol Biofuels 6(1), 52. JBEI
201310.1039/c3ra44847aCulbertson, A., M. Jin, L. da Costa Sousa, B. E. Dale, and V. Balan. 2013. In-house cellulase production from AFEX™ pretreated corn stover using Trichoderma reesei RUT C-30, RSC Advances 3(48), 25960. GLBRC
201310.1186/1754-6834-6-32Currie, D. H., C. D. Herring, A. M. Guss, D. G. Olson, D. A. Hogsett, and L. R. Lynd. 2013. Functional heterologous expression of an engineered full length CipA from Clostridium thermocellum in Thermoanaerobacterium saccharolyticum, Biotechnol Biofuels 6(1), 32. BESC
2013 10.1371/journal.pone.0068465D'Haeseleer, P., J. M. Gladden, M. Allgaier, P. S. Chain, S. G. Tringe, S. A. Malfatti, J. T. Aldrich, C. D. Nicora, E. W. Robinson, L. Pasa-Tolic, P. Hugenholtz, B. A. Simmons, and S. W. Singer. 2013. Proteogenomic analysis of a thermophilic bacterial consortium adapted to deconstruct switchgrass, PLoS One 8(7), e68465. JBEI
201310.1038/nbt.2689Dahl, R. H., F. Zhang, J. Alonso-Gutierrez, E. Baidoo, T. S. Batth, A. M. Redding-Johanson, C. J. Petzold, A. Mukhopadhyay, T. S. Lee, P. D. Adams, and J. D. Keasling. 2013. Engineering dynamic pathway regulation using stress-response promoters, Nat Biotechnol 31(11), 1039-1046. JBEI
2013Davison, B. H., J. Parks, M. F. Davis, B. Donohoe, P. Sannigrahi, and A. J. Ragauskas. 2013. Fundamentals of biomass pretreatment by fractionation. In Aqueous Pretreatment of Plant Biomass for Biological and Chemical Conversion to Fuels and Chemicals, 23-36. Ed. C. E. Wyman.BESC
2013de Leon, N., S. M. Kaeppler, and J. G. Lauer. 2013. Breeding maize for lignocellulosic biofuel production. In Bioenergy Feedstocks: Breeding and Genetics, 151-172. Wiley Blackwell.GLBRC
201310.7554/eLife.00800De Michele, R., C. Ast, D. Loque, C. H. Ho, S. Andrade, V. Lanquar, G. Grossmann, S. Gehne, M. U. Kumke, and W. B. Frommer. 2013. Fluorescent sensors reporting the activity of ammonium transceptors in live cells, Elife 2, e00800. JBEI
201310.1007/s00216-013-6888-zde Rond, T., P. Peralta-Yahya, X. Cheng, T. R. Northen, and J. D. Keasling. 2013. Versatile synthesis of probes for high-throughput enzyme activity screening, Anal Bioanal Chem 405(14), 4969-4973. JBEI
201310.1093/jpe/rtt057Deal, M. W., J. Xu, R. John, T. Zenone, J. Chen, H. Chu, P. Jasrotia, K. Kahmark, J. Bossenbroek, and C. Mayer. 2013. Net primary production in three bioenergy crop systems following land conversion, Journal of Plant Ecology 7(5), 451-460. GLBRC
201310.1016/j.soilbio.2013.06.010DeAngelis, K. M., D. Chivian, J. L. Fortney, A. P. Arkin, B. Simmons, T. C. Hazen, and W. L. Silver. 2013. Changes in microbial dynamics during long-term decomposition in tropical forests, Soil Biology and Biochemistry 66, 60-68. JBEI
201310.3389/fmicb.2013.00280Deangelis, K. M., D. Sharma, R. Varney, B. Simmons, N. G. Isern, L. M. Markilllie, C. Nicora, A. D. Norbeck, R. C. Taylor, J. T. Aldrich, and E. W. Robinson. 2013. Evidence supporting dissimilatory and assimilatory lignin degradation in Enterobacter lignolyticus SCF1, Front Microbiol 4, 280. JBEI
201310.4056/sigs.3377516Deangelis, K. M., P. D'Haeseleer, D. Chivian, B. Simmons, A. P. Arkin, K. Mavromatis, S. Malfatti, S. Tringe, and T. C. Hazen. 2013. Metagenomes of tropical soil-derived anaerobic switchgrass-adapted consortia with and without iron, Stand Genomic Sci 7(3), 382-398. JBEI
201310.1186/1471-2180-13-130Decanio, M. S., R. Landick, and R. J. Haft. 2013. The non-pathogenic Escherichia coli strain W secretes SslE via the virulence-associated type II secretion system beta, BMC Microbiol 13, 130. GLBRC
201310.1039/c3ee23801fDeMartini, J. D., S. Pattathil, J. S. Miller, H. Li, M. G. Hahn, and C. E. Wyman. 2013. Investigating plant cell wall components that affect biomass recalcitrance in poplar and switchgrass, Energy & Environmental Science 6(3), 898. BESC
2013Demartini, J., and C. E. Wyman. 2013. High-throughput pretreatment and hydrolysis systems for screening biomass species in aqueous pretreatment of plant biomass. In Aqueous Pretreatment of Plant Biomass for Biological and Chemical Conversion to Fuels and Chemicals, 471-486. Ed. C. E. Wyman.BESC
201310.1016/j.ymben.2012.11.006Deng, Y., D. G. Olson, J. Zhou, C. D. Herring, A. Joe Shaw, and L. R. Lynd. 2013. Redirecting carbon flux through exogenous pyruvate kinase to achieve high ethanol yields in Clostridium thermocellum, Metab Eng 15, 151-158. BESC
2013Dietrich, J. A., D. L. Shis, A. Alikhani, and J. D. Keasling. 2013. Transcription Factor-Based Screens and Synthetic Selections for Microbial Small-Molecule Biosynthesis. In ACS Synthetic Biology, 47-58.JBEI
2013Ding, S. Y. 2013. Overview of Lignocellulose: Structure and Chemistry. In Biological Conversion of Biomass for Fuels and Chemicals: Explorations from Natural Utilization Systems, 14-25. Eds. J. Sun, S.-Y. Ding, and J. D. Peterson.BESC
201310.1007/s10570-013-0147-5Ding, S.-Y., S. Zhao, and Y. Zeng. 2013. Size, shape, and arrangement of native cellulose fibrils in maize cell walls, Cellulose 21(2), 863-871. BESC
201310.1186/1754-6834-6-175Dumitrache, A., G. M. Wolfaardt, D. G. Allen, S. N. Liss, and L. R. Lynd. 2013. Tracking the cellulolytic activity of Clostridium thermocellum biofilms, Biotechnol Biofuels 6(1), 175. BESC
201310.2136/sssaj2013.01.0023Duran, B. E. L., and C. J. Kucharik. 2013. Comparison of Two Chamber Methods for Measuring Soil Trace-Gas Fluxes in Bioenergy Cropping Systems, Soil Science Society of America Journal 77(5), 1601. GLBRC
201310.1021/es303829wEgbendewe-Mondzozo, A., S. M. Swinton, B. D. Bals, and B. E. Dale. 2013. Can dispersed biomass processing protect the environment and cover the bottom line for biofuel?, Environ Sci Technol 47(3), 1695-1703. GLBRC
201310.1016/j.enpol.2013.02.021Egbendewe-Mondzozo, A., S. M. Swinton, R. C. Izaurralde, D. H. Manowitz, and X. Zhang. 2013. Maintaining environmental quality while expanding biomass production: Sub-regional U.S. policy simulations, Energy Policy 57, 518-531. GLBRC
201310.1111/1462-2920.12159Eichorst, S. A., P. Varanasi, V. Stavila, M. Zemla, M. Auer, S. Singh, B. A. Simmons, and S. W. Singer. 2013. Community dynamics of cellulose-adapted thermophilic bacterial consortia, Environ Microbiol 15(9), 2573-2587. JBEI
201310.1128/genomeA.00162-13Elkins, J. G., S. D. Hamilton-Brehm, S. Lucas, J. Han, A. Lapidus, J. F. Cheng, L. A. Goodwin, S. Pitluck, L. Peters, N. Mikhailova, K. W. Davenport, J. C. Detter, C. S. Han, R. Tapia, M. L. Land, L. Hauser, N. C. Kyrpides, N. N. Ivanova, I. Pagani, D. Bruce, T. Woyke, and R. W. Cottingham. 2013. Complete Genome Sequence of the Hyperthermophilic Sulfate-Reducing Bacterium Thermodesulfobacterium geofontis OPF15T, Genome Announc 1(2), e0016213. BESC
201310.1002/bbb.1426Eranki, P. L., D. H. Manowitz, B. D. Bals, R. C. Izaurralde, S. Kim, and B. E. Dale. 2013. The watershed-scale optimized and rearranged landscape design (WORLD) model and local biomass processing depots for sustainable biofuel production: Integrated life cycle assessments, Biofuels, Bioproducts and Biorefining 7(5), 537-550. GLBRC
201310.1186/1475-2859-12-62Eudes, A., D. Juminaga, E. E. Baidoo, F. W. Collins, J. D. Keasling, and D. Loque. 2013. Production of hydroxycinnamoyl anthranilates from glucose in Escherichia coli, Microb Cell Fact 12, 62. JBEI
201310.1007/s10295-012-1202-1Farkas, J., D. Chung, M. Cha, J. Copeland, P. Grayeski, and J. Westpheling. 2013. Improved growth media and culture techniques for genetic analysis and assessment of biomass utilization by Caldicellulosiruptor bescii, J Ind Microbiol Biotechnol 40(1), 41-49. BESC
201310.1128/genomeA.01039-13Fineran, P. C., M. C. Iglesias Cans, J. P. Ramsay, N. M. Wilf, D. Cossyleon, M. B. McNeil, N. R. Williamson, R. E. Monson, S. A. Becher, J. A. Stanton, K. Brugger, S. D. Brown, and G. P. Salmond. 2013. Draft Genome Sequence of Serratia sp. Strain ATCC 39006, a Model Bacterium for Analysis of the Biosynthesis and Regulation of Prodigiosin, a Carbapenem, and Gas Vesicles, Genome Announc 1(6). BESC
201310.3389/fmicb.2013.00291Fish, J. A., B. Chai, Q. Wang, Y. Sun, C. T. Brown, J. M. Tiedje, and J. R. Cole. 2013. FunGene: the functional gene pipeline and repository, Front Microbiol 4, 291. GLBRC
201310.1002/biot.201200233Flowers, D., R. A. Thompson, D. Birdwell, T. Wang, and C. T. Trinh. 2013. SMET: systematic multiple enzyme targeting - a method to rationally design optimal strains for target chemical overproduction, Biotechnol J 8(5), 605-618. BESC
201310.1016/j.carbon.2012.09.006Foston, M., G. A. Nunnery, X. Meng, Q. Sun, F. S. Baker, and A. Ragauskas. 2013. NMR a critical tool to study the production of carbon fiber from lignin, Carbon 52, 65-73. BESC
2013Fried, D. B., S. Morais, Q. Xu, S. Y. Ding, J. O. Baker, Y. J. Bomble, M. E. Himmel, and E. A. Bayer. 2013. Self-assembly and application of cellulosomal components. In Bionanotechnology: Biological Self-assembly and its Applications. Ed. B. H. A. Rehm. Caister Academic Press.BESC
201310.1128/JB.00634-13Gall, D. L., J. Ralph, T. J. Donohue, and D. R. Noguera. 2013. Benzoyl coenzyme a pathway-mediated metabolism of meta-hydroxy-aromatic acids in Rhodopseudomonas palustris, J Bacteriol 195(18), 4112-4120. GLBRC
201310.1007/s11244-013-0113-3Gallo, J. M. R., D. M. Alonso, M. A. Mellmer, J. H. Yeap, H. C. Wong, and J. A. Dumesic. 2013. Production of Furfural from Lignocellulosic Biomass Using Beta Zeolite and Biomass-Derived Solvent, Topics in Catalysis 56(18-20), 1775-1781. GLBRC
201310.1073/pnas.1213426110Gao, D., S. P. Chundawat, A. Sethi, V. Balan, S. Gnanakaran, and B. E. Dale. 2013. Increased enzyme binding to substrate is not necessary for more efficient cellulose hydrolysis, Proc Natl Acad Sci U S A 110(27), 10922-10927. GLBRC
201310.2134/agronj2012.0420Gao, J., K. D. Thelen, and X. Hao. 2013. Life Cycle Analysis of Corn Harvest Strategies for Bioethanol Production, Agronomy Journal 105(3), 705. GLBRC
201310.1002/bit.24751Gao, X., R. Kumar, J. D. DeMartini, H. Li, and C. E. Wyman. 2013. Application of high throughput pretreatment and co-hydrolysis system to thermochemical pretreatment. Part 1: dilute acid, Biotechnol Bioeng 110(3), 754-762. BESC
201310.1038/nature11811Gelfand, I., R. Sahajpal, X. Zhang, R. C. Izaurralde, K. L. Gross, and G. P. Robertson. 2013. Sustainable bioenergy production from marginal lands in the US Midwest, Nature 493(7433), 514-517. GLBRC
201310.1111/tpj.12281Geshi, N., J. N. Johansen, A. Dilokpimol, A. Rolland, K. Belcram, S. Verger, T. Kotake, Y. Tsumuraya, S. Kaneko, T. Tryfona, P. Dupree, H. V. Scheller, H. Hofte, and G. Mouille. 2013. A galactosyltransferase acting on arabinogalactan protein glycans is essential for embryo development in Arabidopsis, Plant J 76(1), 128-137. JBEI
201310.1016/j.cplett.2013.07.026GhattyVenkataKrishna, P. K., and B. Mostofian. 2013. Dynamics of water in the amphiphilic pore of amyloid ß fibrils, Chemical Physics Letters 582, 1-5. BESC
201310.1016/j.febslet.2013.06.050GhattyVenkataKrishna, P. K., E. C. Uberbacher, and X. Cheng. 2013. Effect of the amyloid beta hairpin's structure on the handedness of helices formed by its aggregates, FEBS Lett 587(16), 2649-2655. BESC
201310.1016/j.bpj.2012.12.052Ghattyvenkatakrishna, P. K., E. M. Alekozai, G. T. Beckham, R. Schulz, M. F. Crowley, E. C. Uberbacher, and X. Cheng. 2013. Initial recognition of a cellodextrin chain in the cellulose-binding tunnel may affect cellobiohydrolase directional specificity, Biophys J 104(4), 904-912. BESC
201310.4161/psb.27141Gidda, S. K., S. Watt, J. Collins-Silva, A. Kilaru, V. Arondel, O. Yurchenko, P. J. Horn, C. N. James, D. Shintani, J. B. Ohlrogge, K. D. Chapman, R. T. Mullen, and J. M. Dyer. 2013. Lipid droplet-associated proteins (LDAPs) are involved in the compartmentalization of lipophilic compounds in plant cells, Plant Signal Behav 8(11), e27141. GLBRC
201310.1093/mp/sst029Gille, S., V. Sharma, E. E. Baidoo, J. D. Keasling, H. V. Scheller, and M. Pauly. 2013. Arabinosylation of a Yariv-precipitable cell wall polymer impacts plant growth as exemplified by the Arabidopsis glycosyltransferase mutant ray1, Mol Plant 6(4), 1369-1372. JBEI
2013Gilna, P. 2013. Cellulosic biofuels, Science Omega Review Europe 2. DOI.BESC
201310.1002/bit.24741Gjersing, E., R. M. Happs, R. W. Sykes, C. Doeppke, and M. F. Davis. 2013. Rapid determination of sugar content in biomass hydrolysates using nuclear magnetic resonance spectroscopy, Biotechnol Bioeng 110(3), 721-728. BESC
201310.1039/c3np20099jGongora-Castillo, E., and C. R. Buell. 2013. Bioinformatics challenges in de novo transcriptome assembly using short read sequences in the absence of a reference genome sequence, Nat Prod Rep 30(4), 490-500. GLBRC
201310.1039/c3gc37086kGroff, D., A. George, N. Sun, N. Sathitsuksanoh, G. Bokinsky, B. A. Simmons, B. M. Holmes, and J. D. Keasling. 2013. Acid enhanced ionic liquid pretreatment of biomass, Green Chemistry 15(5), 1264. JBEI
201310.1002/anie.201207334Gurbuz, E. I., J. M. Gallo, D. M. Alonso, S. G. Wettstein, W. Y. Lim, and J. A. Dumesic. 2013. Conversion of hemicellulose into furfural using solid acid catalysts in gamma-valerolactone, Angew Chem Int Ed Engl 52(4), 1270-1274. GLBRC
201310.1007/s00792-013-0512-1Hamilton-Brehm, S. D., R. A. Gibson, S. J. Green, E. C. Hopmans, S. Schouten, M. T. van der Meer, J. P. Shields, J. S. Damste, and J. G. Elkins. 2013. Thermodesulfobacterium geofontis sp. nov., a hyperthermophilic, sulfate-reducing bacterium isolated from Obsidian Pool, Yellowstone National Park, Extremophiles 17(2), 251-263. BESC
201310.1007/s12155-012-9292-1Hardin, C. F., C. Fu, H. Hisano, X. Xiao, H. Shen, C. N. Stewart, W. Parrott, R. A. Dixon, and Z.-Y. Wang. 2013. Standardization of Switchgrass Sample Collection for Cell Wall and Biomass Trait Analysis, BioEnergy Research 6(2), 755-762. BESC
201310.1186/1754-6834-6-40Harun, S., V. Balan, M. S. Takriff, O. Hassan, J. Jahim, and B. E. Dale. 2013. Performance of AFEX pretreated rice straw as source of fermentable sugars: the influence of particle size, Biotechnol Biofuels 6, 40. GLBRC
201310.1007/s10570-013-0067-4He, J., S. V. Pingali, S. P. S. Chundawat, A. Pack, A. D. Jones, P. Langan, B. H. Davison, V. Urban, B. Evans, and H. O’Neill. 2013. Controlled incorporation of deuterium into bacterial cellulose, Cellulose 21(2), 927-936. GLBRC
201310.1146/annurev-arplant-050312-120237Hirsch, C. N., and C. R. Buell. 2013. Tapping the promise of genomics in species with complex, nonmodel genomes, Annu Rev Plant Biol 64, 89-110. GLBRC
201310.1007/s12155-013-9335-2Hoagland, K. C., M. D. Ruark, M. J. Renz, and R. D. Jackson. 2013. Agricultural Management of Switchgrass for Fuel Quality and Thermal Energy Yield on Highly Erodible Land in the Driftless Area of Southwest Wisconsin, BioEnergy Research 6(3), 1012-1021. GLBRC
201310.1002/bit.24914Holwerda, E. K., and L. R. Lynd. 2013. Testing alternative kinetic models for utilization of crystalline cellulose (Avicel) by batch cultures of Clostridium thermocellum, Biotechnol Bioeng 110(9), 2389-2394. BESC
201310.1002/bit.24915Holwerda, E. K., L. D. Ellis, and L. R. Lynd. 2013. Development and evaluation of methods to infer biosynthesis and substrate consumption in cultures of cellulolytic microorganisms, Biotechnol Bioeng 110(9), 2380-2388. BESC
201310.1104/pp.113.222455Horn, P. J., C. N. James, S. K. Gidda, A. Kilaru, J. M. Dyer, R. T. Mullen, J. B. Ohlrogge, and K. D. Chapman. 2013. Identification of a new class of lipid droplet-associated proteins in plants, Plant Physiol 162(4), 1926-1936. GLBRC
201310.1186/1752-0509-7-89Imam, S., D. R. Noguera, and T. J. Donohue. 2013. Global insights into energetic and metabolic networks in Rhodobacter sphaeroides, BMC Syst Biol 7, 89. GLBRC
2013Iwata, M., F. Shiraishi, and E. O. Voit. 2013. Coarse but efficient identification of metabolic pathway systems, International Journal of Systems Biology 4(1), 57-72. DOI.BESC
201310.1186/1754-6834-6-58Jabbour, D., M. S. Borrusch, G. Banerjee, and J. D. Walton. 2013. Enhancement of fermentable sugar yields by alpha-xylosidase supplementation of commercial cellulases, Biotechnol Biofuels 6(1), 58. GLBRC
201310.3389/fpls.2013.00183Jensen, J. K., N. Johnson, and C. G. Wilkerson. 2013. Discovery of diversity in xylan biosynthetic genes by transcriptional profiling of a heteroxylan containing mucilaginous tissue, Front Plant Sci 4, 183. GLBRC
201310.1002/bit.24797Jin, M., C. Gunawan, V. Balan, X. Yu, and B. E. Dale. 2013. Continuous SSCF of AFEX pretreated corn stover for enhanced ethanol productivity using commercial enzymes and Saccharomyces cerevisiae 424A (LNH-ST), Biotechnol Bioeng 110(5), 1302-1311. GLBRC
2013 10.1186/1754-6834-6-108Jin, M., C. Sarks, C. Gunawan, B. D. Bice, S. P. Simonett, R. Avanasi Narasimhan, L. B. Willis, B. E. Dale, V. Balan, and T. K. Sato. 2013. Phenotypic selection of a wild Saccharomyces cerevisiae strain for simultaneous saccharification and co-fermentation of AFEX pretreated corn stover, Biotechnol Biofuels 6, 108. GLBRC
201310.1016/j.biortech.2013.08.018Jin, M., W. Bothfeld, S. Austin, T. K. Sato, A. La Reau, H. Li, M. Foston, C. Gunawan, R. D. LeDuc, J. F. Quensen, M. McGee, N. Uppugundla, A. Higbee, R. Ranatunga, C. W. Donald, G. Bone, A. J. Ragauskas, J. M. Tiedje, D. R. Noguera, B. E. Dale, Y. Zhang, and V. Balan. 2013. Effect of storage conditions on the stability and fermentability of enzymatic lignocellulosic hydrolysate, Bioresour Technol 147, 212-220. GLBRC
2013, N., L. A. Schulte, C. Williams, d. Mulla, D. Pitt, C. S. Slotterback, R. Jackson, D. Landis, B. Dale, D. Becker, M. Rickenbach, M. Helmers, and B. Bringi. 2013. Landlabs: An Integrated Approach to Creating Agricultural Enterprises That Meet the Triple Botom Line, Journal of Higher Education Outreach and Engagement 26, 175-200. DOI, GLBRC
201310.1371/journal.pone.0084664Joshua, C. J., L. D. Perez, and J. D. Keasling. 2013. Functional characterization of the origin of replication of pRN1 from Sulfolobus islandicus REN1H1, PLoS One 8(12), e84664. JBEI
201310.5539/jas.v5n5p129Kang, S., W. M. Post, J. A. Nichols, D. Wang, T. O. West, V. Bandaru, and R. C. Izaurralde. 2013. Marginal Lands: Concept, Assessment and Management, Journal of Agricultural Science 5(5). GLBRC
201310.1016/j.landusepol.2012.03.002Kang, S., W. Post, D. Wang, J. Nichols, V. Bandaru, and T. West. 2013. Hierarchical marginal land assessment for land use planning, Land Use Policy 30(1), 106-113. GLBRC
201310.1039/c3ee40932eKataeva, I., M. B. Foston, S.-J. Yang, S. Pattathil, A. K. Biswal, F. L. Poole Ii, M. Basen, A. M. Rhaesa, T. P. Thomas, P. Azadi, V. Olman, T. D. Saffold, K. E. Mohler, D. L. Lewis, C. Doeppke, Y. Zeng, T. J. Tschaplinski, W. S. York, M. Davis, D. Mohnen, Y. Xu, A. J. Ragauskas, S.-Y. Ding, R. M. Kelly, M. G. Hahn, and M. W. W. Adams. 2013. Carbohydrate and lignin are simultaneously solubilized from unpretreated switchgrass by microbial action at high temperature, Energy & Environmental Science 6(7), 2186. BESC
201310.1039/c3ee24243aKim, J., S. M. Sen, and C. T. Maravelias. 2013. An optimization-based assessment framework for biomass-to-fuel conversion strategies, Energy & Environmental Science 6(4), 1093. GLBRC
201310.1111/j.1365-313x.2012.05124.xKim, W. C., J. H. Ko, J. Y. Kim, J. Kim, H. J. Bae, and K. H. Han. 2013. MYB46 directly regulates the gene expression of secondary wall-associated cellulose synthases in Arabidopsis, Plant J 73(1), 26-36. GLBRC
201310.1016/j.jplph.2013.04.012Kim, W. C., J. Y. Kim, J. H. Ko, J. Kim, and K. H. Han. 2013. Transcription factor MYB46 is an obligate component of the transcriptional regulatory complex for functional expression of secondary wall-associated cellulose synthases in Arabidopsis thaliana, J Plant Physiol 170(15), 1374-1378. GLBRC
201310.1525/bio.2013.63.2.6King, J. S., R. Ceulemans, J. M. Albaugh, S. Y. Dillen, J.-C. Domec, R. Fichot, M. Fischer, Z. Leggett, E. Sucre, M. Trnka, and T. Zenone. 2013. The Challenge of Lignocellulosic Bioenergy in a Water-Limited World, BioScience 63(2), 102-117. GLBRC
201310.1371/journal.pone.0058387Klassen, J. L., and C. R. Currie. 2013. ORFcor: identifying and accommodating ORF prediction inconsistencies for phylogenetic analysis, PLoS One 8(3), e58387. GLBRC
201310.1002/aic.14245Klein-Marcuschamer, D., and H. W. Blanch. 2013. Survival of the fittest: An economic perspective on the production of novel biofuels, AIChE Journal 59(12), 4454-4460. JBEI
201310.1002/bbb.1404Klein-Marcuschamer, D., C. Turner, M. Allen, P. Gray, R. G. Dietzgen, P. M. Gresshoff, B. Hankamer, K. Heimann, P. T. Scott, E. Stephens, R. Speight, and L. K. Nielsen. 2013. Technoeconomic analysis of renewable aviation fuel from microalgae,Pongamia pinnata, and sugarcane, Biofuels, Bioproducts and Biorefining 7(4), 416-428. JBEI
201310.1002/bit.24967Klein-Marcuschamer, D., Y. Chisti, J. R. Benemann, and D. Lewis. 2013. A matter of detail: assessing the true potential of microalgal biofuels, Biotechnol Bioeng 110(9), 2317-2322. JBEI
201310.1111/tpj.12353Knoch, E., A. Dilokpimol, T. Tryfona, C. P. Poulsen, G. Xiong, J. Harholt, B. L. Petersen, P. Ulvskov, M. Z. Hadi, T. Kotake, Y. Tsumuraya, M. Pauly, P. Dupree, and N. Geshi. 2013. A beta-glucuronosyltransferase from Arabidopsis thaliana involved in biosynthesis of type II arabinogalactan has a role in cell elongation during seedling growth, Plant J 76(6), 1016-1029. JBEI
201310.1021/bi400358vKostylev, M., and D. Wilson. 2013. Two-parameter kinetic model based on a time-dependent activity coefficient accurately describes enzymatic cellulose digestion, Biochemistry 52(33), 5656-5664. BESC
201310.1002/fes3.27Kraatz, S., J. C. Sinistore, and D. J. Reinemann. 2013. Energy intensity and global warming potential of corn grain ethanol production in Wisconsin (USA), Food and Energy Security 2(3), 207-219. GLBRC
201310.1371/journal.pone.0068847Kucharik, C. J., A. Vanloocke, J. D. Lenters, and M. M. Motew. 2013. Miscanthus establishment and overwintering in the Midwest USA: a regional modeling study of crop residue management on critical minimum soil temperatures, PLoS One 8(7), e68847. GLBRC
2013Kumar, R., and C. E. Wyman. 2013. Physical and chemical features of pretreated biomass that influence macro-micro-accessibility and biological processing. In Aqueous Pretreatment of Plant Biomass for Biological and Chemical Conversion to Fuels and Chemicals, 281-296. Ed. C. E. Wyman.BESC
201310.1016/j.biortech.2012.12.028Kumar, R., F. Hu, C. A. Hubbell, A. J. Ragauskas, and C. E. Wyman. 2013. Comparison of laboratory delignification methods, their selectivity, and impacts on physiochemical characteristics of cellulosic biomass, Bioresour Technol 130, 372-381. BESC
201310.1002/bit.24744Kumar, R., F. Hu, P. Sannigrahi, S. Jung, A. J. Ragauskas, and C. E. Wyman. 2013. Carbohydrate derived-pseudo-lignin can retard cellulose biological conversion, Biotechnol Bioeng 110(3), 737-753. BESC
201310.1016/j.copbio.2013.02.028Lennen, R. M., and B. F. Pfleger. 2013. Microbial production of fatty acid-derived fuels and chemicals, Curr Opin Biotechnol 24(6), 1044-1053. GLBRC
201310.1371/journal.pone.0054031Lennen, R. M., and B. F. Pfleger. 2013. Modulating membrane composition alters free fatty acid tolerance in Escherichia coli, PLoS One 8(1), e54031. GLBRC
201310.1128/JB.01477-12Lennen, R. M., M. G. Politz, M. A. Kruziki, and B. F. Pfleger. 2013. Identification of transport proteins involved in free fatty acid efflux in Escherichia coli, J Bacteriol 195(1), 135-144. GLBRC
201310.1186/1754-6834-6-154.Li, C., D. Tanjore, W. He, J. Wong, J. L. Gardner, K. L. Sale, B. A. Simmons, and S. Singh. 2013. Scale-up and evaluation of high solid ionic liquid pretreatment and enzymatic hydrolysis of switchgrass, Biotechnol Biofuels 6(1), 154. JBEI
201310.1007/s10295-013-1254-xLi, H., Q. Qing, R. Kumar, and C. E. Wyman. 2013. Chromatographic determination of 1, 4-beta-xylooligosaccharides of different chain lengths to follow xylan deconstruction in biomass conversion, J Ind Microbiol Biotechnol 40(6), 551-559. BESC
201310.1002/bit.24951Li, H., X. Gao, J. D. Demartini, R. Kumar, and C. E. Wyman. 2013. Application of high throughput pretreatment and co-hydrolysis system to thermochemical pretreatment. Part 2: Dilute alkali, Biotechnol Bioeng 110(11), 2894-2901. BESC
201310.1186/1754-6834-6-119Li, Z., C. H. Chen, E. L. Hegg, and D. B. Hodge. 2013. Rapid and effective oxidative pretreatment of woody biomass at mild reaction conditions and low oxidant loadings, Biotechnol Biofuels 6(1), 119. GLBRC
201310.1002/bit.24793Li, Z., C. H. Chen, T. Liu, V. Mathrubootham, E. L. Hegg, and D. B. Hodge. 2013. Catalysis with Cu(II) (bpy) improves alkaline hydrogen peroxide pretreatment, Biotechnol Bioeng 110(4), 1078-1086. GLBRC
201310.1007/s10570-013-0011-7Lian, P., H.-B. Guo, J. C. Smith, D.-Q. Wei, and H. Guo. 2013. Catalytic mechanism and origin of high activity of cellulase TmCel12A at high temperature: a quantum mechanical/molecular mechanical study, Cellulose 21(2), 937-949. BESC
201310.1016/j.soilbio.2012.09.006Liang, C., D. S. Duncan, T. C. Balser, J. M. Tiedje, and R. D. Jackson. 2013. Soil microbial residue storage linked to soil legacy under biofuel cropping systems in southern Wisconsin, USA, Soil Biology and Biochemistry 57, 939-942. GLBRC
201310.1021/sb300075tLinshiz, G., N. Stawski, S. Poust, C. Bi, J. D. Keasling, and N. J. Hillson. 2013. PaR-PaR laboratory automation platform, ACS Synth Biol 2(5), 216-222. JBEI
201310.1016/j.biortech.2013.08.086Linville, J. L., M. Rodriguez, Jr., J. R. Mielenz, and C. D. Cox. 2013. Kinetic modeling of batch fermentation for Populus hydrolysate tolerant mutant and wild type strains of Clostridium thermocellum, Bioresour Technol 147, 605-613. BESC
201310.1371/journal.pone.0078829Linville, J. L., M. Rodriguez, Jr., M. Land, M. H. Syed, N. L. Engle, T. J. Tschaplinski, J. R. Mielenz, and C. D. Cox. 2013. Industrial robustness: understanding the mechanism of tolerance for the Populus hydrolysate-tolerant mutant strain of Clostridium thermocellum, PLoS One 8(10), e78829. BESC
201310.1038/nrg3583Liu, W., J. S. Yuan, and C. N. Stewart, Jr. 2013. Advanced genetic tools for plant biotechnology, Nat Rev Genet 14(11), 781-793. BESC
2013Liu, Y. S., and S. Y. Ding. 2013. Advances in the measurement and characterization of biomass structure and processing. In Biological Conversion of Biomass for Fuels and Chemicals: Explorations from Natural Utilization Systems, 26-36. Eds. J. Sun, S.-Y. Ding, and J. D. Peterson.BESC
201310.1073/pnas.1308936110Lu, S., Q. Li, H. Wei, M. J. Chang, S. Tunlaya-Anukit, H. Kim, J. Liu, J. Song, Y. H. Sun, L. Yuan, T. F. Yeh, I. Peszlen, J. Ralph, R. R. Sederoff, and V. L. Chiang. 2013. Ptr-miR397a is a negative regulator of laccase genes affecting lignin content in Populus trichocarpa, Proc Natl Acad Sci U S A 110(26), 10848-10853. GLBRC
201310.1007/s12155-013-9352-1Lupoi, J. S., S. Singh, B. A. Simmons, and R. J. Henry. 2013. Assessment of Lignocellulosic Biomass Using Analytical Spectroscopy: an Evolution to High-Throughput Techniques, BioEnergy Research 7(1), 1-23. JBEI
2013Lynd, L., and M. Laser. 2013. Cellulosic Biofuels: Importance, Recalcitrance, and Pretreatment. In Aqueous Pretreatment of Plant Biomass for Biological and Chemical Conversion to Fuels and Chemicals, 17-21. Ed. C. E. Wyman.BESC
201310.1016/j.gpb.2013.01.004Ma, Q., and Y. Xu. 2013. Global genomic arrangement of bacterial genes is closely tied with the total transcriptional efficiency, Genomics Proteomics Bioinformatics 11(1), 66-71. BESC
201310.1093/bioinformatics/btt397Ma, Q., B. Liu, C. Zhou, Y. Yin, G. Li, and Y. Xu. 2013. An integrated toolkit for accurate prediction and analysis of cis-regulatory motifs at a genome scale, Bioinformatics 29(18), 2261-2268. BESC
201310.1093/nar/gkt261Ma, Q., Y. Yin, M. A. Schell, H. Zhang, G. Li, and Y. Xu. 2013. Computational analyses of transcriptomic data reveal the dynamic organization of the Escherichia coli chromosome under different conditions, Nucleic Acids Res 41(11), 5594-5603. BESC
201310.1371/journal.pone.0068887Ma, W., Q. Kong, V. Arondel, A. Kilaru, P. D. Bates, N. A. Thrower, C. Benning, and J. B. Ohlrogge. 2013. Wrinkled1, a ubiquitous regulator in oil accumulating tissues from Arabidopsis embryos to oil palm mesocarp, PLoS One 8(7), e68887. GLBRC
201310.1104/pp.113.225193Manabe, Y., Y. Verhertbruggen, S. Gille, J. Harholt, S. L. Chong, P. M. Pawar, E. J. Mellerowicz, M. Tenkanen, K. Cheng, M. Pauly, and H. V. Scheller. 2013. Reduced Wall Acetylation proteins play vital and distinct roles in cell wall O-acetylation in Arabidopsis, Plant Physiol 163(3), 1107-1117. JBEI
201310.1016/j.jprot.2012.12.009Mann, G. W., H. J. Joshi, C. J. Petzold, and J. L. Heazlewood. 2013. Proteome coverage of the model plant Arabidopsis thaliana: implications for shotgun proteomic studies, J Proteomics 79, 195-199. JBEI
201310.3389/fpls.2013.00411.Mann, G. W., P. C. Calley, H. J. Joshi, and J. L. Heazlewood. 2013. MASCP gator: an overview of the Arabidopsis proteomic aggregation portal, Front Plant Sci 4, 411. JBEI
201310.1371/journal.pone.0056726Mao, F., V. Olman, Y. Wang, and Y. Xu. 2013. Barcode server: a visualization-based genome analysis system, PLoS One 8(2), e56726. 10.1371/journal.pone.0056726.BESC
2013 10.1002/anie.201300766Martin del Campo, J. S., J. Rollin, S. Myung, Y. Chun, S. Chandrayan, R. Patino, M. W. Adams, and Y. H. Zhang. 2013. High-yield production of dihydrogen from xylose by using a synthetic enzyme cascade in a cell-free system, Angew Chem Int Ed Engl 52(17), 4587-4590. BESC
201310.1074/jbc.M113.458356McAndrew, R. P., J. I. Park, R. A. Heins, W. Reindl, G. D. Friedland, P. D'Haeseleer, T. Northen, K. L. Sale, B. A. Simmons, and P. D. Adams. 2013. From soil to structure, a novel dimeric beta-glucosidase belonging to glycoside hydrolase family 3 isolated from compost using metagenomic analysis, J Biol Chem 288(21), 14985-14992. JBEI
201310.1371/journal.pone.0080093Meehan, T. D., C. Gratton, E. Diehl, N. D. Hunt, D. F. Mooney, S. J. Ventura, B. L. Barham, and R. D. Jackson. 2013. Ecosystem-service tradeoffs associated with switching from annual to perennial energy crops in riparian zones of the US Midwest, PLoS One 8(11), e80093. GLBRC
201310.1016/j.biortech.2013.06.091Meng, X., M. Foston, J. Leisen, J. DeMartini, C. E. Wyman, and A. J. Ragauskas. 2013. Determination of porosity of lignocellulosic biomass before and after pretreatment by using Simons' stain and NMR techniques, Bioresour Technol 144, 467-476. BESC
201310.1073/pnas.1218447110Minty, J. J., M. E. Singer, S. A. Scholz, C. H. Bae, J. H. Ahn, C. E. Foster, J. C. Liao, and X. N. Lin. 2013. Design and characterization of synthetic fungal-bacterial consortia for direct production of isobutanol from cellulosic biomass, Proc Natl Acad Sci U S A 110(36), 14592-14597. GLBRC
201310.1007/s10570-013-0018-0Mostofian, B., J. C. Smith, and X. Cheng. 2013. Simulation of a cellulose fiber in ionic liquid suggests a synergistic approach to dissolution, Cellulose 21(2), 983-997. BESC
201310.1371/journal.pone.0054468Muchero, W., M. M. Sewell, P. Ranjan, L. E. Gunter, T. J. Tschaplinski, T. Yin, and G. A. Tuskan. 2013. Genome anchored QTLs for biomass productivity in hybrid Populus grown under contrasting environments, PLoS One 8(1), e54468. BESC
201310.1128/AEM.00973-13Muller, J., D. MacEachran, H. Burd, N. Sathitsuksanoh, C. Bi, Y. C. Yeh, T. S. Lee, N. J. Hillson, S. R. Chhabra, S. W. Singer, and H. R. Beller. 2013. Engineering of Ralstonia eutropha H16 for autotrophic and heterotrophic production of methyl ketones, Appl Environ Microbiol 79(14), 4433-4439. JBEI
201310.1038/nmeth.2404Mutalik, V. K., J. C. Guimaraes, G. Cambray, C. Lam, M. J. Christoffersen, Q. A. Mai, A. B. Tran, M. Paull, J. D. Keasling, A. P. Arkin, and D. Endy. 2013. Precise and reliable gene expression via standard transcription and translation initiation elements, Nat Methods 10(4), 354-360. JBEI
2013 10.1038/nmeth.2403Mutalik, V. K., J. C. Guimaraes, G. Cambray, Q. A. Mai, M. J. Christoffersen, L. Martin, A. Yu, C. Lam, C. Rodriguez, G. Bennett, J. D. Keasling, D. Endy, and A. P. Arkin. 2013. Quantitative estimation of activity and quality for collections of functional genetic elements, Nat Methods 10(4), 347-353. JBEI
2013Muttoni, G., N. Palacios-Rojas, L. Galicia, A. Rosales, and N. de Leon. 2013. Cell wall composition and biomass digestibility diversity in Mexican maize (Zea mays L.) landraces and CIMMYT elite inbred lines, Maydica 58, 21-33. DOI.GLBRC
201310.1371/journal.pgen.1003565Myers, K. S., H. Yan, I. M. Ong, D. Chung, K. Liang, F. Tran, S. Keles, R. Landick, and P. J. Kiley. 2013. Genome-scale analysis of escherichia coli FNR reveals complex features of transcription factor binding, PLoS Genet 9(6), e1003565. GLBRC
201310.1186/1754-6834-6-77Nageswara-Rao, M., J. R. Soneji, C. Kwit, and C. N. Stewart, Jr. 2013. Advances in biotechnology and genomics of switchgrass, Biotechnol Biofuels 6(1), 77. BESC
201310.3389/fmicb.2013.00282Nyyssonen, M., H. M. Tran, U. Karaoz, C. Weihe, M. Z. Hadi, J. B. Martiny, A. C. Martiny, and E. L. Brodie. 2013. Coupled high-throughput functional screening and next generation sequencing for identification of plant polymer decomposing enzymes in metagenomic libraries, Front Microbiol 4, 282. JBEI
201310.1016/j.tplants.2012.07.002Oikawa, A., C. H. Lund, Y. Sakuragi, and H. V. Scheller. 2013. Golgi-localized enzyme complexes for plant cell wall biosynthesis, Trends Plant Sci 18(1), 49-58. JBEI
201310.1128/JB.02014-12Olson, D. G., R. J. Giannone, R. L. Hettich, and L. R. Lynd. 2013. Role of the CipA scaffoldin protein in cellulose solubilization, as determined by targeted gene deletion and complementation in Clostridium thermocellum, J Bacteriol 195(4), 733-739. BESC
201310.1016/j.ymben.2012.07.010Ozaydin, B., H. Burd, T. S. Lee, and J. D. Keasling. 2013. Carotenoid-based phenotypic screen of the yeast deletion collection reveals new genes with roles in isoprenoid production, Metab Eng 15, 174-183. JBEI
201310.1016/j.biombioe.2012.11.029Paap, S. M., T. H. West, D. K. Manley, E. J. Steen, H. R. Beller, J. D. Keasling, D. C. Dibble, S. Chang, and B. A. Simmons. 2013. Biochemical production of ethanol and fatty acid ethyl esters from switchgrass: A comparative analysis of environmental and economic performance, Biomass and Bioenergy 49, 49-62. JBEI
201310.1038/nature12051Paddon, C. J., P. J. Westfall, D. J. Pitera, K. Benjamin, K. Fisher, D. McPhee, M. D. Leavell, A. Tai, A. Main, D. Eng, D. R. Polichuk, K. H. Teoh, D. W. Reed, T. Treynor, J. Lenihan, M. Fleck, S. Bajad, G. Dang, D. Dengrove, D. Diola, G. Dorin, K. W. Ellens, S. Fickes, J. Galazzo, S. P. Gaucher, T. Geistlinger, R. Henry, M. Hepp, T. Horning, T. Iqbal, H. Jiang, L. Kizer, B. Lieu, D. Melis, N. Moss, R. Regentin, S. Secrest, H. Tsuruta, R. Vazquez, L. F. Westblade, L. Xu, M. Yu, Y. Zhang, L. Zhao, J. Lievense, P. S. Covello, J. D. Keasling, K. K. Reiling, N. S. Renninger, and J. D. Newman. 2013. High-level semi-synthetic production of the potent antimalarial artemisinin, Nature 496(7446), 528-532. JBEI
201310.1007/s00253-012-4423-3Paper, J. M., J. S. Scott-Craig, D. Cavalier, A. Faik, R. E. Wiemels, M. S. Borrusch, M. Bongers, and J. D. Walton. 2013. alpha-Fucosidases with different substrate specificities from two species of Fusarium, Appl Microbiol Biotechnol 97(12), 5371-5380. GLBRC
201310.1371/journal.pgen.1003839Park, D. M., M. S. Akhtar, A. Z. Ansari, R. Landick, and P. J. Kiley. 2013. The bacterial response regulator ArcA uses a diverse binding site architecture to regulate carbon oxidation globally, PLoS Genet 9(10), e1003839. GLBRC
201310.1186/1471-2164-14-759Park, J. J., S. Lechno-Yossef, C. P. Wolk, and C. Vieille. 2013. Cell-specific gene expression in Anabaena variabilis grown phototrophically, mixotrophically, and heterotrophically, BMC Genomics 14, 759. GLBRC
201310.1371/journal.pone.0084669Parsons, H. T., C. S. Weinberg, L. J. Macdonald, P. D. Adams, C. J. Petzold, T. J. Strabala, A. Wagner, and J. L. Heazlewood. 2013. Golgi enrichment and proteomic analysis of developing Pinus radiata xylem by free-flow electrophoresis, PLoS One 8(12), e84669. JBEI
2013Parsons, H. T., J. Ito, E. Park, A. W. Carroll, H. J. Joshi, C. J. Petzold, G. Drakakaki, and J. L. Heazlewood. 2013. The current state of the Golgi proteomes. In Proteomics Applications in Biology. Eds. J. L. Heazlewood, and C. J. Petzold. InTechOpen.JBEI
201310.1016/j.ultramic.2013.03.016Passian, A., L. Tetard, and T. Thundat. 2013. Comments on the paper A comprehensive modeling and vibration analysis of AFM microcantilevers subjected to nonlinear tip-sample interaction forces by Sohrab Eslami and Nader Jalili, Ultramicroscopy 131, 92-93. BESC
201310.1007/s12042-013-9129-xPaull, R. E., A. Carroll, and N. J. Chen. 2013. Lotus Cell Walls and the Genes Involved in its Synthesis and Modification, Tropical Plant Biology 6(2-3), 152-160. JBEI
201310.1111/gcbb.12033Peckham, S. D., and S. T. Gower. 2013. Simulating the effects of harvest and biofuel production on the forest system carbon balance of the Midwest, USA, GCB Bioenergy 5(4), 431-444. GLBRC
201310.3389/fmicb.2013.00279Penton, C. R., T. A. Johnson, J. F. Quensen, 3rd, S. Iwai, J. R. Cole, and J. M. Tiedje. 2013. Functional genes to assess nitrogen cycling and aromatic hydrocarbon degradation: primers and processing matter, Front Microbiol 4, 279. GLBRC
201310.1002/er.2897Percival Zhang, Y.-H., J.-H. Xu, and J.-J. Zhong. 2013. A new high-energy density hydrogen carrier-carbohydrate-might be better than methanol, International Journal of Energy Research 37(7), 769-779. BESC
201310.1016/j.biortech.2012.09.124Perez-Pimienta, J. A., M. G. Lopez-Ortega, P. Varanasi, V. Stavila, G. Cheng, S. Singh, and B. A. Simmons. 2013. Comparison of the impact of ionic liquid pretreatment on recalcitrance of agave bagasse and switchgrass, Bioresour Technol 127, 18-24. JBEI
201310.1039/c2cc37107cPolitz, M. C., M. F. Copeland, and B. F. Pfleger. 2013. Artificial repressors for controlling gene expression in bacteria, Chem Commun (Camb) 49(39), 4325-4327. GLBRC
201310.1111/nph.12014Porth, I., J. Klapste, O. Skyba, B. S. Lai, A. Geraldes, W. Muchero, G. A. Tuskan, C. J. Douglas, Y. A. El-Kassaby, and S. D. Mansfield. 2013. Populus trichocarpa cell wall chemistry and ultrastructure trait variation, genetic control and genetic correlations, New Phytol 197(3), 777-790. BESC
2013Pu, Y., B. Hallac, and A. J. Ragauskas. 2013. Plant biomass characterization: application of solution- and solid-state NMR spectroscopy. In Aqueous Pretreatment of Plant Biomass for Biological and Chemical Conversion to Fuels and Chemicals, 369-387. Ed. C. E. Wyman.BESC
201310.1186/1754-6834-6-15Pu, Y., F. Hu, F. Huang, B. H. Davison, and A. J. Ragauskas. 2013. Assessing the molecular structure basis for biomass recalcitrance during dilute acid and hydrothermal pretreatments, Biotechnol Biofuels 6(1), 15. BESC
2013Qing, Q., H. Li, R. Kumar, and C. E. Wyman. 2013. Xylooligosaccharides production, quantification, and characterization in context of lignocellulosic biomass pretreatment. In Aqueous Pretreatment of Plant Biomass for Biological and Chemical Conversion to Fuels and Chemicals, 391-410. Ed. C. E. Wyman.BESC
201310.1002/bbb.1414Ragauskas, A. J. 2013. When to accept no … to yesterday's solutions, Biofuels, Bioproducts and Biorefining 7(3), 217-219. BESC
201310.1021/ja401793nRahimi, A., A. Azarpira, H. Kim, J. Ralph, and S. S. Stahl. 2013. Chemoselective metal-free aerobic alcohol oxidation in lignin, J Am Chem Soc 135(17), 6415-6418. GLBRC
201310.1007/978-1-62703-278-0_2Ramanna, H., X. S. Ding, and R. S. Nelson. 2013. Rationale for developing new virus vectors to analyze gene function in grasses through virus-induced gene silencing, Methods Mol Biol 975, 15-32. BESC
201310.4172/2155-6199.s4-004Ratnaparkhe, S., and S. Venkatachalam. 2013. Analyses using Cell Wall Glycan-directed Monoclonal Antibodies Reveal Xylan-degradation by Two Microbial Glycosyl Hydrolases in Cell Walls from Poplar and Switchgrass Biomass, Journal of Bioremediation & Biodegradation 01(s4). BESC
201310.1371/journal.pone.0077985Reddy, A. P., C. W. Simmons, P. D'Haeseleer, J. Khudyakov, H. Burd, M. Hadi, B. A. Simmons, S. W. Singer, M. P. Thelen, and J. S. Vandergheynst. 2013. Discovery of microorganisms and enzymes involved in high-solids decomposition of rice straw using metagenomic analyses, PLoS One 8(10), e77985. JBEI
201310.1021/jf304686xRencoret, J., J. Ralph, G. Marques, A. Gutierrez, A. Martinez, and J. C. del Rio. 2013. Structural characterization of lignin isolated from coconut (Cocos nucifera) coir fibers, J Agric Food Chem 61(10), 2434-2445. GLBRC
201310.1039/c3ee00019bResch, M. G., B. S. Donohoe, J. O. Baker, S. R. Decker, E. A. Bayer, G. T. Beckham, and M. E. Himmel. 2013. Fungal cellulases and complexed cellulosomal enzymes exhibit synergistic mechanisms in cellulose deconstruction, Energy & Environmental Science 6(6), 1858. BESC
201310.1186/1754-6834-6-93Reyes-Ortiz, V., R. A. Heins, G. Cheng, E. Y. Kim, B. C. Vernon, R. B. Elandt, P. D. Adams, K. L. Sale, M. Z. Hadi, B. A. Simmons, M. S. Kent, and D. Tullman-Ercek. 2013. Addition of a carbohydrate-binding module enhances cellulase penetration into cellulose substrates, Biotechnol Biofuels 6(1), 93. JBEI
201310.1890/0012-9623-94.3.277Ridley, C. E., H. I. Jager, C. M. Clark, R. A. Efroymson, C. Kwit, D. A. Landis, Z. H. Leggett, and D. A. Miller. 2013. Debate: Can Bioenergy Be Produced in a Sustainable Manner That Protects Biodiversity and Avoids the Risk of Invaders?, Bulletin of the Ecological Society of America 94(3), 277-290. GLBRC
2013Robertson, B. A., and P. J. Doran. 2013. Biofuels and biodiversity: The implications of energy sprawl. In Encyclopedia of Biodiversity, 2nd ed., 528-539. Waltham.GLBRC
201310.1186/1471-2164-14-608Rodgers-Melnick, E., M. Culp, and S. P. DiFazio. 2013. Predicting whole genome protein interaction networks from primary sequence data in model and non-model organisms using ENTS, BMC Genomics 14, 608. BESC
201310.1073/pnas.1306164110Rodrigues, J. A., R. Ruan, T. Nishimura, M. K. Sharma, R. Sharma, P. C. Ronald, R. L. Fischer, and D. Zilberman. 2013. Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm, Proc Natl Acad Sci U S A 110(19), 7934-7939. JBEI
201310.1016/j.cbpa.2013.03.039Rothamer, D. A., and T. J. Donohue. 2013. Chemistry and combustion of fit-for-purpose biofuels, Curr Opin Chem Biol 17(3), 522-528. GLBRC
201310.1111/gcb.12216Ruan, L., and G. Philip Robertson. 2013. Initial nitrous oxide, carbon dioxide, and methane costs of converting conservation reserve program grassland to row crops under no-till vs. conventional tillage, Glob Chang Biol 19(8), 2478-2489. GLBRC
201310.1111/tpj.12204Saha, P., T. Ray, Y. Tang, I. Dutta, N. R. Evangelous, M. J. Kieliszewski, Y. Chen, and M. C. Cannon. 2013. Self-rescue of an EXTENSIN mutant reveals alternative gene expression programs and candidate proteins for new cell wall assembly in Arabidopsis, Plant J 75(1), 104-116. BESC
201310.1039/c3ra40578hSamuel, R., S. Cao, B. K. Das, F. Hu, Y. Pu, and A. J. Ragauskas. 2013. Investigation of the fate of poplar lignin during autohydrolysis pretreatment to understand the biomass recalcitrance, RSC Advances 3(16), 5305. BESC
201310.1016/j.soilbio.2013.09.002Sanford, G. R., and C. J. Kucharik. 2013. Effect of methodological consideration on soil carbon parameter estimates obtained via the acid hydrolysis-incubation method, Soil Biology and Biochemistry 67, 295-305. GLBRC
201310.1105/tpc.112.104752Sanjaya, R. Miller, T. P. Durrett, D. K. Kosma, T. A. Lydic, B. Muthan, A. J. Koo, Y. V. Bukhman, G. E. Reid, G. A. Howe, J. Ohlrogge, and C. Benning. 2013. Altered lipid composition and enhanced nutritional value of Arabidopsis leaves following introduction of an algal diacylglycerol acyltransferase 2, Plant Cell 25(2), 677-693. GLBRC
2013Sannigrahi, P., and A. J. Ragauskas. 2013. Fundamentals of biomass pretreatment by fractionation. In Aqueous Pretreatment of Plant Biomass for Biological and Chemical Conversion to Fuels and Chemicals, 201-219. Ed. C. E. Wyman.BESC
201310.1002/jctb.3959Sathitsuksanoh, N., A. George, and Y. H. P. Zhang. 2013. New lignocellulose pretreatments using cellulose solvents: a review, Journal of Chemical Technology & Biotechnology 88(2), 169-180. JBEI BESC
201310.1371/journal.pone.0073523Sathitsuksanoh, N., B. Xu, B. Zhao, and Y. H. Zhang. 2013. Overcoming biomass recalcitrance by combining genetically modified switchgrass and cellulose solvent-based lignocellulose pretreatment, PLoS One 8(9), e73523. BESC
201310.3389/fpls.2013.00076Schwartz, C., and R. Amasino. 2013. Nitrogen recycling and flowering time in perennial bioenergy crops, Front Plant Sci 4, 76. GLBRC
201310.1371/journal.pone.0061005Sekhon, R. S., R. Briskine, C. N. Hirsch, C. L. Myers, N. M. Springer, C. R. Buell, N. de Leon, and S. M. Kaeppler. 2013. Maize gene atlas developed by RNA sequencing and comparative evaluation of transcriptomes based on RNA sequencing and microarrays, PLoS One 8(4), e61005. GLBRC
201310.1007/s12155-013-9315-6Serba, D., L. Wu, G. Daverdin, B. A. Bahri, X. Wang, A. Kilian, J. H. Bouton, E. C. Brummer, M. C. Saha, and K. M. Devos. 2013. Linkage Maps of Lowland and Upland Tetraploid Switchgrass Ecotypes, BioEnergy Research 6(3), 953-965. BESC
201310.1016/j.biortech.2012.11.109Shao, X., and L. Lynd. 2013. Kinetic modeling of xylan hydrolysis in co- and countercurrent liquid hot water flow-through pretreatments, Bioresour Technol 130, 117-124. BESC
201310.1093/mp/sss147Sharma, R., D. De Vleesschauwer, M. K. Sharma, and P. C. Ronald. 2013. Recent advances in dissecting stress-regulatory crosstalk in rice, Mol Plant 6(2), 250-260. JBEI
201310.3389/fpls.2013.00330Sharma, R., P. Cao, K. H. Jung, M. K. Sharma, and P. C. Ronald. 2013. Construction of a rice glycoside hydrolase phylogenomic database and identification of targets for biofuel research, Front Plant Sci 4, 330. JBEI
201310.1186/1754-6834-6-71Shen, H., C. R. Poovaiah, A. Ziebell, T. J. Tschaplinski, S. Pattathil, E. Gjersing, N. L. Engle, R. Katahira, Y. Pu, R. Sykes, F. Chen, A. J. Ragauskas, J. R. Mielenz, M. G. Hahn, M. Davis, C. N. Stewart, Jr., and R. A. Dixon. 2013. Enhanced characteristics of genetically modified switchgrass (Panicum virgatum L.) for high biofuel production, Biotechnol Biofuels 6(1), 71. .BESC
201310.1105/tpc.113.118828Shen, H., M. Mazarei, H. Hisano, L. Escamilla-Trevino, C. Fu, Y. Pu, M. R. Rudis, Y. Tang, X. Xiao, L. Jackson, G. Li, T. Hernandez, F. Chen, A. J. Ragauskas, C. N. Stewart, Jr., Z. Y. Wang, and R. A. Dixon. 2013. A genomics approach to deciphering lignin biosynthesis in switchgrass, Plant Cell 25(11), 4342-4361. BESC
201310.1039/c3gc40545aShi, J., J. M. Gladden, N. Sathitsuksanoh, P. Kambam, L. Sandoval, D. Mitra, S. Zhang, A. George, S. W. Singer, B. A. Simmons, and S. Singh. 2013. One-pot ionic liquid pretreatment and saccharification of switchgrass, Green Chemistry 15(9), 2579. JBEI
2013Singh, S., and B. A. Simmons. 2013. Ionic Liquid Pretreatment: Mechanism, Performance, and Challenges. In Aqueous Pretreatment of Plant Biomass for Biological and Chemical Conversion to Fuels and Chemicals, 223-238. John Wiley & Sons, Ltd.JBEI
201310.1016/j.biombioe.2013.02.035Singh, S., P. Varanasi, P. Singh, P. D. Adams, M. Auer, and B. A. Simmons. 2013. Understanding the impact of ionic liquid pretreatment on cellulose and lignin via thermochemical analysis, Biomass and Bioenergy 54, 276-283. JBEI
201310.1016/j.biombioe.2012.12.017Smith, S. L., K. D. Thelen, and S. J. MacDonald. 2013. Yield and quality analyses of bioenergy crops grown on a regulatory brownfield, Biomass and Bioenergy 49, 123-130. GLBRC
201310.1186/1754-6834-6-61Socha, A. M., S. P. Plummer, V. Stavila, B. A. Simmons, and S. Singh. 2013. Comparison of sugar content for ionic liquid pretreated Douglas-fir woodchips and forestry residues, Biotechnol Biofuels 6(1), 61. JBEI
201310.1039/c2ra20706kSun, L., C. Li, Z. Xue, B. A. Simmons, and S. Singh. 2013. Unveiling high-resolution, tissue specific dynamic changes in corn stover during ionic liquid pretreatment, RSC Adv. 3(6), 2017-2027. JBEI
201310.1186/1754-6834-6-39Sun, N., H. Liu, N. Sathitsuksanoh, V. Stavila, M. Sawant, A. Bonito, K. Tran, A. George, K. L. Sale, S. Singh, B. A. Simmons, and B. M. Holmes. 2013. Production and extraction of sugars from switchgrass hydrolyzed in ionic liquids, Biotechnol Biofuels 6(1), 39. JBEI
201310.1016/j.ces.2013.06.044Szmidt-Middleton, H. L., M. Ouellet, P. D. Adams, J. D. Keasling, and A. Mukhopadhyay. 2013. Utilizing a highly responsive gene, yhjX, in E. coli based production of 1,4-butanediol, Chemical Engineering Science 103, 68-73. JBEI
201310.1128/genomeA.00605-13Taghavi, S., J. A. Izquierdo, and D. van der Lelie. 2013. Complete Genome Sequence of Clostridium sp. Strain DL-VIII, a Novel Solventogenic Clostridium Species Isolated from Anaerobic Sludge, Genome Announc 1(4). BESC
201310.1038/srep01030Takasuka, T. E., A. J. Book, G. R. Lewin, C. R. Currie, and B. G. Fox. 2013. Aerobic deconstruction of cellulosic biomass by an insect-associated Streptomyces, Sci Rep 3, 1030. GLBRC
201310.1105/tpc.112.107334Tan, L., S. Eberhard, S. Pattathil, C. Warder, J. Glushka, C. Yuan, Z. Hao, X. Zhu, U. Avci, J. S. Miller, D. Baldwin, C. Pham, R. Orlando, A. Darvill, M. G. Hahn, M. J. Kieliszewski, and D. Mohnen. 2013. An Arabidopsis cell wall proteoglycan consists of pectin and arabinoxylan covalently linked to an arabinogalactan protein, Plant Cell 25(1), 270-287. BESC
201310.1016/j.febslet.2013.02.021Tjellstrom, H., M. Strawsine, J. Silva, E. B. Cahoon, and J. B. Ohlrogge. 2013. Disruption of plastid acyl:acyl carrier protein synthetases increases medium chain fatty acid accumulation in seeds of transgenic Arabidopsis, FEBS Lett 587(7), 936-942. GLBRC
201310.1111/tpj.12299Tobimatsu, Y., A. Wagner, L. Donaldson, P. Mitra, C. Niculaes, O. Dima, J. I. Kim, N. Anderson, D. Loque, W. Boerjan, C. Chapple, and J. Ralph. 2013. Visualization of plant cell wall lignification using fluorescence-tagged monolignols, Plant J 76(3), 357-366. GLBRC JBEI
201310.1105/tpc.113.113142Tobimatsu, Y., F. Chen, J. Nakashima, L. L. Escamilla-Trevino, L. Jackson, R. A. Dixon, and J. Ralph. 2013. Coexistence but independent biosynthesis of catechyl and guaiacyl/syringyl lignin polymers in seed coats, Plant Cell 25(7), 2587-2600. BESC GLBRC
2013Trajano, H. L., and C. E. Wyman. 2013. Fundamentals of Biomass Pretreatment at Low pH. In Aqueous Pretreatment of Plant Biomass for Biological and Chemical Conversion to Fuels and Chemicals, 103-123. Ed. C. E. Wyman.BESC
201310.1021/ie301869aTrajano, H. L., J. D. DeMartini, M. H. Studer, and C. E. Wyman. 2013. Comparison of the Effectiveness of a Fluidized Sand Bath and a Steam Chamber for Reactor Heating, Industrial & Engineering Chemistry Research 52(13), 4932-4938. BESC
201310.1186/1754-6834-6-110Trajano, H. L., N. L. Engle, M. Foston, A. J. Ragauskas, T. J. Tschaplinski, and C. E. Wyman. 2013. The fate of lignin during hydrothermal pretreatment, Biotechnol Biofuels 6(1), 110. BESC
201310.1016/j.plantsci.2013.01.004Troncoso-Ponce, M. A., X. Cao, Z. Yang, and J. B. Ohlrogge. 2013. Lipid turnover during senescence, Plant Sci 205-206, 13-19. GLBRC
201310.1007/s10295-013-1275-5van der Veen, D., J. Lo, S. D. Brown, C. M. Johnson, T. J. Tschaplinski, M. Martin, N. L. Engle, R. A. van den Berg, A. D. Argyros, N. C. Caiazza, A. M. Guss, and L. R. Lynd. 2013. Characterization of Clostridium thermocellum strains with disrupted fermentation end-product pathways, J Ind Microbiol Biotechnol 40(7), 725-734. BESC
201310.1111/nph.12179Vanholme, B., I. Cesarino, G. Goeminne, H. Kim, F. Marroni, R. Van Acker, R. Vanholme, K. Morreel, B. Ivens, S. Pinosio, M. Morgante, J. Ralph, C. Bastien, and W. Boerjan. 2013. Breeding with rare defective alleles (BRDA): a natural Populus nigra HCT mutant with modified lignin as a case study, New Phytol 198(3), 765-776. GLBRC
201310.1126/science.1241602Vanholme, R., I. Cesarino, K. Rataj, Y. Xiao, L. Sundin, G. Goeminne, H. Kim, J. Cross, K. Morreel, P. Araujo, L. Welsh, J. Haustraete, C. McClellan, B. Vanholme, J. Ralph, G. G. Simpson, C. Halpin, and W. Boerjan. 2013. Caffeoyl shikimate esterase (CSE) is an enzyme in the lignin biosynthetic pathway in Arabidopsis, Science 341(6150), 1103-1106. GLBRC
201310.1186/1754-6834-6-14Varanasi, P., P. Singh, M. Auer, P. D. Adams, B. A. Simmons, and S. Singh. 2013. Survey of renewable chemicals produced from lignocellulosic biomass during ionic liquid pretreatment, Biotechnol Biofuels 6(1), 14. JBEI
201310.4161/psb.23143Vega-Sanchez, M. E., Y. Verhertbruggen, H. V. Scheller, and P. C. Ronald. 2013. Abundance of mixed linkage glucan in mature tissues and secondary cell walls of grasses, Plant Signal Behav 8(2), e23143. JBEI
201310.1039/c3an36709fVismeh, R., F. Lu, S. P. Chundawat, J. F. Humpula, A. Azarpira, V. Balan, B. E. Dale, J. Ralph, and A. D. Jones. 2013. Profiling of diferulates (plant cell wall cross-linkers) using ultrahigh-performance liquid chromatography-tandem mass spectrometry, Analyst 138(21), 6683-6692. GLBRC
201310.1016/j.carbpol.2013.02.005Vismeh, R., J. F. Humpula, S. P. Chundawat, V. Balan, B. E. Dale, and A. D. Jones. 2013. Profiling of soluble neutral oligosaccharides from treated biomass using solid phase extraction and LC-TOF MS, Carbohydr Polym 94(2), 791-799. GLBRC
201310.1155/2013/897658Voit, E. O. 2013. Biochemical Systems Theory: A Review, ISRN Biomathematics 2013, 1-53. BESC
201310.1016/j.mbs.2013.01.008Voit, E. O. 2013. Characterizability of metabolic pathway systems from time series data, Math Biosci 246(2), 315-325. BESC
201310.1007/s11103-012-9985-zWagner, A., Y. Tobimatsu, G. Goeminne, L. Phillips, H. Flint, D. Steward, K. Torr, L. Donaldson, W. Boerjan, and J. Ralph. 2013. Suppression of CCR impacts metabolite profile and cell wall composition in Pinus radiata tracheary elements, Plant Mol Biol 81(1-2), 105-117. GLBRC
201310.1111/1574-6968.12029Waller, B. H., D. G. Olson, D. H. Currie, A. M. Guss, and L. R. Lynd. 2013. Exchange of type II dockerin-containing subunits of the Clostridium thermocellum cellulosome as revealed by SNAP-tags, FEMS Microbiol Lett 338(1), 46-53. BESC
201310.1002/cctc.201200757Wang, D., C. M. Osmundsen, E. Taarning, and J. A. Dumesic. 2013. Selective Production of Aromatics from Alkylfurans over Solid Acid Catalysts, ChemCatChem 5(7), 2044-2050. GLBRC
201310.1039/c3cc43587c.Wang, D., S. H. Hakim, D. M. Alonso, and J. A. Dumesic. 2013. A highly selective route to linear alpha olefins from biomass-derived lactones and unsaturated acids, Chem Commun (Camb) 49(63), 7040-7042. GLBRC
201310.1128/mBio.00592-13Wang, Q., J. F. Quensen, 3rd, J. A. Fish, T. K. Lee, Y. Sun, J. M. Tiedje, and J. R. Cole. 2013. Ecological patterns of nifH genes in four terrestrial climatic zones explored with targeted metagenomics using FrameBot, a new informatics tool, MBio 4(5), e00592-00513. GLBRC
201310.1111/tpj.12019Wang, Y., J. C. Mortimer, J. Davis, P. Dupree, and K. Keegstra. 2013. Identification of an additional protein involved in mannan biosynthesis, Plant J 73(1), 105-117. GLBRC
201310.1016/s1001-0742(12)60104-1Wang, Z.-W., S.-H. Lee, J. G. Elkins, Y. Li, S. Hamilton-Brehm, and J. L. Morrell-Falvey. 2013. Continuous live cell imaging of cellulose attachment by microbes under anaerobic and thermophilic conditions using confocal microscopy, Journal of Environmental Sciences 25(5), 849-856. BESC
201310.2489/jswc.68.6.141AWilliams, C. L., P. Charland, G. Radloff, D. Sample, and R. D. Jackson. 2013. Grass-shed: Place and process for catalyzing perennial grass bioeconomies and their potential multiple benefits, Journal of Soil and Water Conservation 68(6), 141A-146A. GLBRC
201310.1007/s10570-013-0149-3Williams, D. L., and D. B. Hodge. 2013. Impacts of delignification and hot water pretreatment on the water induced cell wall swelling behavior of grasses and its relation to cellulolytic enzyme hydrolysis and binding, Cellulose 21(1), 221-235. GLBRC
201310.1186/1754-6834-6-179Wilson, C. M., M. Rodriguez, Jr., C. M. Johnson, S. L. Martin, T. M. Chu, R. D. Wolfinger, L. J. Hauser, M. L. Land, D. M. Klingeman, M. H. Syed, A. J. Ragauskas, T. J. Tschaplinski, J. R. Mielenz, and S. D. Brown. 2013. Global transcriptome analysis of Clostridium thermocellum ATCC 27405 during growth on dilute acid pretreated Populus and switchgrass, Biotechnol Biofuels 6(1), 179. BESC
201310.1186/1754-6834-6-131Wilson, C. M., S. Yang, M. Rodriguez, Jr., Q. Ma, C. M. Johnson, L. Dice, Y. Xu, and S. D. Brown. 2013. Clostridium thermocellum transcriptomic profiles after exposure to furfural or heat stress, Biotechnol Biofuels 6(1), 131. BESC
201310.1016/j.ces.2013.04.033Woo, H. M., G. W. Murray, T. S. Batth, N. Prasad, P. D. Adams, J. D. Keasling, C. J. Petzold, and T. S. Lee. 2013. 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 103, 21-28. JBEI
201310.1093/treephys/tps081Wullschleger, S. D., D. J. Weston, S. P. DiFazio, and G. A. Tuskan. 2013. Revisiting the sequencing of the first tree genome: Populus trichocarpa, Tree Physiol 33(4), 357-364. BESC
2013Wyman, C. E. 2013. Introduction. In Aqueous Pretreatment of Plant Biomass for Biological and Chemical Conversion to Fuels and Chemicals, 1-20. Ed. C. E. Wyman.BESC
2013Wyman, C. E., and C. J. Wyman. 2013. Chemical and Biological Deconstruction of Aqueous Phase. In Catalysis for the Conversion of Biomass and Its Derivates, 165-182. Eds. M. Behrens, and K. Datye.BESC
201310.1186/1754-6834-6-126Xu, Q., S. Y. Ding, R. Brunecky, Y. J. Bomble, M. E. Himmel, and J. O. Baker. 2013. Improving activity of minicellulosomes by integration of intra- and intermolecular synergies, Biotechnol Biofuels 6(1), 126. BESC
201310.1111/pbi.12016Yang, F., P. Mitra, L. Zhang, L. Prak, Y. Verhertbruggen, J. S. Kim, L. Sun, K. Zheng, K. Tang, M. Auer, H. V. Scheller, and D. Loque. 2013. Engineering secondary cell wall deposition in plants, Plant Biotechnol J 11(3), 325-335. JBEI
201310.1371/journal.pone.0068886Yang, S., C. Pan, T. J. Tschaplinski, G. B. Hurst, N. L. Engle, W. Zhou, P. Dam, Y. Xu, M. Rodriguez, Jr., L. Dice, C. M. Johnson, B. H. Davison, and S. D. Brown. 2013. Systems biology analysis of Zymomonas mobilis ZM4 ethanol stress responses, PLoS One 8(7), e68886. BESC
201310.1111/tpj.12073Ye, C. Y., T. Li, H. Yin, D. J. Weston, G. A. Tuskan, T. J. Tschaplinski, and X. Yang. 2013. Evolutionary analyses of non-family genes in plants, Plant J 73(5), 788-797. BESC
201310.1039/c2cc37883cYeh, Y. C., J. Muller, C. Bi, N. J. Hillson, H. R. Beller, S. R. Chhabra, and S. W. Singer. 2013. Functionalizing bacterial cell surfaces with a phage protein, Chem Commun (Camb) 49(9), 910-912. JBEI
201310.1073/pnas.1302420110You, C., H. Chen, S. Myung, N. Sathitsuksanoh, H. Ma, X. Z. Zhang, J. Li, and Y. H. Zhang. 2013. Enzymatic transformation of nonfood biomass to starch, Proc Natl Acad Sci U S A 110(18), 7182-7187. BESC
201310.1007/s00253-013-4911-0Youngquist, J. T., J. P. Rose, and B. F. Pfleger. 2013. Free fatty acid production in Escherichia coli under phosphate-limited conditions, Appl Microbiol Biotechnol 97(11), 5149-5159. GLBRC
201310.1016/j.ymben.2013.10.006Youngquist, J. T., M. H. Schumacher, J. P. Rose, T. C. Raines, M. C. Politz, M. F. Copeland, and B. F. Pfleger. 2013. Production of medium chain length fatty alcohols from glucose in Escherichia coli, Metab Eng 20, 177-186. GLBRC
201310.1105/tpc.112.108027Yuan, L., R. Gu, Y. Xuan, E. Smith-Valle, D. Loque, W. B. Frommer, and N. von Wiren. 2013. Allosteric regulation of transport activity by heterotrimerization of Arabidopsis ammonium transporter complexes in vivo, Plant Cell 25(3), 974-984. JBEI
201310.1021/bi400520tYuzawa, S., C. H. Eng, L. Katz, and J. D. Keasling. 2013. Broad substrate specificity of the loading didomain of the lipomycin polyketide synthase, Biochemistry 52(22), 3791-3793. JBEI
201310.1016/j.agrformet.2013.07.015Zenone, T., I. Gelfand, J. Chen, S. K. Hamilton, and G. P. Robertson. 2013. From set-aside grassland to annual and perennial cellulosic biofuel crops: Effects of land use change on carbon balance, Agricultural and Forest Meteorology 182-183, 1-12. GLBRC
201310.1111/tpj.12104Zhang, J. Y., Y. C. Lee, I. Torres-Jerez, M. Wang, Y. Yin, W. C. Chou, J. He, H. Shen, A. C. Srivastava, C. Pennacchio, E. Lindquist, J. Grimwood, J. Schmutz, Y. Xu, M. Sharma, R. Sharma, L. E. Bartley, P. C. Ronald, M. C. Saha, R. A. Dixon, Y. Tang, and M. K. Udvardi. 2013. Development of an integrated transcript sequence database and a gene expression atlas for gene discovery and analysis in switchgrass (Panicum virgatum L.), Plant J 74(1), 160-173. JBEI BESC
2013Zhang, X., and Y. P. Zhang. 2013. Cellulases: Characteristics, Sources, Production, and Applications. In Bioprocessing Technologies in Biorefinery for Sustainable Production of Fuels, Chemicals, and Polymers. Eds. S. Yang, H. A. El-Enshasy, and N. Thongchul. John Wiley & Sons, Inc.BESC
201310.1016/j.envsoft.2013.03.013Zhang, X., P. Beeson, R. Link, D. Manowitz, R. C. Izaurralde, A. Sadeghi, A. M. Thomson, R. Sahajpal, R. Srinivasan, and J. G. Arnold. 2013. Efficient multi-objective calibration of a computationally intensive hydrologic model with parallel computing software in Python, Environmental Modelling & Software 46, 208-218. GLBRC
201310.1016/j.scitotenv.2013.06.056Zhang, X., R. C. Izaurralde, J. G. Arnold, J. R. Williams, and R. Srinivasan. 2013. Modifying the Soil and Water Assessment Tool to simulate cropland carbon flux: model development and initial evaluation, Sci Total Environ 463-464, 810-822. GLBRC
201310.1016/j.phytochem.2013.06.014Zhao, N., J. Yao, M. Chaiprasongsuk, G. Li, J. Guan, T. J. Tschaplinski, H. Guo, and F. Chen. 2013. Molecular and biochemical characterization of the jasmonic acid methyltransferase gene from black cottonwood (Populus trichocarpa), Phytochemistry 94, 74-81. BESC
201310.1073/pnas.1312234110Zhao, Q., Y. Tobimatsu, R. Zhou, S. Pattathil, L. Gallego-Giraldo, C. Fu, L. A. Jackson, M. G. Hahn, H. Kim, F. Chen, J. Ralph, and R. A. Dixon. 2013. Loss of function of cinnamyl alcohol dehydrogenase 1 leads to unconventional lignin and a temperature-sensitive growth defect in Medicago truncatula, Proc Natl Acad Sci U S A 110(33), 13660-13665. GLBRC BESC
201310.1105/tpc.113.117788Zhou, C., L. Han, C. Fu, J. Wen, X. Cheng, J. Nakashima, J. Ma, Y. Tang, Y. Tan, M. Tadege, K. S. Mysore, G. Xia, and Z. Y. Wang. 2013. The trans-acting short interfering RNA3 pathway and no apical meristem antagonistically regulate leaf margin development and lateral organ separation, as revealed by analysis of an argonaute7/lobed leaflet1 mutant in Medicago truncatula, Plant Cell 25(12), 4845-4862. BESC
201310.1128/AEM.04037-12Zhou, J., D. G. Olson, D. A. Argyros, Y. Deng, W. M. van Gulik, J. P. van Dijken, and L. R. Lynd. 2013. Atypical glycolysis in Clostridium thermocellum, Appl Environ Microbiol 79(9), 3000-3008. BESC
201310.1534/g3.112.005447Zhu, Q., J. L. Bennetzen, and S. M. Smith. 2013. Isolation and diversity analysis of resistance gene homologues from switchgrass, G3 (Bethesda) 3(6), 1031-1042. BESC
201310.1039/c3ra42818dZhu, Y., M. Regner, F. Lu, H. Kim, A. Mohammadi, T. J. Pearson, and J. Ralph. 2013. Preparation of monolignol ?-acetate, ?-p-hydroxycinnamate, and ?-p-hydroxybenzoate conjugates: selective deacylation of phenolic acetates with hydrazine acetate, RSC Advances 3(44), 21964. GLBRC
201210.1021/pr200851yAbraham, P., R. Adams, R. J. Giannone, U. Kalluri, P. Ranjan, B. Erickson, M. Shah, G. A. Tuskan, and R. L. Hettich. 2012. Defining the boundaries and characterizing the landscape of functional genome expression in vascular tissues of Populus using shotgun proteomics, J Proteome Res 11(1), 449-460. BESC
201210.1016/j.ymben.2012.08.003Agnew, D. E., A. K. Stevermer, J. T. Youngquist, and B. F. Pfleger. 2012. Engineering Escherichia coli for production of C(1)(2)-C(1)(4) polyhydroxyalkanoate from glucose, Metab Eng 14(6), 705-713. GLBRC
201210.1002/pmic.201290018Agrawal, G. K., A. Sarkar, R. Agrawal, B. K. Ndimba, G. Tanou, M. J. Dunn, T. Kieselbach, R. Cramer, S. Wienkoop, S. Chen, M. S. Rafudeen, R. Deswal, B. J. Barkla, W. Weckwerth, J. L. Heazlewood, J. Renaut, D. Job, N. Chakraborty, and R. Rakwal. 2012. Boosting the globalization of plant proteomics through INPPO: current developments and future prospects, Proteomics 12(3), 359-368. JBEI
201210.1111/j.1365-3040.2012.02485.xAllen, D. K., R. W. Laclair, J. B. Ohlrogge, and Y. Shachar-Hill. 2012. Isotope labelling of Rubisco subunits provides in vivo information on subcellular biosynthesis and exchange of amino acids between compartments, Plant Cell Environ 35(7), 1232-1244. GLBRC
201210.1039/c2cs35188aAlonso, D. M., S. G. Wettstein, and J. A. Dumesic. 2012. Bimetallic catalysts for upgrading of biomass to fuels and chemicals, Chem Soc Rev 41(24), 8075-8098. GLBRC
201210.1186/1754-6834-5-49Archambault-Leger, V., X. Shao, and L. R. Lynd. 2012. Integrated analysis of hydrothermal flow through pretreatment, Biotechnol Biofuels 5(1), 49. BESC
201210.3390/insects3010041Aylward, F. O., C. R. Currie, and G. Suen. 2012. The Evolutionary Innovation of Nutritional Symbioses in Leaf-Cutter Ants, Insects 3(1), 41-61. GLBRC
201210.1038/ismej.2012.10Aylward, F. O., K. E. Burnum, J. J. Scott, G. Suen, S. G. Tringe, S. M. Adams, K. W. Barry, C. D. Nicora, P. D. Piehowski, S. O. Purvine, G. J. Starrett, L. A. Goodwin, R. D. Smith, M. S. Lipton, and C. R. Currie. 2012. Metagenomic and metaproteomic insights into bacterial communities in leaf-cutter ant fungus gardens, ISME J 6(9), 1688-1701. GLBRC
201210.1039/c2gc35203fAzadi, P., R. Carrasquillo-Flores, Y. J. Pagán-Torres, E. I. Gürbüz, R. Farnood, and J. A. Dumesic. 2012. Catalytic conversion of biomass using solvents derived from lignin, Green Chemistry 14(6), 1573. GLBRC
2012Backhaus, J., and D. Rothamer. 2012. Design methodology for volatility characteristics of bio-derived drop-in gasoline fuels. In Spring Technical Meeting of the Central States Section of the Combustion Institute, Curran Associates, Inc., Dayton, Ohio.GLBRC
201210.1007/978-1-61779-827-6_9Baidoo, E. E., P. I. Benke, and J. D. Keasling. 2012. Mass spectrometry-based microbial metabolomics, Methods in Molecular Biology 881, 215-278. JBEI
2012Balan, V., L. da Costa Sousa, S. P. S. Chundawat, J. F. Humpula, and B. E. Dale. 2012. Overview to ammonia pretreatments for lignocellulosic biorefineries, Dynamic Biochemistry, Process Biotechnology and Molecular Biology, 1-11. DOI.GLBRC
2012Balan, V., S. Kumar, B. Bals, S. Chundawat, M. Jin, and B. Dale. 2012. Biochemical and thermochemical conversion of switchgrass to biofuels. In Switchgrass: A Valuable Biomass Crop for Energy, 153-185. Ed. A. Monti. SpringerGLBRC
201210.1016/j.biortech.2011.12.024Bals, B. D., and B. E. Dale. 2012. Developing a model for assessing biomass processing technologies within a local biomass processing depot, Bioresour Technol 106, 161-169. GLBRC
201210.1002/bit.24385.Banerjee, G., S. Car, T. Liu, D. L. Williams, S. L. Meza, J. D. Walton, and D. B. Hodge. 2012. Scale-up and integration of alkaline hydrogen peroxide pretreatment, enzymatic hydrolysis, and ethanolic fermentation, Biotechnol Bioeng 109(4), 922-931. GLBRC
201210.3389/fpls.2012.00092Bar-Peled, M., B. R. Urbanowicz, and M. A. O'Neill. 2012. The Synthesis and Origin of the Pectic Polysaccharide Rhamnogalacturonan II - Insights from Nucleotide Sugar Formation and Diversity, Front Plant Sci 3, 92. BESC
201210.1128/mBio.00053-12Basen, M., J. Sun, and M. W. Adams. 2012. Engineering a hyperthermophilic archaeon for temperature-dependent product formation, MBio 3(2), e00053-00012. BESC
201210.1007/978-1-62703-122-6_17Batth, T. S., J. D. Keasling, and C. J. Petzold. 2012. Targeted proteomics for metabolic pathway optimization, Methods in Molecular Biology 944, 237-249. JBEI
2012Beller, H. R., T. C. Legler, and S. R. Kane. 2012. Genetic manipulation of the obligate chemolithoautotrophic bacterium Thiobacillus denitrificans. In Microbial Systems Biology. Methods in Molecular Biology (Methods and Protocols), 99-136. Ed. A. Navid. Humana Press.JBEI
201210.1021/jp300354qBellesia, G., S. P. Chundawat, P. Langan, A. Redondo, B. E. Dale, and S. Gnanakaran. 2012. Coarse-grained model for the interconversion between native and liquid ammonia-treated crystalline cellulose, J Phys Chem B 116(28), 8031-8037. GLBRC
201210.1038/nbt.2196Bennetzen, J. L., J. Schmutz, H. Wang, R. Percifield, J. Hawkins, A. C. Pontaroli, M. Estep, L. Feng, J. N. Vaughn, J. Grimwood, J. Jenkins, K. Barry, E. Lindquist, U. Hellsten, S. Deshpande, X. Wang, X. Wu, T. Mitros, J. Triplett, X. Yang, C. Y. Ye, M. Mauro-Herrera, L. Wang, P. Li, M. Sharma, R. Sharma, P. C. Ronald, O. Panaud, E. A. Kellogg, T. P. Brutnell, A. N. Doust, G. A. Tuskan, D. Rokhsar, and K. M. Devos. 2012. Reference genome sequence of the model plant Setaria, Nat Biotechnol 30(6), 555-561. JBEI BESC
201210.1016/j.copbio.2011.10.002Blanch, H. W. 2012. Bioprocessing for biofuels, Curr Opin Biotechnol 23(3), 390-395. JBEI
201210.1128/JB.00266-12Blumer-Schuette, S. E., R. J. Giannone, J. V. Zurawski, I. Ozdemir, Q. Ma, Y. Yin, Y. Xu, I. Kataeva, F. L. Poole, 2nd, M. W. Adams, S. D. Hamilton-Brehm, J. G. Elkins, F. W. Larimer, M. L. Land, L. J. Hauser, R. W. Cottingham, R. L. Hettich, and R. M. Kelly. 2012. Caldicellulosiruptor core and pangenomes reveal determinants for noncellulosomal thermophilic deconstruction of plant biomass, J Bacteriol 194(15), 4015-4028. BESC
2012Bokinsky, G., D. Groff, and J. D. Keasling. 2012. Synthetic biology of microbial biofuel production: From enzymes to pathways to organisms. In Synthetic Biology: Tools and Applications, 207-223. Academic Press.JBEI
201210.1016/j.copbio.2011.12.006Borglin, S., D. Joyner, K. M. DeAngelis, J. Khudyakov, P. D'Haeseleer, M. P. Joachimiak, and T. Hazen. 2012. Application of phenotypic microarrays to environmental microbiology, Curr Opin Biotechnol 23(1), 41-48. JBEI
201210.1007/s10570-012-9697-1Brennan, M., J. P. McLean, C. M. Altaner, J. Ralph, and P. J. Harris. 2012. Cellulose microfibril angles and cell-wall polymers in different wood types of Pinus radiata, Cellulose 19(4), 1385-1404. GLBRC
201210.1111/j.1742-4658.2011.08402.xBroach, B., X. Gu, and M. Bar-Peled. 2012. Biosynthesis of UDP-glucuronic acid and UDP-galacturonic acid in Bacillus cereus subsp. cytotoxis NVH 391-98, FEBS J 279(1), 100-112. BESC
201210.1186/1471-2164-13-533Broadbent, J. R., E. C. Neeno-Eckwall, B. Stahl, K. Tandee, H. Cai, W. Morovic, P. Horvath, J. Heidenreich, N. T. Perna, R. Barrangou, and J. L. Steele. 2012. Analysis of the Lactobacillus casei supragenome and its influence in species evolution and lifestyle adaptation, BMC Genomics 13, 533. GLBRC
201210.1002/bbb.1353Brosse, N., A. Dufour, X. Meng, Q. Sun, and A. Ragauskas. 2012. Miscanthus: a fast-growing crop for biofuels and chemicals production, Biofuels, Bioproducts and Biorefining 6(5), 580-598. BESC
201210.1128/JB.00473-12Brown, S. D., R. Lamed, E. Morag, I. Borovok, Y. Shoham, D. M. Klingeman, C. M. Johnson, Z. Yang, M. L. Land, S. M. Utturkar, M. Keller, and E. A. Bayer. 2012. Draft genome sequences for Clostridium thermocellum wild-type strain YS and derived cellulose adhesion-defective mutant strain AD2, J Bacteriol 194(12), 3290-3291. BESC
201210.1007/978-1-61779-956-3_18Brunecky, R., J. O. Baker, H. Wei, L. E. Taylor, M. E. Himmel, and S. R. Decker. 2012. Analysis of transgenic glycoside hydrolases expressed in plants: T. reesei CBH I and A. cellulolyticus EI, Methods in Molecular Biology 908, 197-211. BESC
201210.1107/S0907444912001680Brunecky, R., M. Alahuhta, Y. J. Bomble, Q. Xu, J. O. Baker, S. Y. Ding, M. E. Himmel, and V. V. Lunin. 2012. Structure and function of the Clostridium thermocellum cellobiohydrolase A X1-module repeat: enhancement through stabilization of the CbhA complex, Acta Crystallogr D Biol Crystallogr 68(Pt 3), 292-299. BESC
201210.1186/1939-8433-5-17Cao, P., K. H. Jung, D. Choi, D. Hwang, J. Zhu, and P. C. Ronald. 2012. The Rice Oligonucleotide Array Database: an atlas of rice gene expression, Rice (N Y) 5(1), 17. JBEI
201210.1039/c2ra22045hCao, S., Y. Pu, M. Studer, C. Wyman, and A. J. Ragauskas. 2012. Chemical transformations of Populus trichocarpa during dilute acid pretreatment, RSC Advances 2(29), 10925. BESC
201210.1371/journal.pone.0052820Cetinkol, O. P., A. M. Smith-Moritz, G. Cheng, J. Lao, A. George, K. Hong, R. Henry, B. A. Simmons, J. L. Heazlewood, and B. M. Holmes. 2012. Structural and chemical characterization of hardwood from tree species with applications as bioenergy feedstocks, PLoS One 7(12), e52820. JBEI
201210.1074/jbc.R111.290072Chapman, K. D., and J. B. Ohlrogge. 2012. Compartmentation of triacylglycerol accumulation in plants, J Biol Chem 287(4), 2288-2294. GLBRC
201210.1073/pnas.1120992109Chen, F., Y. Tobimatsu, D. Havkin-Frenkel, R. A. Dixon, and J. Ralph. 2012. A polymer of caffeyl alcohol in plant seeds, Proc Natl Acad Sci U S A 109(5), 1772-1777. BESC GLBRC
201210.1186/1754-1611-6-1Chen, J., D. Densmore, T. S. Ham, J. D. Keasling, and N. J. Hillson. 2012. DeviceEditor visual biological CAD canvas, J Biol Eng 6(1), 1. JBEI
201210.1016/j.carres.2011.12.008Chen, M., Y. J. Bomble, M. E. Himmel, and J. W. Brady. 2012. Molecular dynamics simulations of the interaction of glucose with imidazole in aqueous solution, Carbohydr Res 349, 73-77. BESC
201210.1093/jxb/ers057Chen, X., and Y. Shachar-Hill. 2012. Insights into metabolic efficiency from flux analysis, J Exp Bot 63(6), 2343-2351. GLBRC
201210.1007/978-1-61779-956-3_21Chen, Y. R., S. Sarkanen, and Y. Y. Wang. 2012. Lignin-degrading enzyme activities, Methods in Molecular Biology 908, 251-268. BESC
201210.1074/jbc.M112.362640Chen, Z., G. D. Friedland, J. H. Pereira, S. A. Reveco, R. Chan, J. I. Park, M. P. Thelen, P. D. Adams, A. P. Arkin, J. D. Keasling, H. W. Blanch, B. A. Simmons, K. L. Sale, D. Chivian, and S. R. Chhabra. 2012. Tracing determinants of dual substrate specificity in glycoside hydrolase family 5, J Biol Chem 287(30), 25335-25343. JBEI
201210.1021/la300938bCheng, G., M. S. Kent, L. He, P. Varanasi, D. Dibble, R. Arora, K. Deng, K. Hong, Y. B. Melnichenko, B. A. Simmons, and S. Singh. 2012. Effect of ionic liquid treatment on the structures of lignins in solutions: molecular subunits released from lignin, Langmuir 28(32), 11850-11857. JBEI
201210.1021/jp304538vCheng, G., P. Varanasi, R. Arora, V. Stavila, B. A. Simmons, M. S. Kent, and S. Singh. 2012. Impact of ionic liquid pretreatment conditions on cellulose crystalline structure using 1-ethyl-3-methylimidazolium acetate, J Phys Chem B 116(33), 10049-10054. JBEI
201210.1038/ng.2313Cheng, G., S. Datta, Z. Liu, C. Wang, J. K. Murton, P. A. Brown, M. S. Jablin, M. Dubey, J. Majewski, C. E. Halbert, J. F. Browning, A. R. Esker, B. J. Watson, H. Zhang, S. W. Hutcheson, D. L. Huber, K. L. Sale, B. A. Simmons, and M. S. Kent. 2012. Interactions of endoglucanases with amorphous cellulose films resolved by neutron reflectometry and quartz crystal microbalance with dissipation monitoring, Langmuir 28(22), 8348-8358. 10.1021/la300955q.JBEI
2012Chia, J. M., C. Song, P. J. Bradbury, D. Costich, N. de Leon, J. Doebley, R. J. Elshire, B. Gaut, L. Geller, J. C. Glaubitz, M. Gore, K. E. Guill, J. Holland, M. B. Hufford, J. Lai, M. Li, X. Liu, Y. Lu, R. McCombie, R. Nelson, J. Poland, B. M. Prasanna, T. Pyhajarvi, T. Rong, R. S. Sekhon, Q. Sun, M. I. Tenaillon, F. Tian, J. Wang, X. Xu, Z. Zhang, S. M. Kaeppler, J. Ross-Ibarra, M. D. McMullen, E. S. Buckler, G. Zhang, Y. Xu, and D. Ware. 2012. Maize HapMap2 identifies extant variation from a genome in flux, Nat Genet 44(7), 803-807. GLBRC
201210.1073/pnas.1202079109Chiniquy, D., V. Sharma, A. Schultink, E. E. Baidoo, C. Rautengarten, K. Cheng, A. Carroll, P. Ulvskov, J. Harholt, J. D. Keasling, M. Pauly, H. V. Scheller, and P. C. Ronald. 2012. XAX1 from glycosyltransferase family 61 mediates xylosyltransfer to rice xylan, Proc Natl Acad Sci U S A 109(42), 17117-17122. JBEI
201210.1093/pcp/pcs131Chiu, T. Y., K. Christiansen, I. Moreno, J. Lao, D. Loque, A. Orellana, J. L. Heazlewood, G. Clark, and S. J. Roux. 2012. AtAPY1 and AtAPY2 function as Golgi-localized nucleoside diphosphatases in Arabidopsis thaliana, Plant Cell Physiol 53(11), 1913-1925. JBEI
201210.1128/AEM.01175-12Chou, H. H., and J. D. Keasling. 2012. Synthetic pathway for production of five-carbon alcohols from isopentenyl diphosphate, Appl Environ Microbiol 78(22), 7849-7855. JBEI
201210.1186/1752-0509-6-84Chou, I. C., and E. O. Voit. 2012. Estimation of dynamic flux profiles from metabolic time series data, BMC Syst Biol 6, 84. BESC
201210.1016/j.jcs.2011.10.005Christensen, U., and H. V. Scheller. 2012. Regulation of (1,3;1,4)-ß-d-glucan synthesis in developing endosperm of barley lys mutants, Journal of Cereal Science 55(1), 69-76. JBEI
201210.1016/j.indcrop.2011.07.025Chundawat, S. P. S., L. Chang, C. Gunawan, V. Balan, C. McMahan, and B. E. Dale. 2012. Guayule as a feedstock for lignocellulosic biorefineries using ammonia fiber expansion (AFEX) pretreatment, Industrial Crops and Products 37(1), 486-492. GLBRC
201210.1371/journal.pone.0043844Chung, D., J. Farkas, J. R. Huddleston, E. Olivar, and J. Westpheling. 2012. Methylation by a unique alpha-class N4-cytosine methyltransferase is required for DNA transformation of Caldicellulosiruptor bescii DSM6725, PLoS One 7(8), e43844. BESC
201210.1105/tpc.112.100669Consortium, I. A. I. 2012. Taking the next step: building an Arabidopsis information portal, Plant Cell 24(6), 2248-2256. JBEI
201210.1007/978-1-61779-956-3_20Corea, O. R., C. Ki, C. L. Cardenas, L. B. Davin, and N. G. Lewis. 2012. Laser microdissection and genetic manipulation technologies to probe lignin heterogeneity and configuration in plant cell walls, Methods in Molecular Biology 908, 229-250. BESC
201210.1021/ie300487zCui, Z., C. Wan, J. Shi, R. W. Sykes, and Y. Li. 2012. Enzymatic Digestibility of Corn Stover Fractions in Response to Fungal Pretreatment, Industrial & Engineering Chemistry Research 51(21), 7153-7159. BESC
2012Currie, C. R. 2012. The tangled banks of ants and microbes. In Microbes and Evolution: The World That Darwin Never Saw, 181-190. ASM Press.GLBRC
201210.3389/fpls.2012.00236Czarnecki, O., C. Glasser, J. G. Chen, K. F. Mayer, and B. Grimm. 2012. Evidence for a Contribution of ALA Synthesis to Plastid-To-Nucleus Signaling, Front Plant Sci 3, 236. BESC
201210.1002/btpr.1575Dale, B. E., and R. G. Ong. 2012. Energy, wealth, and human development: why and how biomass pretreatment research must improve, Biotechnol Prog 28(4), 893-898. GLBRC
201210.1089/ind.2012.1527Davison, B. H. 2012. The Increasing Importance and Capabilities of Biomass Characterization, Industrial Biotechnology 8(4), 189-190. BESC
201210.3389/fpls.2012.00062De Michele, R., D. Loque, S. Lalonde, and W. B. Frommer. 2012. Ammonium and urea transporter inventory of the selaginella and physcomitrella genomes, Front Plant Sci 3, 62. JBEI
201210.1007/s12155-012-9268-1de Souza, A. P., D. C. C. Leite, S. Pattathil, M. G. Hahn, and M. S. Buckeridge. 2012. Composition and Structure of Sugarcane Cell Wall Polysaccharides: Implications for Second-Generation Bioethanol Production, BioEnergy Research 6(2), 564-579. BESC
201210.1128/mBio.00249-11DeAngelis, K. M., J. L. Fortney, S. Borglin, W. L. Silver, B. A. Simmons, and T. C. Hazen. 2012. Anaerobic decomposition of switchgrass by tropical soil-derived feedstock-adapted consortia, MBio 3(1). JBEI
201210.1007/978-1-61779-956-3_17Decker, S. R., M. Carlile, M. J. Selig, C. Doeppke, M. Davis, R. Sykes, G. Turner, and A. Ziebell. 2012. Reducing the effect of variable starch levels in biomass recalcitrance screening, Methods in Molecular Biology 908, 181-195. BESC
201210.1021/jf301002ndel Rio, J. C., J. Rencoret, P. Prinsen, A. T. Martinez, J. Ralph, and A. Gutierrez. 2012. Structural characterization of wheat straw lignin as revealed by analytical pyrolysis, 2D-NMR, and reductive cleavage methods, J Agric Food Chem 60(23), 5922-5935. GLBRC
201210.1021/jf300099gdel Rio, J. C., P. Prinsen, J. Rencoret, L. Nieto, J. Jimenez-Barbero, J. Ralph, A. T. Martinez, and A. Gutierrez. 2012. Structural characterization of the lignin in the cortex and pith of elephant grass (Pennisetum purpureum) stems, J Agric Food Chem 60(14), 3619-3634. GLBRC
201210.1002/rcm.6134Deng, K., K. W. George, W. Reindl, J. D. Keasling, P. D. Adams, T. S. Lee, A. K. Singh, and T. R. Northen. 2012. Encoding substrates with mass tags to resolve stereospecific reactions using Nimzyme, Rapid Commun Mass Spectrom 26(6), 611-615. JBEI
201210.1007/978-1-61779-956-3_3Ding, S. Y., and Y. S. Liu. 2012. Imaging cellulose using atomic force microscopy, Methods in Molecular Biology 908, 23-30. BESC
201210.1126/science.1227491Ding, S. Y., Y. S. Liu, Y. Zeng, M. E. Himmel, J. O. Baker, and E. A. Bayer. 2012. How does plant cell wall nanoscale architecture correlate with enzymatic digestibility?, Science 338(6110), 1055-1060. BESC
201210.1186/1472-6750-12-38Dougherty, M. J., P. D'Haeseleer, T. C. Hazen, B. A. Simmons, P. D. Adams, and M. Z. Hadi. 2012. Glycoside hydrolases from a targeted compost metagenome, activity-screening and functional characterization, BMC Biotechnol 12, 38. JBEI
201210.1007/s12155-012-9204-4Duceppe, M.-O., A. Bertrand, S. Pattathil, J. Miller, Y. Castonguay, M. G. Hahn, R. Michaud, and M.-P. Dubé. 2012. Assessment of Genetic Variability of Cell Wall Degradability for the Selection of Alfalfa with Improved Saccharification Efficiency, BioEnergy Research 5(4), 904-914. BESC
201210.1016/B978-0-12-394423-8.00001-9Dufour, Y. S., and T. J. Donohue. 2012. Signal correlations in ecological niches can shape the organization and evolution of bacterial gene regulatory networks, Adv Microb Physiol 61, 1-36. GLBRC
2012Egbendewe-Mondzozo, A., S. M. Swinton, R. C. Izaurralde, D. H. Manowitz, and X. Zhang. 2012. Maintaining environmental quality while expanding energy biomass production: policy simulations from Michigan, USA. In International Association of Agricultural Economists (IAAE) Triennial Conference, Foz do Iguaçu, Brazil.GLBRC
201210.1021/ac203390vEllinger, J. J., D. C. Miller, I. A. Lewis, and J. L. Markley. 2012. Semiautomated device for batch extraction of metabolites from tissue samples, Anal Chem 84(4), 1809-1812. GLBRC
201210.1016/j.biortech.2011.09.128Ellis, L. D., E. K. Holwerda, D. Hogsett, S. Rogers, X. Shao, T. Tschaplinski, P. Thorne, and L. R. Lynd. 2012. Closing the carbon balance for fermentation by Clostridium thermocellum (ATCC 27405), Bioresour Technol 103(1), 293-299. BESC
201210.1186/1754-6834-5-59Elumalai, S., Y. Tobimatsu, J. H. Grabber, X. Pan, and J. Ralph. 2012. Epigallocatechin gallate incorporation into lignin enhances the alkaline delignification and enzymatic saccharification of cell walls, Biotechnol Biofuels 5(1), 59. GLBRC
201210.1111/j.1467-7652.2012.00692.xEudes, A., A. George, P. Mukerjee, J. S. Kim, B. Pollet, P. I. Benke, F. Yang, P. Mitra, L. Sun, O. P. Cetinkol, S. Chabout, G. Mouille, L. Soubigou-Taconnat, S. Balzergue, S. Singh, B. M. Holmes, A. Mukhopadhyay, J. D. Keasling, B. A. Simmons, C. Lapierre, J. Ralph, and D. Loque. 2012. Biosynthesis and incorporation of side-chain-truncated lignin monomers to reduce lignin polymerization and enhance saccharification, Plant Biotechnol J 10(5), 609-620. GLBRC JBEI
201210.1128/AEM.00936-12Farkas, J., K. Stirrett, G. L. Lipscomb, W. Nixon, R. A. Scott, M. W. Adams, and J. Westpheling. 2012. Recombinogenic properties of Pyrococcus furiosus strain COM1 enable rapid selection of targeted mutants, Appl Environ Microbiol 78(13), 4669-4676. BESC
201210.1089/ind.2012.0015Foston, M., and A. J. Ragauskas. 2012. Biomass Characterization: Recent Progress in Understanding Biomass Recalcitrance, Industrial Biotechnology 8(4), 191-208. BESC
201210.1021/jf204853bFoston, M., R. Katahira, E. Gjersing, M. F. Davis, and A. J. Ragauskas. 2012. Solid-state selective (13)C excitation and spin diffusion NMR to resolve spatial dimensions in plant cell walls, J Agric Food Chem 60(6), 1419-1427. BESC
201210.1039/c2an35344jFoston, M., R. Samuel, and A. J. Ragauskas. 2012. 13C cell wall enrichment and ionic liquid NMR analysis: progress towards a high-throughput detailed chemical analysis of the whole plant cell wall, Analyst 137(17), 3904-3909. BESC
201210.1016/j.coche.2012.07.003Frock, A. D., and R. M. Kelly. 2012. Extreme Thermophiles: Moving beyond single-enzyme biocatalysis, Curr Opin Chem Eng 1(4), 363-372. BESC
201210.1111/j.1467-7652.2011.00677.xFu, C., R. Sunkar, C. Zhou, H. Shen, J. Y. Zhang, J. Matts, J. Wolf, D. G. Mann, C. N. Stewart, Jr., Y. Tang, and Z. Y. Wang. 2012. Overexpression of miR156 in switchgrass (Panicum virgatum L.) results in various morphological alterations and leads to improved biomass production, Plant Biotechnol J 10(4), 443-452. BESC
201210.1016/B978-0-12-415931-0.00018-5Gardner, J. G., and D. H. Keating. 2012. Genetic and functional genomic approaches for the study of plant cell wall degradation in Cellvibrio japonicus, Methods Enzymol 510, 331-347. GLBRC
201210.1007/s10529-011-0742-1Gardner, J. G., L. A. Zeitler, W. J. Wigstrom, K. C. Engel, and D. H. Keating. 2012. A high-throughput solid phase screening method for identification of lignocellulose-degrading bacteria from environmental isolates, Biotechnol Lett 34(1), 81-89. GLBRC
201210.1016/j.biombioe.2011.12.036Garlock, R. J., B. Bals, P. Jasrotia, V. Balan, and B. E. Dale. 2012. Influence of variable species composition on the saccharification of AFEX™ pretreated biomass from unmanaged fields in comparison to corn stover, Biomass and Bioenergy 37, 49-59. GLBRC
201210.1016/j.biortech.2011.11.034Garlock, R. J., V. Balan, and B. E. Dale. 2012. Optimization of AFEX pretreatment conditions and enzyme mixtures to maximize sugar release from upland and lowland switchgrass, Bioresour Technol 104, 757-768. GLBRC
201210.1128/AEM.01959-12Gartner, K., S. Lechno-Yossef, A. J. Cornish, C. P. Wolk, and E. L. Hegg. 2012. Expression of Shewanella oneidensis MR-1 [FeFe]-hydrogenase genes in Anabaena sp. strain PCC 7120, Appl Environ Microbiol 78(24), 8579-8586. GLBRC
201210.1007/978-1-61779-956-3_14Gilbert, J., L. L. Li, S. Taghavi, S. M. McCorkle, S. Tringe, and D. van der Lelie. 2012. Bioprospecting metagenomics for new glycoside hydrolases, Methods in Molecular Biology 908, 141-151. BESC
201210.1002/bit.24388Gladden, J. M., S. A. Eichorst, T. C. Hazen, B. A. Simmons, and S. W. Singer. 2012. Substrate perturbation alters the glycoside hydrolase activities and community composition of switchgrass-adapted bacterial consortia, Biotechnol Bioeng 109(5), 1140-1145. JBEI
201210.1128/AEM.06785-11Goh, E. B., E. E. Baidoo, J. D. Keasling, and H. R. Beller. 2012. Engineering of bacterial methyl ketone synthesis for biofuels, Appl Environ Microbiol 78(1), 70-80. JBEI
2012Golberg, A., G. Linshiz, M. Koudritsky, A. Chemodanov, and N. J. Hillson. 2012. Distributed Marine Biorefineries for Developing Economies. In Energy, Parts A and B, 493-501. ASME International Mechanical Engineering Congress and Exposition.JBEI
201210.1038/ismej.2011.163Graham, D. E., M. D. Wallenstein, T. A. Vishnivetskaya, M. P. Waldrop, T. J. Phelps, S. M. Pfiffner, T. C. Onstott, L. G. Whyte, E. M. Rivkina, D. A. Gilichinsky, D. A. Elias, R. Mackelprang, N. C. VerBerkmoes, R. L. Hettich, D. Wagner, S. D. Wullschleger, and J. K. Jansson. 2012. Microbes in thawing permafrost: the unknown variable in the climate change equation, ISME J 6(4), 709-712. JBEI
201210.1007/s00216-012-5908-8Greving, M., X. Cheng, W. Reindl, B. Bowen, K. Deng, K. Louie, M. Nyman, J. Cohen, A. Singh, B. Simmons, P. Adams, G. Siuzdak, and T. Northen. 2012. Acoustic deposition with NIMS as a high-throughput enzyme activity assay, Anal Bioanal Chem 403(3), 707-711. JBEI
201210.1093/ae/58.3.172Grieshop, M. J., B. Werling, K. Buehrer, J. Perrone, R. Isaacs, and D. Landis. 2012. Big Brother is Watching: Studying Insect Predation in the Age of Digital Surveillance, American Entomologist 58(3), 172-182. GLBRC
201210.1128/AEM.06761-11Groff, D., P. I. Benke, T. S. Batth, G. Bokinsky, C. J. Petzold, P. D. Adams, and J. D. Keasling. 2012. Supplementation of intracellular XylR leads to coutilization of hemicellulose sugars, Appl Environ Microbiol 78(7), 2221-2229. JBEI
2012Gunckel, K., L. Mohan, B. A. Covitt, and C. W. Anderson. 2012. Addressing challenges in developing learning progressions for environmental science literacy. In Learning progressions in science: Current challenges and future directions, 39-75. Eds. A. Alonzo, and A. Gotwals. Sense Publishers.GLBRC
201210.1002/cssc.201100608Gurbuz, E. I., S. G. Wettstein, and J. A. Dumesic. 2012. Conversion of hemicellulose to furfural and levulinic acid using biphasic reactors with alkylphenol solvents, ChemSusChem 5(2), 383-387. GLBRC
201210.1186/1754-6834-5-30Guss, A. M., D. G. Olson, N. C. Caiazza, and L. R. Lynd. 2012. Dcm methylation is detrimental to plasmid transformation in Clostridium thermocellum, Biotechnol Biofuels 5(1), 30. BESC
201210.1007/s00253-012-3968-5Haft, R. J., J. G. Gardner, and D. H. Keating. 2012. Quantitative colorimetric measurement of cellulose degradation under microbial culture conditions, Appl Microbiol Biotechnol 94(1), 223-229. GLBRC
201210.1093/nar/gks531Ham, T. S., Z. Dmytriv, H. Plahar, J. Chen, N. J. Hillson, and J. D. Keasling. 2012. Design, implementation and practice of JBEI-ICE: an open source biological part registry platform and tools, Nucleic Acids Res 40(18), e141. JBEI
201210.1007/978-1-61779-956-3_15Hamilton-Brehm, S. D., T. A. Vishnivetskaya, S. L. Allman, J. R. Mielenz, and J. G. Elkins. 2012. Anaerobic high-throughput cultivation method for isolation of thermophiles using biomass-derived substrates, Methods in Molecular Biology 908, 153-168. BESC
201210.3389/fpls.2012.00059Hansen, S. F., J. Harholt, A. Oikawa, and H. V. Scheller. 2012. Plant Glycosyltransferases Beyond CAZy: A Perspective on DUF Families, Front Plant Sci 3, 59. JBEI
201210.1371/journal.pone.0033071Hansey, C. N., B. Vaillancourt, R. S. Sekhon, N. de Leon, S. M. Kaeppler, and C. R. Buell. 2012. Maize (Zea mays L.) genome diversity as revealed by RNA-sequencing, PLoS One 7(3), e33071. GLBRC
201210.1371/journal.pone.0035846Harholt, J., I. Sorensen, J. Fangel, A. Roberts, W. G. Willats, H. V. Scheller, B. L. Petersen, J. A. Banks, and P. Ulvskov. 2012. The glycosyltransferase repertoire of the spikemoss Selaginella moellendorffii and a comparative study of its cell wall, PLoS One 7(5), e35846. JBEI
201210.1007/s00425-012-1592-3Harholt, J., J. K. Jensen, Y. Verhertbruggen, C. Sogaard, S. Bernard, M. Nafisi, C. P. Poulsen, N. Geshi, Y. Sakuragi, A. Driouich, J. P. Knox, and H. V. Scheller. 2012. ARAD proteins associated with pectic Arabinan biosynthesis form complexes when transiently overexpressed in planta, Planta 236(1), 115-128. GLBRC JBEI
201210.1016/j.funbio.2012.07.009Hastrup, A. C., C. Howell, F. H. Larsen, N. Sathitsuksanoh, B. Goodell, and J. Jellison. 2012. Differences in crystalline cellulose modification due to degradation by brown and white rot fungi, Fungal Biol 116(10), 1052-1063. JBEI
201210.1021/sb2000116Hillson, N. J., R. D. Rosengarten, and J. D. Keasling. 2012. j5 DNA assembly design automation software, ACS Synth Biol 1(1), 14-21. JBEI
201210.1007/978-1-61779-956-3_1Himmel, M. E., S. R. Decker, and D. K. Johnson. 2012. Challenges for assessing the performance of biomass degrading biocatalysts, Methods in Molecular Biology 908, 1-8. BESC
201210.1126/science.1224682Hittinger, C. T. 2012. Evolution. Endless rots most beautiful, Science 336(6089), 1649-1650. GLBRC
201210.1007/s10295-012-1091-3Holwerda, E. K., K. D. Hirst, and L. R. Lynd. 2012. A defined growth medium with very low background carbon for culturing Clostridium thermocellum, J Ind Microbiol Biotechnol 39(6), 943-947. BESC
201210.1002/jbio.201100139Hoover, E. E., J. J. Field, D. G. Winters, M. D. Young, E. V. Chandler, J. C. Speirs, J. T. Lapenna, S. M. Kim, S. Y. Ding, R. A. Bartels, J. W. Wang, and J. A. Squier. 2012. Eliminating the scattering ambiguity in multifocal, multimodal, multiphoton imaging systems, J Biophotonics 5(5-6), 425-436. BESC
201210.1002/ep.10599Hoover, S. W., J. T. Youngquist, P. A. Angart, S. T. Withers, R. M. Lennen, and B. F. Pfleger. 2012. Isolation of improved free fatty acid overproducing strains of Escherichia coli via Nile red based high-throughput screening, Environ Prog Sustain Energy 31(1), 17-23. GLBRC
2012Howe, A., J. Pell, R. Canino-Koning, R. Mackelprang, S. G. Tringe, J. K. Jansson, J. M. Tiedje, and C. T. Brown. 2012. Illumina Sequencing Artifacts Revealed by Connectivity Analysis of Metagenomic Datasets.GLBRC
201210.1007/s12155-012-9208-0Hu, F., and A. Ragauskas. 2012. Pretreatment and Lignocellulosic Chemistry, BioEnergy Research 5(4), 1043-1066. BESC
201210.1021/sc300032jHu, F., S. Jung, and A. Ragauskas. 2012. Impact of Pseudolignin versus Dilute Acid-Pretreated Lignin on Enzymatic Hydrolysis of Cellulose, ACS Sustainable Chemistry & Engineering 1(1), 62-65. BESC
201210.1016/j.biortech.2012.04.037Hu, F., S. Jung, and A. Ragauskas. 2012. Pseudo-lignin formation and its impact on enzymatic hydrolysis, Bioresour Technol 117, 7-12. BESC
201210.1038/ng.2309Hufford, M. B., X. Xu, J. van Heerwaarden, T. Pyhajarvi, J. M. Chia, R. A. Cartwright, R. J. Elshire, J. C. Glaubitz, K. E. Guill, S. M. Kaeppler, J. Lai, P. L. Morrell, L. M. Shannon, C. Song, N. M. Springer, R. A. Swanson-Wagner, P. Tiffin, J. Wang, G. Zhang, J. Doebley, M. D. McMullen, D. Ware, E. S. Buckler, S. Yang, and J. Ross-Ibarra. 2012. Comparative population genomics of maize domestication and improvement, Nat Genet 44(7), 808-811. GLBRC
201210.1093/bioinformatics/bts429Hyatt, D., P. F. LoCascio, L. J. Hauser, and E. C. Uberbacher. 2012. Gene and translation initiation site prediction in metagenomic sequences, Bioinformatics 28(17), 2223-2230. BESC
201210.1093/treephys/tps032Induri, B. R., D. R. Ellis, G. T. Slavov, T. Yin, X. Zhang, W. Muchero, G. A. Tuskan, and S. P. DiFazio. 2012. Identification of quantitative trait loci and candidate genes for cadmium tolerance in Populus, Tree Physiol 32(5), 626-638. BESC
2012Izaurralde, R. C., W. B. McGill, and J. R. Williams. 2012. Development and application of the EPIC Model for carbon cycle, greenhouse gas mitigation, and biofuel studies. In Managing Agricultural Greenhouse Gases: Coordinated Agricultural Research through GRACEnet to Address our Changing Climate, 293-308. Eds. M. A. Liebig, A. J. Franzluebbers, and R. F. Follett. Academic Press.GLBRC
201210.4056/sigs.2535732Izquierdo, J. A., L. Goodwin, K. W. Davenport, H. Teshima, D. Bruce, C. Detter, R. Tapia, S. Han, M. Land, L. Hauser, C. D. Jeffries, J. Han, S. Pitluck, M. Nolan, A. Chen, M. Huntemann, K. Mavromatis, N. Mikhailova, K. Liolios, T. Woyke, and L. R. Lynd. 2012. Complete Genome Sequence of Clostridium clariflavum DSM 19732, Stand Genomic Sci 6(1), 104-115. BESC
201210.1093/mp/sss032Jensen, J. K., A. Schultink, K. Keegstra, C. G. Wilkerson, and M. Pauly. 2012. RNA-Seq analysis of developing nasturtium seeds (Tropaeolum majus): identification and characterization of an additional galactosyltransferase involved in xyloglucan biosynthesis, Mol Plant 5(5), 984-992. GLBRC
2012Jin, H., and C. W. Anderson. 2012. Developing assessments for a learning progression on carbon-transforming processes in socio-ecological systems. In Learning progressions in science: Current challenges and future directions, 151-181. Sense Publishers.GLBRC
201210.1039/c2ee03058fJin, M., C. Gunawan, N. Uppugundla, V. Balan, and B. E. Dale. 2012. A novel integrated biological process for cellulosic ethanol production featuring high ethanol productivity, enzyme recycling and yeast cells reuse, Energy & Environmental Science 5(5), 7168. GLBRC
201210.1002/bit.24458Jin, M., C. Gunawan, V. Balan, and B. E. Dale. 2012. Consolidated bioprocessing (CBP) of AFEX-pretreated corn stover for ethanol production using Clostridium phytofermentans at a high solids loading, Biotechnol Bioeng 109(8), 1929-1936. GLBRC
201210.1016/j.biortech.2012.01.150Jin, M., C. Gunawan, V. Balan, M. W. Lau, and B. E. Dale. 2012. Simultaneous saccharification and co-fermentation (SSCF) of AFEX(TM) pretreated corn stover for ethanol production using commercial enzymes and Saccharomyces cerevisiae 424A(LNH-ST), Bioresour Technol 110, 587-594. GLBRC
201210.1016/j.biortech.2012.01.154Jin, M., V. Balan, C. Gunawan, and B. E. Dale. 2012. Quantitatively understanding reduced xylose fermentation performance in AFEX treated corn stover hydrolysate using Saccharomyces cerevisiae 424A (LNH-ST) and Escherichia coli KO11, Bioresour Technol 111, 294-300. GLBRC
201210.1002/pmic.201290014Jones, A. M., R. Aebersold, C. H. Ahrens, R. Apweiler, K. Baerenfaller, M. Baker, E. Bendixen, S. Briggs, P. Brownridge, E. Brunner, M. Daube, E. W. Deutsch, U. Grossniklaus, J. Heazlewood, M. O. Hengartner, H. Hermjakob, M. Jovanovic, C. Lawless, G. Lochnit, L. Martens, C. Ravnsborg, S. P. Schrimpf, Y. H. Shim, D. Subasic, A. Tholey, K. Wijk, C. Mering, M. Weiss, and X. Zheng. 2012. The HUPO initiative on Model Organism Proteomes, iMOP, Proteomics 12(3), 340-345. JBEI
201210.1093/bioinformatics/bts133Joshi, H. J., K. M. Christiansen, J. Fitz, J. Cao, A. Lipzen, J. Martin, A. M. Smith-Moritz, L. A. Pennacchio, W. S. Schackwitz, D. Weigel, and J. L. Heazlewood. 2012. 1001 Proteomes: a functional proteomics portal for the analysis of Arabidopsis thaliana accessions, Bioinformatics 28(10), 1303-1306. JBEI
201210.1016/j.biotechadv.2011.08.006Joyce, B. L., and C. N. Stewart, Jr. 2012. Designing the perfect plant feedstock for biofuel production: using the whole buffalo to diversify fuels and products, Biotechnol Adv 30(5), 1011-1022. BESC
201210.1128/AEM.06017-11Juminaga, D., E. E. Baidoo, A. M. Redding-Johanson, T. S. Batth, H. Burd, A. Mukhopadhyay, C. J. Petzold, and J. D. Keasling. 2012. Modular engineering of L-tyrosine production in Escherichia coli, Appl Environ Microbiol 78(1), 89-98. JBEI
201210.1002/anie.201205243Jung, S., M. Foston, U. C. Kalluri, G. A. Tuskan, and A. J. Ragauskas. 2012. 3D chemical image using TOF-SIMS revealing the biopolymer component spatial and lateral distributions in biomass, Angew Chem Int Ed Engl 51(48), 12005-12008. BESC
201210.5402/2012/682824Kaeppler, S. 2012. Heterosis: Many Genes, Many Mechanisms—End the Search for an Undiscovered Unifying Theory, ISRN Botany 2012, 1-12. GLBRC
201210.1093/nar/gks403Karpinets, T. V., B. H. Park, and E. C. Uberbacher. 2012. Analyzing large biological datasets with association networks, Nucleic Acids Res 40(17), e131. BESC
2012Kashefi, K. 2012. Hyperthermophiles: metabolic diversity and biotechnological applications. In Extremophiles: Microbiology and Biotechnology, 183-232. Caister Academic Press.GLBRC
201210.1104/pp.112.196717Kaur, H., K. Shaker, N. Heinzel, J. Ralph, I. Galis, and I. T. Baldwin. 2012. Environmental stresses of field growth allow cinnamyl alcohol dehydrogenase-deficient Nicotiana attenuata plants to compensate for their structural deficiencies, Plant Physiol 159(4), 1545-1570. GLBRC
201210.1016/j.ymben.2012.01.004Keasling, J. D. 2012. Synthetic biology and the development of tools for metabolic engineering, Metab Eng 14(3), 189-195. JBEI
201210.1038/492188aKeasling, J. D., A. Mendoza, and P. S. Baran. 2012. Synthesis: A constructive debate, Nature 492(7428), 188-189. JBEI
201210.1073/pnas.1112750109Khudyakov, J. I., P. D'Haeseleer, S. E. Borglin, K. M. Deangelis, H. Woo, E. A. Lindquist, T. C. Hazen, B. A. Simmons, and M. P. Thelen. 2012. Global transcriptome response to ionic liquid by a tropical rain forest soil bacterium, Enterobacter lignolyticus, Proc Natl Acad Sci U S A 109(32), E2173-2182. JBEI
201210.1186/gb-2012-13-9-r78Kim, J., and J. L. Reed. 2012. RELATCH: relative optimality in metabolic networks explains robust metabolic and regulatory responses to perturbations, Genome Biol 13(9), R78. GLBRC
201210.3389/fpls.2012.00028Kim, S. J., and F. Brandizzi. 2012. News and Views into the SNARE Complexity in Arabidopsis, Front Plant Sci 3, 28. GLBRC
201210.1016/j.biombioe.2012.07.015Kim, S., B. E. Dale, and R. G. Ong. 2012. An alternative approach to indirect land use change: Allocating greenhouse gas effects among different uses of land, Biomass and Bioenergy 46, 447-452. GLBRC
201210.1007/s11103-012-9880-7Kim, W. C., J. H. Ko, and K. H. Han. 2012. Identification of a cis-acting regulatory motif recognized by MYB46, a master transcriptional regulator of secondary wall biosynthesis, Plant Mol Biol 78(4-5), 489-501. GLBRC
201210.1002/bit.24370Klein-Marcuschamer, D., P. Oleskowicz-Popiel, B. A. Simmons, and H. W. Blanch. 2012. The challenge of enzyme cost in the production of lignocellulosic biofuels, Biotechnol Bioeng 109(4), 1083-1087. JBEI
201210.1038/nbt.2235Knight, R., J. Jansson, D. Field, N. Fierer, N. Desai, J. A. Fuhrman, P. Hugenholtz, D. van der Lelie, F. Meyer, R. Stevens, M. J. Bailey, J. I. Gordon, G. A. Kowalchuk, and J. A. Gilbert. 2012. Unlocking the potential of metagenomics through replicated experimental design, Nat Biotechnol 30(6), 513-520. JBEI
201210.1111/j.1467-7652.2012.00690.xKo, J. H., H. T. Kim, I. Hwang, and K. H. Han. 2012. Tissue-type-specific transcriptome analysis identifies developing xylem-specific promoters in poplar, Plant Biotechnol J 10(5), 587-596. GLBRC
201210.1093/mp/sss076Ko, J. H., W. C. Kim, J. Y. Kim, S. J. Ahn, and K. H. Han. 2012. MYB46-mediated transcriptional regulation of secondary wall biosynthesis, Mol Plant 5(5), 961-963. GLBRC
201210.1016/j.copbio.2011.10.003Kontur, W. S., D. R. Noguera, and T. J. Donohue. 2012. Maximizing reductant flow into microbial H2 production, Curr Opin Biotechnol 23(3), 382-389. GLBRC
201210.1128/JB.01214-12Kontur, W. S., W. S. Schackwitz, N. Ivanova, J. Martin, K. Labutti, S. Deshpande, H. N. Tice, C. Pennacchio, E. Sodergren, G. M. Weinstock, D. R. Noguera, and T. J. Donohue. 2012. Revised sequence and annotation of the Rhodobacter sphaeroides 2.4.1 genome, J Bacteriol 194(24), 7016-7017. GLBRC
201210.1104/pp.112.201822Kosma, D. K., I. Molina, J. B. Ohlrogge, and M. Pollard. 2012. Identification of an Arabidopsis fatty alcohol:caffeoyl-Coenzyme A acyltransferase required for the synthesis of alkyl hydroxycinnamates in root waxes, Plant Physiol 160(1), 237-248. GLBRC
201210.1093/glycob/cwr117Kulkarni, A. R., M. J. Pena, U. Avci, K. Mazumder, B. R. Urbanowicz, S. Pattathil, Y. Yin, M. A. O'Neill, A. W. Roberts, M. G. Hahn, Y. Xu, A. G. Darvill, and W. S. York. 2012. The ability of land plants to synthesize glucuronoxylans predates the evolution of tracheophytes, Glycobiology 22(3), 439-451. BESC
201210.1089/ind.2012.0014Kulkarni, A. R., S. Pattathil, M. G. Hahn, W. S. York, and M. A. O'Neill. 2012. Comparison of Arabinoxylan Structure in Bioenergy and Model Grasses, Industrial Biotechnology 8(4), 222-229. BESC
201210.1016/j.ymben.2011.11.005Kumar, S., F. M. Hahn, E. Baidoo, T. S. Kahlon, D. F. Wood, C. M. McMahan, K. Cornish, J. D. Keasling, H. Daniell, and M. C. Whalen. 2012. Remodeling the isoprenoid pathway in tobacco by expressing the cytoplasmic mevalonate pathway in chloroplasts, Metab Eng 14(1), 19-28. JBEI
201210.1021/sb300074kKung, Y., W. Runguphan, and J. D. Keasling. 2012. From fields to fuels: recent advances in the microbial production of biofuels, ACS Synth Biol 1(11), 498-513. JBEI
201210.1890/11-1516.1Kwit, C., and C. N. Stewart. 2012. Gene flow matters in switchgrass (Panicum virgatumL.), a potential widespread biofuel feedstock, Ecological Applications 22(1), 3-7. BESC
2012Landis, D. A., M. M. Gardiner, and J. Tompkins. 2012. Using native plant species to diversify agriculture. In Biodiversity and Insect Pests: Key Issues for Sustainable Management, 276-292. Eds. G. M. Gurr, S. D. Wratten, W. E. Snyder, and D. M. Y. Read. John Wiley and Sons, Ltd.GLBRC
201210.1039/c2ee03596kLau, M. W., B. D. Bals, S. P. S. Chundawat, M. Jin, C. Gunawan, V. Balan, A. D. Jones, and B. E. Dale. 2012. An integrated paradigm for cellulosic biorefineries: utilization of lignocellulosic biomass as self-sufficient feedstocks for fuel, food precursors and saccharolytic enzyme production, Energy & Environmental Science 5(5), 7100. GLBRC
201210.1186/1754-6834-5-5Lee, S. J., T. A. Warnick, S. Pattathil, J. G. Alvelo-Maurosa, M. J. Serapiglia, H. McCormick, V. Brown, N. F. Young, D. J. Schnell, L. B. Smart, M. G. Hahn, J. F. Pedersen, S. B. Leschine, and S. P. Hazen. 2012. Biological conversion assay using Clostridium phytofermentans to estimate plant feedstock quality, Biotechnol Biofuels 5, 5. BESC
201210.1371/journal.pcbi.1002769Lee, Y., L. Escamilla-Trevino, R. A. Dixon, and E. O. Voit. 2012. Functional analysis of metabolic channeling and regulation in lignin biosynthesis: a computational approach, PLoS Comput Biol 8(11), e1002769. BESC
201210.1016/j.tibtech.2012.09.006Lennen, R. M., and B. F. Pfleger. 2012. Engineering Escherichia coli to synthesize free fatty acids, Trends Biotechnol 30(12), 659-667. GLBRC
201210.4137/GRSB.S9357Leuze, M. R., T. V. Karpinets, M. H. Syed, A. S. Beliaev, and E. C. Uberbacher. 2012. Binding Motifs in Bacterial Gene Promoters Modulate Transcriptional Effects of Global Regulators CRP and ArcA, Gene Regul Syst Bio 6, 93-107. BESC
201210.1534/g3.112.004127Lewis, J. A., and A. P. Gasch. 2012. Natural variation in the yeast glucose-signaling network reveals a new role for the Mig3p transcription factor, G3 (Bethesda) 2(12), 1607-1612. GLBRC
201210.1007/s12155-012-9220-4Li, C., L. Sun, B. A. Simmons, and S. Singh. 2012. Comparing the Recalcitrance of Eucalyptus, Pine, and Switchgrass Using Ionic Liquid and Dilute Acid Pretreatments, BioEnergy Research 6(1), 14-23. JBEI
201210.1039/c2ra20557bLi, H., M. B. Foston, R. Kumar, R. Samuel, X. Gao, F. Hu, A. J. Ragauskas, and C. E. Wyman. 2012. Chemical composition and characterization of cellulose for Agave as a fast-growing, drought-tolerant biofuels feedstock, RSC Advances 2(11), 4951. BESC
201210.1128/JB.01908-12Li, L. L., S. Taghavi, J. A. Izquierdo, and D. van der Lelie. 2012. Complete genome sequence of Clostridium sp. strain BNL1100, a cellulolytic mesophile isolated from corn stover, J Bacteriol 194(24), 6982-6983. BESC
201210.1186/1754-6834-5-38Li, M., C. Foster, S. Kelkar, Y. Pu, D. Holmes, A. Ragauskas, C. M. Saffron, and D. B. Hodge. 2012. Structural characterization of alkaline hydrogen peroxide pretreated grasses exhibiting diverse lignin phenotypes, Biotechnol Biofuels 5(1), 38. BESC GLBRC
201210.1186/1754-6834-5-2Li, Y., T. J. Tschaplinski, N. L. Engle, C. Y. Hamilton, M. Rodriguez, Jr., J. C. Liao, C. W. Schadt, A. M. Guss, Y. Yang, and D. E. Graham. 2012. Combined inactivation of the Clostridium cellulolyticum lactate and malate dehydrogenase genes substantially increases ethanol yield from cellulose and switchgrass fermentations, Biotechnol Biofuels 5(1), 2. BESC
201210.1016/j.apsoil.2011.11.015Liang, C., E. d. C. Jesus, D. S. Duncan, R. D. Jackson, J. M. Tiedje, and T. C. Balser. 2012. Soil microbial communities under model biofuel cropping systems in southern Wisconsin, USA: Impact of crop species and soil properties, Applied Soil Ecology 54, 24-31. GLBRC
201210.3791/3767Liang, C., H. W. Read, and T. C. Balser. 2012. GC-based detection of aldononitrile acetate derivatized glucosamine and muramic acid for microbial residue determination in soil, J Vis Exp(63), e3767. GLBRC
201210.1007/s00253-011-3458-1Liao, H., S. Myung, and Y. H. Zhang. 2012. One-step purification and immobilization of thermophilic polyphosphate glucokinase from Thermobifida fusca YX: glucose-6-phosphate generation without ATP, Appl Microbiol Biotechnol 93(3), 1109-1117. BESC
201210.3389/fpls.2012.00109Liepman, A. H., and D. M. Cavalier. 2012. The CELLULOSE SYNTHASE-LIKE A and CELLULOSE SYNTHASE-LIKE C families: recent advances and future perspectives, Front Plant Sci 3, 109. GLBRC
201210.1016/j.biombioe.2011.12.009Lindedam, J., S. B. Andersen, J. DeMartini, S. Bruun, H. Jørgensen, C. Felby, J. Magid, B. Yang, and C. E. Wyman. 2012. Cultivar variation and selection potential relevant to the production of cellulosic ethanol from wheat straw, Biomass and Bioenergy 37, 221-228. BESC
201210.1353/pbm.2012.0044Linshiz, G., A. Goldberg, T. Konry, and N. J. Hillson. 2012. The fusion of biology, computer science, and engineering: towards efficient and successful synthetic biology, Perspect Biol Med 55(4), 503-520. JBEI
201210.1021/jp301673hLiu, H., G. Cheng, M. Kent, V. Stavila, B. A. Simmons, K. L. Sale, and S. Singh. 2012. Simulations reveal conformational changes of methylhydroxyl groups during dissolution of cellulose Ibeta in ionic liquid 1-ethyl-3-methylimidazolium acetate, J Phys Chem B 116(28), 8131-8138. JBEI
201210.1007/978-1-61779-956-3_13Liu, Y. S., S. Y. Ding, and M. E. Himmel. 2012. Single-molecule tracking of carbohydrate-binding modules on cellulose using fluorescence microscopy, Methods in Molecular Biology 908, 129-140. BESC
201210.1105/tpc.112.106625Liwanag, A. J., B. Ebert, Y. Verhertbruggen, E. A. Rennie, C. Rautengarten, A. Oikawa, M. C. Andersen, M. H. Clausen, and H. V. Scheller. 2012. Pectin biosynthesis: GALS1 in Arabidopsis thaliana is a beta-1,4-galactan beta-1,4-galactosyltransferase, Plant Cell 24(12), 5024-5036. JBEI
201210.1128/AEM.00374-12Long, T. M., Y. K. Su, J. Headman, A. Higbee, L. B. Willis, and T. W. Jeffries. 2012. Cofermentation of glucose, xylose, and cellobiose by the beetle-associated yeast Spathaspora passalidarum, Appl Environ Microbiol 78(16), 5492-5500. GLBRC
201210.1021/jf302140kLu, F., L. Wei, A. Azarpira, and J. Ralph. 2012. Rapid syntheses of dehydrodiferulates via biomimetic radical coupling reactions of ethyl ferulate, J Agric Food Chem 60(34), 8272-8277. GLBRC
201210.1186/1472-6750-12-17Mann, D. G., L. L. Abercrombie, M. R. Rudis, R. J. Millwood, J. R. Dunlap, and C. N. Stewart, Jr. 2012. Very bright orange fluorescent plants: endoplasmic reticulum targeting of orange fluorescent proteins as visual reporters in transgenic plants, BMC Biotechnol 12, 17. BESC
201210.1111/j.1467-7652.2011.00658.xMann, D. G., P. R. Lafayette, L. L. Abercrombie, Z. R. King, M. Mazarei, M. C. Halter, C. R. Poovaiah, H. Baxter, H. Shen, R. A. Dixon, W. A. Parrott, and C. Neal Stewart, Jr. 2012. Gateway-compatible vectors for high-throughput gene functional analysis in switchgrass (Panicum virgatum L.) and other monocot species, Plant Biotechnol J 10(2), 226-236. BESC
201210.1038/nprot.2012.064Mansfield, S. D., H. Kim, F. Lu, and J. Ralph. 2012. Whole plant cell wall characterization using solution-state 2D NMR, Nat Protoc 7(9), 1579-1589. GLBRC
201210.1093/nar/gks605Mao, X., H. Zhang, Y. Yin, and Y. Xu. 2012. The percentage of bacterial genes on leading versus lagging strands is influenced by multiple balancing forces, Nucleic Acids Res 40(17), 8210-8218. BESC
201210.1371/journal.pone.0051252Mao, X., X. Chen, Y. Zhang, S. Pangle, and Y. Xu. 2012. CINPER: an interactive web system for pathway prediction for prokaryotes, PLoS One 7(12), e51252. BESC
201210.1074/jbc.M111.287367Martinez, V., M. Ingwers, J. Smith, J. Glushka, T. Yang, and M. Bar-Peled. 2012. Biosynthesis of UDP-4-keto-6-deoxyglucose and UDP-rhamnose in pathogenic fungi Magnaporthe grisea and Botryotinia fuckeliana, J Biol Chem 287(2), 879-892. BESC
201210.1007/s13280-012-0275-4Masukawa, H., M. Kitashima, K. Inoue, H. Sakurai, and R. P. Hausinger. 2012. Genetic engineering of cyanobacteria to enhance biohydrogen production from sunlight and water, Ambio 41 Suppl 2, 169-173. GLBRC
201210.1007/978-1-61779-879-5_18Masukawa, H., M. Mochimaru, and S. Takaichi. 2012. Characterization of carotenogenesis genes in the cyanobacterium Anabaena sp. PCC 7120, Methods in Molecular Biology 892, 297-306. GLBRC
201210.1007/978-1-61779-956-3_19Mazumder, K., M. J. Pena, M. A. O'Neill, and W. S. York. 2012. Structural characterization of the heteroxylans from poplar and switchgrass, Methods in Molecular Biology 908, 215-228. BESC
201210.1186/1754-6834-5-54McClendon, S. D., T. Batth, C. J. Petzold, P. D. Adams, B. A. Simmons, and S. W. Singer. 2012. Thermoascus aurantiacus is a promising source of enzymes for biomass deconstruction under thermophilic conditions, Biotechnol Biofuels 5(1), 54. JBEI
201210.1186/1475-2859-11-79McKee, A. E., B. J. Rutherford, D. C. Chivian, E. K. Baidoo, D. Juminaga, D. Kuo, P. I. Benke, J. A. Dietrich, S. M. Ma, A. P. Arkin, C. J. Petzold, P. D. Adams, J. D. Keasling, and S. R. Chhabra. 2012. Manipulation of the carbon storage regulator system for metabolite remodeling and biofuel production in Escherichia coli, Microb Cell Fact 11, 79. JBEI
201210.1073/pnas.1117686109McKee, L. S., M. J. Pena, A. Rogowski, A. Jackson, R. J. Lewis, W. S. York, K. B. Krogh, A. Vikso-Nielsen, M. Skjot, H. J. Gilbert, and J. Marles-Wright. 2012. Introducing endo-xylanase activity into an exo-acting arabinofuranosidase that targets side chains, Proc Natl Acad Sci U S A 109(17), 6537-6542. BESC
201210.1016/, L. S., R. J. Haft, and K. T. Forest. 2012. Structural insights into the Type II secretion nanomachine, Curr Opin Struct Biol 22(2), 208-216. GLBRC
201210.4056/sigs.2605792Mead, D. A., S. Lucas, A. Copeland, A. Lapidus, J. F. Cheng, D. C. Bruce, L. A. Goodwin, S. Pitluck, O. Chertkov, X. Zhang, J. C. Detter, C. S. Han, R. Tapia, M. Land, L. J. Hauser, Y. J. Chang, N. C. Kyrpides, N. N. Ivanova, G. Ovchinnikova, T. Woyke, C. Brumm, R. Hochstein, T. Schoenfeld, and P. Brumm. 2012. Complete Genome Sequence of Paenibacillus strain Y4.12MC10, a Novel Paenibacillus lautus strain Isolated from Obsidian Hot Spring in Yellowstone National Park, Stand Genomic Sci 6(3), 381-400. GLBRC
201210.1186/1471-2180-12-180Mearls, E. B., J. A. Izquierdo, and L. R. Lynd. 2012. Formation and characterization of non-growth states in Clostridium thermocellum: spores and L-forms, BMC Microbiol 12, 180. BESC
201210.1371/journal.pone.0041728Meehan, T. D., B. P. Werling, D. A. Landis, and C. Gratton. 2012. Pest-suppression potential of midwestern landscapes under contrasting bioenergy scenarios, PLoS One 7(7), e41728. GLBRC
201210.1007/s10841-012-9523-yMeehan, T. D., J. Glassberg, and C. Gratton. 2012. Butterfly community structure and landscape composition in agricultural landscapes of the central United States, Journal of Insect Conservation 17(2), 411-419. GLBRC
201210.1016/j.fuel.2011.06.026Melnichenko, Y. B., L. He, R. Sakurovs, A. L. Kholodenko, T. Blach, M. Mastalerz, A. P. Radlinski, G. Cheng, and D. F. R. Mildner. 2012. Accessibility of pores in coal to methane and carbon dioxide, Fuel 91(1), 200-208. JBEI
201210.1093/ajae/aar142Miao, R., D. A. Hennessy, and B. A. Babcock. 2012. Investment in Cellulosic Biofuel Refineries: Do Waivable Biofuel Mandates Matter?, American Journal of Agricultural Economics 94(3), 750-762. GLBRC
2012 10.1016/j.biombioe.2011.10.018Miesel, J. R., M. J. Renz, J. E. Doll, and R. D. Jackson. 2012. Effectiveness of weed management methods in establishment of switchgrass and a native species mixture for biofuels in Wisconsin, Biomass and Bioenergy 36, 121-131. GLBRC
2012Mitchell, J. C., T. J. Rutkoski, R. M. Bannen, and G. N. Phillips. 2012. Combined computational and experimental approaches to sequence-based design of protein thermal stability. In Thermostable Proteins: Structural Stability and Design, 105-116. CRC Press.GLBRC
2012Mukhopadhyay, A., N. J. Hillson, and J. D. Keasling. 2012. Control of Stress Tolerance in Bacterial Host Organisms for Bioproduction of Fuels. In Microbial Stress Tolerance: From Genomics to Biofuels, 209-238. Ed. Z. L. Liu. Springer-Verlag.JBEI
201210.1016/j.ces.2011.07.022Murat Sen, S., C. A. Henao, D. J. Braden, J. A. Dumesic, and C. T. Maravelias. 2012. Catalytic conversion of lignocellulosic biomass to fuels: Process development and technoeconomic evaluation, Chemical Engineering Science 67(1), 57-67. GLBRC
201210.1104/pp.112.198374Nadakuduti, S. S., M. Pollard, D. K. Kosma, C. Allen, Jr., J. B. Ohlrogge, and C. S. Barry. 2012. Pleiotropic phenotypes of the sticky peel mutant provide new insight into the role of CUTIN DEFICIENT2 in epidermal cell function in tomato, Plant Physiol 159(3), 945-960. GLBRC
201210.1093/database/bas013Nag, A., T. V. Karpinets, C. H. Chang, and M. Bar-Peled. 2012. Enhancing a Pathway-Genome Database (PGDB) to capture subcellular localization of metabolites and enzymes: the nucleotide-sugar biosynthetic pathways of Populus trichocarpa, Database (Oxford) 2012, bas013. BESC
201210.1007/s10722-012-9903-xNageswara-Rao, M., C. N. Stewart, and C. Kwit. 2012. Genetic diversity and structure of natural and agronomic switchgrass (Panicum virgatum L.) populations, Genetic Resources and Crop Evolution 60(3), 1057-1068. BESC
201210.1016/j.biombioe.2012.01.037Nikièma, P., D. E. Rothstein, and R. O. Miller. 2012. Initial greenhouse gas emissions and nitrogen leaching losses associated with converting pastureland to short-rotation woody bioenergy crops in northern Michigan, USA, Biomass and Bioenergy 39, 413-426. GLBRC
2012 10.1016/j.biortech.2011.11.060Oleskowicz-Popiel, P., Z. Kadar, S. Heiske, D. Klein-Marcuschamer, B. A. Simmons, H. W. Blanch, and J. E. Schmidt. 2012. Co-production of ethanol, biogas, protein fodder and natural fertilizer in organic farming--evaluation of a concept for a farm-scale biorefinery, Bioresour Technol 104, 440-446. JBEI
201210.1186/1754-1611-6-5Olson, D. G., and L. R. Lynd. 2012. Computational design and characterization of a temperature-sensitive plasmid replicon for gram positive thermophiles, J Biol Eng 6(1), 5. BESC
201210.1016/B978-0-12-415931-0.00017-3Olson, D. G., and L. R. Lynd. 2012. Transformation of Clostridium thermocellum by electroporation, Methods Enzymol 510, 317-330. BESC
201210.1016/j.copbio.2011.11.026Olson, D. G., J. E. McBride, A. J. Shaw, and L. R. Lynd. 2012. Recent progress in consolidated bioprocessing, Curr Opin Biotechnol 23(3), 396-405. BESC
201210.1007/s00425-012-1596-zOrfila, C., F. Dal Degan, B. Jorgensen, H. V. Scheller, P. M. Ray, and P. Ulvskov. 2012. Expression of mung bean pectin acetyl esterase in potato tubers: effect on acetylation of cell wall polymers and tuber mechanical properties, Planta 236(1), 185-196. JBEI
201210.1128/AEM.07031-11Ozdemir, I., S. E. Blumer-Schuette, and R. M. Kelly. 2012. S-layer homology domain proteins Csac_0678 and Csac_2722 are implicated in plant polysaccharide deconstruction by the extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus, Appl Environ Microbiol 78(3), 768-777. BESC
201210.1016/j.jcat.2012.03.014O’Neill, B. J., E. I. Gürbüz, and J. A. Dumesic. 2012. Reaction kinetics studies of the conversions of formic acid and butyl formate over carbon-supported palladium in the liquid phase, Journal of Catalysis 290, 193-201. GLBRC
201210.1016/j.biortech.2012.04.065Papa, G., P. Varanasi, L. Sun, G. Cheng, V. Stavila, B. Holmes, B. A. Simmons, F. Adani, and S. Singh. 2012. Exploring the effect of different plant lignin content and composition on ionic liquid pretreatment efficiency and enzymatic saccharification of Eucalyptus globulus L. mutants, Bioresour Technol 117, 352-359. JBEI
201210.1371/journal.pone.0037010Park, J. I., E. J. Steen, H. Burd, S. S. Evans, A. M. Redding-Johnson, T. Batth, P. I. Benke, P. D'Haeseleer, N. Sun, K. L. Sale, J. D. Keasling, T. S. Lee, C. J. Petzold, A. Mukhopadhyay, S. W. Singer, B. A. Simmons, and J. M. Gladden. 2012. A thermophilic ionic liquid-tolerant cellulase cocktail for the production of cellulosic biofuels, PLoS One 7(5), e37010. JBEI
201210.3389/fpls.2012.00298Parsons, H. T., G. Drakakaki, and J. L. Heazlewood. 2012. Proteomic dissection of the Arabidopsis Golgi and trans-Golgi network, Front Plant Sci 3, 298. JBEI
201210.1104/pp.111.193151Parsons, H. T., K. Christiansen, B. Knierim, A. Carroll, J. Ito, T. S. Batth, A. M. Smith-Moritz, S. Morrison, P. McInerney, M. Z. Hadi, M. Auer, A. Mukhopadhyay, C. J. Petzold, H. V. Scheller, D. Loque, and J. L. Heazlewood. 2012. Isolation and proteomic characterization of the Arabidopsis Golgi defines functional and novel components involved in plant cell wall biosynthesis, Plant Physiol 159(1), 12-26. JBEI
201210.1089/ind.2012.0013Pattathil, S., T. Saffold, L. Gallego-Giraldo, M. O'Neill, W. S. York, R. A. Dixon, and M. G. Hahn. 2012. Changes in Cell Wall Carbohydrate Extractability Are Correlated with Reduced Recalcitrance of HCT Downregulated Alfalfa Biomass, Industrial Biotechnology 8(4), 217-221. BESC
201210.1007/978-1-61779-956-3_6Pattathil, S., U. Avci, J. S. Miller, and M. G. Hahn. 2012. Immunological approaches to plant cell wall and biomass characterization: Glycome Profiling, Methods in Molecular Biology 908, 61-72. BESC
201210.1073/pnas.1121464109Pell, J., A. Hintze, R. Canino-Koning, A. Howe, J. M. Tiedje, and C. T. Brown. 2012. Scaling metagenome sequence assembly with probabilistic de Bruijn graphs, Proc Natl Acad Sci U S A 109(33), 13272-13277. GLBRC
201210.1016/B978-0-12-415931-0.00007-0Pena, M. J., S. T. Tuomivaara, B. R. Urbanowicz, M. A. O'Neill, and W. S. York. 2012. Methods for structural characterization of the products of cellulose- and xyloglucan-hydrolyzing enzymes, Methods Enzymol 510, 121-139. BESC
201210.1038/nature11478Peralta-Yahya, P. P., F. Zhang, S. B. del Cardayre, and J. D. Keasling. 2012. Microbial engineering for the production of advanced biofuels, Nature 488(7411), 320-328. JBEI
201210.1107/S0907444912028351Pereira, J. H., E. B. Goh, J. D. Keasling, H. R. Beller, and P. D. Adams. 2012. Structure of FabH and factors affecting the distribution of branched fatty acids in Micrococcus luteus, Acta Crystallogr D Biol Crystallogr 68(Pt 10), 1320-1328. JBEI
201210.1371/journal.pone.0043775Perez-Gil, J., E. M. Uros, S. Sauret-Gueto, L. M. Lois, J. Kirby, M. Nishimoto, E. E. Baidoo, J. D. Keasling, A. Boronat, and M. Rodriguez-Concepcion. 2012. Mutations in Escherichia coli aceE and ribB genes allow survival of strains defective in the first step of the isoprenoid biosynthesis pathway, PLoS One 7(8), e43775. JBEI
201210.1101/gad.196741.112Peters, J. M., R. A. Mooney, J. A. Grass, E. D. Jessen, F. Tran, and R. Landick. 2012. Rho and NusG suppress pervasive antisense transcription in Escherichia coli, Genes Dev 26(23), 2621-2633. GLBRC
201210.1186/1754-6834-5-84Petersen, P. D., J. Lau, B. Ebert, F. Yang, Y. Verhertbruggen, J. S. Kim, P. Varanasi, A. Suttangkakul, M. Auer, D. Loque, and H. V. Scheller. 2012. Engineering of plants with improved properties as biofuels feedstocks by vessel-specific complementation of xylan biosynthesis mutants, Biotechnol Biofuels 5(1), 84. JBEI
201210.1128/AEM.02130-12Podkaminer, K. K., A. M. Guss, H. L. Trajano, D. A. Hogsett, and L. R. Lynd. 2012. Characterization of xylan utilization and discovery of a new endoxylanase in Thermoanaerobacterium saccharolyticum through targeted gene deletions, Appl Environ Microbiol 78(23), 8441-8447. BESC
201210.1186/1754-6834-5-43Podkaminer, K. K., W. R. Kenealy, C. D. Herring, D. A. Hogsett, and L. R. Lynd. 2012. Ethanol and anaerobic conditions reversibly inhibit commercial cellulase activity in thermophilic simultaneous saccharification and fermentation (tSSF), Biotechnol Biofuels 5(1), 43. BESC
201210.1186/1471-2105-13-295Poskar, C. H., J. Huege, C. Krach, M. Franke, Y. Shachar-Hill, and B. H. Junker. 2012. iMS2Flux--a high-throughput processing tool for stable isotope labeled mass spectrometric data used for metabolic flux analysis, BMC Bioinformatics 13, 295. GLBRC
201210.1007/s12155-012-9218-yRalph, J., T. Akiyama, H. D. Coleman, and S. D. Mansfield. 2012. Effects on Lignin Structure of Coumarate 3-Hydroxylase Downregulation in Poplar, Bioenergy Res 5(4), 1009-1019. GLBRC
201210.1104/pp.111.187187Rautengarten, C., B. Ebert, M. Ouellet, M. Nafisi, E. E. Baidoo, P. Benke, M. Stranne, A. Mukhopadhyay, J. D. Keasling, Y. Sakuragi, and H. V. Scheller. 2012. Arabidopsis Deficient in Cutin Ferulate encodes a transferase required for feruloylation of omega-hydroxy fatty acids in cutin polyester, Plant Physiol 158(2), 654-665. JBEI
201210.1101/sqb.2013.77.014449Ream, T. S., D. P. Woods, and R. M. Amasino. 2012. The molecular basis of vernalization in different plant groups, Cold Spring Harb Symp Quant Biol 77, 105-115. GLBRC
201210.1111/jam.12002Reddy, A. P., C. W. Simmons, J. Claypool, L. Jabusch, H. Burd, M. Z. Hadi, B. A. Simmons, S. W. Singer, and J. S. VanderGheynst. 2012. Thermophilic enrichment of microbial communities in the presence of the ionic liquid 1-ethyl-3-methylimidazolium acetate, J Appl Microbiol 113(6), 1362-1370. JBEI
201210.1371/journal.pcbi.1002662Reed, J. L. 2012. Shrinking the metabolic solution space using experimental datasets, PLoS Comput Biol 8(8), e1002662. GLBRC
201210.1002/9780470559277.ch110221Reindl, W., K. Deng, X. Cheng, A. K. Singh, B. A. Simmons, P. D. Adams, and T. R. Northen. 2012. Nanostructure-initiator mass spectrometry (NIMS) for the analysis of enzyme activities, Current Protocols in Chemical Biology 4, 123-142. JBEI
201210.1104/pp.112.200964Rennie, E. A., S. F. Hansen, E. E. Baidoo, M. Z. Hadi, J. D. Keasling, and H. V. Scheller. 2012. Three members of the Arabidopsis glycosyltransferase family 8 are xylan glucuronosyltransferases, Plant Physiol 159(4), 1408-1417. JBEI
201210.1007/s12155-012-9258-3Robertson, B. A., D. A. Landis, T. S. Sillett, E. R. Loomis, and R. A. Rice. 2012. Perennial Agroenergy Feedstocks as En Route Habitat for Spring Migratory Birds, BioEnergy Research 6(1), 311-320. GLBRC
201210.1525/cond.2012.110136Robertson, B. A., R. A. Rice, T. S. Sillett, C. A. Ribic, B. A. Babcock, D. A. Landis, J. R. Herkert, R. J. Fletcher, J. J. Fontaine, P. J. Doran, and D. W. Schemske. 2012. Are Agrofuels a Conservation Threat or Opportunity for Grassland Birds in the United States?, The Condor 114(4), 679-688. GLBRC
201210.1007/s10533-012-9802-4.Robertson, G. P., T. W. Bruulsema, R. J. Gehl, D. Kanter, D. L. Mauzerall, C. A. Rotz, and C. O. Williams. 2012. Nitrogen-climate interactions in US agriculture, Biogeochemistry 114(1-3), 41-70. GLBRC
201210.1101/gr.125146.111Rodgers-Melnick, E., S. P. Mane, P. Dharmawardhana, G. T. Slavov, O. R. Crasta, S. H. Strauss, A. M. Brunner, and S. P. Difazio. 2012. Contrasting patterns of evolution following whole genome versus tandem duplication events in Populus, Genome Res 22(1), 95-105. BESC
201210.1016/j.fuel.2012.03.049Rothamer, D. A., and J. H. Jennings. 2012. Study of the knocking propensity of 2,5-dimethylfuran-gasoline and ethanol-gasoline blends, Fuel 98, 203-212. GLBRC
201210.3389/fpls.2012.00117Ruiz-May, E., S. J. Kim, F. Brandizzi, and J. K. Rose. 2012. The secreted plant N-glycoproteome and associated secretory pathways, Front Plant Sci 3, 117. GLBRC
2012Rutherford, B. J., and A. Mukhopadhyay. 2012. Engineering Stress Tolerance in Microbial Systems for Bioproduction of Fuels. In Microbial Biotechnology: Energy and Environment. Ed. R. Arora. CABI.JBEI
201210.1016/j.agee.2012.08.011Sanford, G. R., J. L. Posner, R. D. Jackson, C. J. Kucharik, J. L. Hedtcke, and T.-L. Lin. 2012. Soil carbon lost from Mollisols of the North Central U.S.A. with 20 years of agricultural best management practices, Agriculture, Ecosystems & Environment 162, 68-76. GLBRC
201210.1021/jp2122449Sangha, A. K., J. M. Parks, R. F. Standaert, A. Ziebell, M. Davis, and J. C. Smith. 2012. Radical coupling reactions in lignin synthesis: a density functional theory study, J Phys Chem B 116(16), 4760-4768. BESC
201210.1002/ep.10628Sangha, A. K., L. Petridis, J. C. Smith, A. Ziebell, and J. M. Parks. 2012. Molecular simulation as a tool for studying lignin, Environmental Progress & Sustainable Energy 31(1), 47-54. BESC
201210.1007/s10570-012-9719-zSathitsuksanoh, N., Z. Zhu, and Y. H. P. Zhang. 2012. Cellulose solvent-based pretreatment for corn stover and avicel: concentrated phosphoric acid versus ionic liquid [BMIM]Cl, Cellulose 19(4), 1161-1172. BESC
201210.1016/j.biortech.2012.04.088Sathitsuksanoh, N., Z. Zhu, and Y. H. Zhang. 2012. Cellulose solvent- and organic solvent-based lignocellulose fractionation enabled efficient sugar release from a variety of lignocellulosic feedstocks, Bioresour Technol 117, 228-233. BESC
201210.1021/jf203256fSatoh, Y., K. Tajima, M. Munekata, J. D. Keasling, and T. S. Lee. 2012. Engineering of a tyrosol-producing pathway, utilizing simple sugar and the central metabolic tyrosine, in Escherichia coli, J Agric Food Chem 60(4), 979-984. JBEI
201210.1016/j.ymben.2012.08.002Satoh, Y., K. Tajima, M. Munekata, J. D. Keasling, and T. S. Lee. 2012. Engineering of L-tyrosine oxidation in Escherichia coli and microbial production of hydroxytyrosol, Metab Eng 14(6), 603-610. JBEI
201210.1002/pmic.201290015Schrimpf, S. P., C. von Mering, E. Bendixen, J. L. Heazlewood, D. Bumann, G. Omenn, and M. O. Hengartner. 2012. The initiative on Model Organism Proteomes (iMOP) Session September 6, 2011, Geneva, Switzerland, Proteomics 12(3), 346-350. JBEI
201210.1128/AEM.07329-11Schwalbach, M. S., D. H. Keating, M. Tremaine, W. D. Marner, Y. Zhang, W. Bothfeld, A. Higbee, J. A. Grass, C. Cotten, J. L. Reed, L. da Costa Sousa, M. Jin, V. Balan, J. Ellinger, B. Dale, P. J. Kiley, and R. Landick. 2012. Complex physiology and compound stress responses during fermentation of alkali-pretreated corn stover hydrolysate by an Escherichia coli ethanologen, Appl Environ Microbiol 78(9), 3442-3457. GLBRC
201210.1104/pp.112.199224Sekhon, R. S., K. L. Childs, N. Santoro, C. E. Foster, C. R. Buell, N. de Leon, and S. M. Kaeppler. 2012. Transcriptional and metabolic analysis of senescence induced by preventing pollination in maize, Plant Physiol 159(4), 1730-1744. GLBRC
201210.1039/c2gc35881fSen, S. M., E. I. Gürbüz, S. G. Wettstein, D. M. Alonso, J. A. Dumesic, and C. T. Maravelias. 2012. Production of butene oligomers as transportation fuels using butene for esterification of levulinic acid from lignocellulosic biomass: process synthesis and technoeconomic evaluation, Green Chemistry 14(12), 3289. GLBRC
201210.1002/bbb.1336Sen, S. M., J. B. Binder, R. T. Raines, and C. T. Maravelias. 2012. Conversion of biomass to sugars via ionic liquid hydrolysis: process synthesis and economic evaluation, Biofuels, Bioproducts and Biorefining 6(4), 444-452. GLBRC
201210.1371/journal.pone.0033892Sharma, M. K., R. Sharma, P. Cao, J. Jenkins, L. E. Bartley, M. Qualls, J. Grimwood, J. Schmutz, D. Rokhsar, and P. C. Ronald. 2012. A genome-wide survey of switchgrass genome structure and organization, PLoS One 7(4), e33892. JBEI
2012Sharma, V., D. Chiniquy, E. Baidoo, J. Keasling, P. Ronald, and H. V. Scheller. 2012. Tools for Developing Glycosyl-Transferase Assays and Methods for Xylan Profiling in Plants. In Pharmaceutical Biology, 607.JBEI
201210.1111/j.1469-8137.2011.03922.xShen, H., X. He, C. R. Poovaiah, W. A. Wuddineh, J. Ma, D. G. Mann, H. Wang, L. Jackson, Y. Tang, C. N. Stewart, Jr., F. Chen, and R. A. Dixon. 2012. Functional characterization of the switchgrass (Panicum virgatum) R2R3-MYB transcription factor PvMYB4 for improvement of lignocellulosic feedstocks, New Phytol 193(1), 121-136. BESC
2012Simmons, B. A. 2012. Bioenergy from Plants and Plant Residues. In Plant Biotechnology and Agriculture - Prospects for the 21st Century, 495-506. Eds. A. Altman, and P. M. Hasegawa. Academic Press.JBEI
201210.1002/pmic.201100482Singh, P., T. S. Batth, D. Juminaga, R. H. Dahl, J. D. Keasling, P. D. Adams, and C. J. Petzold. 2012. Application of targeted proteomics to metabolically engineered Escherichia coli, Proteomics 12(8), 1289-1299. JBEI
201210.1111/j.1469-8137.2012.04258.xSlavov, G. T., S. P. DiFazio, J. Martin, W. Schackwitz, W. Muchero, E. Rodgers-Melnick, M. F. Lipphardt, C. P. Pennacchio, U. Hellsten, L. A. Pennacchio, L. E. Gunter, P. Ranjan, K. Vining, K. R. Pomraning, L. J. Wilhelm, M. Pellegrini, T. C. Mockler, M. Freitag, A. Geraldes, Y. A. El-Kassaby, S. D. Mansfield, Q. C. Cronk, C. J. Douglas, S. H. Strauss, D. Rokhsar, and G. A. Tuskan. 2012. Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa, New Phytol 196(3), 713-725. BESC
201210.1016/j.bpj.2011.11.3219Smith-Moritz, A. M., J. Lao, J. L. Heazlewood, P. C. Ronald, and M. E. Vega-Sanchez. 2012. Dependence of Plant Cell Wall Composition and Structure on Cellulose Synthase-Like Knock Out Mutant, Biophysical Journal 102(3), 590a-591a. JBEI
201210.1371/journal.pone.0031324Sogaard, C., A. Stenbaek, S. Bernard, M. Hadi, A. Driouich, H. V. Scheller, and Y. Sakuragi. 2012. GO-PROMTO illuminates protein membrane topologies of glycan biosynthetic enzymes in the Golgi apparatus of living tissues, PLoS One 7(2), e31324. JBEI
201210.1074/jbc.M112.405720Sukharnikov, L. O., M. Alahuhta, R. Brunecky, A. Upadhyay, M. E. Himmel, V. V. Lunin, and I. B. Zhulin. 2012. Sequence, structure, and evolution of cellulases in glycoside hydrolase family 48, J Biol Chem 287(49), 41068-41077. BESC
201210.1016/j.pep.2012.01.017Sun, F., X. Z. Zhang, S. Myung, and Y. H. Zhang. 2012. Thermophilic Thermotoga maritima ribose-5-phosphate isomerase RpiB: optimized heat treatment purification and basic characterization, Protein Expr Purif 82(2), 302-307. BESC
201210.1371/journal.pone.0032017Sun, G., C. N. Stewart, Jr., P. Xiao, and B. Zhang. 2012. MicroRNA expression analysis in the cellulosic biofuel crop switchgrass (Panicum virgatum) under abiotic stress, PLoS One 7(3), e32017. BESC
201210.1002/bit.24348Sun, L., P. Varanasi, F. Yang, D. Loque, B. A. Simmons, and S. Singh. 2012. Rapid determination of syringyl: guaiacyl ratios using FT-Raman spectroscopy, Biotechnol Bioeng 109(3), 647-656. JBEI
201210.1111/j.1757-1707.2012.01166.xSurendran Nair, S., S. Kang, X. Zhang, F. E. Miguez, R. C. Izaurralde, W. M. Post, M. C. Dietze, L. R. Lynd, and S. D. Wullschleger. 2012. Bioenergy crop models: descriptions, data requirements, and future challenges, GCB Bioenergy 4(6), 620-633. GLBRC
201210.1093/bioinformatics/bts016Syed, M. H., T. V. Karpinets, M. Parang, M. R. Leuze, B. H. Park, D. Hyatt, S. D. Brown, S. Moulton, M. D. Galloway, and E. C. Uberbacher. 2012. BESC knowledgebase public portal, Bioinformatics 28(5), 750-751. BESC
201210.1016/j.agee.2011.12.007Syswerda, S. P., B. Basso, S. K. Hamilton, J. B. Tausig, and G. P. Robertson. 2012. Long-term nitrate loss along an agricultural intensity gradient in the Upper Midwest USA, Agriculture, Ecosystems & Environment 149, 10-19. GLBRC
201210.1089/ind.2012.0017Tetard, L., A. Passian, S. Jung, A. J. Ragauskas, and B. H. Davison. 2012. Development of New Methods in Scanning Probe Microscopy for Lignocellulosic Biomass Characterization, Industrial Biotechnology 8(4), 245-249. BESC
201210.1016/j.compag.2012.04.010Thelen, K. D., J. Gao, J. Hoben, L. Qian, C. Saffron, and K. Withers. 2012. A spreadsheet-based model for teaching the agronomic, economic, and environmental aspects of bioenergy cropping systems, Computers and Electronics in Agriculture 85, 157-163. GLBRC
201210.1104/pp.111.186122Tjellstrom, H., Z. Yang, D. K. Allen, and J. B. Ohlrogge. 2012. Rapid kinetic labeling of Arabidopsis cell suspension cultures: implications for models of lipid export from plastids, Plant Physiol 158(2), 601-611. GLBRC
201210.1002/cssc.201100573Tobimatsu, Y., S. Elumalai, J. H. Grabber, C. L. Davidson, X. Pan, and J. Ralph. 2012. Hydroxycinnamate conjugates as potential monolignol replacements: in vitro lignification and cell wall studies with rosmarinic acid, ChemSusChem 5(4), 676-686. GLBRC
201210.1039/c2gc16362dTorr, K. M., K. T. Love, Ö. P. Çetinkol, L. A. Donaldson, A. George, B. M. Holmes, and B. A. Simmons. 2012. The impact of ionic liquid pretreatment on the chemistry and enzymatic digestibility of Pinus radiata compression wood, Green Chemistry 14(3), 778. JBEI
201210.1186/1754-6834-5-71Tschaplinski, T. J., R. F. Standaert, N. L. Engle, M. Z. Martin, A. K. Sangha, J. M. Parks, J. C. Smith, R. Samuel, N. Jiang, Y. Pu, A. J. Ragauskas, C. Y. Hamilton, C. Fu, Z. Y. Wang, B. H. Davison, R. A. Dixon, and J. R. Mielenz. 2012. Down-regulation of the caffeic acid O-methyltransferase gene in switchgrass reveals a novel monolignol analog, Biotechnol Biofuels 5(1), 71. BESC
201210.1111/j.1469-185X.2011.00216.xTscharntke, T., J. M. Tylianakis, T. A. Rand, R. K. Didham, L. Fahrig, P. Batary, J. Bengtsson, Y. Clough, T. O. Crist, C. F. Dormann, R. M. Ewers, J. Frund, R. D. Holt, A. Holzschuh, A. M. Klein, D. Kleijn, C. Kremen, D. A. Landis, W. Laurance, D. Lindenmayer, C. Scherber, N. Sodhi, I. Steffan-Dewenter, C. Thies, W. H. van der Putten, and C. Westphal. 2012. Landscape moderation of biodiversity patterns and processes - eight hypotheses, Biol Rev Camb Philos Soc 87(3), 661-685. GLBRC
201210.1007/s11295-012-0495-6Tuskan, G. A., S. DiFazio, P. Faivre-Rampant, M. Gaudet, A. Harfouche, V. Jorge, J. L. Labbé, P. Ranjan, M. Sabatti, G. Slavov, N. Street, T. J. Tschaplinski, and T. Yin. 2012. The obscure events contributing to the evolution of an incipient sex chromosome in Populus: a retrospective working hypothesis, Tree Genetics & Genomes 8(3), 559-571. BESC
201210.1007/s12155-012-9263-6Uppalapati, S. R., D. D. Serba, Y. Ishiga, L. J. Szabo, S. Mittal, H. S. Bhandari, J. H. Bouton, K. S. Mysore, and M. C. Saha. 2012. Characterization of the Rust Fungus, Puccinia emaculata, and Evaluation of Genetic Variability for Rust Resistance in Switchgrass Populations, BioEnergy Research 6(2), 458-468. BESC
201210.1073/pnas.1208097109Urbanowicz, B. R., M. J. Pena, S. Ratnaparkhe, U. Avci, J. Backe, H. F. Steet, M. Foston, H. Li, M. A. O'Neill, A. J. Ragauskas, A. G. Darvill, C. Wyman, H. J. Gilbert, and W. S. York. 2012. 4-O-methylation of glucuronic acid in Arabidopsis glucuronoxylan is catalyzed by a domain of unknown function family 579 protein, Proc Natl Acad Sci U S A 109(35), 14253-14258. BESC
201210.1371/journal.pone.0036740van der Lelie, D., S. Taghavi, S. M. McCorkle, L. L. Li, S. A. Malfatti, D. Monteleone, B. S. Donohoe, S. Y. Ding, W. S. Adney, M. E. Himmel, and S. G. Tringe. 2012. The metagenome of an anaerobic microbial community decomposing poplar wood chips, PLoS One 7(5), e36740. BESC
201210.1111/j.1469-8137.2012.04337.xVanholme, R., K. Morreel, C. Darrah, P. Oyarce, J. H. Grabber, J. Ralph, and W. Boerjan. 2012. Metabolic engineering of novel lignin in biomass crops, New Phytol 196(4), 978-1000. GLBRC
201210.1089/ind.2012.0011Varanasi, P., J. Katsnelson, D. M. Larson, R. Sharma, M. K. Sharma, M. E. Vega-Sánchez, M. Zemla, D. Loque, P. C. Ronald, B. A. Simmons, S. Singh, P. D. Adams, and M. Auer. 2012. Mechanical Stress Analysis as a Method to Understand the Impact of Genetically Engineered Rice and Arabidopsis Plants, Industrial Biotechnology 8, 238-244. JBEI
201210.1016/j.biortech.2012.08.070Varanasi, P., P. Singh, R. Arora, P. D. Adams, M. Auer, B. A. Simmons, and S. Singh. 2012. Understanding changes in lignin of Panicum virgatum and Eucalyptus globulus as a function of ionic liquid pretreatment, Bioresour Technol 126, 156-161. JBEI
201210.1104/pp.112.195495Vega-Sanchez, M. E., Y. Verhertbruggen, U. Christensen, X. Chen, V. Sharma, P. Varanasi, S. A. Jobling, M. Talbot, R. G. White, M. Joo, S. Singh, M. Auer, H. V. Scheller, and P. C. Ronald. 2012. Loss of Cellulose synthase-like F6 function affects mixed-linkage glucan deposition, cell wall mechanical properties, and defense responses in vegetative tissues of rice, Plant Physiol 159(1), 56-69. JBEI
201210.2489/jswc.67.1.17AVentura, S., S. Hull, R. Jackson, G. Radloff, D. Sample, S. Walling, and C. Williams. 2012. Guidelines for sustainable planting and harvest of nonforest biomass in Wisconsin, Journal of Soil and Water Conservation 67(1), 17A-20A. GLBRC
201210.1007/s10529-011-0821-3Vickers, C. E., D. Klein-Marcuschamer, and J. O. Kromer. 2012. Examining the feasibility of bulk commodity production in Escherichia coli, Biotechnol Lett 34(4), 585-596. JBEI
201210.1371/journal.pgen.1003064Vieler, A., G. Wu, C. H. Tsai, B. Bullard, A. J. Cornish, C. Harvey, I. B. Reca, C. Thornburg, R. Achawanantakun, C. J. Buehl, M. S. Campbell, D. Cavalier, K. L. Childs, T. J. Clark, R. Deshpande, E. Erickson, A. Armenia Ferguson, W. Handee, Q. Kong, X. Li, B. Liu, S. Lundback, C. Peng, R. L. Roston, Sanjaya, J. P. Simpson, A. Terbush, J. Warakanont, S. Zauner, E. M. Farre, E. L. Hegg, N. Jiang, M. H. Kuo, Y. Lu, K. K. Niyogi, J. Ohlrogge, K. W. Osteryoung, Y. Shachar-Hill, B. B. Sears, Y. Sun, H. Takahashi, M. Yandell, S. H. Shiu, and C. Benning. 2012. Genome, functional gene annotation, and nuclear transformation of the heterokont oleaginous alga Nannochloropsis oceanica CCMP1779, PLoS Genet 8(11), e1003064. GLBRC
2012Vishnivetskaya, T. A., B. Raman, T. J. Phelps, M. Podar, and J. G. Elkins. 2012. Cellulolytic Microorganisms from Thermal Environments. In Extremophiles: Microbiology and Biotechnology, 131-158. Ed. R. Anitori. Caister Academic Press.BESC
201210.1007/s00248-011-9987-4Visser, A. A., T. Nobre, C. R. Currie, D. K. Aanen, and M. Poulsen. 2012. Exploring the potential for actinobacteria as defensive symbionts in fungus-growing termites, Microb Ecol 63(4), 975-985. GLBRC
2012Wagner, A., L. Donaldson, and J. Ralph. 2012. Lignification and lignin manipulations in conifers. In Advances in Botanical Research: Lignins, 37-76. Eds. L. Jouanin, and C. Lapierre. Academic Press.GLBRC
201210.1039/c2an15938dWang, L., Y. Wang, and A. J. Ragauskas. 2012. Determination of cellulase colocalization on cellulose fiber with quantitative FRET measured by acceptor photobleaching and spectrally unmixing fluorescence microscopy, Analyst 137(6), 1319-1324. BESC
201210.1002/bit.23330Wang, Q. Q., Z. He, Z. Zhu, Y. H. Zhang, Y. Ni, X. L. Luo, and J. Y. Zhu. 2012. Evaluations of cellulose accessibilities of lignocelluloses by solute exclusion and protein adsorption techniques, Biotechnol Bioeng 109(2), 381-389. BESC
201210.1186/1471-2229-12-138Wang, S., Y. Yin, Q. Ma, X. Tang, D. Hao, and Y. Xu. 2012. Genome-scale identification of cell-wall related genes in Arabidopsis based on co-expression network analysis, BMC Plant Biol 12, 138. BESC
201210.1007/s11103-012-9909-yWang, Y., A. P. Alonso, C. G. Wilkerson, and K. Keegstra. 2012. Deep EST profiling of developing fenugreek endosperm to investigate galactomannan biosynthesis and its regulation, Plant Mol Biol 79(3), 243-258. GLBRC
201210.1093/aob/mcs027Wang, Z. Y., and E. C. Brummer. 2012. Is genetic engineering ever going to take off in forage, turf and bioenergy crop breeding?, Ann Bot 110(6), 1317-1325. BESC
201210.1186/1754-6834-5-20Wei, H., M. P. Tucker, J. O. Baker, M. Harris, Y. Luo, Q. Xu, M. E. Himmel, and S. Y. Ding. 2012. Tracking dynamics of plant biomass composting by changes in substrate structure, microbial community, and enzyme activity, Biotechnol Biofuels 5(1), 20. BESC
201210.1111/j.1467-7652.2012.00684.xWeise, S. E., K. Aung, Z. J. Jarou, P. Mehrshahi, Z. Li, A. C. Hardy, D. J. Carr, and T. D. Sharkey. 2012. Engineering starch accumulation by manipulation of phosphate metabolism of starch, Plant Biotechnol J 10(5), 545-554. GLBRC
201210.1039/c2cp23248kWelz, O., J. Zador, J. D. Savee, M. Y. Ng, G. Meloni, R. X. Fernandes, L. Sheps, B. A. Simmons, T. S. Lee, D. L. Osborn, and C. A. Taatjes. 2012. Low-temperature combustion chemistry of biofuels: pathways in the initial low-temperature (550 K-750 K) oxidation chemistry of isopentanol, Phys Chem Chem Phys 14(9), 3112-3127. JBEI
2012Werling, B. P., D. Pennington, and D. A. Landis. 2012. Ecosystem services and bioenergy landscapes. Extension Bulletin E-3164 Michigan State UniversityGLBRC
201210.1016/j.coche.2012.04.002Wettstein, S. G., D. M. Alonso, E. I. Gürbüz, and J. A. Dumesic. 2012. A roadmap for conversion of lignocellulosic biomass to chemicals and fuels, Current Opinion in Chemical Engineering 1(3), 218-224. GLBRC
201210.1039/c2ee22111jWettstein, S. G., D. M. Alonso, Y. Chong, and J. A. Dumesic. 2012. Production of levulinic acid and gamma-valerolactone (GVL) from cellulose using GVL as a solvent in biphasic systems, Energy & Environmental Science 5(8), 8199. GLBRC
201210.1016/j.apcatb.2012.01.033Wettstein, S. G., J. Q. Bond, D. M. Alonso, H. N. Pham, A. K. Datye, and J. A. Dumesic. 2012. RuSn bimetallic catalysts for selective hydrogenation of levulinic acid to ?-valerolactone, Applied Catalysis B: Environmental 117-118, 321-329. GLBRC
201210.1007/s00253-011-3701-9Wilson, D. B. 2012. Processive and nonprocessive cellulases for biofuel production--lessons from bacterial genomes and structural analysis, Appl Microbiol Biotechnol 93(2), 497-502. BESC
201210.1007/978-1-61779-956-3_9Wilson, D. B., and M. Kostylev. 2012. Cellulase processivity, Methods in Molecular Biology 908, 93-99. BESC
2012Wipat, A., A. Villalobos, G.-B. Stan, T. Smith, H. Sauro, N. Roehner, M. Pocock, H. Plahar, J. Peccoud, C. Myers, G. Misirli, C. Madsen, M. Lux, A. Kuchinsky, T. Ham, R. Grünberg, J. Gennari, D. Endy, O. Drory, D. Densmore, D. Chandran, J. Beal, J. C. Anderson, A. Adler, L. Adam, C. Rodriguez, M. Wilson, and M. Galdzicki. 2012. Synthetic Biology Open Language (SBOL) Version 1.0.0. In BioBricks Foundation Request for Comments.JBEI
201210.3389/fpls.2012.00036Wipf, D., D. Loque, S. Lalonde, and W. B. Frommer. 2012. Amino Acid transporter inventory of the selaginella genome, Front Plant Sci 3, 36. JBEI
201210.1074/jbc.M111.284497Withers, S., F. Lu, H. Kim, Y. Zhu, J. Ralph, and C. G. Wilkerson. 2012. Identification of grass-specific enzyme that acylates monolignols with p-coumarate, J Biol Chem 287(11), 8347-8355. GLBRC
2012Woltz, J. M., B. P. Werling, and D. A. Landis. 2012. Natural enemies and insect outbreaks in agriculture: a landscape perspective. In Insect Outbreaks, 355-370. John Wiley and Sons, Ltd.GLBRC
201210.1016/j.cell.2012.04.038Xiao, Y., T. Savchenko, E. E. Baidoo, W. E. Chehab, D. M. Hayden, V. Tolstikov, J. A. Corwin, D. J. Kliebenstein, J. D. Keasling, and K. Dehesh. 2012. Retrograde signaling by the plastidial metabolite MEcPP regulates expression of nuclear stress-response genes, Cell 149(7), 1525-1535. JBEI
201210.1371/journal.pone.0047399Xu, B., N. Sathitsuksanoh, Y. Tang, M. K. Udvardi, J. Y. Zhang, Z. Shen, M. Balota, K. Harich, P. Y. Zhang, and B. Zhao. 2012. Overexpression of AtLOV1 in Switchgrass alters plant architecture, lignin content, and flowering time, PLoS One 7(12), e47399. BESC
201210.1007/978-1-61779-483-4_9Yang, S., D. M. Klingeman, and S. D. Brown. 2012. Ethanol-tolerant gene identification in Clostridium thermocellum using pyro-resequencing for metabolic engineering, Methods in Molecular Biology 834, 111-136. BESC
2012Yang, S., M. Keller, and S. D. Brown. 2012. Genomics on Pretreatment Inhibitor Tolerance of Zymomonas mobilis. In Microbial Stress Tolerance for Biofuels, 161-175. Ed. Z. L. Liu. Springer.BESC
201210.1186/1471-2164-13-336Yang, S., R. J. Giannone, L. Dice, Z. K. Yang, N. L. Engle, T. J. Tschaplinski, R. L. Hettich, and S. D. Brown. 2012. Clostridium thermocellum ATCC27405 transcriptomic, metabolomic and proteomic profiles after ethanol stress, BMC Genomics 13, 336. BESC
201210.1016/j.ab.2011.12.028Yang, T., Y. Bar-Peled, J. A. Smith, J. Glushka, and M. Bar-Peled. 2012. In-microbe formation of nucleotide sugars in engineered Escherichia coli, Anal Biochem 421(2), 691-698. BESC
201210.1039/c2mb05492bYe, X., C. Zhang, and Y. H. Zhang. 2012. Engineering a large protein by combined rational and random approaches: stabilizing the Clostridium thermocellum cellobiose phosphorylase, Mol Biosyst 8(6), 1815-1823. BESC
201210.1186/1754-6834-5-81Yee, K. L., M. Rodriguez, Jr., T. J. Tschaplinski, N. L. Engle, M. Z. Martin, C. Fu, Z. Y. Wang, S. D. Hamilton-Brehm, and J. R. Mielenz. 2012. Evaluation of the bioconversion of genetically modified switchgrass using simultaneous saccharification and fermentation and a consolidated bioprocessing approach, Biotechnol Biofuels 5(1), 81. BESC
201210.1007/s12155-012-9247-6Yelle, D. J., P. Kaparaju, C. G. Hunt, K. Hirth, H. Kim, J. Ralph, and C. Felby. 2012. Two-Dimensional NMR Evidence for Cleavage of Lignin and Xylan Substituents in Wheat Straw Through Hydrothermal Pretreatment and Enzymatic Hydrolysis, BioEnergy Research 6(1), 211-221. GLBRC
201210.1093/nar/gks479Yin, Y., X. Mao, J. Yang, X. Chen, F. Mao, and Y. Xu. 2012. dbCAN: a web resource for automated carbohydrate-active enzyme annotation, Nucleic Acids Res 40(Web Server issue), W445-451. BESC
201210.1016/j.ab.2012.05.022You, C., and Y. H. Percival Zhang. 2012. Easy preparation of a large-size random gene mutagenesis library in Escherichia coli, Anal Biochem 428(1), 7-12. BESC
201210.1002/anie.201202441You, C., S. Myung, and Y. H. Zhang. 2012. Facilitated substrate channeling in a self-assembled trifunctional enzyme complex, Angew Chem Int Ed Engl 51(35), 8787-8790. BESC
201210.1128/AEM.07105-11You, C., X. Z. Zhang, and Y. H. Zhang. 2012. Simple cloning via direct transformation of PCR product (DNA Multimer) to Escherichia coli and Bacillus subtilis, Appl Environ Microbiol 78(5), 1593-1595. BESC
201210.1128/AEM.07138-11You, C., X. Z. Zhang, N. Sathitsuksanoh, L. R. Lynd, and Y. H. Zhang. 2012. Enhanced microbial utilization of recalcitrant cellulose by an ex vivo cellulosome-microbe complex, Appl Environ Microbiol 78(5), 1437-1444. BESC
201210.1016/j.bej.2012.01.011You, C., X.-Z. Zhang, and Y. H. P. Zhang. 2012. Mini-scaffoldin enhanced mini-cellulosome hydrolysis performance on low-accessibility cellulose (Avicel) more than on high-accessibility amorphous cellulose, Biochemical Engineering Journal 63, 57-65. BESC
201210.1002/bit.24420Youngquist, J. T., R. M. Lennen, D. R. Ranatunga, W. H. Bothfeld, W. D. Marner, 2nd, and B. F. Pfleger. 2012. Kinetic modeling of free fatty acid production in Escherichia coli based on continuous cultivation of a plasmid free strain, Biotechnol Bioeng 109(6), 1518-1527. GLBRC
201210.1021/jf204481xYue, F., F. Lu, R. C. Sun, and J. Ralph. 2012. Syntheses of lignin-derived thioacidolysis monomers and their uses as quantitation standards, J Agric Food Chem 60(4), 922-928. GLBRC
201210.1002/chem.201201506Yue, F., F. Lu, R. Sun, and J. Ralph. 2012. Synthesis and characterization of new 5-linked pinoresinol lignin models, Chemistry 18(51), 16402-16410. GLBRC
201210.1021/bi301414qYuzawa, S., N. Chiba, L. Katz, and J. D. Keasling. 2012. Construction of a part of a 3-hydroxypropionate cycle for heterologous polyketide biosynthesis in Escherichia coli, Biochemistry 51(49), 9779-9781. JBEI
201210.1016/j.copbio.2011.12.029Yuzawa, S., W. Kim, L. Katz, and J. D. Keasling. 2012. Heterologous production of polyketides by modular type I polyketide synthases in Escherichia coli, Curr Opin Biotechnol 23(5), 727-735. JBEI
201210.1104/pp.112.198119Zabotina, O. A., U. Avci, D. Cavalier, S. Pattathil, Y. H. Chou, S. Eberhard, L. Danhof, K. Keegstra, and M. G. Hahn. 2012. Mutations in multiple XXT genes of Arabidopsis reveal the complexity of xyloglucan biosynthesis, Plant Physiol 159(4), 1367-1384. GLBRC
201210.1002/bit.24395Zendejas, F. J., P. I. Benke, P. D. Lane, B. A. Simmons, and T. W. Lane. 2012. Characterization of the acylglycerols and resulting biodiesel derived from vegetable oil and microalgae (Thalassiosira pseudonana and Phaeodactylum tricornutum), Biotechnol Bioeng 109(5), 1146-1154. JBEI
201210.1007/978-1-61779-956-3_5Zeng, Y., M. E. Himmel, and S. Y. Ding. 2012. Coherent Raman microscopy analysis of plant cell walls, Methods in Molecular Biology 908, 49-60. BESC
201210.1038/nbt.2149Zhang, F., J. M. Carothers, and J. D. Keasling. 2012. Design of a dynamic sensor-regulator system for production of chemicals and fuels derived from fatty acids, Nat Biotechnol 30(4), 354-359. JBEI
201210.1016/j.ymben.2012.08.009Zhang, F., M. Ouellet, T. S. Batth, P. D. Adams, C. J. Petzold, A. Mukhopadhyay, and J. D. Keasling. 2012. Enhancing fatty acid production by the expression of the regulatory transcription factor FadR, Metab Eng 14(6), 653-660. JBEI
201210.1371/journal.pone.0029496Zhang, H., Y. Yin, V. Olman, and Y. Xu. 2012. Genomic arrangement of regulons in bacterial genomes, PLoS One 7(1), e29496. BESC
201210.1105/tpc.112.101287Zhang, K., M. W. Bhuiya, J. R. Pazo, Y. Miao, H. Kim, J. Ralph, and C. J. Liu. 2012. An engineered monolignol 4-o-methyltransferase depresses lignin biosynthesis and confers novel metabolic capability in Arabidopsis, Plant Cell 24(7), 3135-3152. GLBRC
201210.1111/j.1469-8137.2012.04268.xZhou, C., L. Han, C. Fu, M. Chai, W. Zhang, G. Li, Y. Tang, and Z. Y. Wang. 2012. Identification and characterization of petiolule-like pulvinus mutants with abolished nyctinastic leaf movement in the model legume Medicago truncatula, New Phytol 196(1), 92-100. BESC
201210.1371/journal.pone.0032660.Zhou, F., Q. Ma, G. Li, and Y. Xu. 2012. QServer: a biclustering server for prediction and assessment of co-expressed gene clusters, PLoS One 7(3), e32660. BESC
2012 10.1016/j.bios.2012.04.001Zhu, Z., F. Sun, X. Zhang, and Y. H. Zhang. 2012. Deep oxidation of glucose in enzymatic fuel cells through a synthetic enzymatic pathway containing a cascade of two thermostable dehydrogenases, Biosens Bioelectron 36(1), 110-115. BESC
201110.1038/ismej.2011.14Adams, A. S., M. S. Jordan, S. M. Adams, G. Suen, L. A. Goodwin, K. W. Davenport, C. R. Currie, and K. F. Raffa. 2011. Cellulose-degrading bacteria associated with the invasive woodwasp Sirex noctilio, ISME J 5(8), 1323-1331. GLBRC
201110.1107/S1744309111038449Alahuhta, M., P. Chandrayan, I. Kataeva, M. W. Adams, M. E. Himmel, and V. V. Lunin. 2011. A 1.5 A resolution X-ray structure of the catalytic module of Caldicellulosiruptor bescii family 3 pectate lyase, Acta Crystallogr Sect F Struct Biol Cryst Commun 67(Pt 12), 1498-1500. BESC
201110.1107/S1744309111003307Alahuhta, M., Y. Luo, S. Y. Ding, M. E. Himmel, and V. V. Lunin. 2011. Structure of CBM4 from Clostridium thermocellum cellulase K, Acta Crystallogr Sect F Struct Biol Cryst Commun 67(Pt 5), 527-530. BESC
201110.1016/j.ymben.2010.10.002Alonso, A. P., D. L. Val, and Y. Shachar-Hill. 2011. Central metabolic fluxes in the endosperm of developing maize seeds and their implications for metabolic engineering, Metab Eng 13(1), 96-107. GLBRC
201110.1002/cssc.201100256Alonso, D. M., S. G. Wettstein, J. Q. Bond, T. W. Root, and J. A. Dumesic. 2011. Production of biofuels from cellulose and corn stover using alkylphenol solvents, ChemSusChem 4(8), 1078-1081. GLBRC
201110.1128/AEM.00646-11Argyros, D. A., S. A. Tripathi, T. F. Barrett, S. R. Rogers, L. F. Feinberg, D. G. Olson, J. M. Foden, B. B. Miller, L. R. Lynd, D. A. Hogsett, and N. C. Caiazza. 2011. High ethanol titers from cellulose by using metabolically engineered thermophilic, anaerobic microbes, Appl Environ Microbiol 77(23), 8288-8294. BESC
201110.1073/pnas.1112816108Atmodjo, M. A., Y. Sakuragi, X. Zhu, A. J. Burrell, S. S. Mohanty, J. A. Atwood, 3rd, R. Orlando, H. V. Scheller, and D. Mohnen. 2011. Galacturonosyltransferase (GAUT)1 and GAUT7 are the core of a plant cell wall pectin biosynthetic homogalacturonan:galacturonosyltransferase complex, Proc Natl Acad Sci U S A 108(50), 20225-20230. JBEI BESC
201110.1039/c1ob05677hAzarpira, A., F. Lu, and J. Ralph. 2011. Reactions of dehydrodiferulates with ammonia, Org Biomol Chem 9(19), 6779-6787. GLBRC
201110.1016/j.enpol.2010.10.044Babcock, B. A., S. Marette, and D. Tréguer. 2011. Opportunity for profitable investments in cellulosic biofuels, Energy Policy 39(2), 714-719. GLBRC
201110.1007/s12155-011-9140-8Bals, B. D., F. Teymouri, T. Campbell, M. Jin, and B. E. Dale. 2011. Low Temperature and Long Residence Time AFEX Pretreatment of Corn Stover, BioEnergy Research 5(2), 372-379. GLBRC
201110.1002/bit.22973Bals, B., and B. E. Dale. 2011. Economic comparison of multiple techniques for recovering leaf protein in biomass processing, Biotechnol Bioeng 108(3), 530-537. GLBRC
201110.1016/j.biortech.2010.08.058Bals, B., C. Wedding, V. Balan, E. Sendich, and B. Dale. 2011. Evaluating the impact of ammonia fiber expansion (AFEX) pretreatment conditions on the cost of ethanol production, Bioresour Technol 102(2), 1277-1283. GLBRC
201110.1186/1754-6834-4-16Banerjee, G., S. Car, J. S. Scott-Craig, D. B. Hodge, and J. D. Walton. 2011. Alkaline peroxide pretreatment of corn stover: effects of biomass, peroxide, and enzyme loading and composition on yields of glucose and xylose, Biotechnol Biofuels 4(1), 16. GLBRC
201110.1126/science.1203810Banks, J. A., T. Nishiyama, M. Hasebe, J. L. Bowman, M. Gribskov, C. dePamphilis, V. A. Albert, N. Aono, T. Aoyama, B. A. Ambrose, N. W. Ashton, M. J. Axtell, E. Barker, M. S. Barker, J. L. Bennetzen, N. D. Bonawitz, C. Chapple, C. Cheng, L. G. Correa, M. Dacre, J. DeBarry, I. Dreyer, M. Elias, E. M. Engstrom, M. Estelle, L. Feng, C. Finet, S. K. Floyd, W. B. Frommer, T. Fujita, L. Gramzow, M. Gutensohn, J. Harholt, M. Hattori, A. Heyl, T. Hirai, Y. Hiwatashi, M. Ishikawa, M. Iwata, K. G. Karol, B. Koehler, U. Kolukisaoglu, M. Kubo, T. Kurata, S. Lalonde, K. Li, Y. Li, A. Litt, E. Lyons, G. Manning, T. Maruyama, T. P. Michael, K. Mikami, S. Miyazaki, S. Morinaga, T. Murata, B. Mueller-Roeber, D. R. Nelson, M. Obara, Y. Oguri, R. G. Olmstead, N. Onodera, B. L. Petersen, B. Pils, M. Prigge, S. A. Rensing, D. M. Riano-Pachon, A. W. Roberts, Y. Sato, H. V. Scheller, B. Schulz, C. Schulz, E. V. Shakirov, N. Shibagaki, N. Shinohara, D. E. Shippen, I. Sorensen, R. Sotooka, N. Sugimoto, M. Sugita, N. Sumikawa, M. Tanurdzic, G. Theissen, P. Ulvskov, S. Wakazuki, J. K. Weng, W. W. Willats, D. Wipf, P. G. Wolf, L. Yang, A. D. Zimmer, Q. Zhu, T. Mitros, U. Hellsten, D. Loque, R. Otillar, A. Salamov, J. Schmutz, H. Shapiro, E. Lindquist, S. Lucas, D. Rokhsar, and I. V. Grigoriev. 2011. The Selaginella genome identifies genetic changes associated with the evolution of vascular plants, Science 332(6032), 960-963. JBEI
201110.1146/annurev-arplant-042110-103918Bar-Peled, M., and M. A. O'Neill. 2011. Plant nucleotide sugar formation, interconversion, and salvage by sugar recycling, Annu Rev Plant Biol 62, 127-155. BESC
201110.1093/nar/gkr433Bates, J. T., D. Chivian, and A. P. Arkin. 2011. GLAMM: Genome-Linked Application for Metabolic Maps, Nucleic Acids Res 39(Web Server issue), W400-405. JBEI
201110.1016/j.copbio.2010.11.005Beckham, G. T., Y. J. Bomble, E. A. Bayer, M. E. Himmel, and M. F. Crowley. 2011. Applications of computational science for understanding enzymatic deconstruction of cellulose, Curr Opin Biotechnol 22(2), 231-238. BESC
201110.1074/jbc.L110.216127Beller, H. R., E. B. Goh, and J. D. Keasling. 2011. Definitive alkene identification needed for in vitro studies with ole (olefin biosynthesis) proteins, J Biol Chem 286(26), le11; author reply le12-13. JBEI
201110.1021/jp2048844Bellesia, G., S. P. Chundawat, P. Langan, B. E. Dale, and S. Gnanakaran. 2011. Probing the early events associated with liquid ammonia pretreatment of native crystalline cellulose, J Phys Chem B 115(32), 9782-9788. GLBRC
201110.1016/j.biortech.2010.08.108Bharadwaj, R., A. Wong, B. Knierim, S. Singh, B. M. Holmes, M. Auer, B. A. Simmons, P. D. Adams, and A. K. Singh. 2011. High-throughput enzymatic hydrolysis of lignocellulosic biomass via in-situ regeneration, Bioresour Technol 102(2), 1329-1337. JBEI
201110.1016/j.agee.2011.01.005Bhardwaj, A. K., P. Jasrotia, S. K. Hamilton, and G. P. Robertson. 2011. Ecological management of intensively cropped agro-ecosystems improves soil quality with sustained productivity, Agriculture, Ecosystems & Environment 140(3-4), 419-429. GLBRC
201110.1111/j.1757-1707.2010.01074.xBhardwaj, A. K., T. Zenone, P. Jasrotia, G. P. Robertson, J. Chen, and S. K. Hamilton. 2011. Water and energy footprints of bioenergy crop production on marginal lands, GCB Bioenergy 3(3), 208-222. GLBRC
201110.1002/cem.1398Biagioni, D. J., D. P. Astling, P. Graf, and M. F. Davis. 2011. Orthogonal projection to latent structures solution properties for chemometrics and systems biology data, Journal of Chemometrics 25(9), 514-525. BESC
201110.1107/S1744309111032660Bianchetti, C. M., N. L. Elsen, B. G. Fox, and G. N. Phillips, Jr. 2011. Structure of cellobiose phosphorylase from Clostridium thermocellum in complex with phosphate, Acta Crystallogr Sect F Struct Biol Cryst Commun 67(Pt 11), 1345-1349. GLBRC
201110.1002/biot.201000180Blanch, H. W., B. A. Simmons, and D. Klein-Marcuschamer. 2011. Biomass deconstruction to sugars, Biotechnol J 6(9), 1086-1102. JBEI
201110.1128/JB.01515-10Blumer-Schuette, S. E., I. Ozdemir, D. Mistry, S. Lucas, A. Lapidus, J. F. Cheng, L. A. Goodwin, S. Pitluck, M. L. Land, L. J. Hauser, T. Woyke, N. Mikhailova, A. Pati, N. C. Kyrpides, N. Ivanova, J. C. Detter, K. Walston-Davenport, S. Han, M. W. Adams, and R. M. Kelly. 2011. Complete genome sequences for the anaerobic, extremely thermophilic plant biomass-degrading bacteria Caldicellulosiruptor hydrothermalis, Caldicellulosiruptor kristjanssonii, Caldicellulosiruptor kronotskyensis, Caldicellulosiruptor owensensis, and Caldicellulosiruptor lactoaceticus, J Bacteriol 193(6), 1483-1484. BESC
201110.1073/pnas.1106958108Bokinsky, G., P. P. Peralta-Yahya, A. George, B. M. Holmes, E. J. Steen, J. Dietrich, T. S. Lee, D. Tullman-Ercek, C. A. Voigt, B. A. Simmons, and J. D. Keasling. 2011. Synthesis of three advanced biofuels from ionic liquid-pretreated switchgrass using engineered Escherichia coli, Proc Natl Acad Sci U S A 108(50), 19949-19954. JBEI
201110.1074/jbc.M110.186031Bomble, Y. J., G. T. Beckham, J. F. Matthews, M. R. Nimlos, M. E. Himmel, and M. F. Crowley. 2011. Modeling the self-assembly of the cellulosome enzyme complex, J Biol Chem 286(7), 5614-5623. BESC
201110.1073/pnas.1106502108Bourgis, F., A. Kilaru, X. Cao, G. F. Ngando-Ebongue, N. Drira, J. B. Ohlrogge, and V. Arondel. 2011. Comparative transcriptome and metabolite analysis of oil palm and date palm mesocarp that differ dramatically in carbon partitioning, Proc Natl Acad Sci U S A 108(30), 12527-12532. GLBRC
201110.1039/c1gc15047bBraden, D. J., C. A. Henao, J. Heltzel, C. C. Maravelias, and J. A. Dumesic. 2011. Production of liquid hydrocarbon fuels by catalytic conversion of biomass-derived levulinic acid, Green Chemistry 13(7), 1755. GLBRC
201110.1073/pnas.1102444108Brown, S. D., A. M. Guss, T. V. Karpinets, J. M. Parks, N. Smolin, S. Yang, M. L. Land, D. M. Klingeman, A. Bhandiwad, M. Rodriguez, Jr., B. Raman, X. Shao, J. R. Mielenz, J. C. Smith, M. Keller, and L. R. Lynd. 2011. Mutant alcohol dehydrogenase leads to improved ethanol tolerance in Clostridium thermocellum, Proc Natl Acad Sci U S A 108(33), 13752-13757. BESC
201110.1128/JB.05209-11Brown, S. D., M. B. Begemann, M. R. Mormile, J. D. Wall, C. S. Han, L. A. Goodwin, S. Pitluck, M. L. Land, L. J. Hauser, and D. A. Elias. 2011. Complete genome sequence of the haloalkaliphilic, hydrogen-producing bacterium Halanaerobium hydrogeniformans, J Bacteriol 193(14), 3682-3683. BESC
2011Brown, T., and J. M. Tiedje. 2011. Metagenomics: the paths forward. In Handbook of Molecular Microbial Ecology II: Metagenomics in Different Habitats, 581-588. Ed. F. J. de Bruijn. Wiley-Blackwell.GLBRC
2011Brumm, P. J., S. Hermanson, J. Luedtke, and D. A. Mead. 2011. Identification, cloning and characterization of Dictyoglomus turgidum CelA, an endoglucanase with cellulase and mannanase activity, Journal of Life Sciences 5, 488-496. DOI.GLBRC
2011Brumm, P., D. Mead, J. Boyum, C. Drinkwater, J. Deneke, K. Gowda, D. Stevenson, and P. Weimer. 2011. Functional annotation of Fibrobacter succinogenes S85 carbohydrate active enzymes, Appl Biochem Biotechnol 163(5), 649-657. 10.1007/s12010-010-9070-5.GLBRC
201110.1007/s12010-010-9029-6Brumm, P., S. Hermanson, B. Hochstein, J. Boyum, N. Hermersmann, K. Gowda, and D. Mead. 2011. Mining Dictyoglomus turgidum for enzymatically active carbohydrases, Appl Biochem Biotechnol 163(2), 205-214. GLBRC
201110.1002/cssc.201000397Caes, B. R., and R. T. Raines. 2011. Conversion of fructose into 5-(hydroxymethyl)furfural in sulfolane, ChemSusChem 4(3), 353-356. GLBRC
201110.1039/c1gc15776kCaes, B. R., J. B. Binder, J. J. Blank, and R. T. Raines. 2011. Separable fluorous ionic liquids for the dissolution and saccharification of cellulose, Green Chemistry 13(10), 2719. GLBRC
201110.1186/1471-2105-12-79Cai, B., X. Yang, G. A. Tuskan, and Z. M. Cheng. 2011. MicroSyn: a user friendly tool for detection of microsynteny in a gene family, BMC Bioinformatics 12, 79. BESC
201110.1126/science.1212209Carothers, J. M., J. A. Goler, D. Juminaga, and J. D. Keasling. 2011. Model-driven engineering of RNA devices to quantitatively program gene expression, Science 334(6063), 1716-1719. JBEI
201110.1074/jbc.M110.215962Cartmell, A., L. S. McKee, M. J. Pena, J. Larsbrink, H. Brumer, S. Kaneko, H. Ichinose, R. J. Lewis, A. Vikso-Nielsen, H. J. Gilbert, and J. Marles-Wright. 2011. The structure and function of an arabinan-specific alpha-1,2-arabinofuranosidase identified from screening the activities of bacterial GH43 glycoside hydrolases, J Biol Chem 286(17), 15483-15495. BESC
201110.3835/plantgenome2011.10.0026Casler, M. D., C. M. Tobias, S. M. Kaeppler, C. R. Buell, Z.-Y. Wang, P. Cao, J. Schmutz, and P. Ronald. 2011. The Switchgrass Genome: Tools and Strategies, The Plant Genome Journal 4(3), 273. JBEI BESC
201110.1111/j.1365-313X.2011.04520.xChen, F., D. Tholl, J. Bohlmann, and E. Pichersky. 2011. The family of terpene synthases in plants: a mid-size family of genes for specialized metabolism that is highly diversified throughout the kingdom, Plant J 66(1), 212-229. BESC
201110.1242/jcs.084624Chen, J., G. Stefano, F. Brandizzi, and H. Zheng. 2011. Arabidopsis RHD3 mediates the generation of the tubular ER network and is required for Golgi distribution and motility in plant cells, J Cell Sci 124(Pt 13), 2241-2252. GLBRC
201110.1016/j.ymben.2010.11.004Chen, X., A. P. Alonso, D. K. Allen, J. L. Reed, and Y. Shachar-Hill. 2011. Synergy between (13)C-metabolic flux analysis and flux balance analysis for understanding metabolic adaptation to anaerobiosis in E. coli, Metab Eng 13(1), 38-48. GLBRC
201110.1186/1471-2105-12-S1-S1Chen, Y., F. Mao, G. Li, and Y. Xu. 2011. Genome-wide discovery of missing genes in biological pathways of prokaryotes, BMC Bioinformatics 12 Suppl 1, S1. BESC
201110.1021/bm101240zCheng, G., P. Varanasi, C. Li, H. Liu, Y. B. Melnichenko, B. A. Simmons, M. S. Kent, and S. Singh. 2011. Transition of cellulose crystalline structure and surface morphology of biomass as a function of ionic liquid pretreatment and its relation to enzymatic hydrolysis, Biomacromolecules 12(4), 933-941. JBEI
201110.1021/bm200305uCheng, G., Z. Liu, J. K. Murton, M. Jablin, M. Dubey, J. Majewski, C. Halbert, J. Browning, J. Ankner, B. Akgun, C. Wang, A. R. Esker, K. L. Sale, B. A. Simmons, and M. S. Kent. 2011. Neutron reflectometry and QCM-D study of the interaction of cellulases with films of amorphous cellulose, Biomacromolecules 12(6), 2216-2224. JBEI
201110.4056/sigs.2184986Chertkov, O., A. Copeland, S. Lucas, A. Lapidus, K. W. Berry, J. C. Detter, T. G. Del Rio, N. Hammon, E. Dalin, H. Tice, S. Pitluck, P. Richardson, D. Bruce, L. Goodwin, C. Han, R. Tapia, E. Saunders, J. Schmutz, T. Brettin, F. Larimer, M. Land, L. Hauser, S. Spring, M. Rohde, N. C. Kyrpides, N. Ivanova, M. Goker, H. R. Beller, H. P. Klenk, and T. Woyke. 2011. Complete genome sequence of Tolumonas auensis type strain (TA 4), Stand Genomic Sci 5(1), 112-120. JBEI
2011Chhabra, S. R., and J. Keasling. 2011. The Biological Basis | Metabolic Design and Control for Production in Prokaryotes. In Comprehensive Biotechnology, 243-255. Ed. M. Moo-Young. Elsevier.JBEI
201110.1073/pnas.1113971108Chuck, G. S., C. Tobias, L. Sun, F. Kraemer, C. Li, D. Dibble, R. Arora, J. N. Bragg, J. P. Vogel, S. Singh, B. A. Simmons, M. Pauly, and S. Hake. 2011. Overexpression of the maize Corngrass1 microRNA prevents flowering, improves digestibility, and increases starch content of switchgrass, Proc Natl Acad Sci U S A 108(42), 17550-17555. JBEI
201110.1039/c0ee00574fChundawat, S. P. S., B. S. Donohoe, L. da Costa Sousa, T. Elder, U. P. Agarwal, F. Lu, J. Ralph, M. E. Himmel, V. Balan, and B. E. Dale. 2011. Multi-scale visualization and characterization of lignocellulosic plant cell wall deconstruction during thermochemical pretreatment, Energy & Environmental Science 4(3), 973. GLBRC
201110.1021/ja2011115Chundawat, S. P., G. Bellesia, N. Uppugundla, L. da Costa Sousa, D. Gao, A. M. Cheh, U. P. Agarwal, C. M. Bianchetti, G. N. Phillips, Jr., P. Langan, V. Balan, S. Gnanakaran, and B. E. Dale. 2011. Restructuring the crystalline cellulose hydrogen bond network enhances its depolymerization rate, J Am Chem Soc 133(29), 11163-11174. GLBRC
201110.1146/annurev-chembioeng-061010-114205Chundawat, S. P., G. T. Beckham, M. E. Himmel, and B. E. Dale. 2011. Deconstruction of lignocellulosic biomass to fuels and chemicals, Annu Rev Chem Biomol Eng 2, 121-145. GLBRC BESC
201110.1021/pr101234zChundawat, S. P., M. S. Lipton, S. O. Purvine, N. Uppugundla, D. Gao, V. Balan, and B. E. Dale. 2011. Proteomics-based compositional analysis of complex cellulase-hemicellulase mixtures, J Proteome Res 10(10), 4365-4372. GLBRC
201110.1007/s10295-011-0976-xChung, D. H., J. R. Huddleston, J. Farkas, and J. Westpheling. 2011. Identification and characterization of CbeI, a novel thermostable restriction enzyme from Caldicellulosiruptor bescii DSM 6725 and a member of a new subfamily of HaeIII-like enzymes, J Ind Microbiol Biotechnol 38(11), 1867-1877. BESC
201110.1021/ac200536bChylla, R. A., K. Hu, J. J. Ellinger, and J. L. Markley. 2011. Deconvolution of two-dimensional NMR spectra by fast maximum likelihood reconstruction: application to quantitative metabolomics, Anal Chem 83(12), 4871-4880. GLBRC
2011Cole, J. R., Q. Wang, B. Chai, and J. M. Tiedje. 2011. The Ribosomal Database Project: sequences and software for high-throughput rRNA analysis. In Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches, 313-324. Wiley-Blackwell.GLBRC
201110.1074/jbc.M111.254664Cornish, A. J., K. Gartner, H. Yang, J. W. Peters, and E. L. Hegg. 2011. Mechanism of proton transfer in [FeFe]-hydrogenase from Clostridium pasteurianum, J Biol Chem 286(44), 38341-38347. GLBRC
201110.1074/jbc.M110.217315Correia, M. A., K. Mazumder, J. L. Bras, S. J. Firbank, Y. Zhu, R. J. Lewis, W. S. York, C. M. Fontes, and H. J. Gilbert. 2011. Structure and function of an arabinoxylan-specific xylanase, J Biol Chem 286(25), 22510-22520. BESC
201110.1021/jp109798pDagel, D. J., Y. S. Liu, L. Zhong, Y. Luo, M. E. Himmel, Q. Xu, Y. Zeng, S. Y. Ding, and S. Smith. 2011. In situ imaging of single carbohydrate-binding modules on cellulose microfibrils, J Phys Chem B 115(4), 635-641. BESC
2011Dagel, D., Y.-S. Liu, L. Zhong, Y. Luo, Y. Zeng, M. Himmel, S.-Y. Ding, and S. J. Smith. 2011. DOPI and PALM Imaging of Single Carbohydrate Binding Modules Bound to Cellulose Nanocrystals. In Proceedings of SPIE - The International Society for Optical Engineering.BESC
201110.1093/nar/gkq1281Dam, P., I. Kataeva, S. J. Yang, F. Zhou, Y. Yin, W. Chou, F. L. Poole, 2nd, J. Westpheling, R. Hettich, R. Giannone, D. L. Lewis, R. Kelly, H. J. Gilbert, B. Henrissat, Y. Xu, and M. W. Adams. 2011. Insights into plant biomass conversion from the genome of the anaerobic thermophilic bacterium Caldicellulosiruptor bescii DSM 6725, Nucleic Acids Res 39(8), 3240-3254. BESC
2011Datta, S., and R. Sapra. 2011. Cellulases and Hemicellulases for Biomass Degradation: An Introduction. In Chemical and Biochemical Catalysis for Next Generation Biofuels, 115-135. Ed. B. A. Simmons. Royal Society of Chemistry.JBEI
201110.3835/plantgenome2011.05.0015Davidson, R. M., C. N. Hansey, M. Gowda, K. L. Childs, H. Lin, B. Vaillancourt, R. S. Sekhon, N. de Leon, S. M. Kaeppler, N. Jiang, and C. R. Buell. 2011. Utility of RNA Sequencing for Analysis of Maize Reproductive Transcriptomes, The Plant Genome Journal 4(3), 191. GLBRC
201110.1128/AEM.05262-11DeAngelis, K. M., C. H. Wu, H. R. Beller, E. L. Brodie, R. Chakraborty, T. Z. DeSantis, J. L. Fortney, T. C. Hazen, S. R. Osman, M. E. Singer, L. M. Tom, and G. L. Andersen. 2011. PCR amplification-independent methods for detection of microbial communities by the high-density microarray PhyloChip, Appl Environ Microbiol 77(18), 6313-6322. JBEI
201110.1371/journal.pone.0019306DeAngelis, K. M., M. Allgaier, Y. Chavarria, J. L. Fortney, P. Hugenholtz, B. Simmons, K. Sublette, W. L. Silver, and T. C. Hazen. 2011. Characterization of trapped lignin-degrading microbes in tropical forest soil, PLoS One 6(4), e19306. JBEI
201110.4056/sigs.2104875Deangelis, K. M., P. D'Haeseleer, D. Chivian, J. L. Fortney, J. Khudyakov, B. Simmons, H. Woo, A. P. Arkin, K. W. Davenport, L. Goodwin, A. Chen, N. Ivanova, N. C. Kyrpides, K. Mavromatis, T. Woyke, and T. C. Hazen. 2011. Complete genome sequence of Enterobacter lignolyticus SCF1, Stand Genomic Sci 5(1), 69-85. JBEI
201110.1016/j.biortech.2010.08.123DeMartini, J. D., and C. E. Wyman. 2011. Changes in composition and sugar release across the annual rings of Populus wood and implications on recalcitrance, Bioresour Technol 102(2), 1352-1358. BESC
201110.1186/1754-6834-4-52Demartini, J. D., and C. E. Wyman. 2011. Composition and hydrothermal pretreatment and enzymatic saccharification performance of grasses and legumes from a mixed-species prairie, Biotechnol Biofuels 4, 52. BESC
201110.1002/bit.22937DeMartini, J. D., M. H. Studer, and C. E. Wyman. 2011. Small-scale and automatable high-throughput compositional analysis of biomass, Biotechnol Bioeng 108(2), 306-312. BESC
201110.1039/c1ee02112eDeMartini, J. D., S. Pattathil, U. Avci, K. Szekalski, K. Mazumder, M. G. Hahn, and C. E. Wyman. 2011. Application of monoclonal antibodies to investigate plant cell wall deconstruction for biofuels production, Energy & Environmental Science 4(10), 4332. BESC
2011Deshpande, A., A. C. Pontaroli, S. R. Chaluvadi, F. Lu, and J. L. Bennetzen. 2011. Plant Genetics for Study of the Roles of Root Exudates and Microbes in the Soil. In Root Genomics, 99-111. Eds. A. Costa de Oliveira, and R. K. Varshney.BESC
201110.1039/c1gc15111hDibble, D. C., C. Li, L. Sun, A. George, A. Cheng, Ö. P. Çetinkol, P. Benke, B. M. Holmes, S. Singh, and B. A. Simmons. 2011. A facile method for the recovery of ionic liquid and lignin from biomass pretreatment, Green Chemistry 13(11), 3255. JBEI
201110.1016/j.jala.2010.08.005Donath, M. J., 2nd, M. A. Dominguez, and S. T. Withers, 3rd. 2011. Development of an automated platform for high-throughput P1-phage transduction of Escherichia coli, J Lab Autom 16(2), 141-147. GLBRC
201110.1089/ind.2011.7.255Donohue, T. 2011. Great Lakes Bioenergy Research Center, Industrial Biotechnology 7(4), 255-256. GLBRC
201110.1038/msb.2011.21Dunlop, M. J., Z. Y. Dossani, H. L. Szmidt, H. C. Chu, T. S. Lee, J. D. Keasling, M. Z. Hadi, and A. Mukhopadhyay. 2011. Engineering microbial biofuel tolerance and export using efflux pumps, Mol Syst Biol 7, 487. JBEI
2011Egbendewe-Mondzozo, A., S. M. Swinton, B. D. Bals, and B. E. Dale. 2011. Can dispersed biomass processing protect the environment and cover the bottom line for biofuel? . Michigan State University Staff Paper 2011-15 Michigan State UniversityGLBRC
201110.1016/j.biombioe.2011.09.010Egbendewe-Mondzozo, A., S. M. Swinton, C. R. Izaurralde, D. H. Manowitz, and X. Zhang. 2011. Biomass supply from alternative cellulosic crops and crop residues: A spatially explicit bioeconomic modeling approach, Biomass and Bioenergy 35(11), 4636-4647. GLBRC
201110.1111/j.1757-1707.2011.01096.xEranki, P. L., and B. E. Dale. 2011. Comparative life cycle assessment of centralized and distributed biomass processing systems combined with mixed feedstock landscapes, GCB Bioenergy 3(6), 427-438. GLBRC
201110.1002/bbb.318Eranki, P. L., B. D. Bals, and B. E. Dale. 2011. Advanced Regional Biomass Processing Depots: a key to the logistical challenges of the cellulosic biofuel industry, Biofuels, Bioproducts and Biorefining 5(6), 621-630. GLBRC
201110.1007/s12155-011-9159-xEscamilla-Treviño, L. L. 2011. Potential of Plants from the Genus Agave as Bioenergy Crops, BioEnergy Research 5(1), 1-9. BESC
201110.1007/s00253-010-2939-yEudes, A., E. E. Baidoo, F. Yang, H. Burd, M. Z. Hadi, F. W. Collins, J. D. Keasling, and D. Loque. 2011. Production of tranilast [N-(3',4'-dimethoxycinnamoyl)-anthranilic acid] and its analogs in yeast Saccharomyces cerevisiae, Appl Microbiol Biotechnol 89(4), 989-1000. JBEI
201110.1128/AEM.05057-11Farkas, J., D. Chung, M. DeBarry, M. W. Adams, and J. Westpheling. 2011. Defining components of the chromosomal origin of replication of the hyperthermophilic archaeon Pyrococcus furiosus needed for construction of a stable replicating shuttle vector, Appl Environ Microbiol 77(18), 6343-6349. BESC
2011Fasmer Hansen, S., R. McAndrew, A. Degiovanni, P. McInerney, J. Henrique Pereira, M. Hadi, P. Adams, and H. Scheller. 2011. Structural Comparison of Plant Glycosyltransferases, Glycobiology 21, 1511-1512. DOI.JBEI
201110.1128/AEM.01901-10Fisher, A. C., C. H. Haitjema, C. Guarino, E. Celik, C. E. Endicott, C. A. Reading, J. H. Merritt, A. C. Ptak, S. Zhang, and M. P. DeLisa. 2011. Production of secretory and extracellular N-linked glycoproteins in Escherichia coli, Appl Environ Microbiol 77(3), 871-881. GLBRC
201110.1890/090091Fletcher, R. J., B. A. Robertson, J. Evans, P. J. Doran, J. R. R. Alavalapati, and D. W. Schemske. 2011. Biodiversity conservation in the era of biofuels: risks and opportunities, Frontiers in Ecology and the Environment 9(3), 161-168. GLBRC
201110.1039/c1ee02073kFoston, M., C. A. Hubbell, R. Samuel, S. Jung, H. Fan, S.-Y. Ding, Y. Zeng, S. Jawdy, M. Davis, R. Sykes, E. Gjersing, G. A. Tuskan, U. Kalluri, and A. J. Ragauskas. 2011. Chemical, ultrastructural and supramolecular analysis of tension wood in Populus tremula x alba as a model substrate for reduced recalcitrance, Energy & Environmental Science 4(12), 4962. BESC
201110.1002/jctb.2484Frear, C., Z.-W. Wang, C. Li, and S. Chen. 2011. Biogas potential and microbial population distributions in flushed dairy manure and implications on anaerobic digestion technology, Journal of Chemical Technology & Biotechnology 86(1), 145-152. JBEI
201110.1073/pnas.1100310108Fu, C., J. R. Mielenz, X. Xiao, Y. Ge, C. Y. Hamilton, M. Rodriguez, Jr., F. Chen, M. Foston, A. Ragauskas, J. Bouton, R. A. Dixon, and Z. Y. Wang. 2011. Genetic manipulation of lignin reduces recalcitrance and improves ethanol production from switchgrass, Proc Natl Acad Sci U S A 108(9), 3803-3808. BESC
201110.1007/s12155-010-9109-zFu, C., X. Xiao, Y. Xi, Y. Ge, F. Chen, J. Bouton, R. A. Dixon, and Z.-Y. Wang. 2011. Downregulation of Cinnamyl Alcohol Dehydrogenase (CAD) Leads to Improved Saccharification Efficiency in Switchgrass, BioEnergy Research 4(3), 153-164. BESC
201110.1073/pnas.1117873108Gallego-Giraldo, L., L. Escamilla-Trevino, L. A. Jackson, and R. A. Dixon. 2011. Salicylic acid mediates the reduced growth of lignin down-regulated plants, Proc Natl Acad Sci U S A 108(51), 20814-20819. BESC
201110.1002/bit.23140Gao, D., S. P. Chundawat, N. Uppugundla, V. Balan, and B. E. Dale. 2011. Binding characteristics of Trichoderma reesei cellulases on untreated, ammonia fiber expansion (AFEX), and dilute-acid pretreated lignocellulosic biomass, Biotechnol Bioeng 108(8), 1788-1800. GLBRC
201110.2134/agronj2010.0445Gao, J., L. Qian, K. D. Thelen, X. Hao, L. d. C. Sousa, M. W. Lau, V. Balan, and B. E. Dale. 2011. Corn Harvest Strategies for Combined Starch and Cellulosic Bioprocessing to Ethanol, Agronomy Journal 103(3), 844. GLBRC
201110.1007/s12155-011-9134-6Garlock, R. J., Y. S. Wong, V. Balan, and B. E. Dale. 2011. AFEX Pretreatment and Enzymatic Conversion of Black Locust (Robinia pseudoacacia L.) to Soluble Sugars, BioEnergy Research 5(2), 306-318. GLBRC
201110.2135/cropsci2011.01.0057Ge, Y., C. Fu, H. Bhandari, J. Bouton, E. C. Brummer, and Z.-Y. Wang. 2011. Pollen Viability and Longevity of Switchgrass ( L.), Crop Science 51(6), 2698. BESC
201110.1073/pnas.1017277108Gelfand, I., T. Zenone, P. Jasrotia, J. Chen, S. K. Hamilton, and G. P. Robertson. 2011. Carbon debt of Conservation Reserve Program (CRP) grasslands converted to bioenergy production, Proc Natl Acad Sci U S A 108(33), 13864-13869. GLBRC
201110.1039/c1gc15543aGeorge, A., K. Tran, T. J. Morgan, P. I. Benke, C. Berrueco, E. Lorente, B. C. Wu, J. D. Keasling, B. A. Simmons, and B. M. Holmes. 2011. The effect of ionic liquid cation and anion combinations on the macromolecular structure of lignins, Green Chemistry 13(12), 3375. JBEI
201110.1128/aem.05225-11Ghimire, S. R., and K. D. Craven. 2011. The Ectomycorrhizal Fungus Sebacina vermifera, Enhances Biomass Production of Switchgrass (Panicum virgatum L.) Under Drought Conditions,, Applied Microbiology and Biotechnology 77(19), 7063-7067. BESC
201110.1105/tpc.111.091728Gille, S., A. de Souza, G. Xiong, M. Benz, K. Cheng, A. Schultink, I. B. Reca, and M. Pauly. 2011. O-acetylation of Arabidopsis hemicellulose xyloglucan requires AXY4 or AXY4L, proteins with a TBL and DUF231 domain, Plant Cell 23(11), 4041-4053. GLBRC
201110.1128/AEM.00032-11Gladden, J. M., M. Allgaier, C. S. Miller, T. C. Hazen, J. S. VanderGheynst, P. Hugenholtz, B. A. Simmons, and S. W. Singer. 2011. Glycoside hydrolase activities of thermophilic bacterial consortia adapted to switchgrass, Appl Environ Microbiol 77(16), 5804-5812. JBEI
201110.1073/pnas.1016157108Gonzales-Vigil, E., C. M. Bianchetti, G. N. Phillips, Jr., and G. A. Howe. 2011. Adaptive evolution of threonine deaminase in plant defense against insect herbivores, Proc Natl Acad Sci U S A 108(14), 5897-5902. GLBRC
201110.1128/JB.00330-11Grubbs, K. J., P. H. Biedermann, G. Suen, S. M. Adams, J. A. Moeller, J. L. Klassen, L. A. Goodwin, T. Woyke, A. C. Munk, D. Bruce, C. Detter, R. Tapia, C. S. Han, and C. R. Currie. 2011. Genome sequence of Streptomyces griseus strain XylebKG-1, an ambrosia beetle-associated actinomycete, J Bacteriol 193(11), 2890-2891. GLBRC
201110.1099/mic.0.040758-0Gu, X., S. G. Lee, and M. Bar-Peled. 2011. Biosynthesis of UDP-xylose and UDP-arabinose in Sinorhizobium meliloti 1021: first characterization of a bacterial UDP-xylose synthase, and UDP-xylose 4-epimerase, Microbiology 157(Pt 1), 260-269. BESC
201110.1002/cssc.201000396Gurbuz, E. I., D. M. Alonso, J. Q. Bond, and J. A. Dumesic. 2011. Reactive extraction of levulinate esters and conversion to gamma-valerolactone for production of liquid fuels, ChemSusChem 4(3), 357-361. GLBRC
2011Gürbüz, E. I., D. Braden, and J. A. Dumesic. 2011. Aqueous phase catalytic processing in biomass valorization to H2 and liquid fuels. In Renewable Resources and Renewal Energy: A Global Challenge, 37-66. Eds. P. Fornasiero, and M. Graziani. CRC Press.GLBRC
201110.1186/1754-1611-5-3Hajimorad, M., P. R. Gray, and J. D. Keasling. 2011. A framework and model system to investigate linear system behavior in Escherichia coli, J Biol Eng 5, 3. JBEI
201110.2135/cropsci2010.08.0490Hansey, C. N., and N. de Leon. 2011. Biomass Yield and Cell Wall Composition of Corn with Alternative Morphologies Planted at Variable Densities, Crop Science 51(3), 1005. GLBRC
201110.2135/cropsci2010.03.0178Hansey, C. N., J. M. Johnson, R. S. Sekhon, S. M. Kaeppler, and N. de Leon. 2011. Genetic Diversity of a Maize Association Population with Restricted Phenology, Crop Science 51(2), 704. GLBRC
201110.3389/fpls.2011.00006Heazlewood, J. L. 2011. The green proteome: challenges in plant proteomics, Front Plant Sci 2, 6. JBEI
201110.1128/AEM.02454-10Higashide, W., Y. Li, Y. Yang, and J. C. Liao. 2011. Metabolic engineering of Clostridium cellulolyticum for production of isobutanol from cellulose, Appl Environ Microbiol 77(8), 2727-2733. BESC
2011Hillson, N. J. 2011. DNA Assembly Method Standardization for Synthetic Biomolecular Circuits and Systems. In Design and Analysis of Biomolecular Circuits: Engineering Approaches to Systems and Synthetic Biology, 295-314. Eds. H. Koeppl, D. Densmore, M. d. Bernardo, and G. Setti. Springer-Verlag.JBEI
201110.1007/s00253-011-3344-xHoover, S. W., W. D. Marner, 2nd, A. K. Brownson, R. M. Lennen, T. M. Wittkopp, J. Yoshitani, S. Zulkifly, L. E. Graham, S. D. Chaston, K. D. McMahon, and B. F. Pfleger. 2011. Bacterial production of free fatty acids from freshwater macroalgal cellulose, Appl Microbiol Biotechnol 91(2), 435-446. GLBRC
201110.1021/ac201948fHu, K., J. J. Ellinger, R. A. Chylla, and J. L. Markley. 2011. Measurement of absolute concentrations of individual compounds in metabolite mixtures by gradient-selective time-zero 1H-13C HSQC with two concentration references and fast maximum likelihood reconstruction analysis, Anal Chem 83(24), 9352-9360. GLBRC
201110.1021/ja1095304Hu, K., W. M. Westler, and J. L. Markley. 2011. Simultaneous quantification and identification of individual chemicals in metabolite mixtures by two-dimensional extrapolated time-zero (1)H-(13)C HSQC (HSQC(0)), J Am Chem Soc 133(6), 1662-1665. GLBRC
201110.1007/s10858-011-9494-4Hu, K., W. M. Westler, and J. L. Markley. 2011. Two-dimensional concurrent HMQC-COSY as an approach for small molecule chemical shift assignment and compound identification, J Biomol NMR 49(3-4), 291-296. GLBRC
201110.1371/journal.pone.0022113Huang, W. D., and Y. H. Zhang. 2011. Energy efficiency analysis: biomass-to-wheel efficiency related with biofuels production, fuel distribution, and powertrain systems, PLoS One 6(7), e22113. BESC
201110.1039/c0ee00069hHuang, W.-D., and Y. H. Percival Zhang. 2011. Analysis of biofuels production from sugar based on three criteria: Thermodynamics, bioenergetics, and product separation, Energy Environ. Sci. 4(3), 784-792. BESC
201110.1007/s00248-010-9797-0Hulcr, J., A. S. Adams, K. Raffa, R. W. Hofstetter, K. D. Klepzig, and C. R. Currie. 2011. Presence and diversity of Streptomyces in Dendroctonus and sympatric bark beetle galleries across North America, Microb Ecol 61(4), 759-768. GLBRC
2011Hull, S., J. Arntzen, C. Bleser, A. Crossley, R. Jackson, E. Lobner, L. Paine, G. Radloff, C. Ribic, D. Sample, J. Vanderbrook, S. Ventura, S. Walling, J. Widholm, and C. Williams. 2011: Wisconsin sustainable planting and harvest guidelines for nonforest biomass. Report to the Wisconsin Bioenergy Council. 88 pp.GLBRC
201110.1016/j.jchromb.2011.02.049Humpula, J. F., S. P. Chundawat, R. Vismeh, A. D. Jones, V. Balan, and B. E. Dale. 2011. Rapid quantification of major reaction products formed during thermochemical pretreatment of lignocellulosic biomass using GC-MS, J Chromatogr B Analyt Technol Biomed Life Sci 879(13-14), 1018-1022. GLBRC
201110.1186/1752-0509-5-116Imam, S., S. Yilmaz, U. Sohmen, A. S. Gorzalski, J. L. Reed, D. R. Noguera, and T. J. Donohue. 2011. iRsp1095: a genome-scale reconstruction of the Rhodobacter sphaeroides metabolic network, BMC Syst Biol 5, 116. GLBRC
2011 10.1021/pr1009433Ito, J., T. S. Batth, C. J. Petzold, A. M. Redding-Johanson, A. Mukhopadhyay, R. Verboom, E. H. Meyer, A. H. Millar, and J. L. Heazlewood. 2011. Analysis of the Arabidopsis cytosolic proteome highlights subcellular partitioning of central plant metabolism, J Proteome Res 10(4), 1571-1582. JBEI
2011Iwai, S., B. Chai, E. da C. Jesus, R. Penton C., T. K. Lee, J. R. Cole, and J. M. Tiedje. 2011. Gene-targeted metagenomics (GT-metagenomics) to explore the extensive diversity of genes of interest in microbial communities. In Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches, 235-243. Ed. F. J. de Bruijn. Wiley-Blackwell.GLBRC
201110.1371/journal.pone.0025757Jakubowski, A. R., M. D. Casler, and R. D. Jackson. 2011. Has selection for improved agronomic traits made reed canarygrass invasive?, PLoS One 6(10), e25757. GLBRC
201110.1071/cp11232Jakubowski, A. R., R. D. Jackson, R. C. Johnson, J. Hu, and M. D. Casler. 2011. Genetic diversity and population structure of Eurasian populations of reed canarygrass: cytotypes, cultivars, and interspecific hybrids, Crop and Pasture Science 62(11), 982. GLBRC
201110.1111/j.1365-313X.2010.04475.xJensen, J. K., H. Kim, J. C. Cocuron, R. Orler, J. Ralph, and C. G. Wilkerson. 2011. The DUF579 domain containing proteins IRX15 and IRX15-L affect xylan synthesis in Arabidopsis, Plant J 66(3), 387-400. GLBRC
201110.1002/bit.23059Jin, M., V. Balan, C. Gunawan, and B. E. Dale. 2011. Consolidated bioprocessing (CBP) performance of Clostridium phytofermentans on AFEX-treated corn stover for ethanol production, Biotechnol Bioeng 108(6), 1290-1297. GLBRC
201110.1104/pp.110.168195Joshi, H. J., M. Hirsch-Hoffmann, K. Baerenfaller, W. Gruissem, S. Baginsky, R. Schmidt, W. X. Schulze, Q. Sun, K. J. van Wijk, V. Egelhofer, S. Wienkoop, W. Weckwerth, C. Bruley, N. Rolland, T. Toyoda, H. Nakagami, A. M. Jones, S. P. Briggs, I. Castleden, S. K. Tanz, A. H. Millar, and J. L. Heazlewood. 2011. MASCP Gator: an aggregation portal for the visualization of Arabidopsis proteomics data, Plant Physiol 155(1), 259-270. JBEI
201110.1128/JB.01219-10Joshua, C. J., R. Dahl, P. I. Benke, and J. D. Keasling. 2011. Absence of diauxie during simultaneous utilization of glucose and Xylose by Sulfolobus acidocaldarius, J Bacteriol 193(6), 1293-1301. JBEI
201110.1016/j.agee.2011.08.020Kallenbach, C., and A. S. Grandy. 2011. Controls over soil microbial biomass responses to carbon amendments in agricultural systems: A meta-analysis, Agriculture, Ecosystems & Environment 144(1), 241-252. GLBRC
201110.1089/ind.2011.7.259Keasling, J. 2011. Joint BioEnergy Institute, Industrial Biotechnology 7(4), 259-260. JBEI
201110.1371/journal.pone.0024162Kim, J., J. L. Reed, and C. T. Maravelias. 2011. Large-scale bi-level strain design approaches and mixed-integer programming solution techniques, PLoS One 6(9), e24162. GLBRC
201110.1016/j.biombioe.2011.04.039Kim, S., and B. E. Dale. 2011. Indirect land use change for biofuels: Testing predictions and improving analytical methodologies, Biomass and Bioenergy 35(7), 3235-3240. GLBRC
201110.1128/JB.06257-11Klassen, J. L., S. M. Adams, S. Bramhacharya, S. S. Giles, L. A. Goodwin, T. Woyke, and C. R. Currie. 2011. Draft genome sequence of Streptomyces sp. strain Wigar10, isolated from a surface-sterilized garlic bulb, J Bacteriol 193(24), 6999-7000. GLBRC
201110.1002/bbb.303Klein-Marcuschamer, D., B. A. Simmons, and H. W. Blanch. 2011. Techno-economic analysis of a lignocellulosic ethanol biorefinery with ionic liquid pre-treatment, Biofuels, Bioproducts and Biorefining 5(5), 562-569. JBEI
2011Klein-Marcuschamer, D., B. Holmes, B. A. Simmons, and H. W. Blanch. 2011. Biofuel Economics. In Plant Biomass Conversion 329-348. Eds. E. Hood, R. Powell, and P. Nelson. John Wiley & Sons.JBEI
201110.1093/treephys/tpq109Ko, J. H., C. Prassinos, D. Keathley, and K. H. Han. 2011. Novel aspects of transcriptional regulation in the winter survival and maintenance mechanism of poplar, Tree Physiol 31(2), 208-225. GLBRC
201110.1128/AEM.05273-11Kontur, W. S., E. C. Ziegelhoffer, M. A. Spero, S. Imam, D. R. Noguera, and T. J. Donohue. 2011. Pathways involved in reductant distribution during photobiological H(2) production by Rhodobacter sphaeroides, Appl Environ Microbiol 77(20), 7425-7429. GLBRC
201110.1128/AEM.05532-11.Kostylev, M., and D. B. Wilson. 2011. Determination of the catalytic base in family 48 glycosyl hydrolases, Appl Environ Microbiol 77(17), 6274-6276. BESC
201110.2136/sssaj2010.0076Kravchenko, A. N., and G. P. Robertson. 2011. Whole-Profile Soil Carbon Stocks: The Danger of Assuming Too Much from Analyses of Too Little, Soil Science Society of America Journal 75(1), 235. GLBRC
201110.1073/pnas.1110384108Lee, I., Y. S. Seo, D. Coltrane, S. Hwang, T. Oh, E. M. Marcotte, and P. C. Ronald. 2011. Genetic dissection of the biotic stress response using a genome-scale gene network for rice, Proc Natl Acad Sci U S A 108(45), 18548-18553. JBEI
201110.1186/1754-1611-5-12Lee, T. S., R. A. Krupa, F. Zhang, M. Hajimorad, W. J. Holtz, N. Prasad, S. K. Lee, and J. D. Keasling. 2011. BglBrick vectors and datasheets: A synthetic biology platform for gene expression, J Biol Eng 5, 12. JBEI
201110.1371/journal.pcbi.1002047Lee, Y., F. Chen, L. Gallego-Giraldo, R. A. Dixon, and E. O. Voit. 2011. Integrative analysis of transgenic alfalfa (Medicago sativa L.) suggests new metabolic control mechanisms for monolignol biosynthesis, PLoS Comput Biol 7(5), e1002047. BESC
201110.1016/j.mbs.2011.03.001Lee, Y., P. W. Chen, and E. O. Voit. 2011. Analysis of operating principles with S-system models, Math Biosci 231(1), 49-60. BESC
201110.1128/AEM.05421-11Lennen, R. M., M. A. Kruziki, K. Kumar, R. A. Zinkel, K. E. Burnum, M. S. Lipton, S. W. Hoover, D. R. Ranatunga, T. M. Wittkopp, W. D. Marner, 2nd, and B. F. Pfleger. 2011. Membrane stresses induced by overproduction of free fatty acids in Escherichia coli, Appl Environ Microbiol 77(22), 8114-8128. GLBRC
201110.1038/ismej.2011.40Levine, U. Y., T. K. Teal, G. P. Robertson, and T. M. Schmidt. 2011. Agriculture's impact on microbial diversity and associated fluxes of carbon dioxide and methane, ISME J 5(10), 1683-1691. GLBRC
201110.1016/j.biortech.2011.04.005Li, C., G. Cheng, V. Balan, M. S. Kent, M. Ong, S. P. Chundawat, L. Sousa, Y. B. Melnichenko, B. E. Dale, B. A. Simmons, and S. Singh. 2011. Influence of physico-chemical changes on enzymatic digestibility of ionic liquid and AFEX pretreated corn stover, Bioresour Technol 102(13), 6928-6936. JBEI GLBRC
201110.1093/nar/gkq948Li, G., B. Liu, Q. Ma, and Y. Xu. 2011. A new framework for identifying cis-regulatory motifs in prokaryotes, Nucleic Acids Res 39(7), e42. BESC
201110.1093/nar/gkr766Li, G., Q. Ma, X. Mao, Y. Yin, X. Zhu, and Y. Xu. 2011. Integration of sequence-similarity and functional association information can overcome intrinsic problems in orthology mapping across bacterial genomes, Nucleic Acids Res 39(22), e150. BESC
201110.1186/1754-6834-4-23Li, L. L., S. Taghavi, S. M. McCorkle, Y. B. Zhang, M. G. Blewitt, R. Brunecky, W. S. Adney, M. E. Himmel, P. Brumm, C. Drinkwater, D. A. Mead, S. G. Tringe, and D. van der Lelie. 2011. Bioprospecting metagenomics of decaying wood: mining for new glycoside hydrolases, Biotechnol Biofuels 4(1), 23. GLBRC BESC
201110.1038/nrmicro2386-c1Liang, C., and T. C. Balser. 2011. Microbial production of recalcitrant organic matter in global soils: implications for productivity and climate policy, Nat Rev Microbiol 9(1), 75; author reply 75. GLBRC
201110.4236/as.2011.22019Liang, C., G. R. Sanford, R. D. Jackson, and T. C. Balser. 2011. Potential legacy effects of biofuel cropping systems on soil microbial communities in southern Wisconsin, USA, Agricultural Sciences 02(02), 131-137. GLBRC
201110.1016/j.mimet.2011.05.007Liang, C., X. Zhang, L. Wei, H. He, A. J. Higbee, and T. C. Balser. 2011. Investigation of the molecular ion structure for aldononitrile acetate derivatized muramic acid, J Microbiol Methods 86(2), 224-230. GLBRC
201110.1002/biot.201100157Liao, H., X. Z. Zhang, J. A. Rollin, and Y. H. Zhang. 2011. A minimal set of bacterial cellulases for consolidated bioprocessing of lignocellulose, Biotechnol J 6(11), 1409-1418. BESC
201110.1021/jp111738qLiu, H., K. L. Sale, B. A. Simmons, and S. Singh. 2011. Molecular dynamics study of polysaccharides in binary solvent mixtures of an ionic liquid and water, J Phys Chem B 115(34), 10251-10258. JBEI
201110.1128/JB.05523-11Liu, J., and C. P. Wolk. 2011. Mutations in genes patA and patL of Anabaena sp. strain PCC 7120 result in similar phenotypes, and the proteins encoded by those genes may interact, J Bacteriol 193(21), 6070-6074. GLBRC
201110.1074/jbc.M110.216556Liu, Y. S., J. O. Baker, Y. Zeng, M. E. Himmel, T. Haas, and S. Y. Ding. 2011. Cellobiohydrolase hydrolyzes crystalline cellulose on hydrophobic faces, J Biol Chem 286(13), 11195-11201. BESC
201110.1021/pr200536jLochner, A., R. J. Giannone, M. Keller, G. Antranikian, D. E. Graham, and R. L. Hettich. 2011. Label-free quantitative proteomics for the extremely thermophilic bacterium Caldicellulosiruptor obsidiansis reveal distinct abundance patterns upon growth on cellobiose, crystalline cellulose, and switchgrass, J Proteome Res 10(12), 5302-5314. BESC
201110.1128/AEM.02811-10Lochner, A., R. J. Giannone, M. Rodriguez, Jr., M. B. Shah, J. R. Mielenz, M. Keller, G. Antranikian, D. E. Graham, and R. L. Hettich. 2011. Use of label-free quantitative proteomics to distinguish the secreted cellulolytic systems of Caldicellulosiruptor bescii and Caldicellulosiruptor obsidiansis, Appl Environ Microbiol 77(12), 4042-4054. BESC
2011Loque, D., A. Eudes, and F. Yang. 2011. Biomass Availability and Sustainability for BioFuels. In Chemical and Biochemical Catalysis for Next Generation Biofuels, 5-32. Ed. B. A. Simmons. Royal Society of Chemistry.JBEI
201110.1166/jbmb.2011.1131Lu, F., and J. Ralph. 2011. Solution-State NMR of Lignocellulosic Biomass, Journal of Biobased Materials and Bioenergy 5(2), 169-180. GLBRC
201110.1016/j.ymben.2011.07.001Ma, S. M., D. E. Garcia, A. M. Redding-Johanson, G. D. Friedland, R. Chan, T. S. Batth, J. R. Haliburton, D. Chivian, J. D. Keasling, C. J. Petzold, T. S. Lee, and S. R. Chhabra. 2011. Optimization of a heterologous mevalonate pathway through the use of variant HMG-CoA reductases, Metab Eng 13(5), 588-597. JBEI
201110.1016/j.virusres.2011.05.010Malmstrom, C. M., U. Melcher, and N. A. Bosque-Perez. 2011. The expanding field of plant virus ecology: historical foundations, knowledge gaps, and research directions, Virus Res 159(2), 84-94. GLBRC
201110.1104/pp.110.168989Manabe, Y., M. Nafisi, Y. Verhertbruggen, C. Orfila, S. Gille, C. Rautengarten, C. Cherk, S. E. Marcus, S. Somerville, M. Pauly, J. P. Knox, Y. Sakuragi, and H. V. Scheller. 2011. Loss-of-function mutation of REDUCED WALL ACETYLATION2 in Arabidopsis leads to reduced cell wall acetylation and increased resistance to Botrytis cinerea, Plant Physiol 155(3), 1068-1078. JBEI
2011Mann, D. G. J., P. R. LaFayette, L. L. Abercrombie, W. A. Parrott, and C. N. Stewart. 2011. pANIC: A Versatile Set of Gateway-Compatible Vectors for Gene Overexpression and RNAi-Mediated down-Regulation in Monocots. In Plant Transformation Technologies, 161-168. Eds. C. Neal Stewart Jr., Alisher Touraev, Vitaly Citovsky, and Tzvi Tzfira.BESC
201110.1186/1472-6750-11-74Mann, D. G., Z. R. King, W. Liu, B. L. Joyce, R. J. Percifield, J. S. Hawkins, P. R. LaFayette, B. J. Artelt, J. N. Burris, M. Mazarei, J. L. Bennetzen, W. A. Parrott, and C. N. Stewart, Jr. 2011. Switchgrass (Panicum virgatum L.) polyubiquitin gene (PvUbi1 and PvUbi2) promoters for use in plant transformation, BMC Biotechnol 11, 74. BESC
201110.1371/journal.pone.0022556Mao, X., Y. Zhang, and Y. Xu. 2011. SEAS: a system for SEED-based pathway enrichment analysis, PLoS One 6(7), e22556. BESC
201110.1016/j.plantsci.2010.12.010Mazarei, M., H. Al-Ahmad, M. R. Rudis, B. L. Joyce, and C. N. Stewart, Jr. 2011. Switchgrass (Panicum virgatum L.) cell suspension cultures: Establishment, characterization, and application, Plant Sci 181(6), 712-715. BESC
2011 10.1016/j.str.2011.09.013McAndrew, R. P., P. P. Peralta-Yahya, A. DeGiovanni, J. H. Pereira, M. Z. Hadi, J. D. Keasling, and P. D. Adams. 2011. Structure of a three-domain sesquiterpene synthase: a prospective target for advanced biofuels production, Structure 19(12), 1876-1884. JBEI
201110.1073/pnas.1100751108Meehan, T. D., B. P. Werling, D. A. Landis, and C. Gratton. 2011. Agricultural landscape simplification and insecticide use in the Midwestern United States, Proc Natl Acad Sci U S A 108(28), 11500-11505. GLBRC
201110.1128/AEM.00467-11Mendez-Perez, D., M. B. Begemann, and B. F. Pfleger. 2011. Modular synthase-encoding gene involved in alpha-olefin biosynthesis in Synechococcus sp. strain PCC 7002, Appl Environ Microbiol 77(12), 4264-4267. GLBRC
201110.1186/gb-2011-12-5-r44Miller, C. S., B. J. Baker, B. C. Thomas, S. W. Singer, and J. F. Banfield. 2011. EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data, Genome Biol 12(5), R44. JBEI
201110.1128/JB.00239-11Miller, D. A., G. Suen, D. Bruce, A. Copeland, J. F. Cheng, C. Detter, L. A. Goodwin, C. S. Han, L. J. Hauser, M. L. Land, A. Lapidus, S. Lucas, L. Meincke, S. Pitluck, R. Tapia, H. Teshima, T. Woyke, B. G. Fox, E. R. Angert, and C. R. Currie. 2011. Complete genome sequence of the cellulose-degrading bacterium Cellulosilyticum lentocellum, J Bacteriol 193(9), 2357-2358. GLBRC
201110.1126/science.1208641Mohnen, D., and M. L. Tierney. 2011. Plant science. Plants get Hyp to O-glycosylation, Science 332(6036), 1393-1394. BESC
201110.1094/MPMI-06-10-0146Mukherjee, A., and J. M. Ane. 2011. Germinating spore exudates from arbuscular mycorrhizal fungi: molecular and developmental responses in plants and their regulation by ethylene, Mol Plant Microbe Interact 24(2), 260-270. GLBRC
2011Mukherjee, A., and J.-M. Ané. 2011. Plant hormones and initiation of legume nodulation and arbuscular mycorrhization. In Ecological Aspects of Nitrogen Metabolism in Plants, 354-396. Eds. J. C. Polacco, and C. D. Todd. Wiley Blackwell Press.GLBRC
2011 10.4056/sigs.1483693Muyzer, G., D. Y. Sorokin, K. Mavromatis, A. Lapidus, A. Clum, N. Ivanova, A. Pati, P. d'Haeseleer, T. Woyke, and N. C. Kyrpides. 2011. Complete genome sequence of Thioalkalivibrio sulfidophilus HL-EbGr7, Stand Genomic Sci 4(1), 23-35. JBEI
201110.1016/j.geoderma.2011.07.017Muñoz, J. D., and A. Kravchenko. 2011. Soil carbon mapping using on-the-go near infrared spectroscopy, topography and aerial photographs, Geoderma 166(1), 102-110. GLBRC
201110.1002/btpr.606Myung, S., X. Z. Zhang, and Y. H. Zhang. 2011. Ultra-stable phosphoglucose isomerase through immobilization of cellulose-binding module-tagged thermophilic enzyme on low-cost high-capacity cellulosic adsorbent, Biotechnol Prog 27(4), 969-975. BESC
201110.1016/j.compag.2011.08.012Nichols, J., S. Kang, W. Post, D. Wang, V. Bandaru, D. Manowitz, X. Zhang, and R. Izaurralde. 2011. HPC-EPIC for high resolution simulations of environmental and sustainability assessment, Computers and Electronics in Agriculture 79(2), 112-115. GLBRC
201110.1038/nbt.1937Nielsen, J., and J. D. Keasling. 2011. Synergies between synthetic biology and metabolic engineering, Nat Biotechnol 29(8), 693-695. JBEI
2011Ohlrogge, J. B., and K. Chapman. 2011: The seeds of green energy - expanding the contribution of plant oils as biofuels. The Biochemist, 34-38.GLBRC
201110.1039/c1gc15327gOuellet, M., S. Datta, D. C. Dibble, P. R. Tamrakar, P. I. Benke, C. Li, S. Singh, K. L. Sale, P. D. Adams, J. D. Keasling, B. A. Simmons, B. M. Holmes, and A. Mukhopadhyay. 2011. Impact of ionic liquid pretreated plant biomass on Saccharomyces cerevisiae growth and biofuel production, Green Chemistry 13(10), 2743. JBEI
201110.1016/j.biortech.2011.02.036Park, J. I., M. S. Kent, S. Datta, B. M. Holmes, Z. Huang, B. A. Simmons, K. L. Sale, and R. Sapra. 2011. Enzymatic hydrolysis of cellulose by the cellobiohydrolase domain of CelB from the hyperthermophilic bacterium Caldicellulosiruptor saccharolyticus, Bioresour Technol 102(10), 5988-5994. JBEI
201110.1021/jp203620xParthasarathi, R., G. Bellesia, S. P. Chundawat, B. E. Dale, P. Langan, and S. Gnanakaran. 2011. Insights into hydrogen bonding and stacking interactions in cellulose, J Phys Chem A 115(49), 14191-14202. GLBRC
201110.1111/j.1757-1707.2010.01067.xPeckham, S. D., and S. T. Gower. 2011. Simulated long-term effects of harvest and biomass residue removal on soil carbon and nitrogen content and productivity for two Upper Great Lakes forest ecosystems, GCB Bioenergy 3(2), 135-147. GLBRC
201110.1038/ncomms1494Peralta-Yahya, P. P., M. Ouellet, R. Chan, A. Mukhopadhyay, J. D. Keasling, and T. S. Lee. 2011. Identification and microbial production of a terpene-based advanced biofuel, Nat Commun 2, 483. JBEI
201110.1002/bit.23050Podkaminer, K. K., X. Shao, D. A. Hogsett, and L. R. Lynd. 2011. Enzyme inactivation by ethanol and development of a kinetic model for thermophilic simultaneous saccharification and fermentation at 50 degrees C with Thermoanaerobacterium saccharolyticum ALK2, Biotechnol Bioeng 108(6), 1268-1278. BESC
201110.1007/s00253-011-3350-zPu, Y., M. Kosa, U. C. Kalluri, G. A. Tuskan, and A. J. Ragauskas. 2011. Challenges of the utilization of wood polymers: how can they be overcome?, Appl Microbiol Biotechnol 91(6), 1525-1536. BESC
201110.1039/c1ee01201kPu, Y., S. Cao, and A. J. Ragauskas. 2011. Application of quantitative 31P NMR in biomass lignin and biofuel precursors characterization, Energy & Environmental Science 4(9), 3154. BESC
201110.1186/1471-2180-11-134Raman, B., C. K. McKeown, M. Rodriguez, Jr., S. D. Brown, and J. R. Mielenz. 2011. Transcriptomic analysis of Clostridium thermocellum ATCC 27405 cellulose fermentation, BMC Microbiol 11, 134. BESC
201110.1105/tpc.111.083931Rautengarten, C., B. Ebert, T. Herter, C. J. Petzold, T. Ishii, A. Mukhopadhyay, B. Usadel, and H. V. Scheller. 2011. The interconversion of UDP-arabinopyranose and UDP-arabinofuranose is indispensable for plant development in Arabidopsis, Plant Cell 23(4), 1373-1390. JBEI
201110.1016/j.ymben.2010.12.005Redding-Johanson, A. M., T. S. Batth, R. Chan, R. Krupa, H. L. Szmidt, P. D. Adams, J. D. Keasling, T. S. Lee, A. Mukhopadhyay, and C. J. Petzold. 2011. Targeted proteomics for metabolic pathway optimization: application to terpene production, Metab Eng 13(2), 194-203. JBEI
201110.1002/bit.23176Reddy, A. P., M. Allgaier, S. W. Singer, T. C. Hazen, B. A. Simmons, P. Hugenholtz, and J. S. VanderGheynst. 2011. Bioenergy feedstock-specific enrichment of microbial populations during high-solids thermophilic deconstruction, Biotechnol Bioeng 108(9), 2088-2098. JBEI
201110.1039/c1ee01112jReindl, W., K. Deng, J. M. Gladden, G. Cheng, A. Wong, S. W. Singer, S. Singh, J. C. Lee, C. H. Yao, T. C. Hazen, A. K. Singh, B. A. Simmons, P. D. Adams, and T. R. Northen. 2011. Colloid-based multiplexed screening for plant biomass-degrading glycoside hydrolase activities in microbial communities, Energy & Environmental Science 4(8), 2884. JBEI
201110.1104/pp.110.167254Rencoret, J., A. Gutierrez, L. Nieto, J. Jimenez-Barbero, C. B. Faulds, H. Kim, J. Ralph, A. T. Martinez, and J. C. Del Rio. 2011. Lignin composition and structure in young versus adult Eucalyptus globulus plants, Plant Physiol 155(2), 667-682. GLBRC
201110.1007/s12010-011-9174-6Rezaei, F., L. D. Joh, H. Kashima, A. P. Reddy, and J. S. VanderGheynst. 2011. Selection of conditions for cellulase and xylanase extraction from switchgrass colonized by Acidothermus cellulolyticus, Appl Biochem Biotechnol 164(6), 793-803. JBEI
201110.1128/AEM.02008-10Riederer, A., T. E. Takasuka, S. Makino, D. M. Stevenson, Y. V. Bukhman, N. L. Elsen, and B. G. Fox. 2011. Global gene expression patterns in Clostridium thermocellum as determined by microarray analysis of chemostat cultures on cellulose or cellobiose, Appl Environ Microbiol 77(4), 1243-1253. GLBRC
201110.1007/s12155-011-9161-3Robertson, B. A., C. Porter, D. A. Landis, and D. W. Schemske. 2011. Agroenergy Crops Influence the Diversity, Biomass, and Guild Structure of Terrestrial Arthropod Communities, BioEnergy Research 5(1), 179-188. GLBRC
201110.1371/journal.pone.0016941Robertson, B. A., P. J. Doran, E. R. Loomis, J. R. Robertson, and D. W. Schemske. 2011. Avian use of perennial biomass feedstocks as post-breeding and migratory stopover habitat, PLoS One 6(3), e16941. GLBRC
201110.1111/j.1757-1707.2010.01080.xRobertson, B. A., P. J. Doran, L. R. Loomis, J. R. Robertson, and D. W. Schemske. 2011. Perennial biomass feedstocks enhance avian diversity, GCB Bioenergy 3(3), 235-246. GLBRC
201110.1890/09-0456.1Robertson, G. P., S. K. Hamilton, S. J. Del Grosso, and W. J. Parton. 2011. The biogeochemistry of bioenergy landscapes: carbon, nitrogen, and water considerations, Ecological Applications 21(4), 1055-1067. GLBRC
201110.1002/bit.22919Rollin, J. A., Z. Zhu, N. Sathitsuksanoh, and Y. H. Zhang. 2011. Increasing cellulose accessibility is more important than removing lignin: a comparison of cellulose solvent-based lignocellulose fractionation and soaking in aqueous ammonia, Biotechnol Bioeng 108(1), 22-30. BESC
201110.1534/genetics.111.128553Ronald, P. 2011. Plant genetics, sustainable agriculture and global food security, Genetics 188(1), 11-20. JBEI
2011S.P., D., G. T. Slavov, and C. S. Joshi. 2011. Populus: A premier pioneer system for plant genomics. In Poplar, 1-28. Eds. C. P. Joshi, and S. P. DiFazio. Science Publishers.BESC
2011Sakuragi, Y., M. H. Norholm, and H. V. Scheller. 2011. Visual mapping of cell wall biosynthesis. In The Plant Cell Wall: Methods and Protocols, 153-167. Ed. Z. A. Popper. Springer Science.JBEI
201110.1016/j.fuel.2011.04.021Samuel, R., M. Foston, N. Jaing, S. Cao, L. Allison, M. Studer, C. Wyman, and A. J. Ragauskas. 2011. HSQC (heteronuclear single quantum coherence) 13C-1H correlation spectra of whole biomass in perdeuterated pyridinium chloride-DMSO system: An effective tool for evaluating pretreatment, Fuel 90(9), 2836-2842. BESC
201110.1016/j.polymdegradstab.2011.08.015Samuel, R., M. Foston, N. Jiang, L. Allison, and A. J. Ragauskas. 2011. Structural changes in switchgrass lignin and hemicelluloses during pretreatments by NMR analysis, Polymer Degradation and Stability 96(11), 2002-2009. BESC
201110.1111/j.1467-7652.2011.00599.xSanjaya, T. P. Durrett, S. E. Weise, and C. Benning. 2011. Increasing the energy density of vegetative tissues by diverting carbon from starch to oil biosynthesis in transgenic Arabidopsis, Plant Biotechnology Journal 9(8), 874-883. GLBRC
201110.1166/jbmb.2011.1170Sannigrahi, P., and A. J. Ragauskas. 2011. Characterization of Fermentation Residues from the Production of Bio-Ethanol from Lignocellulosic Feedstocks, Journal of Biobased Materials and Bioenergy 5(4), 514-519. BESC
201110.1039/c0ee00378fSannigrahi, P., D. H. Kim, S. Jung, and A. Ragauskas. 2011. Pseudo-lignin and pretreatment chemistry, Energy Environ. Sci. 4(4), 1306-1310. BESC
201110.1002/bit.22964Sathitsuksanoh, N., Z. Zhu, S. Wi, and Y. H. Zhang. 2011. Cellulose solvent-based biomass pretreatment breaks highly ordered hydrogen bonds in cellulose fibers of switchgrass, Biotechnol Bioeng 108(3), 521-529. BESC
201110.1186/1752-0509-5-28Satish Kumar, V., J. G. Ferry, and C. D. Maranas. 2011. Metabolic reconstruction of the archaeon methanogen Methanosarcina Acetivorans, BMC Syst Biol 5, 28. JBEI
201110.1111/j.1757-1707.2011.01093.xSchrotenboer, A. C., M. S. Allen, and C. M. Malmstrom. 2011. Modification of native grasses for biofuel production may increase virus susceptibility, GCB Bioenergy 3(5), 360-374. GLBRC
201110.1074/jbc.M111.307397Scott-Craig, J. S., M. S. Borrusch, G. Banerjee, C. M. Harvey, and J. D. Walton. 2011. Biochemical and molecular characterization of secreted alpha-xylosidase from Aspergillus niger, J Biol Chem 286(50), 42848-42854. GLBRC
201110.1111/j.1365-313X.2011.04527.xSekhon, R. S., H. Lin, K. L. Childs, C. N. Hansey, C. R. Buell, N. de Leon, and S. M. Kaeppler. 2011. Genome-wide atlas of transcription during maize development, Plant J 66(4), 553-563. GLBRC
201110.1007/s10529-011-0526-7Selig, M. J., M. P. Tucker, C. Law, C. Doeppke, M. E. Himmel, and S. R. Decker. 2011. High throughput determination of glucan and xylan fractions in lignocelluloses, Biotechnol Lett 33(5), 961-967. BESC
201110.1371/journal.pgen.1002020Seo, Y. S., M. Chern, L. E. Bartley, M. Han, K. H. Jung, I. Lee, H. Walia, T. Richter, X. Xu, P. Cao, W. Bai, R. Ramanan, F. Amonpant, L. Arul, P. E. Canlas, R. Ruan, C. J. Park, X. Chen, S. Hwang, J. S. Jeon, and P. C. Ronald. 2011. Towards establishment of a rice stress response interactome, PLoS Genet 7(4), e1002020. JBEI
201110.1039/c0ee00436gSerrano-Ruiz, J. C., and J. A. Dumesic. 2011. Catalytic routes for the conversion of biomass into liquid hydrocarbon transportation fuels, Energy Environ. Sci. 4(1), 83-99. GLBRC
201110.1007/s00253-011-3492-zShao, X., B. Raman, M. Zhu, J. R. Mielenz, S. D. Brown, A. M. Guss, and L. R. Lynd. 2011. Mutant selection and phenotypic and genetic characterization of ethanol-tolerant strains of Clostridium thermocellum, Appl Microbiol Biotechnol 92(3), 641-652. BESC
201110.1016/j.biortech.2011.05.021Shao, X., M. Jin, A. Guseva, C. Liu, V. Balan, D. Hogsett, B. E. Dale, and L. Lynd. 2011. Conversion for Avicel and AFEX pretreated corn stover by Clostridium thermocellum and simultaneous saccharification and fermentation: insights into microbial conversion of pretreated cellulosic biomass, Bioresour Technol 102(17), 8040-8045. BESC
201110.1007/s11103-011-9819-4Sharma, R., F. Tan, K. H. Jung, M. K. Sharma, Z. Peng, and P. C. Ronald. 2011. Transcriptional dynamics during cell wall removal and regeneration reveals key genes involved in cell wall development in rice, Plant Mol Biol 77(4-5), 391-406. JBEI
2011Simmons, B. A. 2011. Introduction to Catalysis for Biofuels. In Chemical and Biochemical Catalysis for Next Generation Biofuels, 1-4. Ed. B. A. Simmons. Royal Society of Chemistry.JBEI
2011Simmons, B. A. 2011. Synthetic enzymes: catalysis on demand, Microbial Biotechnology 4(2), 130-131. DOI.JBEI
201110.1111/j.1365-2672.2011.04959.xSinger, S. W., A. P. Reddy, J. M. Gladden, H. Guo, T. C. Hazen, B. A. Simmons, and J. S. VanderGheynst. 2011. Enrichment, isolation and characterization of fungi tolerant to 1-ethyl-3-methylimidazolium acetate, J Appl Microbiol 110(4), 1023-1031. JBEI
201110.1128/AEM.01219-10Sizova, M. V., J. A. Izquierdo, N. S. Panikov, and L. R. Lynd. 2011. Cellulose- and xylan-degrading thermophilic anaerobic bacteria from biocompost, Appl Environ Microbiol 77(7), 2282-2291. BESC
2011 10.1186/1746-4811-7-26Smith-Moritz, A. M., M. Chern, J. Lao, W. H. Sze-To, J. L. Heazlewood, P. C. Ronald, and M. E. Vega-Sanchez. 2011. Combining multivariate analysis and monosaccharide composition modeling to identify plant cell wall variations by Fourier Transform Near Infrared spectroscopy, Plant Methods 7, 26. JBEI
201110.1093/ajae/aar018Song, F., J. Zhao, and S. M. Swinton. 2011. Switching to Perennial Energy Crops Under Uncertainty and Costly Reversibility, American Journal of Agricultural Economics 93(3), 768-783. GLBRC
201110.1111/j.1365-313X.2011.04686.xSorensen, I., F. A. Pettolino, A. Bacic, J. Ralph, F. Lu, M. A. O'Neill, Z. Fei, J. K. Rose, D. S. Domozych, and W. G. Willats. 2011. The charophycean green algae provide insights into the early origins of plant cell walls, Plant J 68(2), 201-211. GLBRC
201110.1104/pp.110.168278Srivastava, A. C., P. A. Ramos-Parra, M. Bedair, A. L. Robledo-Hernandez, Y. Tang, L. W. Sumner, R. I. Diaz de la Garza, and E. B. Blancaflor. 2011. The folylpolyglutamate synthetase plastidial isoform is required for postembryonic root development in Arabidopsis, Plant Physiol 155(3), 1237-1251. BESC
201110.4161/psb.6.5.15403Srivastava, A. C., Y. Tang, R. I. Díaz de la Garza, and E. B. Blancaflor. 2011. The plastidial folylpolyglutamate synthetase and root apical meristem maintenance, Plant Signaling & Behavior 6(5), 751-754. BESC
201110.1016/j.plantsci.2011.09.001Stewart, C. N., Jr., and G. S. Liu. 2011. Bioenergy plants in the United States and China, Plant Sci 181(6), 621-622. BESC
201110.1073/pnas.1009252108Studer, M. H., J. D. DeMartini, M. F. Davis, R. W. Sykes, B. Davison, M. Keller, G. A. Tuskan, and C. E. Wyman. 2011. Lignin content in natural Populus variants affects sugar release, Proc Natl Acad Sci U S A 108(15), 6300-6305. BESC
201110.1186/1754-6834-4-19Studer, M. H., S. Brethauer, J. D. DeMartini, H. L. McKenzie, and C. E. Wyman. 2011. Co-hydrolysis of hydrothermal and dilute acid pretreated populus slurries to support development of a high-throughput pretreatment system, Biotechnol Biofuels 4(1), 19. BESC
201110.1371/journal.pgen.1002007Suen, G., C. Teiling, L. Li, C. Holt, E. Abouheif, E. Bornberg-Bauer, P. Bouffard, E. J. Caldera, E. Cash, A. Cavanaugh, O. Denas, E. Elhaik, M. J. Fave, J. Gadau, J. D. Gibson, D. Graur, K. J. Grubbs, D. E. Hagen, T. T. Harkins, M. Helmkampf, H. Hu, B. R. Johnson, J. Kim, S. E. Marsh, J. A. Moeller, M. C. Munoz-Torres, M. C. Murphy, M. C. Naughton, S. Nigam, R. Overson, R. Rajakumar, J. T. Reese, J. J. Scott, C. R. Smith, S. Tao, N. D. Tsutsui, L. Viljakainen, L. Wissler, M. D. Yandell, F. Zimmer, J. Taylor, S. C. Slater, S. W. Clifton, W. C. Warren, C. G. Elsik, C. D. Smith, G. M. Weinstock, N. M. Gerardo, and C. R. Currie. 2011. The genome sequence of the leaf-cutter ant Atta cephalotes reveals insights into its obligate symbiotic lifestyle, PLoS Genet 7(2), e1002007. GLBRC
201110.1128/JB.05621-11Suen, G., D. M. Stevenson, D. C. Bruce, O. Chertkov, A. Copeland, J. F. Cheng, C. Detter, J. C. Detter, L. A. Goodwin, C. S. Han, L. J. Hauser, N. N. Ivanova, N. C. Kyrpides, M. L. Land, A. Lapidus, S. Lucas, G. Ovchinnikova, S. Pitluck, R. Tapia, T. Woyke, J. Boyum, D. Mead, and P. J. Weimer. 2011. Complete genome of the cellulolytic ruminal bacterium Ruminococcus albus 7, J Bacteriol 193(19), 5574-5575. GLBRC
2011Suen, G., J. J. Scott, F. O. Aylward, and C. R. Currie. 2011. The microbiome of leaf-cutter ant fungus gardens. In Handbook of Molecular Microbial Ecology II, 367-379. Ed. F. J. de Bruijn. Wiley-Blackwell.GLBRC
201110.1371/journal.pone.0018814Suen, G., P. J. Weimer, D. M. Stevenson, F. O. Aylward, J. Boyum, J. Deneke, C. Drinkwater, N. N. Ivanova, N. Mikhailova, O. Chertkov, L. A. Goodwin, C. R. Currie, D. Mead, and P. J. Brumm. 2011. The complete genome sequence of Fibrobacter succinogenes S85 reveals a cellulolytic and metabolic specialist, PLoS One 6(4), e18814. GLBRC
201110.1016/j.tibtech.2011.04.008Sukharnikov, L. O., B. J. Cantwell, M. Podar, and I. B. Zhulin. 2011. Cellulases: ambiguous nonhomologous enzymes in a genomic perspective, Trends Biotechnol 29(10), 473-479. BESC
201110.1002/bit.22931Sun, L., B. A. Simmons, and S. Singh. 2011. Understanding tissue specific compositions of bioenergy feedstocks through hyperspectral Raman imaging, Biotechnol Bioeng 108(2), 286-295. JBEI
201110.1016/j.enpol.2011.05.039Swinton, S. M., B. A. Babcock, L. K. James, and V. Bandaru. 2011. Higher US crop prices trigger little area expansion so marginal land for biofuel crops is limited, Energy Policy 39(9), 5254-5258. GLBRC
201110.2136/sssaj2009.0414Syswerda, S. P., A. T. Corbin, D. L. Mokma, A. N. Kravchenko, and G. P. Robertson. 2011. Agricultural Management and Soil Carbon Storage in Surface vs. Deep Layers, Soil Science Society of America Journal 75(1), 92. GLBRC
201110.1002/pmic.201000620Taylor, N. L., J. L. Heazlewood, and A. H. Millar. 2011. The Arabidopsis thaliana 2-D gel mitochondrial proteome: Refining the value of reference maps for assessing protein abundance, contaminants and post-translational modifications, Proteomics 11(9), 1720-1733. JBEI
201110.1088/0022-3727/44/44/445102Tetard, L., A. Passian, R. H. Farahi, B. H. Davison, A. L. Lereu, and T. Thundat. 2011. Optical and plasmonic spectroscopy with cantilever shaped materials, Journal of Physics D: Applied Physics 44(44), 445102. BESC
201110.1364/OL.36.003251Tetard, L., A. Passian, R. H. Farahi, B. H. Davison, and T. Thundat. 2011. Optomechanical spectroscopy with broadband interferometric and quantum cascade laser sources, Opt Lett 36(16), 3251-3253. BESC
201110.1088/0957-4484/22/46/465702Tetard, L., A. Passian, R. H. Farahi, B. H. Davison, S. Jung, A. J. Ragauskas, A. L. Lereu, and T. Thundat. 2011. Nanometrology of delignified Populus using mode synthesizing atomic force microscopy, Nanotechnology 22(46), 465702. BESC
201110.1103/PhysRevLett.106.180801Tetard, L., A. Passian, S. Eslami, N. Jalili, R. H. Farahi, and T. Thundat. 2011. Virtual resonance and frequency difference generation by van der Waals interaction, Phys Rev Lett 106(18), 180801. BESC
201110.1021/bm200136xTobimatsu, Y., C. L. Davidson, J. H. Grabber, and J. Ralph. 2011. Fluorescence-tagged monolignols: synthesis, and application to studying in vitro lignification, Biomacromolecules 12(5), 1752-1761. GLBRC
201110.1111/j.1365-313X.2011.04751.xTroncoso-Ponce, M. A., A. Kilaru, X. Cao, T. P. Durrett, J. Fan, J. K. Jensen, N. A. Thrower, M. Pauly, C. Wilkerson, and J. B. Ohlrogge. 2011. Comparative deep transcriptional profiling of four developing oilseeds, Plant J 68(6), 1014-1027. GLBRC
2011Tsai, C. J., P. Ranjan, S. P. DiFazio, G. A. Tuskan, and V. E. Johnson. 2011. Poplar Genome Microarrays. In Genetics, Genomics and Breeding of Popular, 112-127. Eds. C. P. Joshi, S. P. DiFazio, and C. Kole. CRC Press.BESC
201110.1186/1753-6561-5-s7-i23Van Acker, R., V. Storme, G. Goeminne, B. Ivens, R. Custers, D. Aerts, W. Soetaert, J. Ralph, N. Santoro, J.-C. Leplé, G. Pilate, and W. Boerjan. 2011. Science, society and biosafety of a field trial with transgenic biofuel poplars, BMC Proceedings 5(Suppl 7), I23. GLBRC
201110.1128/AEM.00508-11Vanden Wymelenberg, A., J. Gaskell, M. Mozuch, S. S. BonDurant, G. Sabat, J. Ralph, O. Skyba, S. D. Mansfield, R. A. Blanchette, I. V. Grigoriev, P. J. Kersten, and D. Cullen. 2011. Significant alteration of gene expression in wood decay fungi Postia placenta and Phanerochaete chrysosporium by plant species, Appl Environ Microbiol 77(13), 4499-4507. GLBRC
201110.1002/bit.23093VanFossen, A. L., I. Ozdemir, S. L. Zelin, and R. M. Kelly. 2011. Glycoside hydrolase inventory drives plant polysaccharide deconstruction by the extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus, Biotechnol Bioeng 108(7), 1559-1569. BESC
2011Varanasi, P., L. Sun, B. Knierim, E. Bosneaga, P. Sakar, S. Singh, and M. Auer. 2011. Quantifying Bio-Engineering: The Importance of Biophysics in Biofuel Research. In Biofuel’s Engineering Process Technology, 493-520. Ed. M. A. d. S. Bernades. InTech.JBEI
201110.1104/pp.111.184358Varbanova, M., K. Porter, F. Lu, J. Ralph, R. Hammerschmidt, A. D. Jones, and B. Day. 2011. Molecular and biochemical basis for stress-induced accumulation of free and bound p-coumaraldehyde in cucumber, Plant Physiol 157(3), 1056-1066. GLBRC
201110.4161/psb.6.10.17989Verhertbruggen, Y., L. Yin, A. Oikawa, and H. V. Scheller. 2011. Mannan synthase activity in the CSLD family, Plant Signal Behav 6(10), 1620-1623. JBEI
2011Voit, E. O. 2011. What if the fit is unfit? Criteria for biological systems estimation beyond residual errors. In Applied Statistics for Biological Networks, 183-200. Eds. M. Dehmer, F. Emmert-Streib, and A. Salvador. J. Wiley and Sons.BESC
201110.1111/j.1365-313X.2011.04580.xWagner, A., Y. Tobimatsu, L. Phillips, H. Flint, K. Torr, L. Donaldson, L. Pears, and J. Ralph. 2011. CCoAOMT suppression modifies lignin composition in Pinus radiata, Plant J 67(1), 119-129. GLBRC
201110.3791/3314Walton, J., G. Banerjee, and S. Car. 2011. GENPLAT: an automated platform for biomass enzyme discovery and cocktail optimization, J Vis Exp(56). GLBRC
201110.1016/j.chembiol.2010.12.019Wang, Y., W. Huang, N. Sathitsuksanoh, Z. Zhu, and Y. H. Zhang. 2011. Biohydrogenation from biomass sugar mediated by in vitro synthetic enzymatic pathways, Chem Biol 18(3), 372-380. BESC
201110.1016/j.biortech.2010.10.104Wang, Z. W., S. D. Hamilton-Brehm, A. Lochner, J. G. Elkins, and J. L. Morrell-Falvey. 2011. Mathematical modeling of hydrolysate diffusion and utilization in cellulolytic biofilms of the extreme thermophile Caldicellulosiruptor obsidiansis, Bioresour Technol 102(3), 3155-3162. BESC
201110.1186/2191-0855-1-30Wang, Z. W., S. H. Lee, J. G. Elkins, and J. L. Morrell-Falvey. 2011. fSpatial and temporal dynamics of cellulose degradation and biofilm formation by Caldicellulosiruptor obsidiansis and Clostridium thermocellum, AMB Express 1, 30. BESC
201110.1093/jxb/err035Weise, S. E., K. J. van Wijk, and T. D. Sharkey. 2011. The role of transitory starch in C(3), CAM, and C(4) metabolism and opportunities for engineering leaf starch accumulation, J Exp Bot 62(9), 3109-3118. GLBRC
201110.1105/tpc.110.081547Weng, J. K., T. Akiyama, J. Ralph, and C. Chapple. 2011. Independent recruitment of an O-methyltransferase for syringyl lignin biosynthesis in Selaginella moellendorffii, Plant Cell 23(7), 2708-2724. GLBRC
201110.1111/j.1757-1707.2011.01092.xWerling, B. P., T. D. Meehan, B. A. Robertson, C. Gratton, and D. A. Landis. 2011. Biocontrol potential varies with changes in biofuel-crop plant communities and landscape perenniality, GCB Bioenergy 3(5), 347-359. GLBRC
201110.1016/j.biocontrol.2011.06.014Werling, B. P., T. D. Meehan, C. Gratton, and D. A. Landis. 2011. Influence of habitat and landscape perenniality on insect natural enemies in three candidate biofuel crops, Biological Control 59(2), 304-312. GLBRC
201110.1016/j.mib.2011.04.004Wilson, D. B. 2011. Microbial diversity of cellulose hydrolysis, Curr Opin Microbiol 14(3), 259-263. BESC
201110.1371/journal.pgen.1002430Wisniewski-Dye, F., K. Borziak, G. Khalsa-Moyers, G. Alexandre, L. O. Sukharnikov, K. Wuichet, G. B. Hurst, W. H. McDonald, J. S. Robertson, V. Barbe, A. Calteau, Z. Rouy, S. Mangenot, C. Prigent-Combaret, P. Normand, M. Boyer, P. Siguier, Y. Dessaux, C. Elmerich, G. Condemine, G. Krishnen, I. Kennedy, A. H. Paterson, V. Gonzalez, P. Mavingui, and I. B. Zhulin. 2011. Azospirillum genomes reveal transition of bacteria from aquatic to terrestrial environments, PLoS Genet 7(12), e1002430. BESC
201110.1073/pnas.1103039108Wohlbach, D. J., A. Kuo, T. K. Sato, K. M. Potts, A. A. Salamov, K. M. Labutti, H. Sun, A. Clum, J. L. Pangilinan, E. A. Lindquist, S. Lucas, A. Lapidus, M. Jin, C. Gunawan, V. Balan, B. E. Dale, T. W. Jeffries, R. Zinkel, K. W. Barry, I. V. Grigoriev, and A. P. Gasch. 2011. Comparative genomics of xylose-fermenting fungi for enhanced biofuel production, Proc Natl Acad Sci U S A 108(32), 13212-13217. GLBRC
201110.1002/bit.22910Xia, J., A. D. Jones, M. W. Lau, Y. J. Yuan, B. E. Dale, and V. Balan. 2011. Comparative lipidomic profiling of xylose-metabolizing S. cerevisiae and its parental strain in different media reveals correlations between membrane lipids and fermentation capacity, Biotechnol Bioeng 108(1), 12-21. GLBRC
201110.1111/j.1469-8137.2011.03830.xXu, B., L. L. Escamilla-Trevino, N. Sathitsuksanoh, Z. Shen, H. Shen, Y. H. Zhang, R. A. Dixon, and B. Zhao. 2011. Silencing of 4-coumarate:coenzyme A ligase in switchgrass leads to reduced lignin content and improved fermentable sugar yields for biofuel production, New Phytol 192(3), 611-625. BESC
201110.1038/nrmicro2439-c1Xu, C., C. Liang, S. Wullschleger, C. Wilson, and N. McDowell. 2011. Importance of feedback loops between soil inorganic nitrogen and microbial communities in the heterotrophic soil respiration response to global warming, Nat Rev Microbiol 9(3), 222. GLBRC
2011Xu, Q., Y. Luo, S.-Y. Ding, M. E. Himmel, L. Bu, R. Lamed, and E. A. Bayer. 2011. 3.03 - Multifunctional Enzyme Systems for Plant Cell Wall Degradation. In Comprehensive Biotechnology, 2nd ed., 15-25. Ed. M. Moo-Young. Academic Press.BESC
201110.1016/j.plantsci.2011.01.020Yang, X., C. Y. Ye, A. Bisaria, G. A. Tuskan, and U. C. Kalluri. 2011. Identification of candidate genes in Arabidopsis and Populus cell wall biosynthesis using text-mining, co-expression network analysis and comparative genomics, Plant Sci 181(6), 675-687. BESC
201110.1101/gr.109280.110Yang, X., T. J. Tschaplinski, G. B. Hurst, S. Jawdy, P. E. Abraham, P. K. Lankford, R. M. Adams, M. B. Shah, R. L. Hettich, E. Lindquist, U. C. Kalluri, L. E. Gunter, C. Pennacchio, and G. A. Tuskan. 2011. Discovery and annotation of small proteins using genomics, proteomics, and computational approaches, Genome Res 21(4), 634-641. BESC
2011Yang, X., T. Li, D. Weston, A. Karve, J. L. Labbe, L. E. Gunter, P. Sukumar, A. Borland, J.-G. Chen, S. D. Wullschleger, T. J. Tschaplinski, and G. A. Tuskan. 2011. Innovative Biological Solutions to Challenges in Sustainable Biofuels Production. In Biofuel Production-Recent Developments and Prospects, 375-414. Ed. M. A. dos Santos Bernardes. InTechOpen.BESC
201110.1021/jp1086812Yao, J., Q. Xu, F. Chen, and H. Guo. 2011. QM/MM free energy simulations of salicylic acid methyltransferase: effects of stabilization of TS-like structures on substrate specificity, J Phys Chem B 115(2), 389-396. BESC
201110.1016/j.plantsci.2011.01.021Ye, C. Y., T. Li, G. A. Tuskan, T. J. Tschaplinski, and X. Yang. 2011. Comparative analysis of GT14/GT14-like gene family in Arabidopsis, Oryza, Populus, Sorghum and Vitis, Plant Sci 181(6), 688-695. BESC
201110.1007/s11295-011-0431-1Ye, X., S. Yuan, H. Guo, F. Chen, G. A. Tuskan, and Z.-M. Cheng. 2011. Evolution and divergence in the coding and promoter regions of the Populus gene family encoding xyloglucan endotransglycosylase/hydrolases, Tree Genetics & Genomes 8(1), 177-194. BESC
201110.1080/07352689.2011.605737Ye, X., V. Busov, N. Zhao, R. Meilan, L. M. McDonnell, H. D. Coleman, S. D. Mansfield, F. Chen, Y. Li, and Z.-M. Cheng. 2011. Transgenic Populus Trees for Forest Products, Bioenergy, and Functional Genomics, Critical Reviews in Plant Sciences 30(5), 415-434. BESC
201110.1007/s00253-011-3346-8Ye, X., Z. Zhu, C. Zhang, and Y. H. Zhang. 2011. Fusion of a family 9 cellulose-binding module improves catalytic potential of Clostridium thermocellum cellodextrin phosphorylase on insoluble cellulose, Appl Microbiol Biotechnol 92(3), 551-560. BESC
201110.1111/j.1462-2920.2010.02417.xYelle, D. J., D. Wei, J. Ralph, and K. E. Hammel. 2011. Multidimensional NMR analysis reveals truncated lignin structures in wood decayed by the brown rot basidiomycete Postia placenta, Environ Microbiol 13(4), 1091-1100. GLBRC
201110.1515/hf.2011.028Yelle, D. J., J. Ralph, and C. R. Frihart. 2011. Delineating pMDI model reactions with loblolly pine via solution-state NMR spectroscopy. Part 1. Catalyzed reactions with wood models and wood polymers, Holzforschung 65(2). GLBRC
201110.1515/hf.2011.029Yelle, D. J., J. Ralph, and C. R. Frihart. 2011. Delineating pMDI model reactions with loblolly pine via solution-state NMR spectroscopy. Part 2. Non-catalyzed reactions with the wood cell wall, Holzforschung 65(2). GLBRC
201110.1093/mp/ssr026Yin, L., Y. Verhertbruggen, A. Oikawa, C. Manisseri, B. Knierim, L. Prak, J. K. Jensen, J. P. Knox, M. Auer, W. G. Willats, and H. V. Scheller. 2011. The cooperative activities of CSLD2, CSLD3, and CSLD5 are required for normal Arabidopsis development, Mol Plant 4(6), 1024-1037. JBEI
201110.1371/journal.pone.0027995Yin, Y., J. Huang, X. Gu, M. Bar-Peled, and Y. Xu. 2011. Evolution of plant nucleotide-sugar interconversion enzymes, PLoS One 6(11), e27995. BESC
201110.1007/s00122-010-1488-1Zalapa, J. E., D. L. Price, S. M. Kaeppler, C. M. Tobias, M. Okada, and M. D. Casler. 2011. Hierarchical classification of switchgrass genotypes using SSR and chloroplast sequences: ecotypes, ploidies, gene pools, and cultivars, Theor Appl Genet 122(4), 805-817. GLBRC
201110.1111/j.1757-1707.2011.01098.xZenone, T., J. Chen, M. W. Deal, B. Wilske, P. Jasrotia, J. Xu, A. K. Bhardwaj, S. K. Hamilton, and G. Philip Robertson. 2011. CO2 fluxes of transitional bioenergy crops: effect of land conversion during the first year of cultivation, GCB Bioenergy 3(5), 401-412. GLBRC
201110.1016/j.tim.2011.05.003Zhang, F., and J. Keasling. 2011. Biosensors and their applications in microbial metabolic engineering, Trends Microbiol 19(7), 323-329. JBEI
201110.1016/j.copbio.2011.04.024Zhang, F., S. Rodriguez, and J. D. Keasling. 2011. Metabolic engineering of microbial pathways for advanced biofuels production, Curr Opin Biotechnol 22(6), 775-783. JBEI
201110.1039/c1gc15193bZhang, T., S. Datta, J. Eichler, N. Ivanova, S. D. Axen, C. A. Kerfeld, F. Chen, N. Kyrpides, P. Hugenholtz, J.-F. Cheng, K. L. Sale, B. Simmons, and E. Rubin. 2011. Identification of a haloalkaliphilic and thermostable cellulase with improved ionic liquid tolerance, Green Chemistry 13(8), 2083. JBEI
201110.1111/j.1751-7915.2010.00230.xZhang, X. Z., and Y. Zhang. 2011. Simple, fast and high-efficiency transformation system for directed evolution of cellulase in Bacillus subtilis, Microb Biotechnol 4(1), 98-105. BESC
201110.1016/j.ymben.2011.04.003Zhang, X. Z., N. Sathitsuksanoh, Z. Zhu, and Y. H. Percival Zhang. 2011. One-step production of lactate from cellulose as the sole carbon source without any other organic nutrient by recombinant cellulolytic Bacillus subtilis, Metab Eng 13(4), 364-372. BESC
201110.1016/j.jhydrol.2011.09.002Zhang, X., F. Liang, B. Yu, and Z. Zong. 2011. Explicitly integrating parameter, input, and structure uncertainties into Bayesian Neural Networks for probabilistic hydrologic forecasting, Journal of Hydrology 409(3-4), 696-709. GLBRC
201110.1021/es201463xZhang, X., R. C. Izaurralde, J. G. Arnold, N. B. Sammons, D. H. Manowitz, A. M. Thomson, and J. R. Williams. 2011. Comment on Modeling miscanthus in the soil and water assessment tool (SWAT) to simulate its water quality effects as a bioenergy crop, Environ Sci Technol 45(14), 6211-6212; author reply 6213-6214. GLBRC
201110.1016/j.biotechadv.2011.05.020Zhang, Y. H. 2011. Substrate channeling and enzyme complexes for biotechnological applications, Biotechnol Adv 29(6), 715-725. BESC
2011Zhang, Y. H. P. 2011. Hydrogen Production from Carbohydrates: A Mini-Review. In Sustainable Production of Fuels, Chemicals, and Fibers from Forest Biomass, 203-216. American Chemical Society.BESC
201110.1021/cs200218fZhang, Y. H. P. 2011. Simpler Is Better: High-Yield and Potential Low-Cost Biofuels Production through Cell-Free Synthetic Pathway Biotransformation (SyPaB), ACS Catalysis 1(9), 998-1009. BESC
201110.1016/j.procbio.2011.08.005Zhang, Y. H. P. 2011. What is vital (and not vital) to advance economically-competitive biofuels production, Process Biochemistry 46(11), 2091-2110. BESC
201110.3390/en4020254Zhang, Y. H. P., and J. R. Mielenz. 2011. Renewable Hydrogen Carrier — Carbohydrate: Constructing the Carbon-Neutral Carbohydrate Economy, Energies 4(2), 254-275. BESC
201110.1039/c1jm12078fZhang, Y. H. P., S. Myung, C. You, Z. Zhu, and J. A. Rollin. 2011. Toward low-cost biomanufacturing through in vitro synthetic biology: bottom-up design, Journal of Materials Chemistry 21(47), 18877. BESC
201110.1007/s10709-011-9597-6Zhang, Y., J. E. Zalapa, A. R. Jakubowski, D. L. Price, A. Acharya, Y. Wei, E. C. Brummer, S. M. Kaeppler, and M. D. Casler. 2011. Post-glacial evolution of Panicum virgatum: centers of diversity and gene pools revealed by SSR markers and cpDNA sequences, Genetica 139(7), 933-948. BESC GLBRC
201110.2135/cropsci2011.02.0104Zhang, Y., J. Zalapa, A. R. Jakubowski, D. L. Price, A. Acharya, Y. Wei, E. C. Brummer, S. M. Kaeppler, and M. D. Casler. 2011. Natural Hybrids and Gene Flow between Upland and Lowland Switchgrass, Crop Science 51(6), 2626. BESC GLBRC
201110.1105/tpc.111.085464Zhou, C., L. Han, C. Hou, A. Metelli, L. Qi, M. Tadege, K. S. Mysore, and Z. Y. Wang. 2011. Developmental analysis of a Medicago truncatula smooth leaf margin1 mutant reveals context-dependent effects on compound leaf development, Plant Cell 23(6), 2106-2124. BESC
201110.1002/prot.23094Zhu, X., and J. C. Mitchell. 2011. KFC2: a knowledge-based hot spot prediction method based on interface solvation, atomic density, and plasticity features, Proteins 79(9), 2671-2683. GLBRC
201110.1007/s12155-011-9151-5Zhu, Y., A. Mohammadi, and J. Ralph. 2011. Facile Synthesis of 4-Hydroxycinnamaldehydes, BioEnergy Research 5(2), 407-411. GLBRC
201110.1016/j.tetlet.2011.05.038Zhu, Y., and J. Ralph. 2011. Stereoselective synthesis of 1-O-ß-feruloyl and 1-O-ß-sinapoyl glucopyranoses, Tetrahedron Letters 52(29), 3729-3731. GLBRC
201110.1016/j.jpowsour.2011.04.038Zhu, Z., Y. Wang, S. D. Minteer, and Y. H. Percival Zhang. 2011. Maltodextrin-powered enzymatic fuel cell through a non-natural enzymatic pathway, Journal of Power Sources 196(18), 7505-7509. BESC
2010Abulencia, C. B., Wells, S. M., Gray, K. A., Keller, M., Kreps, J.A., . 2010. Accessing microbial communities relevant to biofuels production. In Industrial Microbiology and Biotechnology, 3rd ed., 565-576. Eds. R. H. Baltz, J. E. Davies, and A. L. Demain. ASM press.BESC
201010.3390/molecules15118641Achyuthan, K. E., A. M. Achyuthan, P. D. Adams, S. M. Dirk, J. C. Harper, B. A. Simmons, and A. K. Singh. 2010. Supramolecular self-assembled chaos: polyphenolic lignin's barrier to cost-effective lignocellulosic biofuels, Molecules 15(12), 8641-8688. JBEI
201010.3390/molecules15031645Achyuthan, K. E., P. D. Adams, S. Datta, B. A. Simmons, and A. K. Singh. 2010. Hitherto unrecognized fluorescence properties of coniferyl alcohol, Molecules 15(3), 1645-1667. JBEI
201010.1107/S1744309110022529Alahuhta, M., Q. Xu, R. Brunecky, W. S. Adney, S. Y. Ding, M. E. Himmel, and V. V. Lunin. 2010. Structure of a fibronectin type III-like module from Clostridium thermocellum, Acta Crystallogr Sect F Struct Biol Cryst Commun 66(Pt 8), 878-880. BESC
201010.1016/j.jmb.2010.07.028Alahuhta, M., Q. Xu, Y. J. Bomble, R. Brunecky, W. S. Adney, S. Y. Ding, M. E. Himmel, and V. V. Lunin. 2010. The unique binding mode of cellulosomal CBM4 from Clostridium thermocellum cellobiohydrolase A, J Mol Biol 402(2), 374-387. BESC
2010Albersheim, P., A. Darvill, K. Roberts, R. Sederoff, and A. Staehelin. 2010. Plant Cell Walls. Crc Press Inc, 430 pp.BESC
2010 10.1371/journal.pone.0008812Allgaier, M., A. Reddy, J. I. Park, N. Ivanova, P. D'Haeseleer, S. Lowry, R. Sapra, T. C. Hazen, B. A. Simmons, J. S. VanderGheynst, and P. Hugenholtz. 2010. Targeted discovery of glycoside hydrolases from a switchgrass-adapted compost community, PLoS One 5(1), e8812. JBEI
201010.1104/pp.110.155713Alonso, A. P., R. J. Piasecki, Y. Wang, R. W. LaClair, and Y. Shachar-Hill. 2010. Quantifying the labeling and the levels of plant cell wall precursors using ion chromatography tandem mass spectrometry, Plant Physiol 153(3), 915-924. GLBRC
201010.1016/j.ymben.2010.04.002Alonso, A. P., V. L. Dale, and Y. Shachar-Hill. 2010. Understanding fatty acid synthesis in developing maize embryos using metabolic flux analysis, Metab Eng 12(5), 488-497. GLBRC
201010.1007/s00216-010-3955-6Andrews, G., D. Lewis, J. Notey, R. Kelly, and D. Muddiman. 2010. Part I: characterization of the extracellular proteome of the extreme thermophile Caldicellulosiruptor saccharolyticus by GeLC-MS2, Anal Bioanal Chem 398(1), 377-389. BESC
201010.1007/s00216-010-3929-8Andrews, G., D. Lewis, J. Notey, R. Kelly, and D. Muddiman. 2010. Part II: defining and quantifying individual and co-cultured intracellular proteomes of two thermophilic microorganisms by GeLC-MS2 and spectral counting, Anal Bioanal Chem 398(1), 391-404. BESC
201010.1007/s12155-010-9087-1Arora, R., C. Manisseri, C. Li, M. D. Ong, H. V. Scheller, K. Vogel, B. A. Simmons, and S. Singh. 2010. Monitoring and Analyzing Process Streams Towards Understanding Ionic Liquid Pretreatment of Switchgrass (Panicum virgatum L.), BioEnergy Research 3(2), 134-145. JBEI
201010.1038/msb.2010.98Atsumi, S., T. Y. Wu, I. M. Machado, W. C. Huang, P. Y. Chen, M. Pellegrini, and J. C. Liao. 2010. Evolution, genomic analysis, and reconstruction of isobutanol tolerance in Escherichia coli, Mol Syst Biol 6, 449. BESC
201010.1186/1754-6834-3-1Bals, B., C. Rogers, M. Jin, V. Balan, and B. Dale. 2010. Evaluation of ammonia fibre expansion (AFEX) pretreatment for enzymatic hydrolysis of switchgrass harvested in different seasons and locations, Biotechnol Biofuels 3(1), 1. GLBRC
201010.1007/s12155-009-9067-5Banerjee, G., J. S. Scott-Craig, and J. D. Walton. 2010. Improving Enzymes for Biomass Conversion: A Basic Research Perspective, BioEnergy Research 3(1), 82-92. GLBRC
201010.1186/1754-6834-3-22Banerjee, G., S. Car, J. S. Scott-Craig, M. S. Borrusch, and J. D. Walton. 2010. Rapid optimization of enzyme mixtures for deconstruction of diverse pretreatment/biomass feedstock combinations, Biotechnol Biofuels 3, 22. GLBRC
201010.1016/j.biortech.2010.07.028Banerjee, G., S. Car, J. S. Scott-Craig, M. S. Borrusch, M. Bongers, and J. D. Walton. 2010. Synthetic multi-component enzyme mixtures for deconstruction of lignocellulosic biomass, Bioresour Technol 101(23), 9097-9105. GLBRC
201010.1002/bit.22741.Banerjee, G., S. Car, J. S. Scott-Craig, M. S. Borrusch, N. Aslam, and J. D. Walton. 2010. Synthetic enzyme mixtures for biomass deconstruction: production and optimization of a core set, Biotechnol Bioeng 106(5), 707-720. GLBRC
201010.1371/journal.pgen.1001123Bart, R. S., M. Chern, M. E. Vega-Sanchez, P. Canlas, and P. C. Ronald. 2010. Rice Snl6, a cinnamoyl-CoA reductase-like gene family member, is required for NH1-mediated immunity to Xanthomonas oryzae pv. oryzae, PLoS Genet 6(9), e1001123. JBEI
2010Bartley, L. E., and P. C. Ronald. 2010. Plant and microbial research seeks biofuel production from lignocellulose, California Agriculture 63, 178-184. DOI.JBEI
201010.1371/journal.pcbi.1000970Barua, D., J. Kim, and J. L. Reed. 2010. An automated phenotype-driven approach (GeneForce) for refining metabolic and regulatory models, PLoS Comput Biol 6(10), e1000970. GLBRC
201010.1128/AEM.02312-09Beller, H. R., E. B. Goh, and J. D. Keasling. 2010. Genes involved in long-chain alkene biosynthesis in Micrococcus luteus, Appl Environ Microbiol 76(4), 1212-1223. JBEI
201010.1016/j.carres.2010.06.017Bergenstrahle, M., J. Wohlert, M. E. Himmel, and J. W. Brady. 2010. Simulation studies of the insolubility of cellulose, Carbohydr Res 345(14), 2060-2066. BESC
201010.1021/ac102243fBharadwaj, R., Z. Chen, S. Datta, B. M. Holmes, R. Sapra, B. A. Simmons, P. D. Adams, and A. K. Singh. 2010. Microfluidic glycosyl hydrolase screening for biomass-to-biofuel conversion, Anal Chem 82(22), 9513-9520. JBEI
201010.1039/b923961hBinder, J. B., A. V. Cefali, J. J. Blank, and R. T. Raines. 2010. Mechanistic insights on the conversion of sugars into 5-hydroxymethylfurfural, Energy & Environmental Science 3(6), 765. GLBRC
201010.1073/pnas.0912073107Binder, J. B., and R. T. Raines. 2010. Fermentable sugars by chemical hydrolysis of biomass, Proc Natl Acad Sci U S A 107(10), 4516-4521. GLBRC
201010.1002/cssc.201000181Binder, J. B., J. J. Blank, A. V. Cefali, and R. T. Raines. 2010. Synthesis of furfural from xylose and xylan, ChemSusChem 3(11), 1268-1272. GLBRC
201010.1128/AEM.01400-10Blumer-Schuette, S. E., D. L. Lewis, and R. M. Kelly. 2010. Phylogenetic, microbiological, and glycoside hydrolase diversities within the extremely thermophilic, plant biomass-degrading genus Caldicellulosiruptor, Appl Environ Microbiol 76(24), 8084-8092. BESC
201010.1007/s12010-009-8842-2Bochner, B., V. Gomez, M. Ziman, S. Yang, and S. D. Brown. 2010. Phenotype microarray profiling of Zymomonas mobilis ZM4, Appl Biochem Biotechnol 161(1-8), 116-123. BESC
2010Bomble, Y. J., M. F. Crowley, Q. I. Xu, and M. E. Himmel. 2010. Modeling the Cellulosome Using Multiscale Models. In Computational Modeling in Lignocellulosic Biofuel Production, 75-98. Eds. M. R. Nimlos, and M. F. Crowley.BESC
201010.1126/science.1184362Bond, J. Q., D. M. Alonso, D. Wang, R. M. West, and J. A. Dumesic. 2010. Integrated catalytic conversion of gamma-valerolactone to liquid alkenes for transportation fuels, Science 327(5969), 1110-1114. GLBRC
201010.1007/s12155-010-9091-5Brennan, T. C. R., S. Datta, H. W. Blanch, B. A. Simmons, and B. M. Holmes. 2010. Recovery of Sugars from Ionic Liquid Biomass Liquor by Solvent Extraction, BioEnergy Research 3(2), 123-133. JBEI
201010.1007/s12155-010-9082-6Cao, P., K.-H. Jung, and P. C. Ronald. 2010. A Survey of Databases for Analysis of Plant Cell Wall-Related Enzymes, BioEnergy Research 3(2), 108-114. JBEI
201010.1093/nar/gkq082Carothers, J. M., J. A. Goler, Y. Kapoor, L. Lara, and J. D. Keasling. 2010. Selecting RNA aptamers for synthetic biology: investigating magnesium dependence and predicting binding affinity, Nucleic Acids Res 38(8), 2736-2747. JBEI
201010.1007/s12155-009-9071-9Casler, M. D. 2010. Changes in Mean and Genetic Variance During Two Cycles of Within-family Selection in Switchgrass, BioEnergy Research 3(1), 47-54. GLBRC
201010.1007/s12155-009-9076-4Casler, M. D. 2010. DOE Bioenergy Center Special Issue: The Great Lakes Bioenergy Research Center (GLBRC), BioEnergy Research 3(1), 1-2. GLBRC
201010.1021/pr1003938Chandrasekaran, A., R. Bharadwaj, J. I. Park, R. Sapra, P. D. Adams, and A. K. Singh. 2010. A microscale platform for integrated cell-free expression and activity screening of cellulases, J Proteome Res 9(11), 5677-5683. JBEI
201010.1186/1754-6834-3-9Chen, X., R. Equi, H. Baxter, K. Berk, J. Han, S. Agarwal, and J. Zale. 2010. A high-throughput transient gene expression system for switchgrass (Panicum virgatum L.) seedlings, Biotechnol Biofuels 3, 9. BESC
201010.1016/j.phytochem.2009.11.012Chen, Y. R., and S. Sarkanen. 2010. Macromolecular replication during lignin biosynthesis, Phytochemistry 71(4), 453-462. BESC
201010.1093/bioinformatics/btq446Chou, W. C., Y. Yin, and Y. Xu. 2010. GolgiP: prediction of Golgi-resident proteins in plants, Bioinformatics 26(19), 2464-2465. BESC
201010.1016/j.phytochem.2009.09.019Christensen, U., A. Alonso-Simon, H. V. Scheller, W. G. Willats, and J. Harholt. 2010. Characterization of the primary cell walls of seedlings of Brachypodium distachyon--a potential model plant for temperate grasses, Phytochemistry 71(1), 62-69. JBEI
2010Chundawat, S. P. S., V. Balan, L. d. C. Sousa, and B. E. Dale. 2010. Thermochemical pretreatment of lignocellulosic biomass. In Bioalcohol Production-Biochemical Conversion of Lignocellulosic Biomass, 24-72. Woodhead Publishing Ltd., (CRC Press).GLBRC
201010.1016/j.biortech.2010.06.027Chundawat, S. P., R. Vismeh, L. N. Sharma, J. F. Humpula, L. da Costa Sousa, C. K. Chambliss, A. D. Jones, V. Balan, and B. E. Dale. 2010. Multifaceted characterization of cell wall decomposition products formed during ammonia fiber expansion (AFEX) and dilute acid based pretreatments, Bioresour Technol 101(21), 8429-8438. GLBRC
201010.1073/pnas.0913774107Cong, Y., M. L. Baker, J. Jakana, D. Woolford, E. J. Miller, S. Reissmann, R. N. Kumar, A. M. Redding-Johanson, T. S. Batth, A. Mukhopadhyay, S. J. Ludtke, J. Frydman, and W. Chiu. 2010. 4.0-A resolution cryo-EM structure of the mammalian chaperonin TRiC/CCT reveals its unique subunit arrangement, Proc Natl Acad Sci U S A 107(11), 4967-4972. JBEI
201010.1186/1471-2229-10-273Cote, C. L., F. Boileau, V. Roy, M. Ouellet, C. Levasseur, M. J. Morency, J. E. Cooke, A. Seguin, and J. J. MacKay. 2010. Gene family structure, expression and functional analysis of HD-Zip III genes in angiosperm and gymnosperm forest trees, BMC Plant Biol 10, 273. JBEI
201010.1007/s12155-009-9073-7da C. Jesus, E., E. Susilawati, S. L. Smith, Q. Wang, B. Chai, R. Farris, J. L. M. Rodrigues, K. D. Thelen, and J. M. Tiedje. 2010. Bacterial Communities in the Rhizosphere of Biofuel Crops Grown on Marginal Lands as Evaluated by 16S rRNA Gene Pyrosequences, BioEnergy Research 3(1), 20-27. GLBRC
201010.1021/es101864bDale, B. E., B. D. Bals, S. Kim, and P. Eranki. 2010. Biofuels Done Right: Land Efficient Animal Feeds Enable Large Environmental and Energy Benefits, Environmental Science & Technology 44(22), 8385-8389. GLBRC
2010Dale, V. H., R. Lowrance, P. Mulholland, and G. P. Robertson. 2010. Bioenergy sustainability at the regional scale, Ecology and Society 15, 23-28. DOI.GLBRC
201010.1039/b916564aDatta, S., B. Holmes, J. I. Park, Z. Chen, D. C. Dibble, M. Hadi, H. W. Blanch, B. A. Simmons, and R. Sapra. 2010. Ionic liquid tolerant hyperthermophilic cellulases for biomass pretreatment and hydrolysis, Green Chemistry 12(2), 338. JBEI
201010.1039/b926617hDavid, K., and A. J. Ragauskas. 2010. Switchgrass as an energy crop for biofuel production: A review of its ligno-cellulosic chemical properties, Energy & Environmental Science 3(9), 1182. BESC
201010.1111/j.1365-313X.2010.04392.xDavis, J., F. Brandizzi, A. H. Liepman, and K. Keegstra. 2010. Arabidopsis mannan synthase CSLA9 and glucan synthase CSLC4 have opposite orientations in the Golgi membrane, Plant J 64(6), 1028-1037. GLBRC
201010.1007/s12155-010-9089-zDeAngelis, K. M., J. M. Gladden, M. Allgaier, P. D’haeseleer, J. L. Fortney, A. Reddy, P. Hugenholtz, S. W. Singer, J. S. Vander Gheynst, W. L. Silver, B. A. Simmons, and T. C. Hazen. 2010. Strategies for Enhancing the Effectiveness of Metagenomic-based Enzyme Discovery in Lignocellulolytic Microbial Communities, BioEnergy Research 3(2), 146-158. JBEI
201010.1093/nar/gkp919Dehal, P. S., M. P. Joachimiak, M. N. Price, J. T. Bates, J. K. Baumohl, D. Chivian, G. D. Friedland, K. H. Huang, K. Keller, P. S. Novichkov, I. L. Dubchak, E. J. Alm, and A. P. Arkin. 2010. MicrobesOnline: an integrated portal for comparative and functional genomics, Nucleic Acids Res 38(Database issue), D396-400. JBEI
201010.1146/annurev-biochem-062608-095938Dietrich, J. A., A. E. McKee, and J. D. Keasling. 2010. High-throughput metabolic engineering: advances in small-molecule screening and selection, Annu Rev Biochem 79, 563-590. JBEI
2010DiFazio, S. 2010. The Populus Genome Initiative. In Advanced Genomics, 243-274. Eds. C. Kole, and A. G. Abbott. Science Publishers,.BESC
201010.1007/s11693-010-9052-5Dunlop, M. J., J. D. Keasling, and A. Mukhopadhyay. 2010. A model for improving microbial biofuel production using a synthetic feedback loop, Syst Synth Biol 4(2), 95-104. JBEI
201010.1093/nar/gkp810Durek, P., R. Schmidt, J. L. Heazlewood, A. Jones, D. MacLean, A. Nagel, B. Kersten, and W. X. Schulze. 2010. PhosPhAt: the Arabidopsis thaliana phosphorylation site database. An update, Nucleic Acids Res 38(Database issue), D828-834. JBEI
201010.1073/pnas.1001707107Durrett, T. P., D. D. McClosky, A. W. Tumaney, D. A. Elzinga, J. Ohlrogge, and M. Pollard. 2010. A distinct DGAT with sn-3 acetyltransferase activity that synthesizes unusual, reduced-viscosity oils in Euonymus and transgenic seeds, Proc Natl Acad Sci U S A 107(20), 9464-9469. GLBRC
2010Egbendewe-Mondzozo, A., S. M. Swinton, R. C. Izaurralde, D. H. Manowitz, and X. Zhang. 2010. Biomass supply from alternative cellulosic crops and crop residues: a preliminary spatial bioeconomic modeling approach. Department of Agricultural, Food, and Resource Economics. Staff Paper No. 2010-07 Michigan State UniversityGLBRC
201010.1128/JB.00950-10Elkins, J. G., A. Lochner, S. D. Hamilton-Brehm, K. W. Davenport, M. Podar, S. D. Brown, M. L. Land, L. J. Hauser, D. M. Klingeman, B. Raman, L. A. Goodwin, R. Tapia, L. J. Meincke, J. C. Detter, D. C. Bruce, C. S. Han, A. V. Palumbo, R. W. Cottingham, M. Keller, and D. E. Graham. 2010. Complete genome sequence of the cellulolytic thermophile Caldicellulosiruptor obsidiansis OB47T, J Bacteriol 192(22), 6099-6100. BESC
201010.1016/j.copbio.2010.05.008Elkins, J. G., B. Raman, and M. Keller. 2010. Engineered microbial systems for enhanced conversion of lignocellulosic biomass, Curr Opin Biotechnol 21(5), 657-662. BESC
201010.1111/j.1469-8137.2009.03018.xEscamilla-Trevino, L. L., H. Shen, S. R. Uppalapati, T. Ray, Y. Tang, T. Hernandez, Y. Yin, Y. Xu, and R. A. Dixon. 2010. Switchgrass (Panicum virgatum) possesses a divergent family of cinnamoyl CoA reductases with distinct biochemical properties, New Phytol 185(1), 143-155. BESC
201010.1126/science.1186834Fedoroff, N. V., D. S. Battisti, R. N. Beachy, P. J. Cooper, D. A. Fischhoff, C. N. Hodges, V. C. Knauf, D. Lobell, B. J. Mazur, D. Molden, M. P. Reynolds, P. C. Ronald, M. W. Rosegrant, P. A. Sanchez, A. Vonshak, and J. K. Zhu. 2010. Radically rethinking agriculture for the 21st century, Science 327(5967), 833-834. JBEI
2010Fortenbery, T. R., and T. J. Donohue. 2010. Opportunities and challenges for next generation biofuels. In From Evolution to Energy, 203-213. Eds. J. Delborne, D. L. Kleinman, K. A. Cloud-Hansen, and J. Handelsman. Mary Ann Liebert, Inc.GLBRC
201010.3791/1745Foster, C. E., T. M. Martin, and M. Pauly. 2010. Comprehensive compositional analysis of plant cell walls (Lignocellulosic biomass) part I: lignin, J Vis Exp(37). GLBRC
201010.1016/j.biombioe.2010.07.023Foston, M., and A. J. Ragauskas. 2010. Changes in lignocellulosic supramolecular and ultrastructure during dilute acid pretreatment of Populus and switchgrass, Biomass and Bioenergy 34(12), 1885-1895. BESC
201010.1021/ef100882tFoston, M., and A. J. Ragauskas. 2010. Changes in the Structure of the Cellulose Fiber Wall during Dilute Acid Pretreatment inPopulusStudied by1H and2H NMR, Energy & Fuels 24(10), 5677-5685. BESC
201010.1016/j.biortech.2009.10.056Gao, D., S. P. Chundawat, C. Krishnan, V. Balan, and B. E. Dale. 2010. Mixture optimization of six core glycosyl hydrolases for maximizing saccharification of ammonia fiber expansion (AFEX) pretreated corn stover, Bioresour Technol 101(8), 2770-2781. GLBRC
201010.1007/s12155-009-9065-7Gardiner, M. A., J. K. Tuell, R. Isaacs, J. Gibbs, J. S. Ascher, and D. A. Landis. 2010. Implications of Three Biofuel Crops for Beneficial Arthropods in Agricultural Landscapes, BioEnergy Research 3(1), 6-19. GLBRC
201010.1128/AEM.00454-10Gardner, J. G., and D. H. Keating. 2010. Requirement of the type II secretion system for utilization of cellulosic substrates by Cellvibrio japonicus, Appl Environ Microbiol 76(15), 5079-5087. GLBRC
201010.1021/es903385gGelfand, I., S. S. Snapp, and G. P. Robertson. 2010. Energy efficiency of conventional, organic, and alternative cropping systems for food and fuel at a site in the U.S. Midwest, Environ Sci Technol 44(10), 4006-4011. GLBRC
201010.1111/j.1749-6632.2009.05267.xGeshi, N., B. L. Petersen, and H. V. Scheller. 2010. Toward tailored synthesis of functional polysaccharides in plants, Annals of the New York Academy of Sciences 1190, 50-57. JBEI
201010.1007/s13225-010-0085-6Ghimire, S. R., N. D. Charlton, J. D. Bell, Y. L. Krishnamurthy, and K. D. Craven. 2010. Biodiversity of fungal endophyte communities inhabiting switchgrass (Panicum virgatum L.) growing in the native tallgrass prairie of northern Oklahoma, Fungal Diversity 47(1), 19-27. BESC
201010.1074/jbc.M110.125872Gu, X., J. Glushka, S. G. Lee, and M. Bar-Peled. 2010. Biosynthesis of a new UDP-sugar, UDP-2-acetamido-2-deoxyxylose, in the human pathogen Bacillus cereus subspecies cytotoxis NVH 391-98, J Biol Chem 285(32), 24825-24833. BESC
201010.1074/jbc.M109.066803Gu, X., J. Glushka, Y. Yin, Y. Xu, T. Denny, J. Smith, Y. Jiang, and M. Bar-Peled. 2010. Identification of a bifunctional UDP-4-keto-pentose/UDP-xylose synthase in the plant pathogenic bacterium Ralstonia solanacearum strain GMI1000, a distinct member of the 4,6-dehydratase and decarboxylase family, J Biol Chem 285(12), 9030-9040. BESC
201010.1039/b920369aGürbüz, E. I., E. L. Kunkes, and J. A. Dumesic. 2010. Dual-bed catalyst system for C-C coupling of biomass-derived oxygenated hydrocarbons to fuel-grade compounds, Green Chemistry 12(2), 223. GLBRC
201010.1016/j.apcatb.2009.11.001Gürbüz, E. I., E. L. Kunkes, and J. A. Dumesic. 2010. Integration of C-C coupling reactions of biomass-derived oxygenates to fuel-grade compounds, Applied Catalysis B: Environmental 94(1-2), 134-141. GLBRC
201010.1128/AEM.01903-09Hamilton-Brehm, S. D., J. J. Mosher, T. Vishnivetskaya, M. Podar, S. Carroll, S. Allman, T. J. Phelps, M. Keller, and J. G. Elkins. 2010. Caldicellulosiruptor obsidiansis sp. nov., an anaerobic, extremely thermophilic, cellulolytic bacterium isolated from Obsidian Pool, Yellowstone National Park, Appl Environ Microbiol 76(4), 1014-1020. BESC
201010.1007/s12155-009-9068-4Hansey, C. N., A. J. Lorenz, and N. de Leon. 2010. Cell Wall Composition and Ruminant Digestibility of Various Maize Tissues Across Development, BioEnergy Research 3(1), 28-37. GLBRC
201010.1094/cm-2010-1203-01-rsHao, X., K. Thelen, and J. Gao. 2010. Earlier-Maturing Hybrids Improve Corn Grain Profitability in the Northern Corn Belt, Crop Management 9(1), 0. GLBRC
201010.2134/agronj2009.0481Hao, X., K. Thelen, and J. Gao. 2010. Effects of Soil and Topographic Properties on Spatial Variability of Corn Grain Ethanol Yield, Agronomy Journal 102(3), 998. GLBRC
201010.1104/pp.110.156588Harholt, J., A. Suttangkakul, and H. Vibe Scheller. 2010. Biosynthesis of pectin, Plant Physiol 153(2), 384-395. JBEI
201010.1111/j.1467-7652.2009.00490.xHarholt, J., I. C. Bach, S. Lind-Bouquin, K. J. Nunan, S. M. Madrid, H. Brinch-Pedersen, P. B. Holm, and H. V. Scheller. 2010. Generation of transgenic wheat (Triticum aestivum L.) accumulating heterologous endo-xylanase or ferulic acid esterase in the endosperm, Plant Biotechnol J 8(3), 351-362. JBEI
201010.1016/j.cell.2009.12.029Holtz, W. J., and J. D. Keasling. 2010. Engineering static and dynamic control of synthetic pathways, Cell 140(1), 19-23. JBEI
201010.1111/j.1523-1739.2010.01518.xHorvath, G., M. Blaho, A. Egri, G. Kriska, I. Seres, and B. Robertson. 2010. Reducing the maladaptive attractiveness of solar panels to polarotactic insects, Conserv Biol 24(6), 1644-1653. GLBRC
201010.1016/j.biortech.2009.12.033Hu, Z., R. Sykes, M. F. Davis, E. Charles Brummer, and A. J. Ragauskas. 2010. Chemical profiles of switchgrass, Bioresour Technol 101(9), 3253-3257. BESC
201010.1016/j.biortech.2010.04.029Hubbell, C. A., and A. J. Ragauskas. 2010. Effect of acid-chlorite delignification on cellulose degree of polymerization, Bioresour Technol 101(19), 7410-7415. BESC
201010.1038/nature08747International Brachypodium Initiative. 2010. Genome sequencing and analysis of the model grass Brachypodium distachyon, Nature 463(7282), 763-768. JBEI BESC
201010.2174/157016410791330543Ito, J., C. J. Petzold, A. Mukhopadhyay, and J. L. Heazlewood. 2010. The Role of Proteomics in the Development of Cellulosic Biofuels, Current Proteomics 7(2), 121-134. JBEI
201010.1128/AEM.02689-09Izquierdo, J. A., M. V. Sizova, and L. R. Lynd. 2010. Diversity of bacteria and glycosyl hydrolase family 48 genes in cellulolytic consortia enriched from thermophilic biocompost, Appl Environ Microbiol 76(11), 3545-3553. BESC
201010.1111/j.1526-100X.2010.00738.xJakubowski, A. R., M. D. Casler, and R. D. Jackson. 2010. The Benefits of Harvesting Wetland Invaders for Cellulosic Biofuel: An Ecosystem Services Perspective, Restoration Ecology 18(6), 789-795. GLBRC
201010.2134/agronj2009.0289James, L. K., S. M. Swinton, and K. D. Thelen. 2010. Profitability Analysis of Cellulosic Energy Crops Compared with Corn, Agronomy Journal 102(2), 675. GLBRC
201010.1002/cssc.201000120Jiang, N., Y. Pu, and A. J. Ragauskas. 2010. Rapid determination of lignin content via direct dissolution and (1)H NMR analysis of plant cell walls, ChemSusChem 3(11), 1285-1289. BESC
201010.1016/j.bpj.2010.08.014Jiang, Y., T. McKinnon, J. Varatharajan, J. Glushka, J. H. Prestegard, A. T. Sornborger, H. B. Schuttler, and M. Bar-Peled. 2010. Time-resolved NMR: extracting the topology of complex enzyme networks, Biophys J 99(7), 2318-2326. BESC
201010.1016/j.biortech.2010.06.026Jin, M., M. W. Lau, V. Balan, and B. E. Dale. 2010. Two-step SSCF to convert AFEX-treated switchgrass to ethanol using commercial enzymes and Saccharomyces cerevisiae 424A(LNH-ST), Bioresour Technol 101(21), 8171-8178. GLBRC
2010Ju, H., S. Singh, S. Lan, B. Simmons, M. Auer, and B. Parvin. 2010. Chemical profiling of the plant cell wall through Raman microspectroscopy. In Proceedings 2010 7th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 1273-1276.JBEI
201010.1016/j.tplants.2010.08.004Jung, K. H., P. Cao, Y. S. Seo, C. Dardick, and P. C. Ronald. 2010. The Rice Kinase Phylogenomics Database: a guide for systematic analysis of the rice kinase super-family, Trends Plant Sci 15(11), 595-599. JBEI
201010.1104/pp.109.152157Jung, K. H., Y. S. Seo, H. Walia, P. Cao, T. Fukao, P. E. Canlas, F. Amonpant, J. Bailey-Serres, and P. C. Ronald. 2010. The submergence tolerance regulator Sub1A mediates stress-responsive expression of AP2/ERF transcription factors, Plant Physiol 152(3), 1674-1692. JBEI
201010.1021/ef901062pJung, S., M. Foston, M. C. Sullards, and A. J. Ragauskas. 2010. Surface Characterization of Dilute Acid Pretreated Populus deltoides by ToF-SIMS, Energy & Fuels 24(2), 1347-1357. BESC
201010.1002/rcm.4757Jung, S., Y. Chen, M. C. Sullards, and A. J. Ragauskas. 2010. Direct analysis of cellulose in poplar stem by matrix-assisted laser desorption/ionization imaging mass spectrometry, Rapid Commun Mass Spectrom 24(22), 3230-3236. BESC
201010.1098/rsif.2009.0564Kalluri, U. C., and M. Keller. 2010. Bioenergy research: a new paradigm in multidisciplinary research, J R Soc Interface 7(51), 1391-1401. BESC
201010.1007/s00299-010-0850-8Kang, B. G., X. Ye, L. D. Osburn, C. N. Stewart, Jr., and Z. M. Cheng. 2010. Transgenic hybrid aspen overexpressing the Atwbc19 gene encoding an ATP-binding cassette transporter confers resistance to four aminoglycoside antibiotics, Plant Cell Rep 29(6), 643-650. BESC
201010.1016/j.enpol.2010.05.008Kaufman, A. S., P. J. Meier, J. C. Sinistore, and D. J. Reinemann. 2010. Applying life-cycle assessment to low carbon fuel standards—How allocation choices influence carbon intensity for renewable transportation fuels, Energy Policy 38(9), 5229-5241. GLBRC
2010Kausch, A. P., J. Hague, M. Oliver, L. S. Watrud, C. Mallory-Smith, V. Meier, A. Snow, and J. C. N. Stewart. 2010. Gene flow in genetically engineered perennial grasses: lessons for modification of dedicated bioenergy crop. In Plant Biotechnology for Sustainable Production of Energy and Co-products, 285-298. Eds. P. N. Mascia, J. Scheffran, and J. M. Widholm. Springer Verlag.BESC
2010Kausch, A. P., J. Hague, M. Oliver, Y. Li, H. Daniell, P.Mascia, and C.N. Stewart, Jr. . 2010. Genetic modification in dedicated bioenergy crops and strategies for gene confinement. In Plant Biotechnology for Sustainable Production of Energy and Co-products, 299-315. Eds. P. N. Mascia, J. Scheffran, and J. M. Widholm. Springer Verlag.BESC
2010Keasling, J. 2010. Engineering Microorganisms with Plant-derived Genes to Produce Drugs and Fuels. Speaker Abstract: 2010 In Vitro Biology Meeting And IAPB 12th World Congress Abstract Issue, In Vitro Cellular & Developmental Biology - Animal 46(Suppl 1), 38-39. DOI.JBEI
201010.1126/science.1193990Keasling, J. D. 2010. Manufacturing molecules through metabolic engineering, Science 330(6009), 1355-1358. JBEI
201010.1104/pp.110.161240Keegstra, K. 2010. Plant cell walls, Plant Physiol 154(2), 483-486. GLBRC
201010.1021/bm9008952Kent, M. S., G. Cheng, J. K. Murton, E. L. Carles, D. C. Dibble, F. Zendejas, M. A. Rodriquez, H. Tran, B. Holmes, B. A. Simmons, B. Knierim, M. Auer, J. L. Banuelos, J. Urquidi, and R. P. Hjelm. 2010. Study of enzymatic digestion of cellulose by small angle neutron scattering, Biomacromolecules 11(2), 357-368. JBEI
2010Kiley, P. J., and T. J. Donohue. 2010. Global responses of bacteria to oxygen deprivation. In Bacterial Stress Responses, 175-189. ASM Press.GLBRC
201010.1039/b916070aKim, H., and J. Ralph. 2010. Solution-state 2D NMR of ball-milled plant cell wall gels in DMSO-d(6)/pyridine-d(5), Org Biomol Chem 8(3), 576-591. GLBRC
201010.1186/1752-0509-4-53Kim, J., and J. L. Reed. 2010. OptORF: Optimal metabolic and regulatory perturbations for metabolic engineering of microbial strains, BMC Syst Biol 4, 53. GLBRC
201010.1016/j.biombioe.2010.07.033Klein-Marcuschamer, D., P. Oleskowicz-Popiel, B. A. Simmons, and H. W. Blanch. 2010. Technoeconomic analysis of biofuels: A wiki-based platform for lignocellulosic biorefineries, Biomass and Bioenergy 34(12), 1914-1921. JBEI
201010.1007/s11816-010-0159-7Ko, J.-H., H.-T. Kim, and K.-H. Han. 2010. Biotechnological improvement of lignocellulosic feedstock for enhanced biofuel productivity and processing, Plant Biotechnology Reports 5(1), 1-7. GLBRC
2010Krauskopf, S. 2010. A life-cycle assessment of biofuels: tracing energy and carbon through a fuel-production system, The Science Teacher 77, 35-40. DOI.GLBRC
201010.1002/bit.22824Krishnan, C., C. Sousa Lda, M. Jin, L. Chang, B. E. Dale, and V. Balan. 2010. Alkali-based AFEX pretreatment for the conversion of sugarcane bagasse and cane leaf residues to ethanol, Biotechnol Bioeng 107(3), 441-450. GLBRC
201010.1104/pp.110.155242Lacayo, C. I., A. J. Malkin, H. Y. Holman, L. Chen, S. Y. Ding, M. S. Hwang, and M. P. Thelen. 2010. Imaging cell wall architecture in single Zinnia elegans tracheary elements, Plant Physiol 154(1), 121-133. JBEI BESC
201010.3389/fphys.2010.00024Lalonde, S., A. Sero, R. Pratelli, G. Pilot, J. Chen, M. I. Sardi, S. A. Parsa, D. Y. Kim, B. R. Acharya, E. V. Stein, H. C. Hu, F. Villiers, K. Takeda, Y. Yang, Y. S. Han, R. Schwacke, W. Chiang, N. Kato, D. Loque, S. M. Assmann, J. M. Kwak, J. I. Schroeder, S. Y. Rhee, and W. B. Frommer. 2010. A membrane protein/signaling protein interaction network for Arabidopsis version AMPv2, Front Physiol 1, 24. JBEI
201010.1111/j.1744-7917.2009.01310.xLandis, D. A., and B. P. Werling. 2010. Arthropods and biofuel production systems in North America, Insect Science 17(3), 220-236. GLBRC
201010.1007/s12010-010-8962-8Lau, M. J., M. W. Lau, C. Gunawan, and B. E. Dale. 2010. Ammonia fiber expansion (AFEX) pretreatment, enzymatic hydrolysis, and fermentation on empty palm fruit bunch fiber (EPFBF) for cellulosic ethanol production, Appl Biochem Biotechnol 162(7), 1847-1857. GLBRC
201010.1016/j.biortech.2010.04.076Lau, M. W., and B. E. Dale. 2010. Effect of primary degradation-reaction products from Ammonia Fiber Expansion (AFEX)-treated corn stover on the growth and fermentation of Escherichia coli KO11, Bioresour Technol 101(20), 7849-7855. GLBRC
201010.1186/1754-6834-3-11Lau, M. W., C. Gunawan, V. Balan, and B. E. Dale. 2010. Comparing the fermentation performance of Escherichia coli KO11, Saccharomyces cerevisiae 424A(LNH-ST) and Zymomonas mobilis AX101 for cellulosic ethanol production, Biotechnol Biofuels 3, 11. GLBRC
201010.2144/000113451Lee, D. Y., B. P. Bowen, and T. R. Northen. 2010. Mass spectrometry-based metabolomics, analysis of metabolite-protein interactions, and imaging, Biotechniques 49(2), 557-565. JBEI
201010.1016/j.mbs.2010.08.009Lee, Y., and E. O. Voit. 2010. Mathematical modeling of monolignol biosynthesis in Populus xylem, Math Biosci 228(1), 78-89. BESC
201010.1002/bit.22660Lennen, R. M., D. J. Braden, R. A. West, J. A. Dumesic, and B. F. Pfleger. 2010. A process for microbial hydrocarbon synthesis: Overproduction of fatty acids in Escherichia coli and catalytic conversion to alkanes, Biotechnol Bioeng 106(2), 193-202. GLBRC
201010.1021/ac100565bLewis, I. A., R. H. Karsten, M. E. Norton, M. Tonelli, W. M. Westler, and J. L. Markley. 2010. NMR method for measuring carbon-13 isotopic enrichment of metabolites in complex solutions, Anal Chem 82(11), 4558-4563. GLBRC
201010.1534/genetics.110.121871Lewis, J. A., I. M. Elkon, M. A. McGee, A. J. Higbee, and A. P. Gasch. 2010. Exploiting natural variation in Saccharomyces cerevisiae to identify genes for increased ethanol resistance, Genetics 186(4), 1197-1205. GLBRC
201010.1016/j.biortech.2009.09.044Li, B. Z., V. Balan, Y. J. Yuan, and B. E. Dale. 2010. Process optimization to convert forage and sweet sorghum bagasse to ethanol based on ammonia fiber expansion (AFEX) pretreatment, Bioresour Technol 101(4), 1285-1292. GLBRC
201010.1016/j.biortech.2009.10.066Li, C., B. Knierim, C. Manisseri, R. Arora, H. V. Scheller, M. Auer, K. P. Vogel, B. A. Simmons, and S. Singh. 2010. Comparison of dilute acid and ionic liquid pretreatment of switchgrass: Biomass recalcitrance, delignification and enzymatic saccharification, Bioresour Technol 101(13), 4900-4906. JBEI
201010.1128/AEM.02735-09Li, Y., D. C. Irwin, and D. B. Wilson. 2010. Increased crystalline cellulose activity via combinations of amino acid changes in the family 9 catalytic domain and family 3c cellulose binding module of Thermobifida fusca Cel9A, Appl Environ Microbiol 76(8), 2582-2588. BESC
201010.1016/j.soilbio.2010.02.006Liang, C., and T. C. Balser. 2010. Mass spectrometric characterization of amino sugar aldononitrile acetate derivatives used for isotope enrichment assessment of microbial residues, Soil Biology and Biochemistry 42(6), 904-909. GLBRC
201010.1007/s10533-010-9525-3Liang, C., G. Cheng, D. L. Wixon, and T. C. Balser. 2010. An Absorbing Markov Chain approach to understanding the microbial role in soil carbon stabilization, Biogeochemistry 106(3), 303-309. GLBRC
201010.1111/j.1365-313X.2010.04161.xLiepman, A. H., R. Wightman, N. Geshi, S. R. Turner, and H. V. Scheller. 2010. Arabidopsis - a powerful model system for plant cell wall research, Plant J 61(6), 1107-1121. JBEI
201010.1534/genetics.110.116665Liko, D., M. K. Conway, D. S. Grunwald, and W. Heideman. 2010. Stb3 plays a role in the glucose-induced transition from quiescence to growth in Saccharomyces cerevisiae, Genetics 185(3), 797-810. GLBRC
201010.1166/jbmb.2010.1104Lindedam, J., S. Bruun, J. DeMartini, H. Jørgensen, C. Felby, B. Yang, C. E. Wyman, and J. Magid. 2010. Near Infrared Spectroscopy as a Screening Tool for Sugar Release and Chemical Composition of Wheat Straw, Journal of Biobased Materials and Bioenergy 4(4), 378-383. BESC
201010.1016/j.bpj.2009.12.2452Liu, H., J. H. Pereira, P. Adams, B. Simmons, R. Sapra, and K. Sale. 2010. The N-Terminal Ig Domain of Endoglucanase Cel9A from the Thermoacidophilic Alicyclobacillus Acidocaldarius Enhances Protein Stability, Biophysical Journal 98(3), 451a. JBEI
201010.1016/j.febslet.2010.06.041Liu, H., J. H. Pereira, P. D. Adams, R. Sapra, B. A. Simmons, and K. L. Sale. 2010. Molecular simulations provide new insights into the role of the accessory immunoglobulin-like domain of Cel9A, FEBS Lett 584(15), 3431-3435. JBEI
201010.1021/jp9117437Liu, H., K. L. Sale, B. M. Holmes, B. A. Simmons, and S. Singh. 2010. Understanding the interactions of cellulose with ionic liquids: a molecular dynamics study, J Phys Chem B 114(12), 4293-4301. JBEI
201010.1007/s12010-009-8782-xLiu, W., D. R. Bevan, and Y. H. Zhang. 2010. The family 1 glycoside hydrolase from Clostridium cellulolyticum H10 is a cellodextrin glucohydrolase, Appl Biochem Biotechnol 161(1-8), 264-273. BESC
201010.1128/AEM.00958-10Liu, W., X. Z. Zhang, Z. Zhang, and Y. H. Zhang. 2010. Engineering of Clostridium phytofermentans Endoglucanase Cel5A for improved thermostability, Appl Environ Microbiol 76(14), 4914-4917. BESC
2010Liu, Y. S., Y. H. Luo, J. O. Baker, Y. N. Zeng, M. E. Himmel, S. Smith, and S. Y. Ding. 2010. A single molecule study of cellulase hydrolysis of crystalline cellulose. In Proc. SPIE 7571, Single Molecule Spectroscopy and Imaging III, 757103 (25 February 2010).BESC
201010.2135/cropsci2009.04.0168Lorenz, A. J., J. G. Coors, C. N. Hansey, S. M. Kaeppler, and N. de Leon. 2010. Genetic Analysis of Cell Wall Traits Relevant to Cellulosic Ethanol Production in Maize ( L.), Crop Science 50(3), 842. GLBRC
201010.2135/cropsci2009.02.0086Lorenz, A. J., T. J. Gustafson, J. G. Coors, and N. d. Leon. 2010. Breeding Maize for a Bioeconomy: A Literature Survey Examining Harvest Index and Stover Yield and Their Relationship to Grain Yield, Crop Science 50(1), 1. GLBRC
201010.1104/pp.110.154278Lu, F., J. M. Marita, C. Lapierre, L. Jouanin, K. Morreel, W. Boerjan, and J. Ralph. 2010. Sequencing around 5-hydroxyconiferyl alcohol-derived units in caffeic acid O-methyltransferase-deficient poplar lignins, Plant Physiol 153(2), 569-579. GLBRC
2010Lucks, J. B., L. S. Qi, V. Mutalik, and A. P. Arkin. 2010. Engineering mRNA structural regulation of transcription using an RNA-sensing riboregulator, The FASEB Journal 24(1_supplement), 495.491-495.491. DOI.JBEI
201010.1016/j.jbiotec.2009.12.016Machina, A., A. Ponosov, and E. O. Voit. 2010. Automated piecewise power-law modeling of biological systems, J Biotechnol 149(3), 154-165. BESC
2010 10.1128/AEM.01056-10Masukawa, H., K. Inoue, H. Sakurai, C. P. Wolk, and R. P. Hausinger. 2010. Site-directed mutagenesis of the Anabaena sp. strain PCC 7120 nitrogenase active site to increase photobiological hydrogen production, Appl Environ Microbiol 76(20), 6741-6750. GLBRC
201010.1002/btpr.382Mattozzi Mde, L., and J. D. Keasling. 2010. Rationally engineered biotransformation of p-nitrophenol, Biotechnol Prog 26(3), 616-621. JBEI
201010.1016/j.carres.2010.07.034Mazumder, K., and W. S. York. 2010. Structural analysis of arabinoxylans isolated from ball-milled switchgrass biomass, Carbohydr Res 345(15), 2183-2193. BESC
201010.4195/jnrlse.2009.0021McSwiney, C. P., S. Bohm, P. R. Grace, and G. P. Robertson. 2010. Greenhouse Gas Emissions Calculator for Grain and Biofuel Farming Systems, Journal of Natural Resources and Life Sciences Education 39(1), 125. GLBRC
201010.1073/pnas.1008475107Meehan, T. D., A. H. Hurlbert, and C. Gratton. 2010. Bird communities in future bioenergy landscapes of the Upper Midwest, Proc Natl Acad Sci U S A 107(43), 18533-18538. GLBRC
201010.1021/la904032pMelnichenko, Y. B., H. Mayama, G. Cheng, and T. Blach. 2010. Monitoring phase behavior of sub- and supercritical CO2 confined in porous fractal silica with 85% porosity, Langmuir 26(9), 6374-6379. JBEI
2010Mielenz, J. R., and D. A. Hogsett. 2010. Improving microbial robutsness using systems biology. In Manual of Industrial Microbiology and Biotechnology, 3rd ed., 605-620.BESC
201010.1039/c004817hMoinuddin, S. G., M. Jourdes, D. D. Laskar, C. Ki, C. L. Cardenas, K. W. Kim, D. Zhang, L. B. Davin, and N. G. Lewis. 2010. Insights into lignin primary structure and deconstruction from Arabidopsis thaliana COMT (caffeic acid O-methyl transferase) mutant Atomt1, Org Biomol Chem 8(17), 3928-3946. BESC
201010.1007/s00267-010-9503-5Moon, H. S., J. M. Abercrombie, A. P. Kausch, and C. N. Stewart, Jr. 2010. Sustainable use of biotechnology for bioenergy feedstocks, Environ Manage 46(4), 531-538. BESC
201010.1016/j.chroma.2010.04.024Morgan, T. J., A. George, P. Alvarez-Rodriguez, M. Millan, A. A. Herod, and R. Kandiyoti. 2010. Estimating molecular masses of petroleum-derived fractions: High mass (>2000u) materials in maltenes and asphaltenes from Maya crude oil, J Chromatogr A 1217(24), 3804-3818. JBEI
201010.1021/ac100968gMorreel, K., H. Kim, F. Lu, O. Dima, T. Akiyama, R. Vanholme, C. Niculaes, G. Goeminne, D. Inze, E. Messens, J. Ralph, and W. Boerjan. 2010. Mass spectrometry-based fragmentation as an identification tool in lignomics, Anal Chem 82(19), 8095-8105. GLBRC
201010.1104/pp.110.156489Morreel, K., O. Dima, H. Kim, F. Lu, C. Niculaes, R. Vanholme, R. Dauwe, G. Goeminne, D. Inze, E. Messens, J. Ralph, and W. Boerjan. 2010. Mass spectrometry-based sequencing of lignin oligomers, Plant Physiol 153(4), 1464-1478. GLBRC
201010.1016/j.procbio.2010.03.017Myung, S., Y. Wang, and Y. H. P. Zhang. 2010. Fructose-1,6-bisphosphatase from a hyper-thermophilic bacterium Thermotoga maritima: Characterization, metabolite stability, and its implications, Process Biochemistry 45(12), 1882-1887. BESC
201010.1371/journal.pone.0015481Oikawa, A., H. J. Joshi, E. A. Rennie, B. Ebert, C. Manisseri, J. L. Heazlewood, and H. V. Scheller. 2010. An integrative approach to the identification of Arabidopsis and rice genes involved in xylan and secondary wall development, PLoS One 5(11), e15481. JBEI
201010.1073/pnas.1003584107.Olson, D. G., S. A. Tripathi, R. J. Giannone, J. Lo, N. C. Caiazza, D. A. Hogsett, R. L. Hettich, A. M. Guss, G. Dubrovsky, and L. R. Lynd. 2010. Deletion of the Cel48S cellulase from Clostridium thermocellum, Proc Natl Acad Sci U S A 107(41), 17727-17732. BESC
201010.1093/glycob/cwq106Park, B. H., T. V. Karpinets, M. H. Syed, M. R. Leuze, and E. C. Uberbacher. 2010. CAZymes Analysis Toolkit (CAT): web service for searching and analyzing carbohydrate-active enzymes in a newly sequenced organism using CAZy database, Glycobiology 20(12), 1574-1584. BESC
2010 10.1039/b819206ePatten, A. M., M. Jourdes, C. L. Cardenas, D. D. Laskar, Y. Nakazawa, B. Y. Chung, V. R. Franceschi, L. B. Davin, and N. G. Lewis. 2010. Probing native lignin macromolecular configuration in Arabidopsis thaliana in specific cell wall types: further insights into limited substrate degeneracy and assembly of the lignins of ref8, fah 1-2 and C4H::F5H lines, Mol Biosyst 6(3), 499-515. BESC
201010.1016/j.pbi.2009.12.009Pauly, M., and K. Keegstra. 2010. Plant cell wall polymers as precursors for biofuels, Curr Opin Plant Biol 13(3), 305-312. GLBRC
201010.1002/biot.200900220Peralta-Yahya, P. P., and J. D. Keasling. 2010. Advanced biofuel production in microbes, Biotechnol J 5(2), 147-162. JBEI
201010.1016/j.jsb.2010.06.018Pereira, J. H., Z. Chen, R. P. McAndrew, R. Sapra, S. R. Chhabra, K. L. Sale, B. A. Simmons, and P. D. Adams. 2010. Biochemical characterization and crystal structure of endoglucanase Cel5A from the hyperthermophilic Thermotoga maritima, J Struct Biol 172(3), 372-379. JBEI
2010Petridis, L., J. Xu, M. F. Crowley, J. C. Smith, and X. Cheng. 2010. Atomistic Simulation of Lignocellulosic Biomass and Associated Cellulosomal Protein Complexes. In ACS Symposium Series - Computational Modeling in Lignocellulosic Biofuel Production, 55-73. Eds. M. R. Nimlos, and M. F. Crowley. ACS.BESC
2010Petzold, C. J., and J. D. Keasling. 2010. Metabolic engineering of E. coli for the production of a precursor to artemisinin, an anti-malarial drug. In The Manual of Industrial Microbiology and Biotechnology, 364-379. Ed. R. Balz. ASM Press.JBEI
2010Ralph, J., and L. L. Landucci. 2010. NMR of lignins. In Lignin and Lignans; Advances in Chemistry, 137-234. CRC Press (Taylor and Francis Group).GLBRC
201010.1007/978-1-60761-783-9_1Rancour, D. M., S. K. Backues, and S. Y. Bednarek. 2010. Protein antigen expression in Escherichia coli for antibody production, Methods Mol Biol 657, 3-20. GLBRC
201010.1007/s12155-010-9085-3Rautengarten, C., E. Baidoo, J. D. Keasling, and H. V. Scheller. 2010. A Simple Method for Enzymatic Synthesis of Unlabeled and Radiolabeled Hydroxycinnamate-CoA, BioEnergy Research 3(2), 115-122. JBEI
201010.1126/science.1189468Ronald, P. C., and B. Beutler. 2010. Plant and animal sensors of conserved microbial signatures, Science 330(6007), 1061-1064. JBEI
201010.1111/j.1749-6632.2009.05261.xRonald, P., and R. Adamchak. 2010. The future of sustainable food production, Ann N Y Acad Sci 1190, 184-185. JBEI
201010.1128/AEM.02323-09Rutherford, B. J., R. H. Dahl, R. E. Price, H. L. Szmidt, P. I. Benke, A. Mukhopadhyay, and J. D. Keasling. 2010. Functional genomic study of exogenous n-butanol stress in Escherichia coli, Appl Environ Microbiol 76(6), 1935-1945. JBEI
201010.1002/ange.201000900Saar, B. G., Y. Zeng, C. W. Freudiger, Y.-S. Liu, M. E. Himmel, X. S. Xie, and S.-Y. Ding. 2010. Label-Free, Real-Time Monitoring of Biomass Processing with Stimulated Raman Scattering Microscopy, Angewandte Chemie 122(32), 5608-5611. BESC
201010.1371/journal.pone.0012947Saharay, M., H. Guo, and J. C. Smith. 2010. Catalytic mechanism of cellulose degradation by a cellobiohydrolase, CelS, PLoS One 5(10), e12947. BESC
201010.1007/s12010-009-8749-ySamuel, R., Y. Pu, B. Raman, and A. J. Ragauskas. 2010. Structural characterization and comparison of switchgrass ball-milled lignin before and after dilute acid pretreatment, Appl Biochem Biotechnol 162(1), 62-74. BESC
201010.1002/bbb.206Sannigrahi, P., A. J. Ragauskas, and G. A. Tuskan. 2010. Poplar as a feedstock for biofuels: A review of compositional characteristics, Biofuels, Bioproducts and Biorefining 4(2), 209-226. BESC
201010.1007/s12155-009-9074-6Santoro, N., S. L. Cantu, C.-E. Tornqvist, T. G. Falbel, J. L. Bolivar, S. E. Patterson, M. Pauly, and J. D. Walton. 2010. A High-Throughput Platform for Screening Milligram Quantities of Plant Biomass for Lignocellulose Digestibility, BioEnergy Research 3(1), 93-102. GLBRC
201010.1016/j.biortech.2009.09.081Sathitsuksanoh, N., Z. Zhu, T. J. Ho, M. D. Bai, and Y. H. Zhang. 2010. Bamboo saccharification through cellulose solvent-based biomass pretreatment followed by enzymatic hydrolysis at ultra-low cellulase loadings, Bioresour Technol 101(13), 4926-4929. BESC
201010.1146/annurev-arplant-042809-112315Scheller, H. V., and P. Ulvskov. 2010. Hemicelluloses, Annu Rev Plant Biol 61, 263-289. JBEI
201010.1007/s12155-010-9086-2Scheller, H. V., S. Singh, H. Blanch, and J. D. Keasling. 2010. The Joint BioEnergy Institute (JBEI): Developing New Biofuels by Overcoming Biomass Recalcitrance, BioEnergy Research 3(2), 105-107. JBEI
201010.1007/s12155-009-9069-3Schwartz, C. J., M. R. Doyle, A. J. Manzaneda, P. J. Rey, T. Mitchell-Olds, and R. M. Amasino. 2010. Natural Variation of Flowering Time and Vernalization Responsiveness in Brachypodium distachyon, BioEnergy Research 3(1), 38-46. GLBRC
201010.1371/journal.pone.0009922Scott, J. J., K. J. Budsberg, G. Suen, D. L. Wixon, T. C. Balser, and C. R. Currie. 2010. Microbial community structure of leaf-cutter ant fungus gardens and refuse dumps, PLoS One 5(3), e9922. GLBRC
201010.1089/ind.2010.0009Selig, M. J., M. P. Tucker, R. W. Sykes, K. L. Reichel, R. Brunecky, M. E. Himmel, M. F. Davis, and S. R. Decker. 2010. ORIGINAL RESEARCH: Lignocellulose recalcitrance screening by integrated high-throughput hydrothermal pretreatment and enzymatic saccharification, Industrial Biotechnology 6(2), 104-111. BESC
201010.1016/j.apcatb.2010.07.029Serrano-Ruiz, J. C., D. J. Braden, R. M. West, and J. A. Dumesic. 2010. Conversion of cellulose to hydrocarbon fuels by progressive removal of oxygen, Applied Catalysis B: Environmental 100(1-2), 184-189. GLBRC
201010.1002/btpr.325Shaikh, A. S., Y. J. Tang, A. Mukhopadhyay, H. G. Martin, J. Gin, P. I. Benke, and J. D. Keasling. 2010. Study of stationary phase metabolism via isotopomer analysis of amino acids from an isolated protein, Biotechnol Prog 26(1), 52-56. JBEI
201010.1186/1754-6834-3-12Shao, Q., S. P. Chundawat, C. Krishnan, B. Bals, C. Sousa Lda, K. D. Thelen, B. E. Dale, and V. Balan. 2010. Enzymatic digestibility and ethanol fermentability of AFEX-treated starch-rich lignocellulosics such as corn silage and whole corn plant, Biotechnol Biofuels 3, 12. GLBRC
201010.1128/AEM.00402-10Shaw, A. J., D. A. Hogsett, and L. R. Lynd. 2010. Natural competence in Thermoanaerobacter and Thermoanaerobacterium species, Appl Environ Microbiol 76(14), 4713-4719. BESC
201010.1016/j.pbi.2010.03.001Simmons, B. A., D. Loque, and J. Ralph. 2010. Advances in modifying lignin for enhanced biofuel production, Curr Opin Plant Biol 13(3), 313-320. GLBRC JBEI
2010Simmons, B. A., S. Singh, B. M. Holmes, and H. W. Blanch. 2010: Ionic liquid pretreatment. Chemical Engineering Progress, 50-55.JBEI
201010.1007/s12155-009-9075-5Slater, S., K. Keegstra, and T. J. Donohue. 2010. The US Department of Energy Great Lakes Bioenergy Research Center: Midwestern Biomass as a Resource for Renewable Fuels, BioEnergy Research 3(1), 3-5. GLBRC
201010.1007/978-1-4419-1541-2_2Slavov, G. T., and P. Zhelev. 2010. Salient Biological Features, Systematics, and Genetic Variation of Populus, Genetics and Genomics of Populus 8(8), 15-38. BESC
201010.1038/hdy.2010.73Slavov, G. T., S. Leonardi, W. T. Adams, S. H. Strauss, and S. P. DiFazio. 2010. Population substructure in continuous and fragmented stands of Populus trichocarpa, Heredity (Edinb) 105(4), 348-357. BESC
2010Smith, A. M., P. Pradhan, D. Loque, C. I. Lacayo, M. Thelen, and J. Heazlewood. 2010. Fluorescent Lifetime Imaging of Lignin in the Plant Cell Wall, Biophysical Journal 98(3, Supplement 1), 581a. DOI.JBEI
2010Song, F., J. Zhao, and S. M. Swinton. 2010. Alternative land use policies: real options with costly reversibility. In Agricultural & Applied Economics Association 2010 AAEA, Denver, Colorado, Agricultural and Applied Economics Association.GLBRC
201010.13031/2013.34903Srinivasan, R., X. Zhang, and J. Arnold. 2010. SWAT Ungauged: Hydrological Budget and Crop Yield Predictions in the Upper Mississippi River Basin, Transactions of the ASABE 53(5), 1533-1546. GLBRC
201010.1007/s12155-010-9080-8Srivastava, A. C., K. Palanichelvam, J. Ma, J. Steele, E. B. Blancaflor, and Y. Tang. 2010. Collection and Analysis of Expressed Sequence Tags Derived from Laser Capture Microdissected Switchgrass (Panicum virgatum L. Alamo) Vascular Tissues, BioEnergy Research 3(3), 278-294. BESC
201010.1038/nature08721Steen, E. J., Y. Kang, G. Bokinsky, Z. Hu, A. Schirmer, A. McClure, S. B. Del Cardayre, and J. D. Keasling. 2010. Microbial production of fatty-acid-derived fuels and chemicals from plant biomass, Nature 463(7280), 559-562. JBEI
201010.1007/s10646-009-0448-5Stewart, C. N., Jr., L. Shugart, G. S. Liu, J. Zhuang, Y. Ma, G. A. Tuskan, R. Meilan, R. W. Gentry, and G. S. Sayler. 2010. China-U.S. workshop on biotechnology of bioenergy plants, Ecotoxicology 19(1), 1-3. BESC
2010 10.1002/bit.22527Studer, M. H., J. D. DeMartini, S. Brethauer, H. L. McKenzie, and C. E. Wyman. 2010. Engineering of a high-throughput screening system to identify cellulosic biomass, pretreatments, and enzyme formulations that enhance sugar release, Biotechnol Bioeng 105(2), 231-238. BESC
2010Suen, G., F. O. Aylward, S. C. Slater, and B. S. Goldman. 2010. From genetics to genomics. In The lure of bacterial genetics: A tribute to John Roth, 257-266. Eds. S. Maloy, K. T. Hughes, and J. Casadesus. American Society for Microbiology Press.GLBRC
201010.1371/journal.pgen.1001129Suen, G., J. J. Scott, F. O. Aylward, S. M. Adams, S. G. Tringe, A. A. Pinto-Tomas, C. E. Foster, M. Pauly, P. J. Weimer, K. W. Barry, L. A. Goodwin, P. Bouffard, L. Li, J. Osterberger, T. T. Harkins, S. C. Slater, T. J. Donohue, and C. R. Currie. 2010. An insect herbivore microbiome with high plant biomass-degrading capacity, PLoS Genet 6(9), e1001129. GLBRC
201010.1038/nnano.2009.454Tetard, L., A. Passian, and T. Thundat. 2010. New modes for subsurface atomic force microscopy through nanomechanical coupling, Nat Nanotechnol 5(2), 105-109. BESC
201010.1016/j.ultramic.2010.02.035Tetard, L., A. Passian, R. H. Farahi, U. C. Kalluri, B. H. Davison, and T. Thundat. 2010. Spectroscopy and atomic force microscopy of biomass, Ultramicroscopy 110(6), 701-707. BESC
201010.1016/j.biombioe.2010.02.004Thelen, K. D., B. E. Fronning, A. Kravchenko, D. H. Min, and G. P. Robertson. 2010. Integrating livestock manure with a corn-soybean bioenergy cropping system improves short-term carbon sequestration rates and net global warming potential, Biomass and Bioenergy 34(7), 960-966. GLBRC
201010.1128/AEM.01484-10Tripathi, S. A., D. G. Olson, D. A. Argyros, B. B. Miller, T. F. Barrett, D. M. Murphy, J. D. McCool, A. K. Warner, V. B. Rajgarhia, L. R. Lynd, D. A. Hogsett, and N. C. Caiazza. 2010. Development of pyrF-based genetic system for targeted gene deletion in Clostridium thermocellum and creation of a pta mutant, Appl Environ Microbiol 76(19), 6591-6599. BESC
201010.1186/1471-2164-11-600Tyler, L., J. N. Bragg, J. Wu, X. Yang, G. A. Tuskan, and J. P. Vogel. 2010. Annotation and comparative analysis of the glycoside hydrolase genes in Brachypodium distachyon, BMC Genomics 11, 600. BESC
201010.1093/nar/gkp940Ulrich, L. E., and I. B. Zhulin. 2010. The MiST2 database: a comprehensive genomics resource on microbial signal transduction, Nucleic Acids Res 38(Database issue), D401-407. BESC
201010.1104/pp.110.154468van Parijs, F. R., K. Morreel, J. Ralph, W. Boerjan, and R. M. Merks. 2010. Modeling lignin polymerization. I. Simulation model of dehydrogenation polymers, Plant Physiol 153(3), 1332-1344. GLBRC
201010.1128/AEM.00058-10Vanden Wymelenberg, A., J. Gaskell, M. Mozuch, G. Sabat, J. Ralph, O. Skyba, S. D. Mansfield, R. A. Blanchette, D. Martinez, I. Grigoriev, P. J. Kersten, and D. Cullen. 2010. Comparative transcriptome and secretome analysis of wood decay fungi Postia placenta and Phanerochaete chrysosporium, Appl Environ Microbiol 76(11), 3599-3610. GLBRC
201010.1104/pp.110.155119Vanholme, R., B. Demedts, K. Morreel, J. Ralph, and W. Boerjan. 2010. Lignin biosynthesis and structure, Plant Physiol 153(3), 895-905. GLBRC
201010.1111/j.1365-313X.2010.04353.xVanholme, R., J. Ralph, T. Akiyama, F. Lu, J. R. Pazo, H. Kim, J. H. Christensen, B. Van Reusel, V. Storme, R. De Rycke, A. Rohde, K. Morreel, and W. Boerjan. 2010. Engineering traditional monolignols out of lignin by concomitant up-regulation of F5H1 and down-regulation of COMT in Arabidopsis, Plant J 64(6), 885-897. GLBRC
2010Vaughn, L. M., K. L. Baldwin, G. Jia, J. C. Verdonk, A. K. Strohm, and P. H. Masson. 2010. The cytoskeleton and root growth behavior. In The Plant Cytoskeleton, 307-326. Ed. B. Liu. Springer Verlag.GLBRC
201010.1016/j.copbio.2010.02.002Vega-Sanchez, M. E., and P. C. Ronald. 2010. Genetic and biotechnological approaches for biofuel crop improvement, Curr Opin Biotechnol 21(2), 218-224. JBEI
201010.1104/pp.110.159269Voelker, S. L., B. Lachenbruch, F. C. Meinzer, M. Jourdes, C. Ki, A. M. Patten, L. B. Davin, N. G. Lewis, G. A. Tuskan, L. Gunter, S. R. Decker, M. J. Selig, R. Sykes, M. E. Himmel, P. Kitin, O. Shevchenko, and S. H. Strauss. 2010. Antisense down-regulation of 4CL expression alters lignification, tree growth, and saccharification potential of field-grown poplar, Plant Physiol 154(2), 874-886. BESC
2010Voit, E. O., and C. I.C. 2010. Parameter Estimation in Canonical Biological Systems Models, International Journal of Systems and Synthetic Biology 1(1), 1-19. DOI.BESC
201010.1002/bit.22838Vuong, T. V., and D. B. Wilson. 2010. Glycoside hydrolases: catalytic base/nucleophile diversity, Biotechnol Bioeng 107(2), 195-205. BESC
201010.1073/pnas.1016436107Wang, H., U. Avci, J. Nakashima, M. G. Hahn, F. Chen, and R. A. Dixon. 2010. Mutation of WRKY transcription factors initiates pith secondary wall formation and increases stem biomass in dicotyledonous plants, Proc Natl Acad Sci U S A 107(51), 22338-22343. BESC
201010.1007/s00216-010-4057-1Wang, L., Y. Wang, and A. J. Ragauskas. 2010. A novel FRET approach for in situ investigation of cellulase-cellulose interaction, Anal Bioanal Chem 398(3), 1257-1262. BESC
201010.1105/tpc.109.073528Weng, J. K., T. Akiyama, N. D. Bonawitz, X. Li, J. Ralph, and C. Chapple. 2010. Convergent evolution of syringyl lignin biosynthesis via distinct pathways in the lycophyte Selaginella and flowering plants, Plant Cell 22(4), 1033-1045. GLBRC
2010Werling, B. P., T. D. Meehan, B. Robertson, and J. K. Tuell. 2010: 2009 Landowner Report: Plants, birds, and insects in three potential biofuel crops GLBRC White Paper. 10 pp.GLBRC
201010.1126/scisignal.2000724Wuichet, K., and I. B. Zhulin. 2010. Origins and diversification of a complex signal transduction system in prokaryotes, Sci Signal 3(128), ra50. BESC
201010.1016/j.mib.2009.12.011Wuichet, K., B. J. Cantwell, and I. B. Zhulin. 2010. Evolution and phyletic distribution of two-component signal transduction systems, Curr Opin Microbiol 13(2), 219-225. BESC
201010.1101/gr.100396.109Wurtzel, O., R. Sapra, F. Chen, Y. Zhu, B. A. Simmons, and R. Sorek. 2010. A single-base resolution map of an archaeal transcriptome, Genome Res 20(1), 133-141. JBEI
201010.1073/pnas.0910055107Xie, Z., L. E. Ulrich, I. B. Zhulin, and G. Alexandre. 2010. PAS domain containing chemoreceptor couples dynamic changes in metabolism with chemotaxis, Proc Natl Acad Sci U S A 107(5), 2235-2240. BESC
201010.1093/protein/gzq049Xu, J., and J. C. Smith. 2010. Probing the mechanism of cellulosome attachment to the Clostridium thermocellum cell surface: computer simulation of the Type II cohesin-dockerin complex and its variants, Protein Eng Des Sel 23(10), 759-768. BESC
201010.1007/s11390-010-9305-5Xu, Y. 2010. Computational Challenges in Deciphering Genomic Structures of Bacteria, Journal of Computer Science and Technology 25(1), 53-70. BESC
201010.1099/ijs.0.017731-0Yang, S. J., I. Kataeva, J. Wiegel, Y. Yin, P. Dam, Y. Xu, J. Westpheling, and M. W. Adams. 2010. Classification of Anaerocellum thermophilum strain DSM 6725 as Caldicellulosiruptor bescii sp. nov, Int J Syst Evol Microbiol 60(Pt 9), 2011-2015. BESC
201010.1186/1471-2180-10-135Yang, S., D. A. Pelletier, T. Y. Lu, and S. D. Brown. 2010. The Zymomonas mobilis regulator hfq contributes to tolerance against multiple lignocellulosic pretreatment inhibitors, BMC Microbiol 10, 135. BESC
201010.1073/pnas.0914506107Yang, S., M. L. Land, D. M. Klingeman, D. A. Pelletier, T. Y. Lu, S. L. Martin, H. B. Guo, J. C. Smith, and S. D. Brown. 2010. Paradigm for industrial strain improvement identifies sodium acetate tolerance loci in Zymomonas mobilis and Saccharomyces cerevisiae, Proc Natl Acad Sci U S A 107(23), 10395-10400. BESC
201010.1042/BJ20100238Yang, T., and M. Bar-Peled. 2010. Identification of a novel UDP-sugar pyrophosphorylase with a broad substrate specificity in Trypanosoma cruzi, Biochem J 429(3), 533-543. BESC
201010.1042/BJ20100315Yang, T., M. Echols, A. Martin, and M. Bar-Peled. 2010. Identification and characterization of a strict and a promiscuous N-acetylglucosamine-1-P uridylyltransferase in Arabidopsis, Biochem J 430(2), 275-284. BESC
201010.1007/s11240-010-9826-1Yang, X., C.-Y. Ye, Z.-M. Cheng, T. J. Tschaplinski, S. D. Wullschleger, W. Yin, X. Xia, and G. A. Tuskan. 2010. Genomic aspects of research involving polyploid plants, Plant Cell, Tissue and Organ Culture (PCTOC) 104(3), 387-397. BESC
201010.4271/2010-01-2164Yang, Y., J. E. Dec, N. Dronniou, and B. Simmons. 2010. Characteristics of Isopentanol as a Fuel for HCCI Engines, SAE International Journal of Fuels and Lubricants 3(2), 725-741. JBEI
201010.1016/j.molcatb.2010.01.015Ye, X., J. Rollin, and Y.-H. P. Zhang. 2010. Thermophilic a-glucan phosphorylase from Clostridium thermocellum: Cloning, characterization and enhanced thermostability, Journal of Molecular Catalysis B: Enzymatic 65(1-4), 110-116. BESC
201010.1007/s12155-009-9072-8Yilmaz, L. S., W. S. Kontur, A. P. Sanders, U. Sohmen, T. J. Donohue, and D. R. Noguera. 2010. Electron Partitioning During Light- and Nutrient-Powered Hydrogen Production by Rhodobacter sphaeroides, BioEnergy Research 3(1), 55-66. GLBRC
201010.1038/nmeth1210-943Yilmaz, S., M. Allgaier, and P. Hugenholtz. 2010. Multiple displacement amplification compromises quantitative analysis of metagenomes, Nat Methods 7(12), 943-944. JBEI
201010.1371/journal.pone.0014021Yin, T., X. Zhang, L. Gunter, R. Priya, R. Sykes, M. Davis, S. D. Wullschleger, and G. A. Tuskan. 2010. Differential detection of genetic Loci underlying stem and root lignin content in Populus, PLoS One 5(11), e14021. BESC
2010Yin, Y., D. Mohnen, I. Gelineo-Albersheim, Y. Xu, and M. G. Hahn. 2010. Glycosyltransferases of the GT8 Family. In Annual Plant Reviews: Plant Polysaccharides, Biosynthesis and Bioengineering. Ed. P. Ulvskov. Wiley-Blackwell.BESC
201010.1104/pp.110.154229Yin, Y., H. Chen, M. G. Hahn, D. Mohnen, and Y. Xu. 2010. Evolution and function of the plant cell wall synthesis-related glycosyltransferase family 8, Plant Physiol 153(4), 1729-1746. BESC
201010.1073/pnas.0911237107Yin, Y., H. Zhang, V. Olman, and Y. Xu. 2010. Genomic arrangement of bacterial operons is constrained by biological pathways encoded in the genome, Proc Natl Acad Sci U S A 107(14), 6310-6315. BESC
201010.1128/JB.01254-09Young, M., V. Artsatbanov, H. R. Beller, G. Chandra, K. F. Chater, L. G. Dover, E. B. Goh, T. Kahan, A. S. Kaprelyants, N. Kyrpides, A. Lapidus, S. R. Lowry, A. Lykidis, J. Mahillon, V. Markowitz, K. Mavromatis, G. V. Mukamolova, A. Oren, J. S. Rokem, M. C. Smith, D. I. Young, and C. L. Greenblatt. 2010. Genome sequence of the Fleming strain of Micrococcus luteus, a simple free-living actinobacterium, J Bacteriol 192(3), 841-860. JBEI
201010.1007/s12155-010-9079-1Zeng, Y., B. G. Saar, M. G. Friedrich, F. Chen, Y.-S. Liu, R. A. Dixon, M. E. Himmel, X. S. Xie, and S.-Y. Ding. 2010. Imaging Lignin-Downregulated Alfalfa Using Coherent Anti-Stokes Raman Scattering Microscopy, BioEnergy Research 3(3), 272-277. BESC
201010.1021/jf103354xZhang, A., F. Lu, C. Liu, and R. C. Sun. 2010. Isolation and characterization of lignins from Eucalyptus tereticornis (12ABL), J Agric Food Chem 58(21), 11287-11293. GLBRC
201010.1002/bit.22811Zhang, J., and L. R. Lynd. 2010. Ethanol production from paper sludge by simultaneous saccharification and co-fermentation using recombinant xylose-fermenting microorganisms, Biotechnol Bioeng 107(2), 235-244. BESC
201010.1016/j.biortech.2010.01.152Zhang, X. Z., N. Sathitsuksanoh, and Y. H. Zhang. 2010. Glycoside hydrolase family 9 processive endoglucanase from Clostridium phytofermentans: heterologous expression, characterization, and synergy with family 48 cellobiohydrolase, Bioresour Technol 101(14), 5534-5538. BESC
201010.1007/s00253-009-2231-1Zhang, X. Z., Z. Zhang, Z. Zhu, N. Sathitsuksanoh, Y. Yang, and Y. H. Zhang. 2010. The noncellulosomal family 48 cellobiohydrolase from Clostridium phytofermentans ISDg: heterologous expression, characterization, and processivity, Appl Microbiol Biotechnol 86(2), 525-533. BESC
201010.1016/j.envsoft.2010.05.012Zhang, X., and R. Srinivasan. 2010. GIS-based spatial precipitation estimation using next generation radar and raingauge data, Environmental Modelling & Software 25(12), 1781-1788. GLBRC
201010.1111/j.1757-1707.2010.01046.xZhang, X., R. C. Izaurralde, D. Manowitz, T. O. West, W. M. Post, A. M. Thomson, V. P. Bandaru, J. Nichols, and J. R. Williams. 2010. An integrative modeling framework to evaluate the productivity and sustainability of biofuel crop production systems, GCB Bioenergy 2(5), 258-277. GLBRC
201010.1002/elsc.201000011Zhang, X.-Z., and Y.-H. P. Zhang. 2010. One-step production of biocommodities from lignocellulosic biomass by recombinant cellulolytic Bacillus subtilis: Opportunities and challenges, Engineering in Life Sciences 10(5), 398-406. BESC
201010.1002/bit.22630Zhang, Y. H. 2010. Production of biocommodities and bioelectricity by cell-free synthetic enzymatic pathway biotransformations: challenges and opportunities, Biotechnol Bioeng 105(4), 663-677. BESC
201010.1016/j.ijhydene.2010.07.132Zhang, Y. H. P. 2010. Renewable carbohydrates are a potential high-density hydrogen carrier, International Journal of Hydrogen Energy 35(19), 10334-10342. BESC
201010.1016/j.copbio.2010.05.005Zhang, Y. H., J. Sun, and J. J. Zhong. 2010. Biofuel production by in vitro synthetic enzymatic pathway biotransformation, Curr Opin Biotechnol 21(5), 663-669. BESC
2010Zhang, Y.-H., Z. Zhu, J. Rollin, and N. Sathisuksanoh. 2010. Advances in cellulose solvent- and organic solvent-based lignocellulose fractionation (COSLIF). In ACS Symposium Series 1033: 365-379 (Cellulose solvents: For analysis, shaping and chemical modification). Oxford University Press.BESC
201010.1073/pnas.1009170107Zhao, Q., H. Wang, Y. Yin, Y. Xu, F. Chen, and R. A. Dixon. 2010. Syringyl lignin biosynthesis is directly regulated by a secondary cell wall master switch, Proc Natl Acad Sci U S A 107(32), 14496-14501. BESC
201010.1111/j.1365-313X.2010.04223.xZhao, Q., L. Gallego-Giraldo, H. Wang, Y. Zeng, S. Y. Ding, F. Chen, and R. A. Dixon. 2010. An NAC transcription factor orchestrates multiple features of cell wall development in Medicago truncatula, Plant J 63(1), 100-114. BESC
201010.1021/pr100249cZhou, C., Y. Yin, P. Dam, and Y. Xu. 2010. Identification of novel proteins involved in plant cell-wall synthesis based on protein-protein interaction data, J Proteome Res 9(10), 5025-5037. BESC
201010.1186/1471-2180-10-69Zhou, F., H. Chen, and Y. Xu. 2010. GASdb: a large-scale and comparative exploration database of glycosyl hydrolysis systems, BMC Microbiol 10, 69. BESC
201010.1002/bit.22814Zhou, W., Y. Xu, and H. B. Schuttler. 2010. Cellulose hydrolysis in evolving substrate morphologies III: time-scale analysis, Biotechnol Bioeng 107(2), 224-234. BESC
201010.1093/mp/ssq023Zhu, X., S. Pattathil, K. Mazumder, A. Brehm, M. G. Hahn, S. P. Dinesh-Kumar, and C. P. Joshi. 2010. Virus-induced gene silencing offers a functional genomics platform for studying plant cell wall formation, Mol Plant 3(5), 818-833. BESC
201010.1074/jbc.M110.137315Ziebell, A., K. Gracom, R. Katahira, F. Chen, Y. Pu, A. Ragauskas, R. A. Dixon, and M. Davis. 2010. Increase in 4-coumaryl alcohol units during lignification in alfalfa (Medicago sativa) alters the extractability and molecular weight of lignin, J Biol Chem 285(50), 38961-38968. BESC
200910.3390/molecules14114758Achyuthan, K. E., P. D. Adams, B. A. Simmons, and A. K. Singh. 2009. Spectroscopic analyses of the biofuels-critical phytochemical coniferyl alcohol and its enzyme-catalyzed oxidation products, Molecules 14(11), 4758-4778. JBEI
200910.2174/138620709788923773Achyuthan, K., J. McClain, and D. Raj. 2009. Orthogonal, Spectroscopic High Throughput Screening of Laccase-Catalyzed p-Cresol Oxidation, Combinatorial Chemistry & High Throughput Screening 12(7), 678-689. JBEI
200910.1111/j.1365-3040.2009.01992.xAllen, D. K., I. G. Libourel, and Y. Shachar-Hill. 2009. Metabolic flux analysis in plants: coping with complexity, Plant Cell Environ 32(9), 1241-1257. GLBRC
200910.1111/j.1365-313X.2008.03771.xAllen, D. K., J. B. Ohlrogge, and Y. Shachar-Hill. 2009. The role of light in soybean seed filling metabolism, Plant J 58(2), 220-234. GLBRC
2009Awai, K., S. Lechno-Yossef, and C. P. Wolk. 2009. Heterocyst envelope glycolipids. In Lipids in Photosynthesis, 179-202. Eds. H. Wada, and N. Murata. Springer Netherlands.GLBRC
200910.1007/978-1-60761-214-8_5Balan, V., B. Bals, S. P. Chundawat, D. Marshall, and B. E. Dale. 2009. Lignocellulosic biomass pretreatment using AFEX, Methods Mol Biol 581, 61-77. GLBRC
200910.1002/btpr.160Balan, V., C. Sousa Lda, S. P. Chundawat, D. Marshall, L. N. Sharma, C. K. Chambliss, and B. E. Dale. 2009. Enzymatic digestibility and pretreatment degradation products of AFEX-treated hardwoods (Populus nigra), Biotechnol Prog 25(2), 365-375. GLBRC
200910.1104/pp.109.137737Bates, P. D., T. P. Durrett, J. B. Ohlrogge, and M. Pollard. 2009. Analysis of acyl fluxes through multiple pathways of triacylglycerol synthesis in developing soybean embryos, Plant Physiol 150(1), 55-72. GLBRC
200910.1021/ja808537jBinder, J. B., and R. T. Raines. 2009. Simple chemical transformation of lignocellulosic biomass into furans for fuels and chemicals, J Am Chem Soc 131(5), 1979-1985. GLBRC
200910.1007/s12155-009-9048-8Burris, J. N., D. G. J. Mann, B. L. Joyce, and C. N. Stewart. 2009. An Improved Tissue Culture System for Embryogenic Callus Production and Plant Regeneration in Switchgrass (Panicum virgatum L.), BioEnergy Research 2(4), 267-274. BESC
200910.1016/j.carres.2009.05.021Caffall, K. H., and D. Mohnen. 2009. The structure, function, and biosynthesis of plant cell wall pectic polysaccharides, Carbohydr Res 344(14), 1879-1900. BESC
200910.1093/mp/ssp062Caffall, K. H., S. Pattathil, S. E. Phillips, M. G. Hahn, and D. Mohnen. 2009. Arabidopsis thaliana T-DNA mutants implicate GAUT genes in the biosynthesis of pectin and xylan in cell walls and seed testa, Mol Plant 2(5), 1000-1014. BESC
200910.1603/022.038.0110Caldera, E. J., M. Poulsen, G. Suen, and C. R. Currie. 2009. Insect Symbios