JBEI logo

 

Management
Partners
For Industry
Contacts
sidebar image

Deconstruction Division

 

Publications

  1. Achyuthan, K. E., A. M. Achyuthan, et al. (2010). "Supramolecular Self-Assembled Chaos: Polyphenolic Lignin's Barrier to Cost-Effective Lignocellulosic Biofuels." Molecules 15(12): 8641-8688.
  2. Achyuthan, K. E., P. D. Adams, et al. (2010). "Hitherto Unrecognized Fluorescence Properties of Coniferyl Alcohol." Molecules 15(3): 1645-1667.
  3. Achyuthan, K. E., P. D. Adams, et al. (2009). "Spectroscopic Analyses of the Biofuels-Critical Phytochemical Coniferyl Alcohol and Its Enzyme-Catalyzed Oxidation Products." Molecules 14(11): 4758-4778.
  4. Allgaier, M., A. Reddy, et al. (2010). "Targeted Discovery of Glycoside Hydrolases from a Switchgrass-Adapted Compost Community." Plos One 5(1): e8812.
  5. Arora, R., C. Manisseri, et al. (2010). "Monitoring and Analyzing Process Streams Towards Understanding Ionic Liquid Pretreatment of Switchgrass (Panicum virgatum L.)." Bioenergy Research 3(2): 134-145.
  6. Bharadwaj, R., Z. Chen, et al. (2010). "Microfluidic Glycosyl Hydrolase Screening for Biomass-to-Biofuel Conversion." Analytical Chemistry 82(22): 9513–9520.
  7. Bharadwaj, R., A. Wong, et al. (2011). "High-throughput enzymatic hydrolysis of lignocellulosic biomass via in-situ regeneration." Bioresource Technology 102(2): 1329-1337.
  8. Blanch, H. W. (2011). "Bioprocessing for biofuels." Current Opinion in Biotechnology 23: 1-6.*
  9. Blanch, H. W., P. D. Adams, et al. (2008). "Addressing the need for alternative transportation fuels: The Joint BioEnergy Institute." ACS Chemical Biology 3(1): 17-20.
  10. Blanch, H. W., B. A. Simmons, et al. (2011). "Biomass deconstruction to sugars." Biotechnology Journal 6(9): 1086-1102.
  11. Bokinsky, G., P. Peralta-Yahya, et al. (2011). "Synthesis of three advanced biofuels from ionic liquid-pretreated switchgrass using engineered." Proceedings of the National Academy of Sciences.*
  12. Brennan, T. C. R., S. Datta, et al. (2010). "Recovery of Sugars from Ionic Liquid Biomass Liquor by Solvent Extraction." Bioenergy Research 3(2): 123-133.
  13. Cetinkol, O. P., D. C. Dibble, et al. (2010). "Understanding the impact of ionic liquid pretreatment on eucalyptus." Biofuels 1(1): 33-46.
  14. Chandrasekaran, A., R. Bharadwaj, et al. (2010). "A Microscale Platform For Integrated Cell-Free Expression And Activity Screening Of Cellulases." Journal of Proteome Research 9(11): 5677-5683.
  15. Cheng, G., Z. Liu, et al. (2011). "Neutron Reflectometry and QCM-D Study of the Interaction of Cellulases with Films of Amorphous Cellulose." Biomacromolecules 12(6): 2216-2224.
  16. Cheng, G., P. Varanasi, et al. (2011). "Transition of cellulose crystalline structure and surface morphology of biomass as a function of ionic liquid pretreatment and its relation to enzymatic hydrolysis." Biomacromolecules 12(4): 933-941.
  17. Chhabra, S. R., G. Butland, et al. (2011). "Generalized Schemes for High-Throughput Manipulation of the Desulfovibrio vulgaris Genome." Applied and Environmental Microbiology 77(21): 7595-7604.
  18. Chhabra, S. R., M. P. Joachimiak, et al. (2011). "Towards a Rigorous Network of Protein-Protein Interactions of the Model Sulfate Reducer Desulfovibrio vulgaris Hildenborough." PLoS One 6(6): e21470.
  19. Chuck, G. S., C. Tobias, et al. (2011). "Overexpression of the maize Corngrass1 microRNA prevents flowering, improves digestibility, and increases starch content of switchgrass." Proceedings of National Academy of Sciences 108(42): 17550-17555.
  20. Datta, S., B. Holmes, et al. (2010). "Ionic liquid tolerant hyperthermophilic cellulases for biomass pretreatment and hydrolysis." Green Chemistry 12(2): 338-345.
  21. Datta, S. and R. Sapra. (2011). Cellulases and Hemicellulases for Biomass Degradation: An Introduction. Chemical and Biochemical Catalysis for Next Generation Biofuels. B. A. Simmons, Royal Society of Chemistry: 115-135.
  22. DeAngelis, K., P. D'Haeseleer, et al. (2011). "Complete genome sequence of Enterobacter lignolyticus SCF1." Standards in Genomic Sciences 5(1): 69-85.
  23. DeAngelis, K. M., M. Allgaier, et al. (2011). "Characterization of Trapped Lignin-Degrading Microbes in Tropical Forest Soil." PLoS ONE 6(4): e19306.
  24. DeAngelis, K. M., J. M. Gladden, et al. (2010). "Strategies for Enhancing the Effectiveness of Metagenomic-based Enzyme Discovery in Lignocellulolytic Microbial Communities." Bioenergy Research 3(2): 146-158.
  25. DeAngelis, K. M., C. H. Wu, et al. (2011). "PCR amplification-independent methods for detection of microbial communities by the high-density microarray PhyloChip." Applied and Environmental Microbiology 77(18): 6313-6322.
  26. Dibble, D., C. Li , et al. (2011). "A facile method for the recovery of ionic liquid and lignin from biomass pretreatment." Green Chemistry 13(11): 3255-3264.
  27. George, A., K. Tran, et al. (2011). "The effect of ionic liquid cation and anion combinations on the macromolecular structure of lignins." Green Chemistry.*
  28. Gladden, J. B., S. A. Eichorst, et al. (2011). "Substrate Perturbation Alters the Glycoside Hydrolase Activities and Community Composition of Switchgrass-Adapted Bacterial Consortia." Biotechnology and Bioengineering.*
  29. Gladden, J. M., M. Allgaier, et al. (2011). "Glycoside hydrolase activities of thermophilic bacterial consortia adapted to switchgrass." Applied and Environmental Microbiology 77(16): 5804-5812.
  30. Han, J., S. Singh, et al. (2010). "Chemical profiling of the plant cell wall through Raman microspectroscopy in 2010 IEEE International Symposium on Biomedical Imaging: From Nano to Macro." IEEE ISBI: 1273-1276.
  31. Kent, M. S., G. Cheng, et al. (2010). "Study of Enzymatic Digestion of Cellulose by Small Angle Neutron Scattering." Biomacromolecules 11(2): 357-368.
  32. Kent, M. S., J. K. Murton, et al. (2009). "Effect of Agitation/Flow on the Enzymatic Digestion of Cellulose: a Structural Study by SANS." Polymer Preprints, ACS-PMSE symposium on Small Angle Neutron Scattering from Polymers and Complex Fluids, 238th ACS National Meeting, Washington DC, Aug 16-20, 2009: 2.
  33. Klein-Marcuschamer, D., B. Holmes, et al. (2011). Biofuel Economics. Plant Biomass Conversion. E. Hood, R. Powell and N. P. New York, John Wiley & Sons: 329-348
  34. Klein-Marcuschamer, D., P. Oleskowicz-Popiel, et al. (2010). "Technoeconomic analysis of biofuels: A wiki-based platform for lignocellulosic biorefineries." Biomass & Bioenergy 34(12): 1914-1921.
  35. Klein-Marcuschamer, D., P. Oleskowicz-Popiel, et al. (2011). "The challenge of enzyme cost in the production of lignocellulosic biofuels." Biotechnology and Bioengineering.*
  36. Klein-Marcuschamer, D., B. A. Simmons, et al. (2011). "Techno-economic analysis of a lignocellulosic ethanol biorefinery with ionic liquid pre-treatment." Biofuels, Bioproducts and Biorefining 5(5): 562-569.
  37. Lacayo, C. I., A. J. Malkin, et al. (2010). "Imaging cell wall architecture in single Zinnia elegans tracheary elements." Plant Physiology 154(1): 121-133.
  38. Li, C., G. Cheng, et al. (2011). "Influence of physico-chemical changes on enzymatic digestibility of ionic liquid and AFEX pretreated corn stover." Bioresource Technology 102(13): 6928-6936.
  39. Li, C., B. Knierim, et al. (2010). "Comparison of dilute acid and ionic liquid pretreatment of switchgrass: Biomass recalcitrance, delignification and enzymatic saccharification." Bioresource Technology 101(13): 4900-4906.
  40. Liu, H., J. H. Pereira, et al. (2010). "Molecular simulations provide new insights into the role of the accessory immunoglobulin-like domain of Cel9A." FEBS Letters 584(15): 3431-3435.
  41. Liu, H., K. L. Sale, et al. (2010). "Understanding the interactions of cellulose with ionic liquids: a molecular dynamics study." Journal of Physical Chemistry B 114(12): 4293-4301.
  42. Liu, H., K. L. Sale, et al. (2011). "Molecular Dynamics Study of Polysaccharides in Binary Solvent Mixtures of an Ionic Liquid and Water." Journal of Physical Chemistry B 115(34): 10251-10258.
  43. Loque, D., A. Eudes, et al. (2011). Biomass Availability and Sustainability for BioFuels. Chemical and Biochemical Catalysis for Next Generation Biofuels. B. A. Simmons, Royal Society of Chemistry: 5-32.
  44. Miller, C. S., B. J. Baker, et al. (2011). "EMIRGE: Reconstruction of full length ribosomal genes from microbial community short read sequencing data." Genome Biology 12(5): R44.
  45. Ouellet, M., S. Datta, et al. (2011). "Impact of ionic liquid pretreated plant biomass on Saccharomyces cerevisiae growth and biofuel production." Green Chemistry 13(10): 2743-2749.
  46. Park, J. I., M. S. Kent, et al. (2011). "Enzymatic hydrolysis of cellulose by the cellobiohydrolase domain of CelB from the hyperthermophilic bacterium Caldicellulosiruptor saccharolyticus." Bioresource Technology 102(10): 5988-5994.
  47. Pereira, J. H., Z. Chen, et al. (2010). "Biochemical characterization and crystal structure of endoglucanase Cel5A from the hyperthermophilic Thermotoga maritima." Journal of Structural Biology 172(3): 372-379.
  48. Pereira, J. H., R. Sapra, et al. (2009). "Structure of endoglucanase Cel9A from the thermoacidophilic Alicyclobacillus acidocaldarius." Acta Crystallographica Section D Biological Crystallography 65(Pt 8): 744-750.
  49. Reddy, A. P., M. Allgaier, et al. (2011). "Bioenergy feedstock-specific enrichment of microbial populations during high-solids thermophilic deconstruction." Biotechnology and Bioengineering 108(9): 2088-2098.
  50. Reindl, W., K. Deng, et al. (2011). "Colloid-based multiplexed screening for plant biomass-degrading glycoside hydrolase activities in microbial communities." Energy & Environmental Science 4(8): 2884-2893.
  51. Rezaei, F., L. D. Joh, et al. (2011). "Selection of Conditions for Cellulase and Xylanase Extraction from Switchgrass Colonized by Acidothermus cellulolyticus." Applied Biochemistry and Biotechnology 164(6): 793-803.
  52. Scheller, H. V., S. Singh, et al. (2010). "The Joint BioEnergy Institute (JBEI): Developing New Biofuels by Overcoming Biomass Recalcitrance." BioEnergy Research 3(2): 105-107.
  53. Shepherd, M., J. Bartle, et al. (2011). "Eucalypts as a biofuel feedstock." Biofuels 2(6): 639-657.
  54. Simmons, B. A. (2011). "Opportunities and challenges in advanced biofuel production: the importance of synthetic biology and combustion science." Biofuels 2(1): 5-7.
  55. Simmons, B. A. (2011). "Synthetic enzymes: catalysis on demand." Microbial Biotechnology 4(2): 130-131.
  56. Simmons, B. A. (2011). Bioenergy from Plants and Plant Residues. Plant Biotechnology and Agriculture - Prospects for the 21st Century. A. Altman and P. M. Hasegawa. Oxford, Academic Press: 495-506.*
  57. Simmons, B. A. (2011). Introduction to Catalysis for Biofuels. Chemical and Biochemical Catalysis for Next Generation Biofuels. B. A. Simmons. Cambridge Royal Society of Chemistry: 1-4.
  58. Simmons, B. A. (2011). "Rethinking renewable energy in Japan." Biofuels 2(4): 365–367.
  59. Simmons, B. A., D. Loque, et al. (2008). "Next-generation biomass feedstocks for biofuel production." Genome Biology 9(12): 242.
  60. Simmons, B. A., D. Loque, et al. (2010). "Advances in modifying lignin for enhanced biofuel production." Current Opinion in Plant Biology 13(3): 313-320.
  61. Simmons, B. A., S. Singh, et al. (2010). "Ionic liquid pretreatment." Chemical Engineering Progress: 50-55.
  62. Singer, S. W., A. P. Reddy, et al. (2011). "Enrichment, Isolation and Characterization of Fungi Tolerant to 1-Ethyl-3-Methylimadazolium Acetate." Journal of Applied Microbiology 110(4): 1023-1031.
  63. Singh, S., B. A. Simmons, et al. (2009). "Visualization of biomass solubilization and cellulose regeneration during ionic liquid pretreatment of switchgrass." Biotechnology and Bioengineering 104(1): 68-75.
  64. Sun, L., B. A. Simmons, et al. (2011). "Understanding tissue specific compositions of bioenergy feedstocks through hyperspectral Raman imaging." Biotechnology and Bioengineering 108(2): 286-295.
  65. Sun, L., P. Varanasi, et al. (2011). "Rapid determination of syringyl: Guaiacyl ratios using FT-Raman spectroscopy." Biotechnology and Bioengineering.*
  66. Tang, Y. J., R. Sapra, et al. (2009). "Analysis of metabolic pathways and fluxes in a newly discovered thermophilic and ethanol-tolerant Geobacillus strain." Biotechnology and Bioengineering 102(5): 1377-1386.
  67. Varanasi, P., L. Sun, et al. (2011). Quantifying Bio-Engineering: The Importance of Biophysics in Biofuel Research. Biofuel's Engineering Process Technology. M. A. dos Santos Bernades, InTech: 493-520.
  68. Wurtzel, O., R. Sapra, et al. (2010). "A single-base resolution map of an archaeal transcriptome." Genome Research 20(1): 133-141.
  69. Yang, Y., J. Dec, et al. (2010). "Characteristics of Isopentanol as a Fuel for HCCI Engines." Society of Automobile Engineers International Journal of Fuels and Lubricants 3(2): 725-741.
  70. Yilmaz, S., M. Allgaier, et al. (2010). "Multiple displacement amplification compromises quantitative analysis of metagenomes." Nature Methods 7(12): 943-944.
  71. Zhang, T., S. Datta, et al. (2011). "Identification of a haloalkaliphilic and thermostable cellulase with improved ionic liquid tolerance." Green Chemistry 13(8): 2083-2090.

 

*Indicates publications "in press"

DOE BioEnergy Research Centers