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Genomic Science Program

DOE Bioenergy Research Centers (2007-2017):
Key Advances for Lignocellulosic Biofuels Production

These three BRCs have generated a number of important breakthroughs toward developing new dedicated bioenergy feedstocks and new products from renewable biomass. These significant achievements include (1) demonstrating that lignin composition and deposition can be genetically engineered to reduce plant cell wall recalcitrance without impacting plant viability; (2) developing effective, commercially adaptable biomass pretreatments to lower costs; (3) discovering novel microbes and enzymatic pathways for more efficient deconstruction of lignocellulosic biomass; (4) conducting proof-of-concept research for consolidated bioprocessing (i.e., the production of ethanol and other biofuels by naturally cellulolytic microbes directly from nonpretreated biomass); (5) metabolically engineering microorganisms and plants for biological production of numerous advanced biofuels or their immediate precursors; and (6) identifying hundreds of new plant genes and developing an understanding of their role in cell wall biosynthesis.

These and other BRC breakthroughs are highlighted below. Through intellectual property licensing agreements, partnerships, and targeted collaborative affiliations, DOE’s BRCs are working to speed the translation of basic research results to industry for contributions to clean energy.

Improved Biomass

Overcome the natural resistance of plant biomass to microbial and chemical hydrolysis through the development and optimization of high-yield, sustainable feedstocks that are easily converted into biofuels.

Advances and Results

  • Discovered that the major plant cell wall polymers (i.e., cellulose, lignin, hemicellulose, and pectin) all contribute to recalcitrance, information that is assisting in fine-tuning cell wall properties to render biomass more amenable to biofuel conversion (Kalluri, Yin, and Davison 2014; Baxter et al. 2014; Biswal et al. 2015).
  • Conducted a comprehensive systems biology study of Populus and switchgrass to identify natural variants with modified composition; findings advance opportunities for rapid discovery of specific genes best suited for producing biofuel from biomass planted in different environments (Serba et al. 2015; Muchero et al. 2015; Evans et al. 2014).
  • Revealed robust, reduced-recalcitrance phenotypes and better growth with field trials of high-performing Populus and switchgrass lines, demonstrating that transgenic feedstocks can be maintained in the field (Baxter et al. 2014).
  • Manipulated transcription factors to reduce cell wall recalcitrance and enhance polysaccharide accumulation, with no significant impacts on plant growth and development (Vega-Sánchez et al. 2015).
  • Identified and characterized several novel plant nucleotide sugar transporters that are powerful tools for cell wall engineering (Ebert et al. 2015).
  • Coupled metabolomics analysis with genetic information to identify metabolite-gene associations, yielding critical insights into biomass formation in Populus (Payyavula et al. 2014).
  • Modified the lignin biosynthetic pathway to enable design of plant cell walls that are easier and cheaper to convert into fuels and chemicals (Wilkerson et al. 2014).
  • Altered lignin content and composition in planta to enhance biomass deconstructibility, significantly reducing the amount of energy required for higher sugar yields from pretreatment (Eudes et al. 2016; Scullin et al. 2015).


Increase the energy efficiency and cost-effectiveness of processes for deconstructing lignocellulosic biomass into its constituent sugars, while minimizing the formation of inhibitors and using as few chemicals as possible.

Advances and Results

  • Developed and demonstrated an affordable, scalable biomass deconstruction technology based on ionic liquids for a wide range of single and blended feedstocks (Sun et al. 2015; Papa et al. 2015; Li et al. 2015).
  • Discovered a renewable solvent (gamma-valerolactone) derived from biomass that can produce sugar and lignin streams from multiple biomass sources without expensive biomass-degrading enzymes (Alonso, Wettstein, and Dumesic 2013; Luterbacher et al. 2014; Luterbacher et al. 2015).
  • Developed a novel pretreatment method (e.g., cosolvent-enhanced lignocellulosic fractionation) that greatly reduces enzyme loadings compared to traditional dilute acid pretreatment and significantly increases biofuel yields (Ngyuyen et al. 2015a; Nguyen et al. 2015b; Smith et al. 2015).
  • Optimized biocatalyst-feedstock combinations to achieve high solubilization, demonstrating the potential for biomass processing with little or no thermochemical pretreatment (Paye et al. 2016).
  • Identified enzymes that can enhance the hydrolyzation of multiple polysaccharides derived from plant cell walls into fermentable sugars (Deng et al. 2014; Takasuka et al. 2014; Deng et al. 2015a; Deng et al. 2015b; Walker et al. 2015).
  • Conducted targeted bioprospecting in unique environments for novel enzymes, revealing diverse microbial communities that potentially could efficiently deconstruct plant polysaccharides (Vishnivetskaya et al. 2014; Yu et al. 2015; Simmons et al. 2014).
  • Discovered and optimized a cellulase mixture that tolerates ionic liquids, which could provide a new, more efficient and tunable biomass pretreatment method (Gladden et al. 2014; Shi et al. 2013).
  • Discovered that Clostridium thermocellum (anaerobic, thermophilic microorganism) performs demonstrably better than industry-standard fungal cellulases; findings are being used to develop optimal systems for breaking down lignocellulosic biomass (Paye et al. 2016; Xu et al. 2016).
  • With Mascoma Inc., engineered yeasts that more efficiently convert cellulose to sugar than previous strains; these yeasts are used in about 20% of corn ethanol production, with C5-utilizing strains now available for cellulosic ethanol production (Guilliams et al. 2016; Henningsen et al. 2015).


Develop improved methods of converting plant sugars into fuels, along with synthesis processes for new fuels in addition to ethanol.

Advances and Results

  • Used genomic knowledge of how various plant-derived compounds negatively impact the performance of biofuel microbes to engineer strains with increased tolerance to individual inhibitors, thereby increasing biomass conversion rates and ethanol yields (Piotrowski et al. 2014; Piotrowski et al. 2015a; Piotrowski et al. 2015b; Dickinson et al. 2016; Pisithkul et al. 2015; Keating et al. 2014; Parreiras et al. 2014).
  • Elucidated the mechanisms of ionic liquid tolerance in microbes, which could advance the development of gene expression systems for tolerance mechanisms of other toxic compounds (Ruegg et al. 2014; Frederix et al. 2014; Dickinson et al. 2016).
  • Used targeted proteomics for biofuel metabolic pathway and protein monitoring, proving its use as an efficient quantitative analysis method (Alonso-Gutierrez et al. 2015; Dickinson et al. 2016).
  • Optimized production of select advanced biofuels using model hydrolysates (Kirby et al. 2015; Kang et al. 2015; Foo et al. 2014).
  • Developed a consolidated process for pretreatment, saccharification, and fermentation using ionic liquids, with potential to significantly reduce biofuel production costs (Xu et al. 2016; Liszka et al. 2016; Frederix et al. 2016).
  • Developed the capability to genetically engineer both C. thermocellum and Caldicellulosiruptor bescii (thermophilic, cellulolytic anaerobes) to produce more desired biofuels and bioproducts (Chung et al. 2013; Olson, Sparling, and Lynd 2015).
  • Efficiently converted mixed lignocellulosic feedstocks into isopentenol and other advanced biofuels using ionic liquids, offering a solution for overcoming biomass supply challenges (Shi et al. 2015).

Lignin as a Valuable Resource Instead of a Waste Product

  • Converted lignin into “bionic liquids,” which could replace ionic liquids derived from nonrenewable sources such as petroleum or natural gas (Socha et al. 2014).
  • Developed methods for removal or bioconversion of aromatic compounds from lignin, potentially leading to higher-value products crucial to the economic viability of integrated biorefineries (Luterbacher et al. 2015; Rahimi et al. 2014; Austin et al. 2015).
  • Characterized the structure and biochemistry of lignin-degrading enzymes, providing new insight into their catalysis mechanisms and informing future enzyme engineering efforts (Pereira et al. 2016; Helmich et al. 2016).
  • Developed a novel assay for lignin-degrading enzymes, potentially enabling rapid assessment of catalytic, enzymatic, and microbial degradation of lignin (Kent et al. 2015).
  • Identified novel lignin-degradation genes in multiple natural environments (Hudson et al. 2015; Woo et al. 2014).

Cross-Cutting Achievements

Enabling Technologies

Develop new technologies to facilitate and accelerate BRC research, including, but not limited to, high-throughput laboratory technologies and computational and information systems, several of which have applications to biological research as a whole.

  • Developed rapid methods for analyzing cell wall structure and integrity in plants and during processing, providing a foundation for high-throughput profiling and correlating pretreatment conditions with biomass digestibility (Lu and Ralph 2014; Kim and Ralph 2014; Vismeh et al. 2013; Tobimatsu 2013; Chylla et al. 2013).
  • Developed glycome profiling to analyze plant cell wall polysaccharides; immunological approach is aimed at understanding the spatial distribution of secondary cell wall components affecting recalcitrance (Pattathil et al. 2015).
  • Developed nanostructure-initiator mass spectrometry (NIMzyme) technology to rapidly screen glycoside hydrolases, which are key plant cell wall-degrading enzymes (Deng et al. 2015b; Deng et al. 2014).
  • Developed and deployed new synthetic biology software tools (i.e., DIVA and j5) for more efficient genetic design, transformation, and manipulation (Hillson 2014; Galdzicki et al. 2014; Hillson, Rosengarten, and Keasling 2012).
  • Created a new suite of bioinformatics tools for metagenomics and plants (Wu, Simmons, and Singer 2015; Lee et al. 2015; Mann et al. 2013).
  • Developed and deployed synthetic biology on a chip; automated microfluidic platform has the potential to significantly reduce the design-build-test cycle (Linshiz et al. 2014; Gach et al. 2016; Shih et al. 2015).

Sustainability and Economic Analysis

Produce biomass for biofuels with no negative impacts on food production or the environment.

  • Determined that marginal lands can provide significant cellulosic biomass, along with substantial climate change mitigation and other environmental benefits, allowing fertile lands to be reserved for food production (Gelfand and Robertson 2015).
  • Incorporated state-of-the-art technologies into an open, wiki-based technoeconomic model that simulates critical factors in the biorefinery process (e.g., production costs and energy balances) under different scenarios, enabling researchers to focus on the most promising strategies for cost-efficient operations (Klein-Marcuschamer and Blanch 2015; Konda et al. 2014).


  • Alonso, D. M., S. G. Wettstein, and J. A. Dumesic. 2013. “Gamma-Valerolactone, a Sustainable Platform Molecule Derived from Lignocellulosic Biomass,” Green Chemistry 15(3), 584-95. DOI:10.1039/C3GC37065H.
  • Alonso-Gutierrez, J., et al. 2015. “Principal Component Analysis of Proteomics (PCAP) as a Tool to Direct Metabolic Engineering,” Metabolic Engineering 28, 123-33. DOI:10.1016/j.ymben.2014.11.011.
  • Austin, S., et al. 2015. “Metabolism of Multiple Aromatic Compounds in Corn Stover Hydrolysate by Rhodopseudomonas palustris,” Environmental Science and Technology 49(14), 8914-22. DOI:10.1021/acs.est.5b02062.
  • Baxter, H. L., et al. 2014. “Two-Year Field Analysis of Reduced Recalcitrance Transgenic Switchgrass,” Plant Biotechnology Journal 12(7), 914-24. DOI:10.1111/pbi.12195.
  • Biswal, A. K., et al. 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,” Biotechnology for Biofuels 8(41). DOI:10.1186/s13068-015-0218-y.
  • Chung, D., et al. 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. DOI:10.1371/journal.pone.0062881.
  • Chylla, R., et al. 2013. “Plant Cell Wall Profiling by Fast Maximum Likelihood Reconstruction (FMLR) and Region-of-Interest (ROI) Segmentation of Solution-State 2D 1H-13C NMR Spectra,” Biotechnology for Biofuels 6(45). DOI:10.1186/1754-6834-6-45.
  • Deng, K., et al. 2015a. “Development of a High Throughput Platform for Screening Glycoside Hydrolases Based on Oxime-NIMS,” Frontiers in Bioengineering and Biotechnology: Methods Article 3(153). DOI:10.3389/fbioe.2015.00153.
  • Deng, K., et al. 2015b. “Use of Nanostructure-Initiator Mass Spectrometry (NIMS) to Deduce Selectivity of Reaction in Glycoside Hydrolases,” Frontiers in Bioengineering and Biotechnology: Methods Article 3(165). DOI:10.3389/fbioe.2015.00165.
  • Deng, K., et al. 2014. “Rapid Kinetic Characterization of Glycosyl Hydrolases Based on Oxime Derivatization and Nanostructure-Initiator Mass Spectrometry (NIMS),” ACS Chemical Biology 9(7), 1470-79. DOI:10.1021/CB5000289.
  • Dickinson, Q., et al. 2016. “Mechanism of Imidazolium Ionic Liquids Toxicity in Saccharomyces cerevisiae and Rational Engineering of a Tolerant, Xylose-Fermenting Strain,” Microbial Cell Factories 15(17). DOI:10.1186/s12934-016-0417-7.
  • Ebert, B., et al. 2015. “Identification and Characterization of a Golgi-Localized UDP-Xylose Transporter Family from Arabidopsis,” The Plant Cell 27(4), 1218-27. DOI:10.1105/tpc.114.133827.
  • Eudes, A., et al. 2016. “Exploiting the Substrate Promiscuity of Hydroxycinnamoyl-CoA:Shikimate Hydroxycinnamoyl Transferase to Reduce Lignin,” Plant and Cell Physiology 57(3), 568-79. DOI:10.1093/pcp/pcw016.
  • Evans, L. M., et al. 2014. “Population Genomics of the Model Tree Populus trichocarpa Identifies Signatures of Selection and Adaptive Trait Associations,” Nature Genetics 46, 1089-96. DOI:10.1038/ng.3075.
  • Foo, J. L., et al. 2014. “Improving Microbial Biogasoline Production in Escherichia coli Using Tolerance Engineering,” mBio 5(6), e01932. DOI:10.1128/mBio.01932-14.
  • Frederix, M., et al. 2016. “Development of an E. coli Strain for One-Pot Biofuel Production from Ionic Liquid Pretreated Cellulose and Switchgrass,” Green Chemistry, DOI:10.1039/C6GC00642F.
  • Frederix, M., et al. 2014. “Development of a Native Escherichia coli Induction System for Ionic Liquid Tolerance,” PLOS ONE 9(7), e101115. DOI:10.1371/journal.pone.0101115.
  • Gach, P. C., et al. 2016. “A Droplet Microfluidic Platform for Automating Genetic Engineering,” ACS Synthetic Biology 5(5), 426-33. DOI:10.1021/acssynbio.6b00011.
  • Galdzicki, M., et al. 2014. “The Synthetic Biology Open Language (SBOL) Provides a Community Standard for Communicating Designs in Synthetic Biology,” Nature Biotechnology 32(6), 545-50. DOI:10.1038/nbt.2891.
  • Gelfand, I., and G. P. Robertson. 2015. “Mitigation of Greenhouse Gases in Agricultural Ecosystems.” In The Ecology of Agricultural Landscapes: Long-Term Research on the Path to Sustainability. Eds. S. K. Hamilton, J. E. Doll, and G. P. Robertson. Oxford University Press, New York: 310-39.
  • Gladden, J. M., et al. 2014. “Discovery and Characterization of Ionic Liquid-Tolerant Thermophilic Cellulases from a Switchgrass-Adapted Microbial Community,” Biotechnology for Biofuels 7(15). DOI:10.1186/1754-6834-7-15.
  • Guilliams, A., et al. 2016. “Physical and Chemical Differences Between One-Stage and Two-Stage Hydrothermal Pretreated Hardwood Substrates for Use in Cellulosic Ethanol Production,” Biotechnology for Biofuels 9(30). DOI:10.1186/s13068-016-0446-9.
  • Helmich, K. E., et al. 2016. “Structural Basis of Stereospecificity in the Bacterial Enzymatic Cleavage of ß-Aryl Ether Bonds in Lignin,” The Journal of Biological Chemistry 291(10), 5234-46. DOI:10.1074/jbc.M115.694307.
  • Henningsen, B. M., et al. 2015. “Increasing Anaerobic Acetate Consumption and Ethanol Yield in Saccharomyces cerevisiae with NADPH-Specific Alcohol Dehydrogenase,” Applied and Environmental Microbiology 81(23), 8108-17. DOI:10.1128/AEM.01689-15.
  • Hillson, N. J. 2014. “j5 DNA Assembly Design Automation.” In DNA Cloning and Assembly Methods, Methods in Molecular Biology series. Eds. S. Valla and R. Lale. Humana Press Inc.: 1116, 245-69. DOI:10.1007/978-1-62703-764-8_17.
  • Hillson, N. J., R. D. Rosengarten, and J. D. Keasling. 2012. “j5 DNA Assembly Design Automation Software,” ACS Synthetic Biology 1(1), 14-21. DOI:10.1021/Sb2000116.
  • Hudson, C. M., et al. 2015. “Lignin-Modifying Processes in the Rhizosphere of Arid Land Grasses,” Environmental Microbiology 17(12), 4965-78. DOI:10.1111/1462-2920.13020.
  • Kalluri, U. C., H. Yin, and B. H. Davison. 2014. “Systems and Synthetic Biology Approaches to Alter Plant Cell Walls and Reduce Biomass Recalcitrance,” Plant Biotechnology Journal 12(9), 1207-16. DOI:10.1111/pbi.12283.
  • Kang, A., et al. 2015. “Isopentenyl Diphosphate (IPP)-Bypass Mevalonate Pathways for Isopentenol Production,” Metabolic Engineering 34, 25-35. DOI:10.1016/j.ymben.2015.12.002.
  • Keating, D. H., et al. 2014. “Aromatic Inhibitors Derived from Ammonia-Pretreated Lignocellulose Hinder Bacterial Ethanologenesis by Activating Regulatory Circuits Controlling Inhibitor Efflux and Detoxification,” Frontiers in Microbiology 5(402). DOI:10.3389/fmicb.2014.00402.
  • Kent, M. S., et al. 2015. “Assay for Lignin Breakdown Based on Lignin Films: Insights into the Fenton Reaction with Insoluble Lignin,” Green Chemistry 10, 4830-45. DOI:10.1039/C5GC01083G.
  • Kim, H., and J. Ralph. 2014. “A Gel-State 2D-NMR Method for Plant Cell Wall Profiling and Analysis: Model Study with the Amorphous Cellulose and Xylan from Ball-Milled Cotton Linters,” RSC Advances 4(15), 7549-60. DOI:10.1039/C3RA46338A.
  • Kirby, J., et al. 2015. “Enhancing Terpene Yield from Sugars via Novel Routes to 1-Deoxy-D-Xylulose 5-Phosphate,” Applied and Environmental Microbiology 81(1), 130-38. DOI:10.1128/AEM.02920-14.
  • Klein-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. DOI:10.1002/aic.14755.
  • Konda, M., et al. 2014. “Understanding Cost Drivers and Economic Potential of Two Variants of Ionic Liquid Pretreatment for Cellulosic Biofuel Production,” Biotechnology for Biofuels 7(86). DOI:10.1186/1754-6834-7-86.
  • Lee, T., et al. 2015. “RiceNet v2: An Improved Network Prioritization Server for Rice Genes,” Nucleic Acids Research 43(W1), W122-27. DOI:10.1093/nar/gkv253.
  • Li, C., et al. 2015. “Scale-Up of Ionic Liquid-Based Fractionation of Single and Mixed Feedstocks,” BioEnergy Research 8(3). DOI:10.1007/s12155-015-9587-0.
  • Linshiz, G., et al. 2014. “PR-PR: Cross-Platform Laboratory Automation System,” ACS Synthetic Biology 3(8), 515-24. DOI:10.1021/sb4001728.
  • Liszka, M. J., et al. 2016. “Switchable Ionic Liquids Based on Di-Carboxylic Acids for One-Pot Conversion of Biomass to an Advanced Biofuel,” Green Chemistry, DOI:10.1039/C6GC00657D.
  • Lu, 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. Ed. F. Lu. Nova Science Publishers, Inc., Hauppauge, New York: 27-66.
  • Luterbacher, J. S., et al. 2015. “Lignin Monomer Production Integrated into the γ-Valerolactone Sugar Platform,” Energy and Environmental Science 8(9), 2657-63. DOI:10.1039/C5EE01322D.
  • Luterbacher, J. S, et al. 2014. “Nonenzymatic Sugar Production from Biomass Using Biomass-Derived γ -Valerolactone,” Science 343(6168), 277-80. DOI:10.1126/science_1246748.
  • Mann, G. W., et al. 2013. “MASCP Gator: An Overview of the Arabidopsis Proteomic Aggregation Portal,” Frontiers in Plant Science 4(411). DOI:10.3389/fpls.2013.00411.
  • Muchero, W., et al. 2015. “High-Resolution Genetic Mapping of Allelic Variants Associated with Cell Wall Chemistry in Populus,” BMC Genomics 16(24). DOI:10.1186/s12864-015-1215-z.
  • Nguyen, T. Y., et al. 2015a. “CELF Pretreatment of Corn Stover Boosts Ethanol Titers and Yields from High Solids SSF with Low Enzyme Loadings,” Green Chemistry 18(6), 1581-89. DOI:10.1039/C5GC01977J.
  • Nguyen, T. Y., et al. 2015b. “Co-Solvent Pretreatment Reduces Costly Enzyme Requirements for High Sugar and Ethanol Yields from Lignocellulosic Biomass,” ChemSusChem 8(10), 1716-25. DOI:10.1002/cssc.201403045.
  • Olson, D. G., R. Sparling, and L. R. Lynd. 2015. “Ethanol Production by Engineered Thermophiles,” Current Opinion in Biotechnology 33, 130-41. DOI:10.1016/j.copbio.2015.02.006.
  • Papa, G., et al. 2015. “Comparison of Different Pretreatments for the Production of Bioethanol and Biomethane from Corn Stover and Switchgrass,” Bioresource Technology 183, 101-10. DOI:10.1016/j.biortech.2015.01.121.
  • Parreiras, L. S., et al. 2014. “Engineering and Two-Stage Evolution of a Lignocellulosic Hydrolysate-Tolerant Saccharomyces cerevisiae Strain for Anaerobic Fermentation of Xylose from AFEXTM Pretreated Corn Stover,” PLOS ONE 9(9), e107499. DOI:10.1371/journal.pone.0107499.
  • Pattathil, S., et al. 2015. “Immunological Approaches to Biomass Characterization and Utilization,” Frontiers in Bioengineering and Biotechnology 3(173). DOI:10.3389/fbioe.2015.00173.
  • Paye, J. M. D., et al. 2016. “Biological Lignocellulose Solubilization: Comparative Evaluation of Biocatalysts and Enhancement via Cotreatment,” Biotechnology for Biofuels 9(8). DOI:10.1186/s13068-015-0412-y.
  • Payyavula, R. S., et al. 2014. “Metabolic Profiling Reveals Altered Sugar and Secondary Metabolism in Response to UGPase Overexpression in Populus,” BMC Plant Biology 14(265). DOI:10.1186/s12870-014-0265-8.
  • Pereira, J. H., et al. 2016. “Structural and Biochemical Characterization of the Early and Late Enzymes in the Lignin ß-Aryl Ether Cleavage Pathway from Sphingobium sp SYK-6,” The Journal of Biological Chemistry 29(19), 10228-238. DOI: 10.1074/jbc.M115.700427.
  • Piotrowski, J. S., et al. 2015a. “Chemical Genomic Profiling via Barcode Sequencing to Predict Compound Mode of Action.” In Chemical Biology: Methods and Protocols, Methods in Molecular Biology series. Eds. J. E. Hempel, C. H. Williams, and C. C. E. Hong. Springer, New York: 1263, 299-318.
  • Piotrowski, J. S., et al. 2015b. “Plant-Derived Antifungal Agent Poacic Acid Targets β-1,3-Glucan,” Proceedings of the National Academy of Sciences USA 112(12), E1490-97. DOI:10.1073/pnas.1410400112.
  • Piotrowski, J. S., et al. 2014. “Death by a Thousand Cuts: The Challenges and Diverse Landscape of Lignocellulosic Hydrolysate Inhibitors,” Frontiers in Microbiology 5(90). DOI:10.3389/FMICB.2014.00090.
  • Pisithkul, T., et al. 2015. “Phenolic Amides Are Potent Inhibitors of De Novo Nucleotide Biosynthesis,” Applied and Environmental Microbiology 81(17), 5761-72. DOI:10.1128/AEM-01324-15.
  • Rahimi, A., et al. 2014. “Formic-Acid-Induced Depolymerization of Oxidized Lignin to Aromatics,” Nature 515(7526), 249-52. DOI:10.1038/nature13867.
  • Ruegg, T. L., et al. 2014. “An Auto-Inducible Mechanism for Ionic Liquid Resistance in Microbial Biofuel Production,” Nature Communications 5, 3490. DOI:10.1038/ncomms4490.
  • Scullin, C., et al. 2015. “Restricting Lignin and Enhancing Sugar Deposition in Secondary Cell Walls Enhances Monomeric Sugar Release After Low Temperature Ionic Liquid Pretreatment,” Biotechnology for Biofuels 8(95). DOI:10.1186/s13068-015-0275-2.
  • Serba, D. D., et al. 2015. “Transcriptome Profiling of Rust Resistance in Switchgrass Using RNA-Seq Analysis,” The Plant Genome 8(2), DOI:10.3835/plantgenome2014.10.0075.
  • Shi, J., et al. 2015. “Impact of Pretreatment Technologies on Saccharification and Isopentenol Fermentation of Mixed Lignocellulosic Feedstocks,” BioEnergy Research 8(3), 1004-13. DOI:10.1007/s12155-015-9588-z.
  • Shi, J., et al. 2013. “One-Pot Ionic Liquid Pretreatment and Saccharification of Switchgrass,” Green Chemistry 15, 2579-89. DOI:10.1039/C3GC40545A.
  • Shih, S. C., et al. 2015. “A Versatile Microfluidic Device for Automating Synthetic Biology,” ACS Synthetic Biology 4(10), 1151-64. DOI:10.1021/acssynbio.5b00062.
  • Simmons, C. W., et al. 2014. “Effect of Inoculum Source on the Enrichment of Microbial Communities on Two Lignocellulosic Bioenergy Crops Under Thermophilic and High-Solids Conditions,” Journal of Applied Microbiology117(4), 1025-34. DOI:10.1111/jam.12609.
  • Smith, M. D., et al. 2015. “Cosolvent Pretreatment in Cellulosic Biofuel Production: Effect of Tetrahydrofuran-Water on Lignin Structure and Dynamics,” Green Chemistry 18(5), 1268-77. DOI:10.1039/C5GC01952D.
  • Socha, A. M., et al. 2014. “Efficient Biomass Pretreatment Using Ionic Liquids Derived from Lignin and Hemicellulose,” Proceedings of the National Academy of Sciences USA, 111(35), E3587-95. DOI:10.1073/pnas.1405685111.
  • Sun, N., et al. 2015. “Blending Municipal Solid Waste with Corn Stover for Sugar Production Using Ionic Liquid Process,” Bioresource Technology 186, 200-06. DOI:10.1016/j.biortech.2015.02.087.
  • Takasuka, T. E., et al. 2014. “Cell-Free Translation of Biofuel Enzymes.” In Cell-Free Protein Synthesis: Methods and Protocols, Methods in Molecular Biology series. Eds. K. Alexandrov and W. A. Johnston. Humana Press Inc.: 118, 71-95.
  • Tobimatsu, Y., et al. 2013. “Visualization of Plant Cell Wall Lignification Using Fluorescence-Tagged Monolignols,” The Plant Journal 76(3), 357-66. DOI:10.1111/tpj.12299.  
  • Vega-Sánchez, M. E., et al. 2015. “Engineering Temporal Accumulation of a Low Recalcitrance Polysaccharide Leads to Increased C6 Sugar Content in Plant Cell Walls,” Plant Biotechnology Journal 13(7), 903-14. DOI:10.1111/pbi.12326.
  • Vishnivetskaya, T. A., et al. 2014. “Community Analysis of Plant Biomass-Degrading Microorganisms from Obsidian Pool, Yellowstone National Park,” Microbial Ecology 69(2), 333-45. DOI:10.1007/s00248-014-0500-8.
  • Vismeh, R., et al. 2013. “Profiling of Diferulates (Plant Cell Wall Cross-Linkers) Using Ultrahigh-Performance Liquid Chromatography-Tandem Mass Spectrometry,” Analyst 138(21), 6683-92. DOI:10.1039/c3an36709f.
  • Walker, J. A., et al. 2015. “Multifunctional Cellulase Catalysis Targeted by Fusion to Different Carbohydrate Binding Modules,” Biotechnology for Biofuels 8(220). DOI:10.1186/s13068-015-0402-0.
  • Wilkerson, C. G., et al. 2014. “Monolignol Ferulate Transferase Introduces Chemically Labile Linkages into the Lignin Backbone,” Science 344(6179), 90-93. DOI:10.1126/science.1250161.
  • Woo, H. L., et al. 2014. “Enzyme Activities of Aerobic Lignocellulolytic Bacteria Isolated from Wet Tropical Forest Soils,” Systematic and Applied Microbiology 37(1), 60-67. DOI:10.1016/j.syapm.2013.10.001.
  • Wu, Y.-W., B. A. Simmons, and S. W. Singer. 2015. “MaxBin 2.0: An Automated Binning Algorithm to Recover Genomes from Multiple Metagenomic Datasets,” Bioinformatics, DOI:10.1093/bioinformatics/btv638.
  • Xu, F., et al. 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 and Environmental Science 9(3), 1042-49. DOI:10.1039/C5EE02940F.
  • Xu, Q., et al. 2016. “Dramatic Performance of Clostridium thermocellum Explained by Its Wide Range of Cellulase Modalities,” Science Advances 2(2), E1501254. DOI:10.1126/sciadv.1501254.
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Plant Feedstock Genomics for Bioenergy Abstracts [9/16]

Bioenergy Research Centers
Key Advances Update: 2014-2016 [06/16]

Systems Biology Research to Advance Sustainable Bioenergy Crop Development (Summary of Funded Projects) [9/15]

Lignocellulosic Biomass for Advanced Biofuels and Bioproducts: Workshop Report [2/15]

Systems Biology-Enabled Research for Microbial Production of Advanced Biofuels (Summary of Funded Projects) [9/14]

Sustainable Bioenergy [05/14]

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Bioenergy Research Centers [02/14]


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