Biofuels Publications

Biofuels Publications 2018-07-25T17:50:22+00:00
  • Shi, 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.
  • Talin, A. A., M. D. Allendorf, F. Leonard and V. Stavila (2017). Multiaxis sensing using metal organic frameworks, Google Patents.
  • Wu, W., R. W. Davis, M. B. Tran-Gyamfi, A. Kuo, K. LaButti, S. Mihaltcheva, H. Hundley, M. Chovatia, E. Lindquist, K. Barry, I. V. Grigoriev, B. Henrissat and J. M. Gladden (2017). “Characterization of four endophytic fungi as potential consolidated bioprocessing hosts for conversion of lignocellulose into advanced biofuels.” Applied Microbiology and Biotechnology: 1-16.
  • Kwang Ho Kim, Blake Simmons, Seema Singh, “Catalytic transfer hydrogenolysis of ionic liquid processed biorefinery lignin to phenolic compounds.” Green Chemistry (Jan 2017)
  • Kwang Ho Kim, Robert C. Brown, Tannon Daugaard, William, F. Tivol, Manfred Auer, Blake Simmons, Seema Singh. “Strategy for extending the stability of bio-oil derived phenolic oligomer via mild hydrotreatment with ionic liquid stabilized nanoparticles.” ChemSusChem 10.1002/cssc.201601515 (Jan 2017)
  • W. Zhao, B. Simmons, S. Singh, A. Ragauskas and G. Cheng. “From Lignin Association to Nano-/Micro-particle Preparation: Extracting Higher Value of Lignin.” Green Chemistry, accepted September 2016. (Jan 2017)
  • J. Shi, D. Wu, L. Zhang, B. Simmons, S. Singh, B. Yang and C. Wyman. “Dynamics Changes of Substrate Reactivity and Enzyme Adsorption on Partially Hydrolyzed Cellulose.” Biotechnology and Bioengineering, accepted September 6, 2016. (Jan 2017)

Notable High Impact Journals

  • Jian Sun, Jian Shi, Ramakrishnan Parthasarathi, Tanmoy Dutta, Feng Xu, Seema Singh et al, CO2 enabled process consolidation for the production of cellulosic ethanol in bionic liquids, Energy & Environmental Science, July 2016. (IMPACT FACTOR: 25)
  • Jian Shi, Sivakumar Pattathil, Parthasarathi Ramakrishnan, Seema Singh, et al. Impact of engineered lignin composition on biomass recalcitrance and ionic liquid pretreatment efficiency, Green Chemistry, June 2016. (IMPACT FACTOR: 8)

Additional Publications 

  • Morgan, T. J., S. Q. Turn, N. Sun and A. George. “Fast Pyrolysis of Tropical Biomass Species and Influence of Water Pretreatment on Product Distributions.” Plos One 11, no. 3 (2016): e0151368.
  • Aymerick Eudes, Seema Singh, et al., Expression of S-adenosylmethionine Hydrolase in Tissues Synthesizing Secondary Cell Walls Alters Specific Methylated Cell Wall Fractions and Improves Biomass Digestibility, Frontiers in Bioengineering and Biotechnology (Bioenergy and Biofuels), July 2016.
  • Corno Luca, Pilu Roberto, Tran Kim, Tambone Fulvia, Singh Seema, Simmons Blake, Adani Fabrizio, Sugars production for green chemistry from 2nd generation crop (Arundo donax L.): a full field approach, ChemistrySelect, July 2016.
  • Adam L. Healey, Jason S. Lupoi, David J. Lee, Robert W. Sykese, Joel M. Guenther, Kim Tran, Stephen R. Decker, Seema Singh, Blake A. Simmons, and Robert J. Henry, Effect of aging on lignin content, composition and enzymatic saccharification in Corymbia hybrids and parental taxa between years 9 and 12, Biomass and Bioenergy, July 2016.
  • Ramakrishnan Parthasarathi, Jian Sun, Tanmoy Dutta, Ning Sun, Sivakumar Pattathil, Murthy Konda, Angelo Gabriel Peralta, Blake Simmons, and Seema Singh, Activation of Lignocellulosic Biomass for Higher Sugar Yields using Aqueous Ionic Liquid at Low Severity Process Conditions, Biotechnology for Biofuels, published online August 2016, 9:160.
  • Jian Shi, Dong Wu, Libing Zhang, Blake A. Simmons, Seema Singh, Bin Yang and Charles E. Wyman, Dynamics Changes of Substrate Reactivity and Enzyme Adsorption on Partially Hydrolyzed Cellulose, Biotechnology and Bioengineering, accepted September 6, 2016.
  1. Laura T. Carney, Joshua S.Wilkenfeld, Pam D. Lane, Owen D. Solberg, Zachary B. Fuqua, Nina G. Cornelius, Shaunette Gillespie, Kelly P.Williams, Tzachi M. Samocha, ToddW. Lane. “Pond Crash Forensics: Presumptive identification of pond crash agents by next generation sequencing in replicate raceway mass cultures of
    Nannochloropsis salina.” Algal Research 17 (2016): ALGAL-00583
  2. Abhyankar, V. V., M. Wu, C. Y. Koh and A. V. Hatch. “A Reversibly Sealed, Easy Access, Modular (Seam) Microfluidic Architecture to Establish in Vitro Tissue Interfaces.” PLoS One 11, no. 5 (2016): e0156341. (May 2016)
  3. Harmon, B., S. W. Bird, B. R. Schudel, A. V. Hatch, A. Rasley and O. A. Negrete. “A Genome-Wide Rnai Screen Identifies a Role for Wnt/Beta-Catenin Signaling During Rift Valley Fever Virus Infection.” J Virol,  (2016). (May 2016)
  4. Billings, Andrew F., Julian L. Fortney, Terry C. Hazen, Blake Simmons, Karen W. Davenport, Lynne Goodwin, Natalia Ivanova, Nikos C. Kyrpides, Konstantinos Mavromatis, Tanja Woyke and Kristen M. DeAngelis. “Genome Sequence and Description of the Anaerobic Lignin-Degrading Bacterium Tolumonas Lignolytica Sp Nov.” Standards in Genomic Sciences 10, (November 2015).
  5. Geng, H., K. L. Sale, M. B. Tran-Gyamfi, T. W. Lane and E. T. Yu. “Longitudinal Analysis of Microbiota in Microalga Nannochloropsis Salina Cultures.” Microb Ecol, (2016).
  6. Healey, A. L., D. J. Lee, A. Furtado, B. A. Simmons and R. J. Henry. “Efficient Eucalypt Cell Wall Deconstruction and Conversion for Sustainable Lignocellulosic Biofuels.” Front Bioeng Biotechnol 3, (November 2015): 190.
  7. Hudson, Corey M., Edward Kirton, Miriam I. Hutchinson, Joanna L. Redfern, Blake Simmons, Eric Ackerman, Seema Singh, Kelly P. Williams, Donald O. Natvig and Amy J. Powell. “Lignin-Modifying Processes in the Rhizosphere of Arid Land Grasses.” Environmental Microbiology 17, no. 12 (December 2015): 4965-4978.
  8. Lupoi, J., B. Simmons and R. Henry. “Editorial: Biomass Modification, Characterization, and Process Monitoring Analytics to Support Biofuel and Biomaterial Production.” Front Bioeng Biotechnol 4, (2016): 25.
  9. Pace, S., S. J. Ceballos, D. Harrold, W. Stannard, B. A. Simmons, S. W. Singer, M. P. Thelen and J. S. VanderGheynst. “Enrichment of Microbial Communities Tolerant to the Ionic Liquids Tetrabutylphosphonium Chloride and Tributylethylphosphonium Diethylphosphate.” Appl Microbiol Biotechnol, (2016).
  10. Pereira, 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. “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, (2016).
  11. Ruffing, Anne M. and Toivo Kallas. “Editorial: Cyanobacteria: The Green E. Coli.” Frontiers in bioengineering and biotechnology 4, (2016): 7-7.
  12. Walker, Johnnie A., Taichi E. Takasuka, Kai Deng, Christopher M. Bianchetti, Hannah S. Udell, Ben M. Prom, Hyunkee Kim, Paul D. Adams, Trent R. Northen and Brian G. Fox. “Multifunctional Cellulase Catalysis Targeted by Fusion to Different Carbohydrate-Binding Modules.” Biotechnology for Biofuels 8, (December 2015).
  13. Xu, Feng, Jian Sun, N. V. S. N. Murthy Konda, Jian Shi, Tanmoy Dutta, Corinne D. Scown, Blake A. Simmons and Seema Singh. “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, no. 3 (2016): 1042-1049.
  14. Yu, C., A. P. Reddy, C. W. Simmons, B. A. Simmons, S. W. Singer and J. S. Vander Gheynst. “Preservation of Microbial Communities Enriched on Lignocellulose under Thermophilic and High-Solid Conditions.” 8, (December 2015): 206.
  1. Allendorf, M. D., R. W. Davis, P. Ramakrishnan, K. L. Sale, and V. Stavila. “Mof-Based Catalysts for Lignin Degradation.” Abstracts of Papers of the American Chemical Society 248, (2014).
  2. Baker, Scott E., Kevin McCluskey, Blake A. Simmons, Jed Lynn, John M. Gladden, and Jon K. Magnuson. “Genomics and Regulation of Fungal Enzyme Secretion ” In Symposium on Biotechnology for Fuels and Chemicals. San Diego, CA. , 2015.
  3. Cheng, Gang, Xin Zhang, Blake Simmons, and Seema Singh. “Theory, Practice and Prospects of X-Ray and Neutron Scattering for Lignocellulosic Biomass Characterization: Towards Understanding Biomass Pretreatment.” Energy and Environmental Science 8, no. 2 (2015): 436-455.
  4. Eudes, Aymerick, Noppadon Sathitsuksanoh, Edward E. K. Baidoo, Anthe George, Yan Liang, Fan Yang, Seema Singh, Jay D. Keasling, Blake A. Simmons, and Dominique Loqué. “Expression of a Bacterial 3-Dehydroshikimate Dehydratase Reduces Lignin Content and Improves Biomass Saccharification Efficiency.” Plant Biotechnology Journal [Early View], (2015).
  5. Furtado, Agnelo, Jason S. Lupoi, Nam V. Hoang, Adam Healey, Seema Singh, Blake A. Simmons, and Robert J. Henry. “Modifying Plants for Biofuel and Biomaterial Production.” Plant Biotechnology Journal 12, no. 9 (2014): 1246-1258.
  6. Gardner, James, Wei He, Chenlin Li, Jessica Wong, Kenneth L. Sale, Blake Simmons, Seema Singh, and Deepti Tanjore. “Calorimetric Evaluation Indicates That Lignin Conversion to Advanced Biofuels Is Vital to Improving Energy Yields.” RSC Advances (2015).
  7. George, Anthe, Agnieszka Brandt, Shahrul Zahari, Daniel Klein-Marcuschamer, Parthasarathi Ramakrishnan, Ning Sun, Noppadon Sathitsuksanoh, Jian Shi, Vitalie Stavila, Kim Tran, Seema Singh, Bradley M. Holmes, Tom Welton, Blake Simmons, and Jason Hallett. “Design of Low-Cost Ionic Liquids for Biomass Pretreatment.” Green Chemistry 17, (2014): 1728-1734.
  8. Hudson, Corey M., Edward Kirton, Miriam I. Hutchinson, Joanna L. Redfern, Blake Simmons, Eric Ackerman, Seema Singh, Kelly P. Williams, Donald O. Natvig, and Amy J. Powell. “Lignin-Modifying Processes in the Rhizosphere of Aridland Grasses.” Environmental Microbiology [Accepted Article], (2015).
  9. Kent, Michael S., Isaac C. Avina, Nadeya Rader, Michael L. Busse, Anthe George, Noppadon Sathitsuksanoh, Edward Baidoo, Jerilyn Timlin, Nicholas H. Giron, Mathias C. Celina, Laura E. Martin, Ronen Polsky, Victor H. Chavez, Dale L. Huber, Jay D. Keasling, Seema Singh, Blake A. Simmons, and Kenneth L. Sale. “Assay for Lignin Breakdown Based on Lignin Films: Insights into the Fenton Reaction with Insoluble Lignin.” Green Chemistry [Advance article], (2015).
  10. Konda, N. V. S. N. Murthy, Seema Singh, Blake A. Simmons, and Daniel Klein-Marcuschamer. “An Investigation on the Economic Feasibility of Macroalgae as a Potential Feedstock for Biorefineries.” BioEnergy Research, (2015): 1-11.
  11. Li, Chenlin, Deepti Tanjore, Wei He, Jessica Wong, James L Gardner, Vicki S Thompson, Neal A Yancey, Kenneth L Sale, Blake A Simmons, and Seema Singh. “Scale-up of Ionic Liquid-Based Fractionation of Single and Mixed Feedstocks.” BioEnergy Research, (2015): 1-10.
  12. Lopez-Ortega, Monica G., Jose A. Chavez-Carvayar, Vitalie Stavila, Gang Cheng, Seema Singh, Blake A. Simmons, José Pérez-Pimienta,Characterization of agave bagasse ad a function of ionic liquid pretreatment, Biomass & Bioenergy, accepted January 2015
  13. Lupoi, Jason S., Adam Healey, Seema Singh, Robert Sykes, Mark Davis, David J. Lee, Merv Shepherd, Blake A. Simmons, and Robert J. Henry. “High-Throughput Prediction of Acacia and Eucalypt Lignin Syringyl/Guaiacyl Content Using Ft-Raman Spectroscopy and Partial Least Squares Modeling.” BioEnergy Research, (2015): 1-11.
  14. Lupoi, Jason S., Seema Singh, Ramakrishnan Parthasarathi, Blake A. Simmons, and Robert J. Henry, Recent Innovations in Analytical Methods for the Qualitative and Quantitative Assessment of Lignin, Renewable & Sustainable Energy Reviews, accepted April 2015.
  15. Lupoi, J. S., A. Smith-Moritz, S. Singh, R. McQualter, H. V. Scheller, B. A. Simmons, and R. J. Henry. “Localization of Polyhydroxybutyrate in Sugarcane Using Fourier-Transform Infrared Microspectroscopy and Multivariate Imaging.” Biotechnology for Biofuels 8, (2015): 98.
  16. Morgan, Trevor J., Anthe George, Aikaterini K. Boulamanti, Patricia Alvarez, Ibtissam Adanouj, Charles Dean, Stanislav V. Vassilev, David Baxter, and Lars Klembt Andersen. “Quantitative X-Ray Fluorescence Analysis of Biomass (Switchgrass, Corn Stover, Eucalyptus, Beech, and Pine Wood) with a Typical Commercial Multi-Element Method on a Wd-Xrf Spectrometer.” Energy & Fuels 29, no. 3 (2015): 1669-1685.
  17. Morgan, Trevor James, Scott Q. Turn, and Anthe George. “Fast Pyrolysis Behavior of Banagrass as a Function of Temperature and Volatiles Residence Time in a Fluidized Bed Reactor.” Plos One 10, no. 8 (2015): e0136511.
  18. Rodriguez, Sarah, James Kirby, Charles M. Denby, and Jay D. Keasling. “Production and Quantification of Sesquiterpenes in Saccharomyces Cerevisiae, Including Extraction, Detection and Quantification of Terpene Products and Key Related Metabolites.” Protocols 9, no. 8 (2014): 1980-1996.
  19. Papa, G., S. Rodriguez, A. George, A. Schievano, V. Orzi, K. L. Sale, S. Singh, F. Adani, and B. A. Simmons. “Comparison of Different Pretreatments for the Production of Bioethanol and Biomethane from Corn Stover and Switchgrass.” Bioresource Technology 183C, (2015): 101-110.
  20. Parthasarathi, R., S. Singh, and B. A. Simmons. “Weak, Strong, Strongest Hydrogen Bonding: Designing Ionic Liquid for Improved Plant Cell Wall Deconstruction.” Abstracts of Papers of the American Chemical Society 248, (2014).
  21. Perez-Pimienta, Jose A., Monica G. Lopez-Ortega, Jose A. Chavez-Carvayar, Patanjali Varanasi, Vitalie Stavila, Gang Cheng, Seema Singh, and Blake A. Simmons. “Characterization of Agave Bagasse as a Function Of ionic Liquid Pretreatment.” Biomass and Bioenergy 75, (2015): 180-188.
  22. Sathitsuksanoh, Noppadon, Manali Sawant, Quoc Troung, Jared Tran, Chris Canlas, Ning Sun, Wei Zhang, Scott Renneckar, Teerawit Prasomsri, Jian Shi, Özgül Çetinkol, Seema Singh, Blake Simmons, and Anthe George, How alkyl chain length of alcohols affects lignin fractionation and ionic liquid recycle during lignocellulose pretreatment, BioEnergy Research, 8(3), 2015: 973-981
  23. Scullin, C., A. G. Cruz, Y. D. Chuang, B. A. Simmons, D. Loque, and S. Singh. “Restricting Lignin and Enhancing Sugar Deposition in Secondary Cell Walls Enhances Monomeric Sugar Release after Low Temperature Ionic Liquid Pretreatment.” Biotechnology for Biofuels 8, (2015): 95.
  24. Siegel, Justin B., Amanda Lee Smith, Sean Poust, Adam J. Wargacki, Arren Bar-Even, Catherine Louw, Betty W. Shen, Christopher B. Eiben, Huu M. Tran, Elad Noor, Jasmine L. Gallaher, Jacob Bale, Yasuo Yoshikuni, Michael H. Gelb, Jay D. Keasling, Barry L. Stoddard, Mary E. Lidstrom, and David Baker, “Computational protein design enables a novel one-carbon assimilation pathway.” PNAS,March 24, 2015  112 no. 12, 3704-3709.
  25. Shi, Jian, Kevin W. George, Ning Sun, Wei He, Chenlin Li, Vitalie Stavila, Jay D. Keasling, Blake A. Simmons, Taek Soon Lee, and Seema Singh. “Impact of Pretreatment Technologies on Saccharification and Isopentenol Fermentation of Mixed Lignocellulosic Feedstocks.” BioEnergy Research, (2015): 1-10.
  26. Shih, S. C., P. C. Gach, J. Sustarich, B. A. Simmons, P. D. Adams, S. Singh, and A. K. Singh. “A Droplet-to-Digital (D2d) Microfluidic Device for Single Cell Assays.” Lab on a Chip 15, no. 1 (2015): 225-236.
  27. Singh, Seema, Gang Cheng, Noppadon Sathitsuksanoh, Dong Wu, Patanjali Varanasi, Anthe George, Venkatesh Balan, Xiadi Gao, Rajeev Kumar, Bruce Dale, Charles Wyman, and Blake Simmons. “Comparison of Different Biomass Pretreatment Techniques and Their Impact on Chemistry, Structure, and Recalcitrance.” Frontiers in Energy Research 2, (2015): Article 62.
  28. Sun, Lan, Seema Singh, Michael Joo, Miguel Vega-Sanchez, Pamela Ronald, Blake A. Simmons, Paul Adams, and Manfred Auer. “Non-Invasive Imaging of Cellulose Microfibril Orientation within Plant Cell Walls by Polarized Raman Microspectroscopy.” Biotechnology and Bioengineering [Early View article], (2015).
  29. Sun, Ning, Feng Xu, Noppadon Sathitsuksanoh, Vicki S. Thompson, Kara Cafferty, Chenlin Li, Deepti Tanjore, Akash Narani, Todd R. Pray, Blake A. Simmons, and Seema Singh. “Blending Municipal Solid Waste with Corn Stover for Sugar Production Using Ionic Liquid Process.” Bioresource Technology, (In Press, Accepted Manuscript).
  30. Tanger, Paul, Miguel E. Vega-Sánchez, Margaret Fleming, Kim Tran, Seema Singh, James B. Abrahamson, Courtney E. Jahn, Nicholas Santoro, Elizabeth B. Naredo, Marietta Baraoidan, John M. C. Danku, David E. Salt, Kenneth L. McNally, Blake A. Simmons, Pamela C. Ronald, Hei Leung, Daniel R. Bush, John K. McKay, and Jan E. Leach. “Cell Wall Composition and Bioenergy Potential of Rice Straw Tissues Are Influenced by Environment, Tissue Type, and Genotype.” BioEnergy Research, (2015): 1-18.
  31. Wu, Yu-Wei, Chijioke Joshua, Stephanie A. Eichorst, John M. Gladden, Blake A. Simmons, and Steven W. Singer. “Genomic Analysis of Xylose Metabolism in Members of the Deinoccocus-Thermus Phylum from Thermophilic Biomass-Deconstructing Bacterial Consortia.” BioEnergy Research, (2015): 1-8.
  1. Batth, T. S., P. Singh, V. R. Ramakrishnan, M. M. Sousa, L. J. Chan, H. M. Tran, E. G. Luning, E. H. Pan, K. M. Vuu, J. D. Keasling, P. D. Adams, and C. J. Petzold. “A Targeted Proteomics Toolkit for High-Throughput Absolute Quantification of Escherichia Coli Proteins.” Metabolic Engineering [In Press, Uncorrected Proof], (2014).
  2. Bergmann, J. C., O. Y. A. Costa, J. M. Gladden, S. Singer, R. Heins, P. D’Haeseleer, B. A. Simmons, and B. F. Quirino. “Discovery of Two Novel Β-Glucosidases from an Amazon Soil Metagenomic Library.” FEMS Microbiology Letters 351, no. 2 (2014): 147-155.
  3. Chen, Zhiwei, Jose H. Pereira, Hanbin Liu, Huu M. Tran, Nathan S. Y. Hsu, Dean Dibble, Seema Singh, Paul D. Adams, Rajat Sapra, Masood Z. Hadi, Blake A. Simmons, and Kenneth L. Sale. “Improved Activity of a Thermophilic Cellulase, Cel5a, from Thermotoga Maritima on Ionic Liquid Pretreated Switchgrass.” Plos One 8, no. 11 (2013): e79725.
  4. Davis RW, Jones HDT, Collins AM, Ricken JB, Sinclair MB, Timlin JA, Singh, S. (2013) Label-free measurement of algal triacylglyceride production using fluorescence hyperspectral imaging. Algal Research  DOI: 10.1016/j.algal.2013.11.010
  5. Davis, Ryan W., Benjamin J. Carvalho, Howland D. T. Jones, and Seema Singh. “The Role of Photo-Osmotic Adaptation in Semi-Continuous Culture and Lipid Particle Release from Dunaliella Viridis.” Journal of Applied Phycology, (2014): 1-15.
  6. Davis, Ryan W., Hauwen Wu, and Seema Singh. “Multispectral Sorter for Rapid, Nondestructive Optical Bioprospecting for Algae Biofuels.” 8947, 89471E-89471E-11, 2014.
  7. Deng, 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. “Rapid Kinetic Characterization of Glycosyl Hydrolases Based on Oxime Derivatization and Nanostructure-Initiator Mass Spectrometry (Nims).” ACS Chem Biol, (2014).
  8. D’Haeseleer, Patrik, John M. Gladden, Martin Allgaier, Patrik S. G. Chain, Susannah G. Tringe, Stephanie A. Malfatti, Joshua T. Aldrich, Carrie D. Nicora, Errol W. Robinson, Ljiljana Paša-Tolić, Philip Hugenholtz, Blake A. Simmons, and Steven W. Singer. “Proteogenomic Analysis of a Thermophilic Bacterial Consortium Adapted to Deconstruct Switchgrass.” Plos One 8, no. 7 (2013): e68465.
  9. Dougherty, Michael J., Huu M. Tran, Vitalie Stavila, Bernhard Knierim, Anthe George, Manfred Auer, Paul D. Adams, and Masood Z. Hadi. “Cellulosic Biomass Pretreatment and Sugar Yields as a Function of Biomass Particle Size ” PLoS ONE 9, no. 6 (2014): e100836.
  10. Eichorst, S. A., C. Joshua, N. Sathitsuksanoh, S. Singh, B. A. Simmons, and S. W. Singer. “Substrate-Specific Development of Thermophilic Bacterial Consortia Using Chemically Pretreated Switchgrass.” Appl Environ Microbiol, (2014).
  11. Gao, Xiadi, Rajeev Kumar, Seema Singh, Blake Simmons, Venkatesh Balan, Bruce Dale, and Charles Wyman. “Comparison of Enzymatic Reactivity of Corn Stover Solids Prepared by Dilute Acid, Afex (Tm), and Ionic Liquid Pretreatments.” Biotechnology for Biofuels 7, no. 1 (2014): 71.
  12. Gladden, John, Joshua Park, Jessica Bergmann, Vimalier Reyes-Ortiz, Patrik Dhaeseleer, Betania Quirino, Kenneth Sale, Blake Simmons, and Steven Singer. “Discovery and Characterization of Ionic Liquid-Tolerant Thermophilic Cellulases from a Swithchgrass-Adapted Microbial Community.” Biotechnology for Biofuels 7, no. 1 (2014): 15.
  13. Heins, Richard; Cheng, Xiaoliang; Nath, Sangeeta; Deng, Kai; Bowen, Benjamin; Chivian, Dylan; Datta, Supratim; Friedland, Gregory; D’Haeseleer, Patrik; Wu, Dongying; Tran-Gyamfi, Mary; Scullin, Chessa; Singh, Seema; Shi, Weibing; Hamilton, Matthew; Bendall, Matthew; Sczyrba, Alexander; Thompson, John; Feldman, Taya; Guenther, Joel; Gladden, John; Cheng, Jan-Fang; Adams, Paul; Rubin, Edward; Simmons, Blake A.; Sale, Kenneth; Northen, Trent; Deutsch, Sam, Phylogenomic Guided Identification of Industrially Relevant GH1 β-Glucosidases Through DNA Synthesis and Nanostructure-Initiator Mass Spectrometry, ACS Chemical Biology, doi:10.1021/cb500244v
  14. Hollinshead, Whitney D., Arul M. Varman, Le You, Zachary Hembree, and Yinjie J. Tang. “Boosting D-Lactate Production in Engineered Cyanobacteria Using Sterilized Anaerobic Digestion Effluents.” Bioresource Technology 169, (2014): 462-467.
  15. Li, C. L., D. Tanjore, W. He, J. Wong, J. L. Gardner, K. L. Sale, B. A. Simmons, and S. Singh. “Scale-up and Evaluation of High Solid Ionic Liquid Pretreatment and Enzymatic Hydrolysis of Switchgrass.” Biotechnology for Biofuels 6, (2013): 154.
  16. V.S.N. Murthy Konda, Jian Shi, Seema Singh, Harvey W Blanch, Blake A Simmons and Daniel Klein-Marcuschamer, Understanding cost drivers and economic potential of two variants of ionic liquid pretreatment for cellulosic biofuel production, Biotechnology for Biofuels, 2014, 7:86
  17. Reyes-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. “Addition of a Carbohydrate-Binding Module Enhances Cellulase Penetration into Cellulose Substrates.” Biotechnology for Biofuels 6, no. 1 (2013): 93.
  18. Scullin, Chessa, Vitalie Stavila, Anita Skarstad, Jay D. Keasling, Blake A. Simmons, and Seema Singh. Optimization of Renewable Pinene Production from the Conversion of Macroalgae Saccharina latissima, Bioresource Technology, DOI: 10.1016/j.biortech.2014.09.105
  19. Shi, Jian, Kanagasabai Balamurugan, Ramakrishnan Parthasarathi, Noppadon Sathitsuksanoh, Sonny Zhang, Vitalie Stavila, Venkatesan Subramanian, Blake Simmons, and Seema Singh. “Understanding the Role of Water During Ionic Liquid Pretreatment of Lignocellulose: Co-Solvent or Anti-Solvent?” Green Chemistry 16, no. 8 (2014): 3830-3840.
  20. Socha, 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. “Efficient Biomass Pretreatment Using Ionic Liquids Derived from Lignin and Hemicellulose.” Proceedings of the National Academy of Sciences of the United States of America 111, no. 35 (2014): E3587-E3595.
  21. Sun, Ning, Ramakrishnan Parthasarathi, Aaron M. Socha, Jian Shi, Sonny Zhang, Vitalie Stavila, Kenneth L. Sale, Blake Simmons, and Seema Singh. “Understanding Pretreatment Efficacy of Four Cholinium and Imidazolium Ionic Liquids by Chemistry and Computation.” Green Chemistry, (2014).
  22. Tran, Huu (Co-PI), Dougherty, Michael J. (Co-PI), Vitalie Stavila, Bernhard Knierim, Anthe George, Manfred Auer, Paul D. Adams, Masood Z. Hadi, Cellulosic Biomass Pretreatment and Sugar Yields as a Function of Biomass Particle Size, June 27, 2014DOI: 10.1371/journal.pone.0100836.
  23. Uppugundla, Nirmal, Leonardo da Costa Sousa, Shishir Chundawat, Xiurong Yu, Blake Simmons, Seema Singh, Xiadi Gao, Rajeev Kumar, Charles Wyman, Bruce Dale, and Venkatesh Balan. “A Comparative Study of Ethanol Production Using Dilute Acid, Ionic Liquid and Afex (Tm) Pretreated Corn Stover.” Biotechnology for Biofuels 7, no. 1 (2014): 72.
  24. Varanasi, Patanjali, Priyanka Singh, Manfred Auer, Paul Adams, Blake Simmons, and Seema Singh. “Survey of Renewable Chemicals Produced from Lignocellulosic Biomass During Ionic Liquid Pretreatment.” Biotechnology for Biofuels 6, no. 1 (2013): 14.
  1. Dawn Chiniquy, Patanjali Varanasi, Taeyun Oh, Jesper Harholt, Jacob Katnelson, Seema Singh, Manfred Auer, Blake Simmons, Paul D. Adams, Henrik V. Scheller, Pamela C. Ronald. Three novel rice genes closely related to the Arabidopsis IRX9, IRX9L, and IRX14 genes and their roles in xylan biosynthesis, Frontiers in PlantBiotechnology, 2013, 4(83), 1-13.
  2. Alejandro G. Cruz, Chessa Scullin, Chen Mu, Gang Cheng, Vitalie Stavila, Patanjali Varanasi, Jeff Mentel, DongYan Xu, Yi-De A. Chung, Blake Simmons and Seema Singh. Impact of High Biomass Loading on Ionic Liquid Pretreatment, Biotechnology for Biofuels, 2013, 6:52.
  3. D’Haeseleer, Patrik, John M. Gladden, Martin Allgaier, Patrik S. G. Chain, Susannah G. Tringe, Stephanie A. Malfatti, Joshua T. Aldrich, Carrie D. Nicora, Errol W. Robinson, Ljiljana Paša-Tolić, Philip Hugenholtz, Blake A. Simmons, and Steven W. Singer. “Proteogenomic Analysis of a Thermophilic Bacterial Consortium Adapted to Deconstruct Switchgrass.” Plos One 8, no. 7 (2013): e68465.
  4. Stephanie A. Eichorst, Pantanjali Varasani, Vatalie Stavila, Marcin Zemla, Manfred Auer, Seems Singh, Blake A. Simmons, Steven W. Singer Community Dynamics of Cellulose-Adapted Thermophilic Consortia, Environmental MIcrobiology, May 2103, doi: 10.1111/1462-2920.12159.
  5. Groff, Dan, Anthe George, Ning Sun, Noppadon Sathitsuksanoh, Gregory Bokinsky, Blake A. Simmons, Bradley M. Holmes, and Jay D. Keasling. “Acid Enhanced Ionic Liquid Pretreatment of Biomass.” Green Chemistry, (2013).
  6. Li, Chenlin; Sun, Lan; Simmons, Blake; Singh, Seema. Comparing the Recalcitrance of Eucalyptus, Pine, and Switchgrass using Ionic Liquid and Dilute Acid Pretreatments, BioEnergy Research, March 2013, 6(1), 14-23.
  7. Jason S. Lupoi, Seema Singh, Blake A. Simmons, and Robert J. Henry Assessment of Lignocellulosic Biomass using Analytical Spectroscopy: An Evolution to High Throughput Techniques,BioEnergy Research, in press, June 2013, DOI 10.1007/s12155-013-9352-1.
  8. McAndrew RP, Park JI, Heins RA, Reindl W, Friedland GD, et al. (2013) From Soil to Structure, a Novel Dimeric β-Glucosidase Belonging to Glycoside Hydrolase Family 3 Isolated from Compost Using Metagenomic Analysis. Journal of Biological Chemistry, 288: 14985–14992.
  9. Nyyssönen, Mari, Huu M. Tran, Ulas Karaoz, Claudia Weihe, Masood Z. Hadi, Jennifer B. H. Martiny, Adam C. Martiny, and Eoin L. Brodie. “Coupled High-Throughput Functional Screening and Next Generation Sequencing for Identification of Plant Polymer Decomposing Enzymes in Metagenomic Libraries.” Frontiers in Microbiology 4, (2013).
  10. Paap, Scott M., Todd H. West, Dawn K. Manley, Eric J. Steen, Harry R. Beller, Jay D. Keasling, Dean C. Dibble, Shiyan Chang, and Blake A. Simmons. “Biochemical Production of Ethanol and Fatty Acid Ethyl Esters from Switchgrass: A Comparative Analysis of Environmental and Economic Performance.” Biomass and Bioenergy 49, (2013): 49-62.
  11. Passell, H., H. Dhaliwal, M. Reno, B. Wu, A. Ben Amotz, E. Ivry, M. Gay, T. Czartoski, L. Laurin, and N. Ayer. “Algae Biodiesel Life Cycle Assessment Using Current Commercial Data.” J Environ Manage 129C, (2013): 103-111.
  12. Jose A. Perez-Pimienta, Monica G. Lopez-Ortega, Patanjali Varanasi, Vitalie Stavila, Gang Cheng, Seema Singh, Blake A. Simmons. Comparing the Impact of Ionic Liquid Pretreatment on Agave Bagasse and Switchgrass, Bioresource Technology, 2013, 127, 18–24.
  13. Petersen, Pia Damm; Lau, Jane; Ebert, Berit; Yang, Fan; Verhertbruggen, Yves; Kim, Jin Sun; Varanasi, Patanjali; Suttangkakul, Anongpat; Auer, Manfred; Loqué, Dominique; Scheller, Henrik Vibe “Engineering of Plants with Improved Properties as Biofuels Feedstocks by Vessel-Specific Complementation of Xylan Biosynthesis Mutants.” Biotechnology for Biofuels 5,  (2012).
  14. Vimalier Reyes-Ortiz, Richard A Heins, Gang Cheng, Edward Y Kim, Briana C Vernon, Ryan B Elandt, Paul D Adams, Kenneth L Sale, Masood Z Hadi, Blake A Simmons, Michael S Kent and Danielle Tullman-Ercek. Addition of a carbohydrate-binding module enhances cellulase penetration into cellulose substrate, Biotechnology for Biofuels, 2013, 6:93.
  15. Jian Shi, John M. Gladden, Noppadon Sathitsuksanoh, Pavan Kambam, Lucas Sandoval, Debjani Mitra, Sonny Zhang, Anthe George, Steven W. Singer, Blake A. Simmons and Seema Singh, One-pot Ionic Liquid Pretreatment and Saccharification of Switchgrass, Green Chemistry, 2013,15, 2579-2589.
  16. Jian Shi, Vicki S. Thompson, Neal A. Yancey, Vitalie Stavila, Blake A. Simmons, and Seema Singh. Impact of Mixed Feedstocks and Feedstock Densification on Ionic Liquid Pretreatment Efficiency, Biofuels, Jan 2013, 4(1), 63-72.
  17. Seema Singh; Patanjali Varanasi; Priyanka Singh; Paul Adams; Manfred Auer; Blake A. Simmons. Understanding the Impact of Ionic Liquid Pretreatment on Cellulose and Lignin via Thermochemical Analysis, Biomass & Bioenergy, July 2013, 54, 276–283.
  18. Seema Singh and Blake Simmons, Ionic Liquid Pretreatment: Mechanism, Performance, and Challenges, Aqueous Pretreatment of Plant Biomass for Biological and Chemical Conversion to Fuels and Chemicals, Wiley Blackwell, ed. Charles Wyman, in press October 2012
  19. Aaron M Socha, Samuel Plummer, Vitalie Stavila, Blake A Simmons and Seema Singh. Comparison of sugar content for ionic liquid pretreated Douglas-fir woodchips and forestry residues.Biotechnology for Biofuels, published online May 1, 2013, doi 10.1186/1754-6834-6-61.
  20. Lan Sun, Chenlin Li, Zhengjun Xue, Blake A. Simmons, and Seema Singh, Unveiling High-Resolution, Tissue Specific Dynamic Changes in Corn Stover during Ionic Liquid Pretreatment, RSC Advances, 2013, 3, 2017-2027.
  21. Ning Sun, Hanbin Liu, Noppadon Sathitsuksanoh, Vitalie Stavila, Manali Sawant, Anaise Bonito, Kim Tran, Anthe George, Kenneth L Sale, Seema Singh, Blake A Simmons and Bradley M Holmes. Production and Extraction of Sugars from Switchgrass Hydrolyzed in Ionic Liquids, Biotechnology for Biofuels, 2013, 6:39.
  22. Ning Sun, Hanbin Liu, Noppadon Sathitsuksanoh, Vitalie Stavila, Manali Sawant, Anaise Bonito, Kim Tran, Anthe George, Kenneth L Sale, Seema Singh, Blake A Simmons and Bradley M Holmes.Production and Extraction of Sugars from Switchgrass Hydrolyzed in Ionic Liquids,Biotechnology for Biofuels, 2013, 6:39.
  23. Varanasi, P.; Singh, P.; Auer, M.; Adams, P.D.; Simmons, B.A.; Singh, S. Survey of Renewable Chemicals Produced from Lignocellulosic Biomass during Ionic Liquid Pretreatment,Biotechnology for Biofuels, 2013, 6(14).
  24. Patanjali Varanasi, Priyanka Singh, Rohit Arora, Paul D. Adams, Manfred Auer, Blake A. Simmons, and Seema Singh. Understanding changes in lignin of Panicum virgatumand Eucalyptus globulus as a function of ionic liquid pretreatment, Bioresource Technology, 2013, 6:14.