Book Chapters
Papa, Gabriella, Simmons, Blake A. and Sun, Ning (2022). Scale-Up of the Ionic Liquid-Based Biomass Conversion Processes. Encyclopedia of Ionic Liquids. (pp. 1183-1190) Singapore: Springer Nature Singapore. doi: 10.1007/978-981-33-4221-7_49
Reilly, Morgann C., Amaike Campen, Saori, Simmons, Blake A., Baker, Scott E., Gladden, John M. and Magnuson, Jon K. (2018). Cloning and expression of heterologous cellulases and enzymes in aspergillus niger. Cellulases. (pp. 123-133) edited by Mette Lübeck. New York, NY, United States: Humana Press Inc.. doi: 10.1007/978-1-4939-7877-9_10
Dutta, Tanmoy, Shi, Jian, Sun, Jian, Zhang, Xin, Cheng, Gang, Simmons, Blake A. and Singh, Seema (2016). Ionic liquid pretreatment of lignocellulosic biomass for biofuels and chemicals. Ionic liquids in the biorefinery concept: challenges and perspectives. (pp. 65-94) edited by Rafal Bogel-Lukasik. Cambridge, United Kingdom: Royal Society of Chemistry. doi: 10.1039/9781782622598
Gao, Xiadi, Kumar, Rajeev, Singh, Seema, Simmons, Blake A., Balan, Venkatesh, Dale, Bruce E. and Wyman, Charles E. (2015). Comparison of enzymatic reactivity of corn stover solids prepared by dilute acid, afex™, and ionic liquid pretreatments. Fuel production from non-food biomass: corn stover. (pp. 181-208) edited by Barnabas Gikonyo. New York, NY, United States: Apple Academic Press. doi: 10.1201/b18437
Singh, Seema and Simmons, Blake A. (2013). Ionic Liquid Pretreatment: Mechanism, Performance, and Challenges. Aqueous Pretreatment of Plant Biomass for Biological and Chemical Conversion to Fuels and Chemicals. (pp. 223-238) edited by Charles E. Wyman. Chichester, West Sussex, United Kingdom: John Wiley and Sons. doi: 10.1002/9780470975831.ch11
Simmons, Blake A. (2012). Bioenergy from plants and plant residues. Plant biotechnology and agriculture. (pp. 495-505) edited by Arie Altman and Paul Michael Hasegawa. London, United Kingdom: Elsevier . doi: 10.1016/B978-0-12-381466-1.00031-6
Klein-Marcuschamer, Daniel, Holmes, Brad, Simmons, Blake A. and Blanch, Harvey W. (2011). Biofuel economics. Plant biomass conversion. (pp. 329-354) edited by Elizabeth E. Hood, Peter Nelson and Randall Powell. Chichester, West Sussex, United Kingdom: John Wiley & Sons. doi: 10.1002/9780470959138.ch14
Journal Articles
Mohan, Mood, Demerdash, Omar N., Simmons, Blake A., Singh, Seema, Kidder, Michelle K. and Smith, Jeremy C. (2024). Physics-Based Machine Learning Models Predict Carbon Dioxide Solubility in Chemically Reactive Deep Eutectic Solvents. ACS Omega. doi: 10.1021/acsomega.4c01175
Kumar, Nikhil, Mohan, Mood, Smith, Jeremy C., Simmons, Blake A., Singh, Seema and Banerjee, Tamal (2024). Inhibition of asphaltene aggregation using deep eutectic solvents: COSMO-RS calculations and experimental validation. Journal of Molecular Liquids, 400 124471, 124471. doi: 10.1016/j.molliq.2024.124471
Healey, A. L., Garsmeur, O., Lovell, J. T., Shengquiang, S., Sreedasyam, A., Jenkins, J., Plott, C. B., Piperidis, N., Pompidor, N., Llaca, V., Metcalfe, C. J., Doležel, J., Cápal, P., Carlson, J. W., Hoarau, J. Y., Hervouet, C., Zini, C., Dievart, A., Lipzen, A., Williams, M., Boston, L. B., Webber, J., Keymanesh, K., Tejomurthula, S., Rajasekar, S., Suchecki, R., Furtado, A., May, G., Parakkal, P. ... D’Hont, A. (2024). The complex polyploid genome architecture of sugarcane. Nature, 628 (8009), 1-7. doi: 10.1038/s41586-024-07231-4
Pham, Le Thanh Mai, Deng, Kai, Choudhary, Hemant, Northen, Trent R., Singer, Steven W., Adams, Paul D., Simmons, Blake A. and Sale, Kenneth L. (2024). An Engineered Laccase from Fomitiporia mediterranea Accelerates Lignocellulose Degradation. Biomolecules, 14 (3) 324, 324. doi: 10.3390/biom14030324
Banerjee, Deepanwita, Yunus, Ian S., Wang, Xi, Kim, Jinho, Srinivasan, Aparajitha, Menchavez, Russel, Chen, Yan, Gin, Jennifer W., Petzold, Christopher J., Martin, Hector Garcia, Magnuson, Jon K., Adams, Paul D., Simmons, Blake A., Mukhopadhyay, Aindrila, Kim, Joonhoon and Lee, Taek Soon (2024). Genome-scale and pathway engineering for the sustainable aviation fuel precursor isoprenol production in Pseudomonas putida. Metabolic Engineering, 82, 157-170. doi: 10.1016/j.ymben.2024.02.004
Schieppati, Dalma, Mohan, Mood, Blais, Bruno, Fattahi, Kobra, Patience, Gregory S., Simmons, Blake A., Singh, Seema and Boffito, Daria C. (2024). Characterization of the acoustic cavitation in ionic liquids in a horn-type ultrasound reactor. Ultrasonics Sonochemistry, 102 106721, 106721. doi: 10.1016/j.ultsonch.2023.106721
Achinivu, Ezinne C., Blankenship, Brian W., Baral, Nawa Raj, Choudhary, Hemant, Kakumanu, Ramu, Mohan, Mood, Baidoo, Edward E.K., Scown, Corinne D., George, Anthe, Simmons, Blake A. and Gladden, John (2024). Biomass pretreatment with distillable ionic liquids for an effective recycling and recovery approach. Chemical Engineering Journal, 479 147824, 1-14. doi: 10.1016/j.cej.2023.147824
Baral, Nawa Raj, Banerjee, Deepanwita, Mukhopadhyay, Aindrila, Simmons, Blake A., Singer, Steven W. and Scown, Corinne D. (2023). Economic and environmental trade-offs of simultaneous sugar and lignin utilization for biobased fuels and chemicals. ACS Sustainable Chemistry and Engineering, 12 (7), 2563-2576. doi: 10.1021/acssuschemeng.3c05541
Dou, Chang, Choudhary, Hemant, Wang, Zilong, Baral, Nawa R., Mohan, Mood, Aguilar, Rolin A., Huang, Shenyue, Holiday, Alexander, Banatao, D. Rey, Singh, Seema, Scown, Corinne D., Keasling, Jay D., Simmons, Blake A. and Sun, Ning (2023). A hybrid chemical-biological approach can upcycle mixed plastic waste with reduced cost and carbon footprint. One Earth, 6 (11), 1576-1590. doi: 10.1016/j.oneear.2023.10.015
Eng, Thomas, Banerjee, Deepanwita, Menasalvas, Javier, Chen, Yan, Gin, Jennifer, Choudhary, Hemant, Baidoo, Edward, Chen, Jian Hua, Ekman, Axel, Kakumanu, Ramu, Diercks, Yuzhong Liu, Codik, Alex, Larabell, Carolyn, Gladden, John, Simmons, Blake A., Keasling, Jay D., Petzold, Christopher J. and Mukhopadhyay, Aindrila (2023). Maximizing microbial bioproduction from sustainable carbon sources using iterative systems engineering. Cell Reports, 42 (9) 113087, 113087. doi: 10.1016/j.celrep.2023.113087
Wolski, Paul, Blankenship, Brian W., Umar, Athiyya, Cabrera, Mica, Simmons, Blake A., Sale, Kenneth L. and Achinivu, Ezinne C. (2023). Factors that influence the activity of biomass-degrading enzymes in the presence of ionic liquids—a review. Frontiers in Energy Research, 11 1212719, 1-28. doi: 10.3389/fenrg.2023.1212719
Garcia, Valentina E., Pidatala, Venkataramana, Barcelos, Carolina A., Liu, Dupeng, Otoupal, Peter, Wendt, Oliver, Choudhary, Hemant, Sun, Ning, Eudes, Aymerick, Sundstrom, Eric R., Scheller, Henrik V., Putnam, Daniel H., Mukhopadhyay, Aindrila, Gladden, John M., Simmons, Blake A. and Rodriguez, Alberto (2023). Enhanced microbial production of protocatechuate from engineered sorghum using an integrated feedstock-to-product conversion technology. Green Chemistry, 25 (17), 6797-6808. doi: 10.1039/d3gc01481a
Lu, Yangsiyu, Zhou, Xiao Yan and Simmons, B. Alexander (2023). Empirical analysis of Chinese overseas power plant investments: Likelihood of suspensions and associated environmental risks. iScience, 26 (8) 107457, 1-19. doi: 10.1016/j.isci.2023.107457
Mohan, Mood, Smith, Micholas Dean, Demerdash, Omar N., Simmons, Blake A., Singh, Seema, Kidder, Michelle K. and Smith, Jeremy C. (2023). Quantum chemistry-driven machine learning approach for the prediction of the surface tension and speed of sound in ionic liquids. ACS Sustainable Chemistry and Engineering, 11 (20), 7809-7821. doi: 10.1021/acssuschemeng.3c00624
Lankiewicz, Thomas S., Choudhary, Hemant, Gao, Yu, Amer, Bashar, Lillington, Stephen P., Leggieri, Patrick A., Brown, Jennifer L., Swift, Candice L., Lipzen, Anna, Na, Hyunsoo, Amirebrahimi, Mojgan, Theodorou, Michael K., Baidoo, Edward E. K., Barry, Kerrie, Grigoriev, Igor V., Timokhin, Vitaliy I., Gladden, John, Singh, Seema, Mortimer, Jenny C., Ralph, John, Simmons, Blake A., Singer, Steven W. and O’Malley, Michelle A. (2023). Lignin deconstruction by anaerobic fungi. Nature Microbiology, 8 (4), 596-610. doi: 10.1038/s41564-023-01336-8
Hirakawa, Matthew P., Rodriguez, Alberto, Tran-Gyamfi, Mary B., Light, Yooli K., Martinez, Salvador, Diamond-Pott, Henry, Simmons, Blake A. and Sale, Kenneth L. (2023). Phenothiazines rapidly induce laccase expression and lignin-degrading properties in the white-rot fungus Phlebia radiata. Journal of Fungi, 9 (3) 371, 1-18. doi: 10.3390/jof9030371
Gauttam, Rahul, Eng, Thomas, Zhao, Zhiying, ul ain Rana, Qurrat, Simmons, Blake A., Yoshikuni, Yasuo, Mukhopadhyay, Aindrila and Singer, Steven W. (2023). Development of genetic tools for heterologous protein expression in a pentose‐utilizing environmental isolate of Pseudomonas putida. Microbial Biotechnology, 16 (3), 645-661. doi: 10.1111/1751-7915.14205
Mohan, Mood, Demerdash, Omar, Simmons, Blake A., Smith, Jeremy C., K. Kidder, Michelle and Singh, Seema (2023). Accurate prediction of carbon dioxide capture by deep eutectic solvents using quantum chemistry and a neural network. Green Chemistry, 25 (9), 3475-3492. doi: 10.1039/d2gc04425k
Choudhary, Hemant, Das, Lalitendu, Pelton, Jeffrey G., Sheps, Leonid, Simmons, Blake A., Gladden, John and Singh, Seema (2023). Funneled depolymerization of ionic liquid‐based biorefinery “Heterogeneous” lignin into guaiacols over reusable palladium catalyst. Chemistry – A European Journal, 29 (27) e202300330. doi: 10.1002/chem.202300330
Choi, Julius, Rodriguez, Alberto, Simmons, Blake A. and Gladden, John M. (2023). Valorization of hemp-based packaging waste with one-pot ionic liquid technology. Molecules, 28 (3) 1427, 1-12. doi: 10.3390/molecules28031427
Park, Mee‐Rye, Gauttam, Rahul, Fong, Bonnie, Chen, Yan, Lim, Hyun Gyu, Feist, Adam M., Mukhopadhyay, Aindrila, Petzold, Christopher J., Simmons, Blake A. and Singer, Steven W. (2023). Revealing oxidative pentose metabolism in new Pseudomonas putida isolates. Environmental Microbiology, 25 (2), 493-504. doi: 10.1111/1462-2920.16296
Martin, Hector G, Radivojevic, Tijana, Zucker, Jeremy, Bouchard, Kristofer, Sustarich, Jess, Peisert, Sean, Arnold, Dan, Hillson, Nathan, Babnigg, Gyorgy, Marti, Jose M, Mungall, Christopher J, Beckham, Gregg T, Waldburger, Lucas, Carothers, James, Sundaram, ShivShankar, Agarwal, Deb, Simmons, Blake A, Backman, Tyler, Banerjee, Deepanwita, Tanjore, Deepti, Ramakrishnan, Lavanya and Singh, Anup (2023). Perspectives for self-driving labs in synthetic biology. Current Opinion in Biotechnology, 79 102881. doi: 10.1016/j.copbio.2022.102881
Deng, Kai, Wang, Xi, Ing, Nicole, Opgenorth, Paul, de Raad, Markus, Kim, Jinho, Simmons, Blake A., Adams, Paul D., Singh, Anup K., Lee, Taek Soon and Northen, Trent R. (2023). Rapid quantification of alcohol production in microorganisms based on nanostructure-initiator mass spectrometry (NIMS). Analytical Biochemistry, 662 114997, 1-6. doi: 10.1016/j.ab.2022.114997
Mohan, Mood, Simmons, Blake A., Sale, Kenneth L. and Singh, Seema (2023). Multiscale molecular simulations for the solvation of lignin in ionic liquids. Scientific Reports, 13 (1) 271. doi: 10.1038/s41598-022-25372-2
Han, Yinglei, Simmons, Blake A. and Singh, Seema (2023). Perspective on oligomeric products from lignin depolymerization: their generation, identification, and further valorization. Industrial Chemistry & Materials, 1 (2), 207-223. doi: 10.1039/d2im00059h
Otoupal, Peter B., Geiselman, Gina M., Oka, Asun M., Barcelos, Carolina A., Choudhary, Hemant, Dinh, Duy, Zhong, Wenqing, Hwang, HeeJin, Keasling, Jay D., Mukhopadhyay, Aindrila, Sundstrom, Eric, Haushalter, Robert W., Sun, Ning, Simmons, Blake A. and Gladden, John M. (2022). Advanced one-pot deconstruction and valorization of lignocellulosic biomass into triacetic acid lactone using Rhodosporidium toruloides. Microbial Cell Factories, 21 (1) 254, 1-17. doi: 10.1186/s12934-022-01977-0
Lin, Chien-Yuan, Geiselman, Gina M., Liu, Di, Magurudeniya, Harsha D., Rodriguez, Alberto, Chen, Yi-Chun, Pidatala, Venkataramana, Unda, Faride, Amer, Bashar, Baidoo, Edward E. K., Mansfield, Shawn D., Simmons, Blake A., Singh, Seema, Scheller, Henrik V., Gladden, John M. and Eudes, Aymerick (2022). Evaluation of engineered low-lignin poplar for conversion into advanced bioproducts. Biotechnology for Biofuels and Bioproducts, 15 (1) 145, 1-12. doi: 10.1186/s13068-022-02245-4
Lin, Chien-Yuan, Tian, Yang, Nelson-Vasilchik, Kimberly, Hague, Joel, Kakumanu, Ramu, Lee, Mi Yeon, Pidatala, Venkataramana R., Trinh, Jessica, De Ben, Christopher M., Dalton, Jutta, Northen, Trent R., Baidoo, Edward E.K., Simmons, Blake A., Gladden, John M., Scown, Corinne D., Putnam, Daniel H., Kausch, Albert P., Scheller, Henrik V. and Eudes, Aymerick (2022). Engineering sorghum for higher 4-hydroxybenzoic acid content. Metabolic Engineering Communications, 15 e00207, 1-7. doi: 10.1016/j.mec.2022.e00207
Jassal, Vidhisha, Dou, Chang, Sun, Ning, Singh, Seema, Simmons, Blake A. and Choudhary, Hemant (2022). Finding values in lignin: a promising yet under-utilized component of the lignocellulosic biomass. Frontiers in Chemical Engineering, 4 1059305, 1-7. doi: 10.3389/fceng.2022.1059305
Mohan, Mood, Kumar, Nikhil, Goud, Vaibhav V, Simmons, Blake A., Sale, Kenneth L., Gladden, John M., Singh, Seema and Banerjee, Tamal (2022). Effect of cosolvent on the solubility of glucose in ionic liquids: experimental and molecular dynamics simulations. Fluid Phase Equilibria, 562 113559, 1-9. doi: 10.1016/j.fluid.2022.113559
Tom, Lauren M., Aulitto, Martina, Wu, Yu-Wei, Deng, Kai, Gao, Yu, Xiao, Naijia, Rodriguez, Beatrice Garcia, Louime, Clifford, Northen, Trent R., Eudes, Aymerick, Mortimer, Jenny C., Adams, Paul D., Scheller, Henrik V., Simmons, Blake A., Ceja-Navarro, Javier A. and Singer, Steven W. (2022). Low-abundance populations distinguish microbiome performance in plant cell wall deconstruction. Microbiome, 10 (1) 183, 1-16. doi: 10.1186/s40168-022-01377-x
Choudhary, Hemant, Pidatala, Venkataramana R., Mohan, Mood, Simmons, Blake A., Gladden, John M. and Singh, Seema (2022). Renewable schiff-base ionic liquids for lignocellulosic biomass pretreatment. Molecules, 27 (19) 6278, 1-15. doi: 10.3390/molecules27196278
Perlo, Virginie, Furtado, Agnelo, Botha, Frederik C., Margarido, Gabriel R. A., Hodgson‐Kratky, Katrina, Choudhary, Hemant, Gladden, John, Simmons, Blake and Henry, Robert J. (2022). Transcriptome and metabolome integration in sugarcane through culm development. Food and Energy Security, 11 (4) e421, 1-16. doi: 10.1002/fes3.421
Achinivu, Ezinne C., Cabrera, Mica, Umar, Athiyya, Yang, Minliang, Baral, Nawa Raj, Scown, Corinne D., Simmons, Blake A. and Gladden, John M. (2022). In situ synthesis of protic ionic liquids for biomass pretreatment. ACS Sustainable Chemistry and Engineering, 10 (37), 12090-12098. doi: 10.1021/acssuschemeng.2c01211
Mohan, Mood, L. Sale, Kenneth, Kalb, Roland S., Simmons, Blake A., Gladden, John M. and Singh, Seema (2022). Multiscale molecular simulation strategies for understanding the delignification mechanism of biomass in cyrene. ACS Sustainable Chemistry and Engineering, 10 (33), 11016-11029. doi: 10.1021/acssuschemeng.2c03373
Yang, Minliang, Liu, Di, Baral, Nawa Raj, Lin, Chien-Yuan, Simmons, Blake A., Gladden, John M., Eudes, Aymerick and Scown, Corinne D. (2022). Comparing
in planta
accumulation with microbial routes to set targets for a cost-competitive bioeconomy. Proceedings of the National Academy of Sciences, 119 (30) e2122309119, 1-10. doi: 10.1073/pnas.2122309119
Pham, Le Thanh Mai, Choudhary, Hemant, Gauttam, Rahul, Singer, Steven W., Gladden, John M., Simmons, Blake A., Singh, Seema and Sale, Kenneth L. (2022). Revisiting theoretical tools and approaches for the valorization of recalcitrant lignocellulosic biomass to value-added chemicals. Frontiers in Energy Research, 10 863153, 1-18. doi: 10.3389/fenrg.2022.863153
Mohan, Mood, Keasling, Jay D., Simmons, Blake A. and Singh, Seema (2022). In silico COSMO-RS predictive screening of ionic liquids for the dissolution of plastic. Green Chemistry, 24 (10), 4140-4152. doi: 10.1039/d1gc03464b
Choudhary, Hemant, Simmons, Blake A. and Gladden, John M. (2022). Comparative study on the pretreatment of aspen and maple with 1-ethyl-3-methylimidazolium acetate and cholinium lysinate. Frontiers in Energy Research, 10 868181, 1-8. doi: 10.3389/fenrg.2022.868181
Park, Mee-Rye, Fong, Bonnie, Tofaha, Taqwa, Simmons, Blake A. and Singer, Steven (2022). Complete genome sequences of five isolated Pseudomonas strains that catabolize pentose sugars and aromatic compounds obtained from lignocellulosic biomass. Microbiology Resource Announcements, 11 (4), 1-3. doi: 10.1128/mra.00987-21
Rahaman, Mohammad Shahinur, Tulaphol, Sarttrawut, Hossain, Md Anwar, Jasinski, Jacek B., Sun, Ning, George, Anthe, Simmons, Blake A., Maihom, Thana, Crocker, Mark and Sathitsuksanoh, Noppadon (2022). Cooperative Brønsted-Lewis acid sites created by phosphotungstic acid encapsulated metal–organic frameworks for selective glucose conversion to 5-hydroxymethylfurfural. Fuel, 310 122459, 1-13. doi: 10.1016/j.fuel.2021.122459
Martinez, Daniella V., Rodriguez, Alberto, Juarros, Miranda A., Martinez, Estevan J., Alam, Todd M., Simmons, Blake A., Sale, Kenneth L., Singer, Steven W. and Kent, Michael S. (2022). Depolymerization of lignin for biological conversion through sulfonation and a chelator-mediated Fenton reaction. Green Chemistry, 24 (4), 1627-1643. doi: 10.1039/d1gc03854k
Bin, Jianhui, Obst-Huebl, Lieselotte, Mao, Jian-Hua, Nakamura, Kei, Geulig, Laura D., Chang, Hang, Ji, Qing, He, Li, De Chant, Jared, Kober, Zachary, Gonsalves, Anthony J., Bulanov, Stepan, Celniker, Susan E., Schroeder, Carl B., Geddes, Cameron G. R., Esarey, Eric, Simmons, Blake A., Schenkel, Thomas, Blakely, Eleanor A., Steinke, Sven and Snijders, Antoine M. (2022). A new platform for ultra-high dose rate radiobiological research using the BELLA PW laser proton beamline. Scientific Reports, 12 (1) 1484, 1-15. doi: 10.1038/s41598-022-05181-3
Leynaud Kieffer Curran, Laure M.C., Pham, Le Thanh Mai, Sale, Kenneth L. and Simmons, Blake A. (2022). Review of advances in the development of laccases for the valorization of lignin to enable the production of lignocellulosic biofuels and bioproducts. Biotechnology Advances, 54 107809, 1-12. doi: 10.1016/j.biotechadv.2021.107809
Pérez Pimienta, José A., Papa, Gabriella, Sun, Jian, Stavila, Vitalie, Sanchez, Arturo, Gladden, John M. and Simmons, Blake A. (2022). One-pot ethanol production under optimized pretreatment conditions using agave bagasse at high solids loading with low-cost biocompatible protic ionic liquid. Green Chemistry, 24 (1), 207-217. doi: 10.1039/d1gc03774a
Mohan, Mood, Huang, Kaixuan, Pidatala, Venkataramana R., Simmons, Blake A., Singh, Seema, Sale, Kenneth L. and Gladden, John M. (2022). Prediction of solubility parameters of lignin and ionic liquids using multi-resolution simulation approaches. Green Chemistry, 24 (3), 1165-1176. doi: 10.1039/d1gc03798f
Rodriguez, Alberto, Meadows, Jamie A., Sun, Ning, Simmons, Blake A. and Gladden, John M. (2021). Evaluation of bacterial hosts for conversion of lignin-derived p-coumaric acid to 4-vinylphenol. Microbial Cell Factories, 20 (1) 181, 1-10. doi: 10.1186/s12934-021-01670-8
Banerjee, Deepanwita, Eng, Thomas, Sasaki, Yusuke, Srinivasan, Aparajitha, Oka, Asun, Herbert, Robin A., Trinh, Jessica, Singan, Vasanth R., Sun, Ning, Putnam, Dan, Scown, Corinne D., Simmons, Blake and Mukhopadhyay, Aindrila (2021). Genomics characterization of an engineered Corynebacterium glutamicum in bioreactor cultivation under ionic liquid stress. Frontiers in Bioengineering and Biotechnology, 9 766674, 1-16. doi: 10.3389/fbioe.2021.766674
Pérez-Pimienta, Jose A., García-López, Rocío M., Méndez-Acosta, Hugo O., González-Álvarez, Víctor, Simmons, Blake A., Méndoza-Pérez, Jorge A. and Arreola-Vargas, Jorge (2021). Ionic liquid-water mixtures enhance pretreatment and anaerobic digestion of agave bagasse. Industrial Crops and Products, 171 113924, 1-10. doi: 10.1016/j.indcrop.2021.113924
Achinivu, Ezinne C., Frank, Skye, Baral, Nawa Raj, Das, Lalitendu, Mohan, Mood, Otoupal, Peter, Shabir, Emara, Utan, Sean, Scown, Corinne D., Simmons, Blake A. and Gladden, John (2021). Alkanolamines as dual functional solvents for biomass deconstruction and bioenergy production. Green Chemistry, 23 (21), 8611-8631. doi: 10.1039/d1gc02667d
Baral, Nawa Raj, Yang, Minliang, Harvey, Benjamin G., Simmons, Blake A., Mukhopadhyay, Aindrila, Lee, Taek Soon and Scown, Corinne D. (2021). Production cost and carbon footprint of biomass-derived dimethylcyclooctane as a high-performance jet fuel blendstock. ACS Sustainable Chemistry and Engineering, 9 (35), 11872-11882. doi: 10.1021/acssuschemeng.1c03772
Mohan, Mood, Choudhary, Hemant, George, Anthe, Simmons, Blake A., Sale, Kenneth and Gladden, John M. (2021). Towards understanding of delignification of grassy and woody biomass in cholinium-based ionic liquids. Green Chemistry, 23 (16), 6020-6035. doi: 10.1039/d1gc01622a
Lim, Hyun Gyu, Eng, Thomas, Banerjee, Deepanwita, Alarcon, Geovanni, Lau, Andrew K., Park, Mee-Rye, Simmons, Blake A., Palsson, Bernhard O., Singer, Steven W., Mukhopadhyay, Aindrila and Feist, Adam M. (2021). Generation of Pseudomonas putida KT2440 strains with efficient utilization of xylose and galactose via adaptive laboratory evolution. ACS Sustainable Chemistry and Engineering, 9 (34) acssuschemeng.1c03765, 11512-11523. doi: 10.1021/acssuschemeng.1c03765
Cole, Benjamin, Bergmann, Dominique, Blaby-Haas, Crysten E., Blaby, Ian K., Bouchard, Kristofer E., Brady, Siobhan M., Ciobanu, Doina, Coleman-Derr, Devin, Leiboff, Samuel, Mortimer, Jenny C., Nobori, Tatsuya, Rhee, Seung Y., Schmutz, Jeremy, Simmons, Blake A., Singh, Anup K., Sinha, Neelima, Vogel, John P., O’Malley, Ronan C., Visel, Axel and Dickel, Diane E. (2021). Plant single-cell solutions for energy and the environment. Communications Biology, 4 (1) 962, 1-12. doi: 10.1038/s42003-021-02477-4
Huang, Kaixuan, Mohan, Mood, George, Anthe, Simmons, Blake A., Xu, Yong and Gladden, John M. (2021). Integration of acetic acid catalysis with one-pot protic ionic liquid configuration to achieve high-efficient biorefinery of poplar biomass. Green Chemistry, 23 (16), 6036-6049. doi: 10.1039/d1gc01727f
Gabriel, Raphael, Thieme, Nils, Liu, Qian, Li, Fangya, Kohler, Lisa T., Harth, Simon, Jecmenica, Marina, Ramamurthy, Maya, Gorman, Jennifer, Simmons, Blake A., McCluskey, Kevin, Baker, Scott E., Tian, Chaoguang, Schuerg, Timo, Singer, Steven W., Fleißner, André and Benz, J. Philipp (2021). The F-box protein gene exo-1 is a target for reverse engineering enzyme hypersecretion in filamentous fungi. Proceedings of the National Academy of Sciences, 118 (26) e2025689118, 1-9. doi: 10.1073/pnas.2025689118
Healey, Adam L., Shepherd, Mervyn, King, Graham J., Butler, Jakob B., Freeman, Jules S., Lee, David J., Potts, Brad M., Silva-Junior, Orzenil B., Baten, Abdul, Jenkins, Jerry, Shu, Shengqiang, Lovell, John T., Sreedasyam, Avinash, Grimwood, Jane, Furtado, Agnelo, Grattapaglia, Dario, Barry, Kerrie W., Hundley, Hope, Simmons, Blake A., Schmutz, Jeremy, Vaillancourt, René E. and Henry, Robert J. (2021). Pests, diseases, and aridity have shaped the genome of Corymbia citriodora. Communications Biology, 4 (1) 537, 1-13. doi: 10.1038/s42003-021-02009-0
Magurudeniya, Harsha D., Baral, Nawa Raj, Rodriguez, Alberto, Scown, Corinne D., Dahlberg, Jeff, Putnam, Daniel, George, Anthe, Simmons, Blake A. and Gladden, John M. (2021). Use of ensiled biomass sorghum increases ionic liquid pretreatment efficiency and reduces biofuel production cost and carbon footprint. Green Chemistry, 23 (8), 3127-3140. doi: 10.1039/d0gc03260c
Das, Lalitendu, Achinivu, Ezinne C., Barcelos, Carolina Araujo, Sundstrom, Eric, Amer, Bashar, Baidoo, Edward E. K., Simmons, Blake A., Sun, Ning and Gladden, John M. (2021). Deconstruction of woody biomass via protic and aprotic ionic liquid pretreatment for ethanol production. ACS Sustainable Chemistry and Engineering, 9 (12), 4422-4432. doi: 10.1021/acssuschemeng.0c07925
Barcelos, Carolina A., Oka, Asun M., Yan, Jipeng, Das, Lalitendu, Achinivu, Ezinne C., Magurudeniya, Harsha, Dong, Jie, Akdemir, Simay, Baral, Nawa Raj, Yan, Chunsheng, Scown, Corinne D., Tanjore, Deepti, Sun, Ning, Simmons, Blake A., Gladden, John and Sundstrom, Eric (2021). High-efficiency conversion of ionic liquid-pretreated woody biomass to ethanol at the pilot scale. ACS Sustainable Chemistry and Engineering, 9 (11), 4042-4053. doi: 10.1021/acssuschemeng.0c07920
Yao, Alexander, Choudhary, Hemant, Mohan, Mood, Rodriguez, Alberto, Magurudeniya, Harsha, Pelton, Jeffrey G., George, Anthe, Simmons, Blake A. and Gladden, John M. (2021). Can multiple ions in an ionic liquid improve the biomass pretreatment efficacy?. ACS Sustainable Chemistry and Engineering, 9 (12), 4371-4376. doi: 10.1021/acssuschemeng.0c09330
Hodgson-Kratky, K., Perlo, V., Furtado, A., Choudhary, H., Gladden, J. M., Simmons, B. A., Botha, F. and Henry, R. J. (2021). Association of gene expression with syringyl to guaiacyl ratio in sugarcane lignin. Plant Molecular Biology, 106 (1-2), 173-192. doi: 10.1007/s11103-021-01136-w
Kim, Jinho, Baidoo, Edward E.K., Amer, Bashar, Mukhopadhyay, Aindrila, Adams, Paul D., Simmons, Blake A. and Lee, Taek Soon (2021). Engineering Saccharomyces cerevisiae for isoprenol production. Metabolic Engineering, 64, 154-166. doi: 10.1016/j.ymben.2021.02.002
Brunner, Manuel, Imberti, Silvia, Simmons, Blake A., Warr, Gregory G. and Atkin, Rob (2021). Liquid nanostructure of cholinium argininate biomass solvents. ACS Sustainable Chemistry and Engineering, 9 (7), 2880-2890. doi: 10.1021/acssuschemeng.0c08829
Das, Lalitendu, Geiselman, Gina M., Rodriguez, Alberto, Magurudeniya, Harsha D., Kirby, James, Simmons, Blake A. and Gladden, John M. (2021). Seawater-based one-pot ionic liquid pretreatment of sorghum for jet fuel production. Bioresource Technology Reports, 13 100622, 1-5. doi: 10.1016/j.biteb.2020.100622
Lawson, Christopher E., Martí, Jose Manuel, Radivojevic, Tijana, Jonnalagadda, Sai Vamshi R., Gentz, Reinhard, Hillson, Nathan J., Peisert, Sean, Kim, Joonhoon, Simmons, Blake A., Petzold, Christopher J., Singer, Steven W., Mukhopadhyay, Aindrila, Tanjore, Deepti, Dunn, Joshua G. and Garcia Martin, Hector (2021). Machine learning for metabolic engineering: a review. Metabolic Engineering, 63, 34-60. doi: 10.1016/j.ymben.2020.10.005
Achinivu, Ezinne C., Mohan, Mood, Choudhary, Hemant, Das, Lalitendu, Huang, Kaixuan, Magurudeniya, Harsha D., Pidatala, Venkataramana R., George, Anthe, Simmons, Blake A. and Gladden, John M. (2021). A predictive toolset for the identification of effective lignocellulosic pretreatment solvents: a case study of solvents tailored for lignin extraction. Green Chemistry, 23 (18), 7269-7289. doi: 10.1039/d1gc01186c
Gauttam, Rahul, Mukhopadhyay, Aindrila, Simmons, Blake A. and Singer, Steven W. (2021). Development of dual-inducible duet-expression vectors for tunable gene expression control and CRISPR interference-based gene repression in Pseudomonas putida KT2440. Microbial Biotechnology, 14 (6), 2659-2678. doi: 10.1111/1751-7915.13832
Mason, Patrick J., Furtado, Agnelo, Marquardt, Annelie, Hodgson-Kratky, Katrina, Hoang, Nam V., Botha, Frederik C., Papa, Gabriella, Mortimer, Jenny C., Simmons, Blake and Henry, Robert J. (2020). Variation in sugarcane biomass composition and enzymatic saccharification of leaves, internodes and roots. Biotechnology for Biofuels, 13 (1) 201, 1-19. doi: 10.1186/s13068-020-01837-2
Mohamed, Elsayed T., Werner, Allison Z., Salvachúa, Davinia, Singer, Christine A., Szostkiewicz, Kiki, Rafael Jiménez-Díaz, Manuel, Eng, Thomas, Radi, Mohammad S., Simmons, Blake A., Mukhopadhyay, Aindrila, Herrgård, Markus J., Singer, Steven W., Beckham, Gregg T. and Feist, Adam M. (2020). Adaptive laboratory evolution of Pseudomonas putida KT2440 improves p-coumaric and ferulic acid catabolism and tolerance. Metabolic Engineering Communications, 11 e00143, 1-11. doi: 10.1016/j.mec.2020.e00143
Geiselman, Gina M., Kirby, James, Landera, Alexander, Otoupal, Peter, Papa, Gabriella, Barcelos, Carolina, Sundstrom, Eric R., Das, Lalitendu, Magurudeniya, Harsha D., Wehrs, Maren, Rodriguez, Alberto, Simmons, Blake A., Magnuson, Jon K., Mukhopadhyay, Aindrila, Lee, Taek Soon, George, Anthe and Gladden, John M. (2020). Conversion of poplar biomass into high-energy density tricyclic sesquiterpene jet fuel blendstocks. Microbial Cell Factories, 19 (1) 208, 1-16. doi: 10.1186/s12934-020-01456-4
Aulitto, Martina, Tom, Lauren M., Ceja-Navarro, Javier A., Simmons, Blake A. and Singer, Steven W. (2020). Whole-genome sequence of brevibacillus borstelensis SDM, isolated from a sorghum-adapted microbial community. Microbiology Resource Announcements, 9 (48) e01046-20, 1-2. doi: 10.1128/MRA.01046-20
Achmon, Yigal, Claypool, Joshua T., Fernández-Bayo, Jesús D., Hernandez, Katie, McCurry, Dlinka G., Harrold, Duff R., Su, Joey, Simmons, Blake A., Singer, Steven W., Dahlquist-Willard, Ruth M., Stapleton, James J., VanderGheynst, Jean S. and Simmons, Christopher W. (2020). Structural changes in bacterial and fungal soil microbiome components during biosolarization as related to volatile fatty acid accumulation. Applied Soil Ecology, 153 103602, 1-12. doi: 10.1016/j.apsoil.2020.103602
Park, Mee-Rye, Chen, Yan, Thompson, Mitchell, Benites, Veronica T., Fong, Bonnie, Petzold, Christopher J., Baidoo, Edward E. K., Gladden, John M., Adams, Paul D., Keasling, Jay D., Simmons, Blake A. and Singer, Steven W. (2020). Response of Pseudomonas putida to Complex, Aromatic-Rich Fractions from Biomass. ChemSusChem, 13 (17) cssc.202000268, 4455-4467. doi: 10.1002/cssc.202000268
Jacquet, Nicolas, Eudes, Aymerick, Dutta, Tanmoy, Kim, Kwang Ho, Bouxin, Florent, Benites, Veronica, Baidoo, Edward, Singh, Seema, Simmons, Blake, Loqué, Dominique and Richel, Aurore (2020). Influence of hydrocracking and ionic liquid pretreatments on composition and properties of Arabidopsis thaliana wild type and CAD mutant lignins. Renewable Energy, 152, 1241-1249. doi: 10.1016/j.renene.2020.01.153
Pérez-Pimienta, José A., Papa, Gabriela, Gladden, John M., Simmons, Blake A. and Sanchez, Arturo (2020). The effect of continuous tubular reactor technologies on the pretreatment of lignocellulosic biomass at pilot-scale for bioethanol production. RSC Advances, 10 (31), 18147-18159. doi: 10.1039/d0ra04031b
Yang, Minliang, Baral, Nawa Raj, Simmons, Blake A., Mortimer, Jenny C., Shih, Patrick M. and Scown, Corinne D. (2020). Accumulation of high-value bioproducts in planta can improve the economics of advanced biofuels. Proceedings of the National Academy of Sciences, 117 (15), 202000053-8648. doi: 10.1073/pnas.2000053117
Kjærbølling, Inge, Vesth, Tammi, Frisvad, Jens C., Nybo, Jane L., Theobald, Sebastian, Kildgaard, Sara, Petersen, Thomas Isbrandt, Kuo, Alan, Sato, Atsushi, Lyhne, Ellen K., Kogle, Martin E., Wiebenga, Ad, Kun, Roland S., Lubbers, Ronnie J. M., Mäkelä, Miia R., Barry, Kerrie, Chovatia, Mansi, Clum, Alicia, Daum, Chris, Haridas, Sajeet, He, Guifen, LaButti, Kurt, Lipzen, Anna, Mondo, Stephen, Pangilinan, Jasmyn, Riley, Robert, Salamov, Asaf, Simmons, Blake A., Magnuson, Jon K. ... Andersen, Mikael R. (2020). A comparative genomics study of 23 Aspergillus species from section Flavi. Nature Communications, 11 (1) 1106, 1106. doi: 10.1038/s41467-019-14051-y
Ju, Zhaoyang, Xiao, Weihua, Yao, Xiaoqian, Tan, Xin, Simmons, Blake A., Sale, Kenneth L. and Sun, Ning (2020). Theoretical study on the microscopic mechanism of lignin solubilization in Keggin-type polyoxometalate ionic liquids. Physical Chemistry Chemical Physics, 22 (5), 2878-2886. doi: 10.1039/c9cp05339e
Hossain, Anwar, Rahaman, Mohammad Shahinur, Lee, David, Phung, Thanh Khoa, Canlas, Christian G., Simmons, Blake A., Renneckar, Scott, Reynolds, William, George, Anthe, Tulaphol, Sarttrawut and Sathitsuksanoh, Noppadon (2020). Enhanced softwood cellulose accessibility by H3PO4 pretreatment: high sugar yield without compromising lignin integrity. Industrial and Engineering Chemistry Research, 59 (2) acs.iecr.9b05873, 1010-1024. doi: 10.1021/acs.iecr.9b05873
Rigual, Victoria, Papa, Gabriella, Rodriguez, Alberto, Wehrs, Maren, Kim, Kwang Ho, Oliet, Mercedes, Alonso, M. Virginia, Gladden, John M., Mukhopadhyay, Aindrila, Simmons, Blake A. and Singh, Seema (2020). Evaluating protic ionic liquid for woody biomass one-pot pretreatment + saccharification, followed by Rhodosporidium toruloides cultivation. ACS Sustainable Chemistry and Engineering, 8 (2), 782-791. doi: 10.1021/acssuschemeng.9b04451
Yabushita, Mizuho, Papa, Gabriella, Li, Peng, Fukuoka, Atsushi, Farha, Omar K., Simmons, Blake A. and Katz, Alexander (2020). Effect of ionic liquid on sugar-aromatic separation selectivity by metal-organic framework NU-1000 in aqueous solution. Fuel Processing Technology, 197 106189, 106189. doi: 10.1016/j.fuproc.2019.106189
Sitepu, Irnayuli, Enriquez, Lauren, Nguyen, Valerie, Fry, Russell, Simmons, Blake, Singer, Steve, Simmons, Christopher and Boundy-Mills, Kyria L. (2020). Ionic liquid tolerance of yeasts in family Dipodascaceae and genus Wickerhamomyces. Applied Biochemistry and Biotechnology, 191 (4), 1580-1593. doi: 10.1007/s12010-020-03293-y
Lim, Hyun Gyu, Fong, Bonnie, Alarcon, Geovanni, Magurudeniya, Harsha D., Eng, Thomas, Szubin, Richard, Olson, Connor A., Palsson, Bernhard O., Gladden, John M., Simmons, Blake A., Mukhopadhyay, Aindrila, Singer, Steven W. and Feist, Adam M. (2020). Generation of ionic liquid tolerant Pseudomonas putida KT2440 strains via adaptive laboratory evolution. Green Chemistry, 22 (17), 5677-5690. doi: 10.1039/d0gc01663b
Carrozza, Chiara Francesca, Papa, Gabriella, Citterio, Attilio, Sebastiano, Roberto, Simmons, Blake A. and Singh, Seema (2019). One-pot bio-derived ionic liquid conversion followed by hydrogenolysis reaction for biomass valorization: a promising approach affecting the morphology and quality of lignin of switchgrass and poplar. Bioresource Technology, 294 122214, 122214. doi: 10.1016/j.biortech.2019.122214
Wehrs, Maren, Gladden, John M., Liu, Yuzhong, Platz, Lukas, Prahl, Jan-Philip, Moon, Jadie, Papa, Gabriella, Sundstrom, Eric, Geiselman, Gina M., Tanjore, Deepti, Keasling, Jay D., Pray, Todd R., Simmons, Blake A. and Mukhopadhyay, Aindrila (2019). Correction: Sustainable bioproduction of the blue pigment indigoidine: Expanding the range of heterologous products in R. toruloides to include non-ribosomal peptides. Green Chemistry, 21 (21), 6027-6029. doi: 10.1039/c9gc90091h
Baral, Nawa Raj, Kavvada, Olga, Perez, Daniel Mendez, Mukhopadhyay, Aindrila, Lee, Taek Soon, Simmons, Blake A. and Scown, Corinne D. (2019). Greenhouse gas footprint, water-intensity, and production cost of bio-based isopentenol as a renewable transportation fuel. ACS Sustainable Chemistry and Engineering, 7 (18), 15434-15444. doi: 10.1021/acssuschemeng.9b02928
Derose, Katherine, Liu, Fang, Davis, Ryan W., Simmons, Blake A. and Quinn, Jason C. (2019). Conversion of distiller's grains to renewable fuels and high value protein: integrated techno-economic and life cycle assessment. Environmental Science and Technology, 53 (17), 10525-10533. doi: 10.1021/acs.est.9b03273
Sitepu, Irnayuli R., Enriquez, Lauren L., Nguyen, Valerie, Doyle, Carolyn, Simmons, Blake A., Singer, Steven W., Fry, Russell, Simmons, Christopher W. and Boundy-Mills, Kyria (2019). Ethanol production in switchgrass hydrolysate by ionic liquid-tolerant yeasts. Bioresource Technology Reports, 7 100275, 1-10. doi: 10.1016/j.biteb.2019.100275
Rodriguez, Alberto, Ersig, Nadine, Geiselman, Gina M., Seibel, Katharina, Simmons, Blake A., Magnuson, Jon K., Eudes, Aymerick and Gladden, John M. (2019). Conversion of depolymerized sugars and aromatics from engineered feedstocks by two oleaginous red yeasts. Bioresource Technology, 286 121365, 121365. doi: 10.1016/j.biortech.2019.121365
Dong, Jie, Chen, Yan, Benites, Veronica Teixeira, Baidoo, Edward E K, Petzold, Christopher J., Beller, Harry R., Eudes, Aymerick, Scheller, Henrik V., Adams, Paul D., Mukhopadhyay, Aindrila, Simmons, Blake A. and Singer, Steven W. (2019). Methyl ketone production by Pseudomonas putida is enhanced by plant-derived amino acids. Biotechnology and Bioengineering, 116 (8), 1909-1922. doi: 10.1002/bit.26995
Higgins, Douglas A., Gladden, John M., Kimbrel, Jeff A., Simmons, Blake A., Singer, Steven W. and Thelen, Michael P. (2019). Guanidine riboswitch-regulated efflux transporters protect bacteria against ionic liquid toxicity. Journal of Bacteriology, 201 (13) e00069-19. doi: 10.1128/JB.00069-19
Nora, Luísa Czamanski, Wehrs, Maren, Kim, Joonhoon, Cheng, Jan-Fang, Tarver, Angela, Simmons, Blake A., Magnuson, Jon, Harmon-Smith, Miranda, Silva-Rocha, Rafael, Gladden, John M., Mukhopadhyay, Aindrila, Skerker, Jeffrey M. and Kirby, James (2019). A toolset of constitutive promoters for metabolic engineering of Rhodosporidium toruloides. Microbial Cell Factories, 18 (1) 117. doi: 10.1186/s12934-019-1167-0
Wang, Shizeng, Cheng, Gang, Dong, Jie, Tian, Tian, Lee, Taek Soon, Mukhopadhyay, Aindrila, Simmons, Blake A., Yuan, Qipeng and Singer, Steven W. (2019). NaCl enhances Escherichia coli growth and isoprenol production in the presence of imidazolium-based ionic liquids. Bioresource Technology Reports, 6, 1-5. doi: 10.1016/j.biteb.2019.01.021
Yang, Mingkun, Zhao, Wenwen, Wang, Shizeng, Yu, Changyuan, Singh, Seema, Simmons, Blake and Cheng, Gang (2019). Dimethyl sulfoxide assisted dissolution of cellulose in 1-ethyl-3-methylimidazoium acetate: small angle neutron scattering and rheological studies. Cellulose, 26 (4), 2243-2253. doi: 10.1007/s10570-018-2218-0
Sasaki, Yusuke, Eng, Thomas, Herbert, Robin A., Trinh, Jessica, Chen, Yan, Rodriguez, Alberto, Gladden, John, Simmons, Blake A., Petzold, Christopher J. and Mukhopadhyay, Aindrila (2019). Engineering Corynebacterium glutamicum to produce the biogasoline isopentenol from plant biomass hydrolysates. Biotechnology for Biofuels, 12 (1) 41, 41. doi: 10.1186/s13068-019-1381-3
Achmon, Yigal, Claypool, Joshua T., Pace, Sara, Simmons, Blake A., Singer, Steven W. and Simmons, Christopher W. (2019). Assessment of biogas production and microbial ecology in a high solid anaerobic digestion of major California food processing residues. Bioresource Technology Reports, 5, 1-11. doi: 10.1016/j.biteb.2018.11.007
Leynaud-Kieffer, Laure M.C., Curran, Samuel C., Kim, Irene, Magnuson, Jon K., Gladden, John M., Baker, Scott E. and Simmons, Blake A. (2019). A new approach to Cas9-based genome editing in Aspergillus niger that is precise, efficient and selectable. PLoS ONE, 14 (1) e0210243, e0210243. doi: 10.1371/journal.pone.0210243
Jiang, Haihui Joy, Imberti, Silvia, Simmons, Blake A., Atkin, Rob and Warr, Gregory G. (2019). Structural design of ionic liquids for optimizing aromatic dissolution. ChemSusChem, 12 (1), 270-274. doi: 10.1002/cssc.201802016
Wang, Shizeng, Cheng, Gang, Dong, Jie, Tian, Tian, Lee, Taek Soon, Mukhopadhyay, Aindrila, Simmons, Blake A., Yuan, Qipeng and Singer, Steven W. (2019). Tolerance characterization and isoprenol production of adapted Escherichia coli in the presence of ionic liquids. ACS Sustainable Chemistry and Engineering, 7 (1), 1457-1463. doi: 10.1021/acssuschemeng.8b05144
Pérez Pimienta, José A., Papa, Gabriella, Rodriguez, Alberto, Barcelos, Carolina A., Liang, Ling, Stavila, Vitalie, Sanchez, Arturo, Gladden, John M. and Simmons, Blake A. (2019). Pilot-scale hydrothermal pretreatment and optimized saccharification enables bisabolene production from multiple feedstocks. Green Chemistry, 21 (11), 3152-3164. doi: 10.1039/c9gc00323a
Baral, Nawa Raj, Kavvada, Olga, Mendez-Perez, Daniel, Mukhopadhyay, Aindrila, Lee, Taek Soon, Simmons, Blake A. and Scown, Corinne D. (2019). Techno-economic analysis and life-cycle greenhouse gas mitigation cost of five routes to bio-jet fuel blendstocks. Energy & Environmental Science, 12 (3), 807-824. doi: 10.1039/c8ee03266a
Martinez-Hernandez, Elias, Cui, Xinguang, Scown, Corinne D., Amezcua-Allieri, Myriam A., Aburto, Jorge and Simmons, Blake A. (2019). Techno-economic and greenhouse gas analyses of lignin valorization to eugenol and phenolic products in integrated ethanol biorefineries. Biofuels, Bioproducts and Biorefining, 13 (4) bbb.1989, 978-993. doi: 10.1002/bbb.1989
Wehrs, Maren, Gladden, John M., Liu, Yuzhong, Platz, Lukas, Prahl, Jan-Philip, Moon, Jadie, Papa, Gabriella, Sundstrom, Eric, Geiselman, Gina M., Tanjore, Deepti, Keasling, Jay D., Pray, Todd R., Simmons, Blake A. and Mukhopadhyay, Aindrila (2019). Sustainable bioproduction of the blue pigment indigoidine: expanding the range of heterologous products in R. toruloides to include non-ribosomal peptides. Green Chemistry, 21 (12), 3394-3406. doi: 10.1039/c9gc00920e
Narani, Akash, Konda, N. V. S. N. Murthy, Chen, Chyi-Shin, Tachea, Firehiwot, Coffman, Phil, Gardner, James, Li, Chenlin, Ray, Allison E., Hartley, Damon S., Simmons, Blake, Pray, Todd R. and Tanjore, Deepti (2019). Simultaneous application of predictive model and least cost formulation can substantially benefit biorefineries outside Corn Belt in United States: a case study in Florida. Bioresource Technology, 271, 218-227. doi: 10.1016/j.biortech.2018.09.103
Pomraning, Kyle R., Bredeweg, Erin L., Kerkhoven, Eduard J., Barry, Kerrie, Haridas, Sajeet, Hundley, Hope, LaButti, Kurt, Lipzen, Anna, Yan, Mi, Magnuson, Jon K., Simmons, Blake A., Grigoriev, Igor V., Nielsen, Jens and Baker, Scott E. (2018). Regulation of Yeast-to-Hyphae Transition in Yarrowia lipolytica. mSphere, 3 (6) e00541-18. doi: 10.1128/mSphere.00541-18
Yuzawa, Satoshi, Mirsiaghi, Mona, Jocic, Renee, Fujii, Tatsuya, Masson, Fabrice, Benites, Veronica T., Baidoo, Edward E. K., Sundstrom, Eric, Tanjore, Deepti, Pray, Todd R., George, Anthe, Davis, Ryan W., Gladden, John M., Simmons, Blake A., Katz, Leonard and Keasling, Jay D. (2018). Short-chain ketone production by engineered polyketide synthases in Streptomyces albus. Nature Communications, 9 (1) 4569, 4569. doi: 10.1038/s41467-018-07040-0
Ruegg, Thomas L., Pereira, Jose H., Chen, Joseph C., DeGiovanni, Andy, Novichkov, Pavel, Mutalik, Vivek K., Tomaleri, Giovani P., Singer, Steven W., Hillson, Nathan J., Simmons, Blake A., Adams, Paul D. and Thelen, Michael P. (2018). Author correction: Jungle Express is a versatile repressor system for tight transcriptional control (Nature communications (2018) 9 1 (3617)). Nature communications, 9 (1) 4596, 4596. doi: 10.1038/s41467-018-07111-2
Vesth, Tammi C., Nybo, Jane L., Theobald, Sebastian, Frisvad, Jens C., Larsen, Thomas O., Nielsen, Kristian F., Hoof, Jakob B., Brandl, Julian, Salamov, Asaf, Riley, Robert, Gladden, John M., Phatale, Pallavi, Nielsen, Morten T., Lyhne, Ellen K., Kogle, Martin E., Strasser, Kimchi, McDonnell, Erin, Barry, Kerrie, Clum, Alicia, Chen, Cindy, LaButti, Kurt, Haridas, Sajeet, Nolan, Matt, Sandor, Laura, Kuo, Alan, Lipzen, Anna, Hainaut, Matthieu, Drula, Elodie, Tsang, Adrian ... Andersen, Mikael R. (2018). Investigation of inter- and intraspecies variation through genome sequencing of Aspergillus section Nigri. Nature Genetics, 50 (12), 1688-1695. doi: 10.1038/s41588-018-0246-1
Villegas Calvo, Mariana, Colombo, Bianca, Corno, Luca, Eisele, Giorgio, Cosentino, Cesare, Papa, Gabriella, Scaglia, Barbara, Pilu, Roberto, Simmons, Blake and Adani, Fabrizio (2018). Bioconversion of giant cane for integrated production of biohydrogen, carboxylic acids, and polyhydroxyalkanoates (PHAs) in a multistage biorefinery approach. ACS Sustainable Chemistry and Engineering, 6 (11), 15361-15373. doi: 10.1021/acssuschemeng.8b03794
Deng, Kai, Zeng, Jijiao, Cheng, Gang, Gao, Jian, Sale, Kenneth L., Simmons, Blake A., Singh, Anup K., Adams, Paul D. and Northen, Trent R. (2018). Rapid characterization of the activities of lignin-modifying enzymes based on nanostructure-initiator mass spectrometry (NIMS). Biotechnology for Biofuels, 11 (1) 266. doi: 10.1186/s13068-018-1261-2
Yang, Mingkun, Zhao, Wenwen, Singh, Seema, Simmons, Blake and Cheng, Gang (2018). On the solution structure of kraft lignin in ethylene glycol and its implication for nanoparticle preparation. Nanoscale Advances, 1 (1), 299-304. doi: 10.1039/c8na00042e
Ruegg, Thomas L., Pereira, Jose H., Chen, Joseph C., DeGiovanni, Andy, Novichkov, Pavel, Mutalik, Vivek K., Tomaleri, Giovani P., Singer, Steven W., Hillson, Nathan J., Simmons, Blake A., Adams, Paul D. and Thelen, Michael P. (2018). Jungle Express is a versatile repressor system for tight transcriptional control. Nature Communications, 9 (1) 3617, 3617. doi: 10.1038/s41467-018-05857-3
Higgins, Douglas A., Young, Megan K. M., Tremaine, Mary, Sardi, Maria, Fletcher, Jenna M., Agnew, Margaret, Liu, Lisa, Dickinson, Quinn, Peris, David, Wrobel, Russell L., Hittinger, Chris Todd, Gasch, Audrey P., Singer, Steven W., Simmons, Blake A., Landick, Robert, Thelen, Michael P. and Sato, Trey K. (2018). Natural variation in the multidrug efflux pump SGE1 underlies ionic liquid tolerance in yeast. Genetics, 210 (1), 219-234. doi: 10.1534/genetics.118.301161
Kohler, Amanda C., Simmons, Blake A. and Sale, Kenneth L. (2018). Structure-based engineering of a plant-fungal hybrid peroxidase for enhanced temperature and pH tolerance. Cell Chemical Biology, 25 (8), 974-983.e3. doi: 10.1016/j.chembiol.2018.04.014
Bouxin, Florent P., Strub, Henri, Dutta, Tanmoy, Aguilhon, Julie, Morgan, Trevor J., Mingardon, Florence, Konda, Murthy, Singh, Seema, Simmons, Blake and George, Anthe (2018). Elucidating transfer hydrogenation mechanisms in non-catalytic lignin depolymerization. Green Chemistry, 20 (15), 3566-3580. doi: 10.1039/c7gc03239k
Liang, Ling, Yan, Jipeng, He, Qian, Luong, Tina, Pray, Todd R., Simmons, Blake A. and Sun, Ning (2018). Scale-up of biomass conversion using 1-ethyl-3-methylimidazolium acetate as the solvent. Green Energy and Environment, 4 (4), 432-438. doi: 10.1016/j.gee.2018.07.002
Kimbrel, Jeffrey A., Ballor, Nicholas, Wu, Yu-Wei, David, Maude M., Hazen, Terry C., Simmons, Blake A., Singer, Steven W. and Jansson, Janet K. (2018). Microbial community structure and functional potential along a hypersaline gradient. Frontiers in Microbiology, 9 (JUL) 1492. doi: 10.3389/fmicb.2018.01492
Garsmeur, Olivier, Droc, Gaetan, Antonise, Rudie, Grimwood, Jane, Potier, Bernard, Aitken, Karen, Jenkins, Jerry, Martin, Guillaume, Charron, Carine, Hervouet, Catherine, Costet, Laurent, Yahiaoui, Nabila, Healey, Adam, Sims, David, Cherukuri, Yesesri, Sreedasyam, Avinash, Kilian, Andrzej, Chan, Agnes, Van Sluys, Marie-Anne, Swaminathan, Kankshita, Town, Christopher, Bergès, Hélène, Simmons, Blake, Glaszmann, Jean Christophe, van der Vossen, Edwin, Henry, Robert, Schmutz, Jeremy and D'Hont, Angélique (2018). A mosaic monoploid reference sequence for the highly complex genome of sugarcane. Nature Communications, 9 (1) 2638, 2638. doi: 10.1038/s41467-018-05051-5
Xu, Feng, Sun, Jian, Wehrs, Maren, Kim, Kwang Ho, Rau, Sameeha S., Chan, Ann M., Simmons, Blake A., Mukhopadhyay, Aindrila and Singh, Seema (2018). Biocompatible choline-based deep eutectic solvents enable one-pot production of cellulosic ethanol. ACS Sustainable Chemistry and Engineering, 6 (7), 8914-8919. doi: 10.1021/acssuschemeng.8b01271
Ellinghaus, Thomas L., Pereira, Jose H., McAndrew, Ryan P., Welner, Ditte H., DeGiovanni, Andy M., Guenther, Joel M., Tran, Huu M., Feldman, Taya, Simmons, Blake A., Sale, Kenneth L. and Adams, Paul D. (2018). Engineering glycoside hydrolase stability by the introduction of zinc binding. Acta Crystallographica Section D: Structural Biology, 74 (7), 702-710. doi: 10.1107/S2059798318006678
Sundstrom, Eric, Yaegashi, Junko, Yan, Jipeng, Masson, Fabrice, Papa, Gabriella, Rodriguez, Alberto, Mirsiaghi, Mona, Liang, Ling, He, Qian, Tanjore, Deepti, Pray, Todd R., Singh, Seema, Simmons, Blake, Sun, Ning, Magnuson, Jon and Gladden, John (2018). Demonstrating a separation-free process coupling ionic liquid pretreatment, saccharification, and fermentation with Rhodosporidium toruloides to produce advanced biofuels. Green Chemistry, 20 (12), 2870-2879. doi: 10.1039/c8gc00518d
Liu, Dajiang, Sun, Jian, Simmons, Blake A. and Singh, Seema (2018). N-Heterocyclic carbene promoted decarboxylation of lignin-derived aromatic acids. ACS Sustainable Chemistry and Engineering, 6 (6), 7232-7238. doi: 10.1021/acssuschemeng.7b03612
Kent, Michael S., Zeng, Jijiao, Rader, Nadeya, Avina, Isaac C., Simoes, Casey T., Brenden, Christopher K., Busse, Michael L., Watt, John, Giron, Nicholas H., Alam, Todd M., Allendorf, Mark D., Simmons, Blake A., Bell, Nelson S. and Sale, Kenneth L. (2018). Efficient conversion of lignin into a water-soluble polymer by a chelator-mediated Fenton reaction: optimization of H2O2 use and performance as a dispersant. Green Chemistry, 20 (13), 3024-3037. doi: 10.1039/c7gc03459h
Butler, Jakob B., Freeman, Jules S., Potts, Brad M., Vaillancourt, René E., Grattapaglia, Dario, Silva-Junior, Orzenil B., Simmons, Blake A., Healey, Adam L., Schmutz, Jeremy, Barry, Kerrie W., Lee, David J., Henry, Robert J., King, Graham J., Baten, Abdul and Shepherd, Mervyn (2018). Annotation of the Corymbia terpene synthase gene family shows broad conservation but dynamic evolution of physical clusters relative to Eucalyptus. Heredity, 121 (1), 1-18. doi: 10.1038/s41437-018-0058-1
Coradetti, Samuel T., Pinel, Dominic, Geiselman, Gina M., Ito, Masakazu, Mondo, Stephen J., Reilly, Morgann C., Cheng, Ya-Fang, Bauer, Stefan, Grigoriev, Igor V., Gladden, John M., Simmons, Blake A., Brem, Rachel B., Arkin, Adam P. and Skerker, Jeffrey M. (2018). Functional genomics of lipid metabolism in the oleaginous yeast Rhodosporidium toruloides. eLife, 7 e32110. doi: 10.7554/eLife.32110
Dutta, Tanmoy, Papa, Gabriella, Wang, Eileen, Sun, Jian, Isern, Nancy G., Cort, John R., Simmons, Blake A. and Singh, Seema (2018). Characterization of lignin streams during bionic liquid-based tretreatment from grass, hardwood, and softwood. ACS Sustainable Chemistry and Engineering, 6 (3), 3079-3090. doi: 10.1021/acssuschemeng.7b02991
Wang, Shizeng, Zhao, Wenwen, Lee, Taek Soon, Singer, Steven W., Simmons, Blake A., Singh, Seema, Yuan, Qipeng and Cheng, Gang (2018). Dimethyl sulfoxide assisted ionic liquid pretreatment of switchgrass for isoprenol production. ACS Sustainable Chemistry and Engineering, 6 (3), 4354-4361. doi: 10.1021/acssuschemeng.7b04908
Sun, Jian, Liu, Dajiang, Young, Robert P., Cruz, Alejandro G., Isern, Nancy G., Schuerg, Timo, Cort, John R., Simmons, Blake A. and Singh, Seema (2018). Solubilization and upgrading of high polyethylene terephthalate loadings in a low-costing bifunctional ionic liquid. ChemSusChem, 11 (4), 781-792. doi: 10.1002/cssc.201701798
Kim, Kwang Ho, Dutta, Tanmoy, Sun, Jian, Simmons, Blake and Singh, Seema (2018). Biomass pretreatment using deep eutectic solvents from lignin derived phenols. Green Chemistry, 20 (4), 809-815. doi: 10.1039/c7gc03029k
Liu, Dajiang, Kim, Kwang Ho, Sun, Jian, Simmons, Blake A. and Singh, Seema (2018). Cascade production of lactic acid from universal types of sugars catalyzed by lanthanum triflate. ChemSusChem, 11 (3), 598-604. doi: 10.1002/cssc.201701902
Reilly, Morgann C., Kim, Joonhoon, Lynn, Jed, Simmons, Blake A., Gladden, John M., Magnuson, Jon K. and Baker, Scott E. (2018). Forward genetics screen coupled with whole-genome resequencing identifies novel gene targets for improving heterologous enzyme production in Aspergillus niger. Applied Microbiology and Biotechnology, 102 (4), 1797-1807. doi: 10.1007/s00253-017-8717-3
Kjærbølling, Inge, Vesth, Tammi C, Frisvad, Jens C, Nybo, Jane L, Theobald, Sebastian, Kuo, Alan, Bowyer, Paul, Matsuda, Yudai, Mondo, Stephen, Lyhne, Ellen K, Kogle, Martin E, Clum, Alicia, Lipzen, Anna, Salamov, Asaf, Ngan, Chew Yee, Daum, Chris, Chiniquy, Jennifer, Barry, Kerrie, LaButti, Kurt, Haridas, Sajeet, Simmons, Blake A, Magnuson, Jon K, Mortensen, Uffe H, Larsen, Thomas O, Grigoriev, Igor V, Baker, Scott E and Andersen, Mikael R (2018). Linking secondary metabolites to gene clusters through genome sequencing of six diverse species. Proceedings of the National Academy of Sciences of the United States of America, 115 (4), E753-E761. doi: 10.1073/pnas.1715954115
Kolinko, Sebastian, Wu, Yu-Wei, Tachea, Firehiwot, Denzel, Evelyn, Hiras, Jennifer, Gabriel, Raphael, Bäcker, Nora, Chan, Leanne Jade G., Eichorst, Stephanie A., Frey, Dario, Chen, Qiushi, Azadi, Parastoo, Adams, Paul D., Pray, Todd R., Tanjore, Deepti, Petzold, Christopher J., Gladden, John M., Simmons, Blake A. and Singer, Steven W. (2018). A bacterial pioneer produces cellulase complexes that persist through community succession. Nature Microbiology, 3 (1), 99-107. doi: 10.1038/s41564-017-0052-z
To, Trang Q., Procter, Kerryn, Simmons, Blake A., Subashchandrabose, Suresh and Atkin, Rob (2018). Low cost ionic liquid-water mixtures for effective extraction of carbohydrate and lipid from algae. Faraday Discussions, 206, 93-112. doi: 10.1039/c7fd00158d
Campen, Saori Amaike, Lynn, Jed, Sibert, Stephanie J., Srikrishnan, Sneha, Phatale, Pallavi, Feldman, Taya, Guenther, Joel M., Hiras, Jennifer, An Tran, Yvette Thuy, Singer, Steven W., Adams, Paul D., Sale, Kenneth L., Simmons, Blake A., Baker, Scott E., Magnuson, Jon K. and Gladden, John M. (2017). Expression of naturally ionic liquid-tolerant thermophilic cellulases in Aspergillus niger. PLoS ONE, 12 (12) e0189604, e0189604. doi: 10.1371/journal.pone.0189604
Sitepu, Irnayuli R., Garay, Luis A., Enriquez, Lauren, Fry, Russell, Butler, John H., Lopez, Julian M., Kanti, Atit, Faulina, Sarah A., Nugroho, Agustinus J., Simmons, Blake A., Singer, Steven W., Simmons, Christopher W. and Boundy-Mills, Kyria (2017). 1-ethyl-3-methylimidazolium tolerance and intracellular lipid accumulation of 38 oleaginous yeast species. Applied Microbiology and Biotechnology, 101 (23-24), 8621-8631. doi: 10.1007/s00253-017-8506-z
Mohamed, Elsayed T., Wang, Shizeng, Lennen, Rebecca M., Herrgård, Markus J., Simmons, Blake A., Singer, Steven W. and Feist, Adam M. (2017). Generation of a platform strain for ionic liquid tolerance using adaptive laboratory evolution. Microbial Cell Factories, 16 (1) 204. doi: 10.1186/s12934-017-0819-1
Neupane, Binod, Konda, N.V.S.N. Murthy, Singh, Seema, Simmons, Blake A. and Scown, Corinne D. (2017). Life-Cycle Greenhouse Gas and Water Intensity of Cellulosic Biofuel Production Using Cholinium Lysinate Ionic Liquid Pretreatment. ACS Sustainable Chemistry and Engineering, 5 (11), 10176-10185. doi: 10.1021/acssuschemeng.7b02116
Dutta, Tanmoy, Isern, Nancy G., Sun, Jian, Wang, Eileen, Hull, Sarah, Cort, John R., Simmons, Blake A. and Singh, Seema (2017). Survey of lignin-structure changes and depolymerization during ionic liquid pretreatment. ACS Sustainable Chemistry and Engineering, 5 (11), 10116-10127. doi: 10.1021/acssuschemeng.7b02123
Mills, Matthew J. L., Sale, Kenneth L., Simmons, Blake A. and Popelier, Paul L. A. (2017). Rhorix: An interface between quantum chemical topology and the 3D graphics program blender. Journal of Computational Chemistry, 38 (29), 2538-2552. doi: 10.1002/jcc.25054
Narani, Akash, Coffman, Phil, Gardner, James, Li, Chenlin, Ray, Allison E., Hartley, Damon S., Stettler, Allison, Konda, N.V.S.N. Murthy, Simmons, Blake, Pray, Todd R. and Tanjore, Deepti (2017). Predictive modeling to de-risk bio-based manufacturing by adapting to variability in lignocellulosic biomass supply. Bioresource Technology, 243, 676-685. doi: 10.1016/j.biortech.2017.06.156
Yaegashi, Junko, Kirby, James, Ito, Masakazu, Sun, Jian, Dutta, Tanmoy, Mirsiaghi, Mona, Sundstrom, Eric R., Rodriguez, Alberto, Baidoo, Edward, Tanjore, Deepti, Pray, Todd, Sale, Kenneth, Singh, Seema, Keasling, Jay D., Simmons, Blake A., Singer, Steven W., Magnuson, Jon K., Arkin, Adam P., Skerker, Jeffrey M. and Gladden, John M. (2017). Rhodosporidium toruloides: a new platform organism for conversion of lignocellulose into terpene biofuels and bioproducts. Biotechnology for Biofuels, 10 (1) 241. doi: 10.1186/s13068-017-0927-5
Yuan, Xueming, He, Lilin, Singh, Seema, Simmons, Blake A. and Cheng, Gang (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 and Fuels, 31 (10), 10874-10879. doi: 10.1021/acs.energyfuels.7b01567
Fernández-Bayo, Jesús D., Achmon, Yigal, Harrold, Duff R., Claypool, Joshua T., Simmons, Blake A., Singer, Steven W., Dahlquist-Willard, Ruth M., Stapleton, James J., VanderGheynst, Jean S. and Simmons, Christopher W. (2017). Comparison of soil biosolarization with mesophilic and thermophilic solid digestates on soil microbial quantity and diversity. Applied Soil Ecology, 119, 183-191. doi: 10.1016/j.apsoil.2017.06.016
Papa, Gabriella, Feldman, Taya, Sale, Kenneth L., Adani, Fabrizio, Singh, Seema and Simmons, Blake A. (2017). Parametric study for the optimization of ionic liquid pretreatment of corn stover. Bioresource Technology, 241, 627-637. doi: 10.1016/j.biortech.2017.05.167
Rodriguez, Alberto, Salvachúa, Davinia, Katahira, Rui, Black, Brenna A., Cleveland, Nicholas S., Reed, Michelle, Smith, Holly, Baidoo, Edward E.K., Keasling, Jay D., Simmons, Blake A., Beckham, Gregg T. and Gladden, John M. (2017). Base-catalyzed depolymerization of solid lignin-rich streams enables microbial conversion. ACS Sustainable Chemistry and Engineering, 5 (9), 8171-8180. doi: 10.1021/acssuschemeng.7b01818
Ceballos, Shannon J., Yu, Chaowei, Claypool, Josh T., Singer, Steven W., Simmons, Blake A., Thelen, Michael P., Simmons, Christopher W. and VanderGheynst, Jean S. (2017). Development and characterization of a thermophilic, lignin degrading microbiota. Process Biochemistry, 63, 193-203. doi: 10.1016/j.procbio.2017.08.018
To, Trang Q., Shah, Kalpit, Tremain, Priscilla, Simmons, Blake A., Moghtaderi, Behdad and Atkin, Rob (2017). Treatment of lignite and thermal coal with low cost amino acid based ionic liquid-water mixtures. Fuel, 202, 296-306. doi: 10.1016/j.fuel.2017.04.051
McAndrew, Ryan P, Sathitsuksanoh, Noppadon, Mbughuni, Michael M, Heins, Richard A, Pereira, Jose H, George, Anthe, Sale, Kenneth L, Fox, Brian G, Simmons, Blake A and Adams, Paul D (2017). Reply to Kiser: dioxygen binding in NOV1 crystal structures. Proceedings of the National Academy of Sciences of the United States of America, 114 (30), E6029-E6030. doi: 10.1073/pnas.1708124114
Liang, Ling, Li, Chenlin, Xu, Feng, He, Qian, Yan, Jipeng, Luong, Tina, Simmons, Blake A., Pray, Todd R., Singh, Seema, Thompson, Vicki S. and Sun, Ning (2017). Conversion of cellulose rich municipal solid waste blends using ionic liquids: Feedstock convertibility and process scale-up. RSC Advances, 7 (58), 36585-36593. doi: 10.1039/c7ra06701a
Zhao, Wenwen, Xiao, Ling-Ping, Song, Guoyong, Sun, Run-Cang, He, Lilin, Singh, Seema, Simmons, Blake A. and Cheng, Gang (2017). From lignin subunits to aggregates: Insights into lignin solubilization. Green Chemistry, 19 (14), 3272-3281. doi: 10.1039/c7gc00944e
Sun, Jian, Konda, N. V. S. N. Murthy, Parthasarathi, Ramakrishnan, Dutta, Tanmoy, Valiev, Marat, Xu, Feng, Simmons, Blake A. and Singh, Seema (2017). One-pot integrated biofuel production using low-cost biocompatible protic ionic liquids. Green Chemistry, 19 (13), 3152-3163. doi: 10.1039/c7gc01179b
d'Espaux, Leo, Ghosh, Amit, Runguphan, Weerawat, Wehrs, Maren, Xu, Feng, Konzock, Oliver, Dev, Ishaan, Nhan, Melissa, Gin, Jennifer, Reider Apel, Amanda, Petzold, Christopher J., Singh, Seema, Simmons, Blake A., Mukhopadhyay, Aindrila, García Martín, Héctor and Keasling, Jay D. (2017). Engineering high-level production of fatty alcohols by Saccharomyces cerevisiae from lignocellulosic feedstocks. Metabolic Engineering, 42, 115-125. doi: 10.1016/j.ymben.2017.06.004
Sun, Jian, Shi, Jian, Murthy Konda, N. V.S.N., Campos, Dan, Liu, Dajiang, Nemser, Stuart, Shamshina, Julia, Dutta, Tanmoy, Berton, Paula, Gurau, Gabriela, Rogers, Robin D., Simmons, Blake A. and Singh, Seema (2017). Efficient dehydration and recovery of ionic liquid after lignocellulosic processing using pervaporation. Biotechnology for Biofuels, 1 (1) 154. doi: 10.1186/s13068-017-0842-9
Eudes, Aymerick, Dutta, Tanmoy, Deng, Kai, Jacquet, Nicolas, Sinha, Anagh, Benites, Veronica T., Baidoo, Edward E. K., Riche, Aurore, Sattler, Scott E., Northen, Trent R., Singh, Seema, Simmons, Blake A. and Loqué, Dominique (2017). SbCOMT (Bmr12) is involved in the biosynthesis of tricin-lignin in sorghum. PLoS ONE, 12 (6) e0178160, e0178160. doi: 10.1371/journal.pone.0178160
Fernandez-Bayo, Jesus D., Toniato, Juliano, Simmons, Blake A. and Simmons, Christopher W. (2017). Structure and activity of thermophilic methanogenic microbial communities exposed to quaternary ammonium sanitizer. Journal of Environmental Sciences, 56, 164-168. doi: 10.1016/j.jes.2016.10.005
Zeng, Jijiao, Mills, Matthew J. L., Simmons, Blake A., Kent, Michael S. and Sale, Kenneth L. (2017). Understanding factors controlling depolymerization and polymerization in catalytic degradation of β-ether linked model lignin compounds by versatile peroxidase. Green Chemistry, 19 (9), 2145-2154. doi: 10.1039/c6gc03379b
Woo, Hannah L., DeAngelis, Kristen M., Teshima, Hazuki, Davenport, Karen, Daligault, Hajnalka, Erkkila, Tracy, Goodwin, Lynne, Gu, Wei, Lo, Chien-Chi, Munk, Christine, Scholz, Matthew, Xu, Yan, Chain, Patrick, Bruce, David, Detter, Chris, Tapia, Roxanne, Han, Cliff, Simmons, Blake A. and Hazena, Terry C. (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 Announcements, 5 (18) e00300-17. doi: 10.1128/genomeA.00300-17
Yuan, Xueming, Duan, Yonghao, He, Lilin, Singh, Seema, Simmons, Blake and Cheng, Gang (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. Bioresource Technology, 232, 113-118. doi: 10.1016/j.biortech.2017.02.014
Kim, Kwang Ho, Dutta, Tanmoy, Walter, Eric D., Isern, Nancy G., Cort, John R., Simmons, Blake A. and Singh, Seema (2017). Chemoselective methylation of phenolic hydroxyl group prevents quinone methide formation and repolymerization during lignin depolymerization. ACS Sustainable Chemistry and Engineering, 5 (5), 3913-3919. doi: 10.1021/acssuschemeng.6b03102
Yuan, Xueming, Singh, Seema, Simmons, Blake A. and Cheng, Gang (2017). Biomass pretreatment using dilute aqueous ionic liquid (IL) solutions with dynamically varying IL concentration and its impact on IL recycling. ACS Sustainable Chemistry and Engineering, 5 (5), 4408-4413. doi: 10.1021/acssuschemeng.7b00480
Kim, Kwang Ho, Dutta, Tanmoy, Ralph, John, Mansfield, Shawn D., Simmons, Blake A. and Singh, Seema (2017). Impact of lignin polymer backbone esters on ionic liquid pretreatment of poplar. Biotechnology for Biofuels, 10 (1) 101. doi: 10.1186/s13068-017-0784-2
Kohler, Amanda C., Mills, Matthew J. L., Adams, Paul D., Simmons, Blake A. and Sale, Kenneth L. (2017). Structure of aryl O-demethylase offers molecular insight into a catalytic tyrosine-dependent mechanism. Proceedings of the National Academy of Sciences of the United States of America, 114 (16), E3205-E3214. doi: 10.1073/pnas.1619263114
Perez-Pimienta, Jose A., Sathitsuksanoh, Noppadon, Thompson, Vicki S., Tran, Kim, Ponce-Noyola, Teresa, Stavila, Vitalie, Singh, Seema and Simmons, Blake A. (2017). Ternary ionic liquid-water pretreatment systems of an agave bagasse and municipal solid waste blend. Biotechnology for Biofuels, 10 (1) 72. doi: 10.1186/s13068-017-0758-4
Kim, Kwang Ho, Brown, Robert C., Daugaard, Tannon, Tivol, William F., Auer, Manfred, Simmons, Blake and Singh, Seema (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. doi: 10.1002/cssc.201601515
Shi, Jian, Wu, Dong, Zhang, Libing, Simmons, Blake A., Singh, Seema, Yang, Bin and Wyman, Charles E. (2017). Dynamic changes of substrate reactivity and enzyme adsorption on partially hydrolyzed cellulose. Biotechnology and Bioengineering, 114 (3), 503-515. doi: 10.1002/bit.26180
Papa, Gabriella, Kirby, James, Murthy Konda, N. V.S.N., Tran, Kim, Singh, Seema, Keasling, Jay D., Peter, Gary F. and Simmons, Blake A. (2017). Development of an integrated approach for α-pinene recovery and sugar production from loblolly pine using ionic liquids. Green Chemistry, 19 (4), 1117-1127. doi: 10.1039/c6gc02637k
Daly, Paul, Van Munster, Jolanda M., Blythe, Martin J., Ibbett, Roger, Kokolski, Matt, Gaddipati, Sanyasi, Lindquist, Erika, Singan, Vasanth R., Barry, Kerrie W., Lipzen, Anna, Ngan, Chew Yee, Petzold, Christopher J., Chan, Leanne Jade G., Pullan, Steven T., Delmas, Stéphane, Waldron, Paul R., Grigoriev, Igor V., Tucker, Gregory A., Simmons, Blake A. and Archer, David B. (2017). Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments. Biotechnology for Biofuels, 10 (1) 35. doi: 10.1186/s13068-017-0700-9
Pérez-Pimienta, Jose A., Vargas-Tah, Alejandra, López-Ortega, Karla M., Medina-López, Yessenia N., Mendoza-Pérez, Jorge A., Avila, Sayeny, Singh, Seema, Simmons, Blake A., Loaces, Inés and Martinez, Alfredo (2017). Sequential enzymatic saccharification and fermentation of ionic liquid and organosolv pretreated agave bagasse for ethanol production. Bioresource Technology, 225, 191-198. doi: 10.1016/j.biortech.2016.11.064
Li, Chenlin, Liang, Ling, Sun, Ning, Thompson, Vicki S., Xu, Feng, Narani, Akash, He, Qian, Tanjore, Deepti, Pray, Todd R., Simmons, Blake A. and Singh, Seema (2017). Scale-up and process integration of sugar production by acidolysis of municipal solid waste/corn stover blends in ionic liquids. Biotechnology for Biofuels, 10 (1) 13. doi: 10.1186/s13068-016-0694-8
Yu, Chaowei, Harrold, Duff R., Claypool, Joshua T., Simmons, Blake A., Singer, Steven W., Simmons, Christopher W. and VanderGheynst, Jean S. (2017). Nitrogen amendment of green waste impacts microbial community, enzyme secretion and potential for lignocellulose decomposition. Process Biochemistry, 52, 214-222. doi: 10.1016/j.procbio.2016.11.002
Kim, Kwang Ho, Simmons, Blake A. and Singh, Seema (2017). Catalytic transfer hydrogenolysis of ionic liquid processed biorefinery lignin to phenolic compounds. Green Chemistry, 19 (1), 215-224. doi: 10.1039/c6gc02473d
McAndrew, Ryan P., Sathitsuksanoh, Noppadon, Mbughuni, Michael M., Heins, Richard A., Pereira, Jose H., George, Anthe, Sale, Kenneth L., Fox, Brian G., Simmons, Blake A. and Adams, Paul D. (2016). Structure and mechanism of NOV1, a resveratrolcleaving Dioxygenase. Proceedings of the National Academy of Sciences of the United States of America, 113 (50), 14324-14329. doi: 10.1073/pnas.1608917113
Yu, Chaowei, Simmons, Blake A., Singer, Steven W., Thelen, Michael P. and VanderGheynst, Jean S. (2016). Ionic liquid-tolerant microorganisms and microbial communities for lignocellulose conversion to bioproducts. Applied Microbiology and Biotechnology, 100 (24), 10237-10249. doi: 10.1007/s00253-016-7955-0
Sun, Jian, Dutta, Tanmoy, Parthasarathi, Ramakrishnan, Kim, Kwang Ho, Tolic, Nikola, Chu, Rosalie K., Isern, Nancy G., Cort, John R., Simmons, Blake A. and Singh, Seema (2016). Rapid room temperature solubilization and depolymerization of polymeric lignin at high loadings. Green Chemistry, 18 (22), 6012-6020. doi: 10.1039/c6gc02258h
Salvachúa, Davinia, Katahira, Rui, Cleveland, Nicholas S., Khanna, Payal, Resch, Michael G., Black, Brenna A., Purvine, Samuel O., Zink, Erika M., Prieto, Alicia, Martínez, María J., Martínez, Angel T., Simmons, Blake A., Gladden, John M. and Beckham, Gregg T. (2016). Lignin depolymerization by fungal secretomes and a microbial sink. Green Chemistry, 18 (22), 6046-6062. doi: 10.1039/c6gc01531j
Healey, Adam L., Lee, David J., Lupoi, Jason S., Papa, Gabriella, Guenther, Joel M., Corno, Luca, Adani, Fabrizio, Singh, Seema, Simmons, Blake A. and Henry, Robert J. (2016). Evaluation of relationships between growth rate, tree size, lignocellulose composition, and enzymatic saccharification in interspecific Corymbia hybrids and parental taxa. Frontiers in Plant Science, 7 (NOVEMBER2016) 1705, 1705. doi: 10.3389/fpls.2016.01705
Zhao, Wenwen, Simmons, Blake, Singh, Seema, Ragauskas, Arthur and Cheng, Gang (2016). From lignin association to nano-/micro-particle preparation: extracting higher value of lignin. Green Chemistry, 18 (21), 5693-5700. doi: 10.1039/c6gc01813k
Wu, Yu-Wei, Higgins, Brendan, Yu, Chaowei, Reddy, Amitha P., Ceballos, Shannon, Joh, Lawrence D., Simmons, Blake A., Singer, Steven W. and VanderGheynst, Jean S. (2016). Ionic liquids impact the bioenergy feedstock-degrading microbiome and transcription of enzymes relevant to polysaccharide hydrolysis. mSystems, 1 (6) e00120. doi: 10.1128/mSystems.00120-16
Whitmore, Leanne S., Davis, Ryan W., McCormick, Robert L., Gladden, John M., Simmons, Blake A., George, Anthe and Hudson, Corey M. (2016). BioCompoundML: A General Biofuel Property Screening Tool for Biological Molecules Using Random Forest Classifiers. Energy and Fuels, 30 (10), 8410-8418. doi: 10.1021/acs.energyfuels.6b01952
Simmons, Christopher W., Higgins, Brendan, Staley, Simon, Joh, Lawrence D., Simmons, Blake A., Singer, Steven W., Stapleton, James J. and VanderGheynst, Jean S. (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. doi: 10.1016/j.apsoil.2016.04.018
Healey, Adam L., Lupoi, Jason S., Lee, David J., Sykes, Robert W., Guenther, Joel M., Tran, Kim, Decker, Stephen R., Singh, Seema, Simmons, Blake A. and Henry, Robert J. (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. doi: 10.1016/j.biombioe.2016.06.016
Shi, Jian, Pattathil, Sivakumar, Parthasarathi, Ramakrishnan, Anderson, Nickolas A., Kim, Jeong Im, Venketachalam, Sivasankari, Hahn, Michael G., Chapple, Clint, Simmons, Blake A. and Singh, Seema (2016). Impact of engineered lignin composition on biomass recalcitrance and ionic liquid pretreatment efficiency. Green Chemistry, 18 (18), 4884-4895. doi: 10.1039/c6gc01193d
Sun, Jian, Murthy Konda, N. V.S.N., Shi, Jian, Parthasarathi, Ramakrishnan, Dutta, Tanmoy, Xu, Feng, Scown, Corinne D., Simmons, Blake A. and Singh, Seema (2016). CO2 enabled process integration for the production of cellulosic ethanol using bionic liquids. Energy and Environmental Science, 9 (9), 2822-2834. doi: 10.1039/c6ee00913a
Frederix, Marijke, Mingardon, Florence, Hu, Matthew, Sun, Ning, Pray, Todd, Singh, Seema, Simmons, Blake A., Keasling, Jay D. and Mukhopadhyay, Aindrila (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. doi: 10.1039/c6gc00642f
Parthasarathi, Ramakrishnan, Sun, Jian, Dutta, Tanmoy, Sun, Ning, Pattathil, Sivakumar, Murthy Konda, N. V.S.N., Peralta, Angelo Gabriel, Simmons, Blake A. and Singh, Seema (2016). Activation of lignocellulosic biomass for higher sugar yields using aqueous ionic liquid at low severity process conditions. Biotechnology for Biofuels, 9 (1) 160. doi: 10.1186/s13068-016-0561-7
Perez-Pimienta, José A., Poggi-Varaldo, Héctor M., Ponce-Noyola, Teresa, Ramos-Valdivia, Ana C., Chavez-Carvayar, José A., Stavila, Vitalie and Simmons, Blake A. (2016). Fractional pretreatment of raw and calcium oxalate-extracted agave bagasse using ionic liquid and alkaline hydrogen peroxide. Biomass and Bioenergy, 91, 48-55. doi: 10.1016/j.biombioe.2016.05.001
Liszka, Michael J., Kang, Aram, Konda, N. V. S. N. Murthy, Tran, Kim, Gladden, John M., Singh, Seema, Keasling, Jay D., Scown, Corinne D., Lee, Taek Soon, Simmons, Blake A. and Sale, Kenneth L. (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. doi: 10.1039/c6gc00657d
Eudes, Aymerick, Zhao, Nanxia, Sathitsuksanoh, Noppadon, Baidoo, Edward E. K., Lao, Jeemeng, Wang, George, Yogiswara, Sasha, Lee, Taek Soon, Singh, Seema, Mortimer, Jenny C., Keasling, Jay D., Simmons, Blake A. and Loque, Dominique (2016). 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, 4 (JUL) 58. doi: 10.3389/fbioe.2016.00058
Corno, Luca, Pilu, Roberto, Tran, Kim, Tambone, Fulvia, Singh, Seema, Simmons, Blake A. and Adani, Fabrizio (2016). Sugars production for green chemistry from 2nd generation crop (Arundo donax L.): a full field approach. ChemistrySelect, 1 (11), 2617-2623. doi: 10.1002/slct.201600733
Hiras, Jennifer, Wu, Yu-Wei, Deng, Kai, Nicora, Carrie D., Aldrich, Joshua T., Frey, Dario, Kolinko, Sebastian, Robinson, Errol W., Jacobs, Jon M., Adams, Paul D., Northen, Trent R., Simmons, Blake A. and Singer, Steven W. (2016). Comparative community proteomics demonstrates the unexpected importance of actinobacterial glycoside hydrolase family 12 protein for crystalline cellulose hydrolysis. mBio, 7 (4) e01106-16. doi: 10.1128/mBio.01106-16
Perez-Pimienta, Jose A., Flores-Gómez, Carlos A., Ruiz, Héctor A., Sathitsuksanoh, Noppadon, Balan, Venkatesh, da Costa Sousa, Leonardo, Dale, Bruce E., Singh, Seema and Simmons, Blake A. (2016). Evaluation of agave bagasse recalcitrance using AFEX™, autohydrolysis, and ionic liquid pretreatments. Bioresource Technology, 211, 216-223. doi: 10.1016/j.biortech.2016.03.103
Pace, Sara, Ceballos, Shannon J., Harrold, Duff, Stannard, Whitney, Simmons, Blake A., Singer, Steven W., Thelen, Michael P. and VanderGheynst, Jean S. (2016). Enrichment of microbial communities tolerant to the ionic liquids tetrabutylphosphonium chloride and tributylethylphosphonium diethylphosphate. Applied Microbiology and Biotechnology, 100 (12), 5639-5652. doi: 10.1007/s00253-016-7525-5
Pereira, Jose Henrique, Heins, Richard A., Gall, Daniel L., McAndrew, Ryan P., Deng, Kai, Holland, Keefe C., Donohue, Timothy J., Noguera, Daniel R., Simmons, Blake A., Sale, Kenneth L., Ralph, John and Adams, Paul D. (2016). Structural and biochemical characterization of the early and late enzymes in the lignin β-aryl ether cleavage pathway from Sphingobium sp. SYK-6. Journal of Biological Chemistry, 291 (19), 10228-10238. doi: 10.1074/jbc.M115.700427
Da Costa Sousa, Leonardo, Jin, Mingjie, Chundawat, Shishir P. S., Bokade, Vijay, Tang, Xiaoyu, Azarpira, Ali, Lu, Fachuang, Avci, Utku, Humpula, James, Uppugundla, Nirmal, Gunawan, Christa, Pattathil, Sivakumar, Cheh, Albert M., Kothari, Ninad, Kumar, Rajeev, Ralph, John, Hahn, Michael G., Wyman, Charles E., Singh, Seema, Simmons, Blake A., Dale, Bruce E. and Balan, Venkatesh (2016). Next-generation ammonia pretreatment enhances cellulosic biofuel production. Energy and Environmental Science, 9 (4), 1215-1223. doi: 10.1039/c5ee03051j
Hiras, Jennifer, Wu, Yu-Wei, Eichorst, Stephanie A., Simmons, Blake A. and Singer, Steven W. (2016). Refining the phylum Chlorobi by resolving the phylogeny and metabolic potential of the representative of a deeply branching, uncultivated lineage. ISME Journal, 10 (4), 833-845. doi: 10.1038/ismej.2015.158
Helmich, Kate E., Pereira, Jose Henrique, Gall, Daniel L., Heins, Richard A., McAndrew, Ryan P., Bingman, Craig, Deng, Kai, Holland, Keefe C., Noguera, Daniel R., Simmons, Blake A., Sale, Kenneth L., Ralph, John, Donohue, Timothy J., Adams, Paul D. and Phillips, George N. (2016). Structural basis of stereospecificity in the bacterial enzymatic cleavage of β-aryl ether bonds in lignin. Journal of Biological Chemistry, 291 (10), 5234-5246. doi: 10.1074/jbc.M115.694307
Xu, Feng, Sun, Jian, Konda, N. V. S. N. Murthy, Shi, Jian, Dutta, Tanmoy, Scown, Corinne D., Simmons, Blake A. and Singh, Seema (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), 1042-1049. doi: 10.1039/c5ee02940f
Torr, Kirk M., Love, Karen T., Simmons, Blake A. and Hill, Stefan J. (2016). Structural features affecting the enzymatic digestibility of pine wood pretreated with ionic liquids. Biotechnology and Bioengineering, 113 (3), 540-549. doi: 10.1002/bit.25831
Wiemann, Stefan, Pennacchio, Christa, Hu, Yanhui, Hunter, Preston, Harbers, Matthias, Amiet, Alexandra, Bethel, Graeme, Busse, Melanie, Carninci, Piero, Diekhans, Mark, Dunham, Ian, Hao, Tong, Harper, J. Wade, Hayashizaki, Yoshihide, Heil, Oliver, Hennig, Steffen, Hotz-Wagenblatt, Agnes, Jang, Wonhee, Jöcker, Anika, Kawai, Jun, Koenig, Christoph, Korn, Bernhard, Lambert, Cristen, LeBeau, Anita, Lu, Sun, Maurer, Johannes, Moore, Troy, Ohara, Osamu, Park, Jin ... Hill, David E. (2016). The ORFeome Collaboration: A genome-scale human ORF-clone resource. Nature Methods, 13 (3), 191-192. doi: 10.1038/nmeth.3776
Lupoi, Jason, Simmons, Blake and Henry, Robert (2016). Biomass modification, characterization and process monitoring analytics to support biofuel and biomaterial production. Frontiers in Bioengineering and Biotechnology, 4 (MAR) 25, 25.1-25.2. doi: 10.3389/fbioe.2016.00025
Wu, Yu-Wei, Simmons, Blake A. and Singer, Steven W. (2016). MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets. Bioinformatics, 32 (4), 605-607. doi: 10.1093/bioinformatics/btv638
Stavila, Vitalie, Parthasarathi, Ramakrishnan, Davis, Ryan W., El Gabaly, Farid, Sale, Kenneth L., Simmons, Blake A., Singh, Seema and Allendorf, Mark D. (2016). MOF-Based catalysts for selective hydrogenolysis of carbon-oxygen ether bonds. ACS Catalysis, 6 (1), 55-59. doi: 10.1021/acscatal.5b02061
Sun, Lan, Singh, Seema, Joo, Michael, Vega-Sanchez, Miguel, Ronald, Pamela, Simmons, Blake A., Adams, Paul and Auer, Manfred (2016). Non-invasive imaging of cellulose microfibril orientation within plant cell walls by polarized Raman microspectroscopy. Biotechnology and Bioengineering, 113 (1), 82-90. doi: 10.1002/bit.25690
Joshua, C. J., Simmons, B. A. and Singer, S. W. (2016). Ferricyanide-based analysis of aqueous lignin suspension revealed sequestration of water-soluble lignin moieties. RSC Advances, 6 (59), 54382-54393. doi: 10.1039/c6ra04443c
Zhang, Wei, Sathitsuksanoh, Noppadon, Simmons, Blake A., Frazier, Charles E., Barone, Justin R. and Renneckar, Scott (2016). Revealing the thermal sensitivity of lignin during glycerol thermal processing through structural analysis. RSC Advances, 6 (36), 30234-30246. doi: 10.1039/C6RA00745G
Baker, Scott E., Schackwitz, Wendy, Lipzen, Anna, Martin, Joel, Haridas, Sajeet, LaButti, Kurt, Grigoriev, Igor V., Simmons, Blake A. and McCluskey, Kevin (2016). Draft genome sequence of Neurospora crassa strain FGSC 73. Genome Announcements, 3 (2) e00074-15. doi: 10.1128/genomeA.00074-15
Hudson, Corey M., Kirton, Edward, Hutchinson, Miriam I., Redfern, Joanna L., Simmons, Blake, Ackerman, Eric, Singh, Seema, Williams, Kelly P., Natvig, Donald O. and Powell, Amy J. (2015). Lignin-modifying processes in the rhizosphere of arid land grasses. Environmental Microbiology, 17 (12), 4965-4978. doi: 10.1111/1462-2920.13020
Eudes, Aymerick, Sathitsuksanoh, Noppadon, Baidoo, Edward E.K., George, Anthe, Liang, Yan, Yang, Fan, Singh, Seema, Keasling, Jay D., Simmons, Blake A. and Loqué, Dominique (2015). Expression of a bacterial 3-dehydroshikimate dehydratase reduces lignin content and improves biomass saccharification efficiency. Plant Biotechnology Journal, 13 (9), 1241-1250. doi: 10.1111/pbi.12310
Healey, Adam L., Lee, David J., Furtado, Agnelo, Simmons, Blake A. and Henry, Robert J. (2015). Efficient eucalypt cell wall deconstruction and conversion for sustainable lignocellulosic biofuels. Frontiers in Bioengineering and Biotechnology, 3 (NOV) 190, 190.1-190.14. doi: 10.3389/fbioe.2015.00190
Billings, Andrew F., Fortney, Julian L., Hazen, Terry C., Simmons, Blake, Davenport, Karen W., Goodwin, Lynne, Ivanova, Natalia, Kyrpides, Nikos C., Mavromatis, Konstantinos, Woyke, Tanja and DeAngelis, Kristen M. (2015). Genome sequence and description of the anaerobic lignin-degrading bacterium Tolumonas lignolytica sp. nov. Standards in Genomic Sciences, 10 (1) 106. doi: 10.1186/s40793-015-0100-3
Hoang, Nam V., Furtado, Agnelo, Botha, Frederik C., Simmons, Blake A. and Henry, Robert J. (2015). Potential for genetic improvement of sugarcane as a source of biomass for biofuels. Frontiers in Bioengineering and Biotechnology, 3 (NOV) 182, 1-15. doi: 10.3389/fbioe.2015.00182
Deng, Kai, Guenther, Joel M., Gao, Jian, Bowen, Benjamin P., Tran, Huu, Reyes-Ortiz, Vimalier, Cheng, Xiaoliang, Sathitsuksanoh, Noppadon, Heins, Richard, Takasuka, Taichi E., Bergeman, Lai F., Geertz-Hansen, Henrik, Deutsch, Samuel, Loqué, Dominique, Sale, Kenneth L., Simmons, Blake A., Adams, Paul D., Singh, Anup K., Fox, Brian G. and Northen, Trent R. (2015). Development of a high throughput platform for screening glycoside hydrolases based on Oxime-NIMS. Frontiers in Bioengineering and Biotechnology, 3 (OCT) 153. doi: 10.3389/fbioe.2015.00153
Lupoi, Jason S., Singh, Seema, Parthasarathi, Ramakrishnan, Simmons, Blake A. and Henry, Robert J. (2015). Recent innovations in analytical methods for the qualitative and quantitative assessment of lignin. Renewable and Sustainable Energy Reviews, 49 4346, 871-906. doi: 10.1016/j.rser.2015.04.091
Parthasarathi, Ramakrishnan, Balamurugan, Kanagasabai, Shi, Jian, Subramanian, Venkatesan, Simmons, Blake A. and Singh, Seema (2015). Theoretical insights into the role of water in the dissolution of cellulose using IL/Water mixed solvent systems. Journal of Physical Chemistry B, 119 (45), 14339-14349. doi: 10.1021/acs.jpcb.5b02680
Slater, Steven C., Simmons, Blake A., Rogers, Tamara S., Phillips, Margaret F., Nordahl, Kristy and Davison, Brian H. (2015). The DOE bioenergy research centers: history, operations, and scientific output. Bioenergy Research, 8 (3), 881-896. doi: 10.1007/s12155-015-9660-8
Sathitsuksanoh, Noppadon, Sawant, Manali, Truong, Quoc, Tan, Jared, Canlas, Christian G., Sun, Ning, Zhang, Wei, Renneckar, Scott, Prasomsri, Teerawit, Shi, Jian, Çetinkol, Özgül, Singh, Seema, Simmons, Blake A. and George, Anthe (2015). How alkyl chain length of alcohols affects lignin fractionation and ionic liquid recycle during lignocellulose pretreatment. BioEnergy Research, 8 (3), 973-981. doi: 10.1007/s12155-015-9643-9
Shi, Jian, George, Kevin W., Sun, Ning, He, Wei, Li, Chenlin, Stavila, Vitalie, Keasling, Jay D., Simmons, Blake A., Lee, Taek Soon and Singh, Seema (2015). Impact of pretreatment technologies on saccharification and isopentenol fermentation of mixed lignocellulosic feedstocks. Bioenergy Research, 8 (3), 1004-1013. doi: 10.1007/s12155-015-9588-z
Tanger, Paul, Vega-Sánchez, Miguel E., Fleming, Margaret, Tran, Kim, Singh, Seema, Abrahamson, James B., Jahn, Courtney E., Santoro, Nicholas, Naredo, Elizabeth B., Baraoidan, Marietta, Danku, John M. C., Salt, David E., McNally, Kenneth L., Simmons, Blake A., Ronald, Pamela C., Leung, Hei, Bush, Daniel R., McKay, John K. and Leach, Jan E. (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. doi: 10.1007/s12155-014-9573-y
Li, Chenlin, Tanjore, Deepti, He, Wei, Wong, Jessica, Gardner, James L., Thompson, Vicki S., Yancey, Neal A., Sale, Kenneth L., Simmons, Blake A. and Singh, Seema (2015). Scale-up of ionic liquid-based fractionation of single and mixed feedstocks. Bioenergy Research, 8 (3), 982-991. doi: 10.1007/s12155-015-9587-0
Wu, Yu-Wei, Joshua, Chijioke, Eichorst, Stephanie A., Gladden, John M., Simmons, Blake A. and Singer, Steven W. (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. doi: 10.1007/s12155-015-9600-7
Kent, Michael S., Avina, Isaac C., Rader, Nadeya, Busse, Michael L., George, Anthe, Sathitsuksanoh, Noppadon, Baidoo, Edward, Timlin, Jerilyn, Giron, Nicholas H., Celina, Mathias C., Martin, Laura E., Polsky, Ronen, Chavez, Victor H., Huber, Dale L., Keasling, Jay D., Singh, Seema, Simmons, Blake A. and Sale, Kenneth L. (2015). Assay for lignin breakdown based on lignin films: insights into the Fenton reaction with insoluble lignin. Green Chemistry, 17 (10), 4830-4845. doi: 10.1039/c5gc01083g
Dolan, Jeffrey A., Sathitsuksanoh, Noppadon, Rodriguez, Katia, Simmons, Blake A., Frazier, Charles E. and Renneckar, Scott (2015). Biocomposite adhesion without added resin: understanding the chemistry of the direct conversion of wood into adhesives. RSC Advances, 5 (82), 67267-67276. doi: 10.1039/c5ra09676f
Lupoi, Jason S, Smith-Moritz, Andreia, Singh, Seema, McQualter, Richard, Scheller, Henrik V, Simmons, Blake A and Henry, Robert J (2015). Localization of polyhydroxybutyrate in sugarcane using Fourier-transform infrared microspectroscopy and multivariate imaging. Biotechnology for Biofuels, 8 (98) 98, 98. doi: 10.1186/s13068-015-0279-y
Scullin, Chessa, Cruz, Alejandro G., Chuang, Yi-De, Simmons, Blake A., Loque, Dominique and Singh, Seema (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 (1) 95. doi: 10.1186/s13068-015-0275-2
Gardner, James L., He, Wei, Li, Chenlin, Wong, Jessica, Sale, Kenneth L., Simmons, Blake A., Singh, Seema and Tanjore, Deepti (2015). Calorimetric evaluation indicates that lignin conversion to advanced biofuels is vital to improving energy yields. RSC Advances, 5 (63), 51092-51101. doi: 10.1039/c5ra01503k
Sun, Ning, Xu, Feng, Sathitsuksanoh, Noppadon, Thompson, Vicki S., Cafferty, Kara, Li, Chenlin, Tanjore, Deepti, Narani, Akash, Pray, Todd R., Simmons, Blake A. and Singh, Seema (2015). Blending municipal solid waste with corn stover for sugar production using ionic liquid process. Bioresource Technology, 186, 200-206. doi: 10.1016/j.biortech.2015.02.087
Scullin, Chessa, Stavila, Vitalie, Skarstad, Anita, Keasling, Jay D., Simmons, Blake A. and Singh, Seema (2015). Optimization of renewable pinene production from the conversion of macroalgae Saccharina latissima. Bioresource Technology, 184, 415-420. doi: 10.1016/j.biortech.2014.09.105
Papa, G., Rodriguez, S., George, A., Schievano, A., Orzi, V., Sale, K. L., Singh, S., Adani, F. and Simmons, B. A. (2015). Comparison of different pretreatments for the production of bioethanol and biomethane from corn stover and switchgrass. Bioresource Technology, 183, 101-110. doi: 10.1016/j.biortech.2015.01.121
Perez-Pimienta, Jose A., Lopez-Ortega, Monica G., Chavez-Carvayar, Jose A., Varanasi, Patanjali, Stavila, Vitalie, Cheng, Gang, Singh, Seema and Simmons, Blake A. (2015). Characterization of agave bagasse as a function ofionic liquid pretreatment. Biomass and Bioenergy, 75, 180-188. doi: 10.1016/j.biombioe.2015.02.026
Konda, N.V.S.N.Murthy, Singh, Seema, Simmons, Blake A and Klein-Marcuschamer, Daniel (2015). An Investigation on the Economic Feasibility of Macroalgae as a Potential Feedstock for Biorefineries. Bioenergy Research, 8 (3), 1046-1056. doi: 10.1007/s12155-015-9594-1
George, Anthe, Brandt, Agnieszka, Tran, Kim, Zahari, Shahrul M. S. Nizan S., Klein-Marcuschamer, Daniel, Sun, Ning, Sathitsuksanoh, Noppadon, Shi, Jian, Stavila, Vitalie, Parthasarathi, Ramakrishnan, Singh, Seema, Holmes, Bradley M., Welton, Tom, Simmons, Blake A. and Hallett, Jason P. (2015). Design of low-cost ionic liquids for lignocellulosic biomass pretreatment. Green Chemistry, 17 (3), 1728-1734. doi: 10.1039/c4gc01208a
Singh, Seema, Cheng, Gang, Sathitsuksanoh, Noppadon, Wu, Dong, Varanasi, Patanjali, George, Anthe, Balan, Venkatesh, Gao, Xiadi, Kumar, Rajeev, Dale, Bruce E., Wyman, Charles E. and Simmons, Blake A. (2015). Comparison of different biomass pretreatment techniques and their impact on chemistry and structure. Frontiers in Energy Research, 3 (FEB) 62. doi: 10.3389/fenrg.2014.00062
Lupoi, Jason S., Healey, Adam, Singh, Seema, Sykes, Robert, Davis, Mark, Lee, David J., Shepherd, Merv, Simmons, Blake A. and Henry, Robert J. (2015). High-throughput prediction of Acacia and eucalypt lignin syringyl/guaiacyl content using FT-Raman spectroscopy and partial least squares modelling. Bioenergy Research, 8 (3), 953-963. doi: 10.1007/s12155-015-9578-1
Shih, Steve C. C., Gach, Philip C., Sustarich, Jess, Simmons, Blake A., Adams, Paul D., Singh, Seema and Singh, Anup K. (2015). A droplet-to-digital (D2D) microfluidic device for single cell assays. Lab on a Chip, 15 (1), 225-236. doi: 10.1039/c4lc00794h
Cheng, Gang, Zhang, Xin, Simmons, Blake and Singh, Seema (2015). Theory, practice and prospects of X-ray and neutron scattering for lignocellulosic biomass characterization: towards understanding biomass pretreatment. Energy and Environmental Science, 8 (2), 436-455. doi: 10.1039/c4ee03147d
Woo, Hannah L., Ballor, Nicholas R., Hazen, Terry C., Fortney, Julian L., Simmons, Blake, Davenport, Karen Walston, Goodwin, Lynne, Ivanova, Natalia, Kyrpides, Nikos C., Mavromatis, Konstantinos, Woyke, Tanja, Jansson, Janet, Kimbrel, Jeff and DeAngelis, Kristen M. (2014). Complete genome sequence of the lignin-degrading bacterium Klebsiella sp. strain BRL6-2. Standards in Genomic Sciences, 9 (1) 19. doi: 10.1186/1944-3277-9-19
Furtado, Agnelo, Lupoi, Jason S., Hoang, Nam V., Healey, Adam, Singh, Seema, Simmons, Blake A. and Henry, Robert J. (2014). Modifying plants for biofuel and biomaterial production. Plant Biotechnology Journal, 12 (9), 1246-1258. doi: 10.1111/pbi.12300
Sitepu, Irnayuli R., Shi, Shuang, Simmons, Blake A., Singer, Steven W., Boundy-Mills, Kyria and Simmons, Christopher W. (2014). Yeast tolerance to the ionic liquid 1-ethyl-3-methylimidazolium acetate. FEMS Yeast Research, 14 (8), 1286-1294. doi: 10.1111/1567-1364.12224
Rotavera, Brandon, Zádor, Judit, Welz, Oliver, Sheps, Leonid, Scheer, Adam M., Savee, John D., Akbar Ali, Mohamad, Lee, Taek Soon, Simmons, Blake A., Osborn, David L., Violi, Angela and Taatjes, Craig A. (2014). Photoionization mass spectrometric measurements of initial reaction pathways in low-temperature oxidation of 2,5-dimethylhexane. Journal of Physical Chemistry A, 118 (44), 10188-10200. doi: 10.1021/jp507811d
Simmons, C. W., Reddy, A. P., Simmons, B. A., Singer, S. W. and Vandergheynst, J. S. (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 Microbiology, 117 (4), 1025-1034. doi: 10.1111/jam.12609
Heins, Richard A., Cheng, Xiaoliang, Nath, Sangeeta, Deng, Kai, Bowen, Benjamin P., Chivian, Dylan C., Datta, Supratim, Friedland, Gregory D., D'Haeseleer, Patrik, Wu, Dongying, Tran-Gyamfi, Mary, Scullin, Chessa S., Singh, Seema, Shi, Weibing, Hamilton, Matthew G., Bendall, Matthew L., Sczyrba, Alexander, Thompson, John, Feldman, Taya, Guenther, Joel M., Gladden, John M., Cheng, Jan-Fang, Adams, Paul D., Rubin, Edward M., Simmons, Blake A., Sale, Kenneth L., Northen, Trent R. and Deutsch, Samuel (2014). Phylogenomically guided identification of industrially relevant GH1 β-glucosidases through DNA synthesis and nanostructure-initiator mass spectrometry. ACS Chemical Biology, 9 (9), 2082-2091. doi: 10.1021/cb500244v
Parreiras, Lucas S., Breuer, Rebecca J., Narasimhan, Ragothaman Avanasi, Higbee, Alan J., La Reau, Alex, Tremaine, Mary, Qin, Li, Willis, Laura B., Bice, Benjamin D., Bonfert, Brandi L., Pinhancos, Rebeca C., Balloon, Allison J., Uppugundla, Nirmal, Liu, Tongjun, Li, Chenlin, Tanjore, Deepti, Ong, Irene M., Li, Haibo, Pohlmann, Edward L., Serate, Jose, Withers, Sydnor T., Simmons, Blake A., Hodge, David B., Westphall, Michael S., Coon, Joshua J., Dale, Bruce E., Balan, Venkatesh, Keating, David H., Zhang, Yaoping ... Sato, Trey K. (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, e107499. doi: 10.1371/journal.pone.0107499
Socha, Aaron M., Parthasarathi, Ramakrishnan, Shi, Jian, Pattathil, Sivakumar, Whyte, Dorian, Bergeron, Maxime, George, Anthe, Tran, Kim, Stavila, Vitalie, Venkatachalam, Sivasankari, Hahn, Michael G., Simmons, Blake A. and Singh, Seema (2014). 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 (35), E3587-E3595. doi: 10.1073/pnas.1405685111
Shi, Jian, Balamurugan, Kanagasabai, Parthasarathi, Ramakrishnan, Sathitsuksanoh, Noppadon, Zhang, Sonny, Stavila, Vitalie, Subramanian, Venkatesan, Simmons, Blake A. and Singh, Seema (2014). Understanding the role of water during ionic liquid pretreatment of lignocellulose: co-solvent or anti-solvent?. Green Chemistry, 16 (8), 3830-3840. doi: 10.1039/c4gc00373j
Deng, Kai, Takasuka, Taichi E., Heins, Richard, Cheng, Xiaoliang, Bergeman, Lai F., Shi, Jian, Aschenbrener, Ryan, Deutsch, Sam, Singh, Seema, Sale, Kenneth L., Simmons, Blake A., Adams, Paul D., Singh, Anup K., Fox, Brian G. and Northen, Trent R. (2014). Rapid kinetic characterization of glycosyl hydrolases based on oxime derivatization and nanostructure-initiator mass spectrometry (NIMS). ACS Chemical Biology, 9 (7), 1470-1479. doi: 10.1021/cb5000289
Frederix, Marijke, Hütter, Kimmo, Leu, Jessica, Batth, Tanveer S., Turner, William J., Rüegg, Thomas L., Blanch, Harvey W., Simmons, Blake A., Adams, Paul D., Keasling, Jay D., Thelen, Michael P., Dunlop, Mary J., Petzold, Christopher J. and Mukhopadhyay, Aindrila (2014). Development of a native Escherichia coli induction system for ionic liquid tolerance. PLoS ONE, 9 (7) e101115, e101115. doi: 10.1371/journal.pone.0101115
Lupoi, Jason S., Singh, Seema, Davis, Mark, Lee, David J., Shepherd, Merv, Simmons, Blake A. and Henry, Robert J. (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. Biotechnology for Biofuels, 7 (1) 93, 93. doi: 10.1186/1754-6834-7-93
Konda, NVSN Murthy, Shi, Jian, Singh, Seema, Blanch, Harvey W., Simmons, Blake A. and Klein-Marcuschamer, Daniel (2014). Understanding cost drivers and economic potential of two variants of ionic liquid pretreatment for cellulosic biofuel production. Biotechnology for Biofuels, 7 (86) 86, 1-11. doi: 10.1186/1754-6834-7-86
Uppugundla, Nirmal, Da Costa Sousa, Leonardo, Chundawat, Shishir P. S., Yu, Xiurong, Simmons, Blake, Singh, Seema, Gao, Xiadi, Kumar, Rajeev, Wyman, Charles E., Dale, Bruce E. and Balan, Venkatesh (2014). A comparative study of ethanol production using dilute acid, ionic liquid and AFEX™ pretreated corn stover. Biotechnology for Biofuels, 7 (1) 72. doi: 10.1186/1754-6834-7-72
Gao, Xiadi, Kumar, Rajeev, Singh, Seema, Simmons, Blake A., Balan, Venkatesh, Dale, Bruce E. and Wyman, Charles E. (2014). Comparison of enzymatic reactivity of corn stover solids prepared by dilute acid, AFEX™, and ionic liquid pretreatments. Biotechnology for Biofuels, 7 (1) 71. doi: 10.1186/1754-6834-7-71
Sun, Ning, Parthasarathi, Ramakrishnan, Socha, Aaron M., Shi, Jian, Zhang, Sonny, Stavila, Vitalie, Sale, Kenneth L., Simmons, Blake A. and Singh, Seema (2014). Understanding pretreatment efficacy of four cholinium and imidazolium ionic liquids by chemistry and computation. Green Chemistry, 16 (5), 2546-2557. doi: 10.1039/c3gc42401d
Oleskowicz-Popiel, Piotr, Klein-Marcuschamer, Daniel, Simmons, Blake A. and Blanch, Harvey W. (2014). Lignocellulosic ethanol production without enzymes - technoeconomic analysis of ionic liquid pretreatment followed by acidolysis. Bioresource Technology, 158, 294-299. doi: 10.1016/j.biortech.2014.02.016
Ruegg, Thomas L., Kim, Eun-Mi, Simmons, Blake A., Keasling, Jay D., Singer, Steven W., Soon Lee, Taek and Thelen, Michael P. (2014). An auto-inducible mechanism for ionic liquid resistance in microbial biofuel production. Nature Communications, 5 (1) 3490. doi: 10.1038/ncomms4490
Wu, Yu-Wei, Tang, Yung-Hsu, Tringe, Susannah G., Simmons, Blake A. and Singer, Steven W. (2014). MaxBin: An automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm. Microbiome, 2 (1) 26. doi: 10.1186/2049-2618-2-26
Sathitsuksanoh, Noppadon, Holtman, Kevin M., Yelle, Daniel J., Morgan, Trevor, Stavila, Vitalie, Pelton, Jeffrey, Blanch, Harvey, Simmons, Blake A. and George, Anthe (2014). Lignin fate and characterization during ionic liquid biomass pretreatment for renewable chemicals and fuels production. Green Chemistry, 16 (3), 1236-1247. doi: 10.1039/c3gc42295j
Bergmann, Jessica C., Costa, Ohana Yonara A., Gladden, John M., Singer, Steven, Heins, Richard, D'haeseleer, Patrik, Simmons, Blake A. and Quirino, Betania F. (2014). Discovery of two novel β-glucosidases from an Amazon soil metagenomic library. FEMS Microbiology Letters, 351 (2), 147-155. doi: 10.1111/1574-6968.12332
Woo, Hannah L., Hazen, Terry C., Simmons, Blake A. and DeAngelis, Kristen M. (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
Gladden, John M., Park, Joshua I., Bergmann, Jessica, Reyes-Ortiz, Vimalier, D'Haeseleer, Patrik, Quirino, Betania F., Sale, Kenneth L., Simmons, Blake A. and Singer, Steven W. (2014). Discovery and characterization of ionic liquid-tolerant thermophilic cellulases from a switchgrass-adapted microbial community. Biotechnology for Biofuels, 7 (1) 15. doi: 10.1186/1754-6834-7-15
Woo, Hannah L., Utturkar, Sagar, Klingeman, Dawn, Simmons, Blake A., DeAngelis, Kristen M., Brown, Steven D. and Hazen, Terry C. (2014). Draft genome sequence of the lignin-degrading Burkholderia sp. strain LIG30, isolated from wet tropical forest soil. Genome Announcements, 2 (3) e00637-14. doi: 10.1128/genomeA.00637-14
Simmons, Christopher W., Claypool, Joshua T., Marshall, Megan N., Jabusch, Lauren K., Reddy, Amitha P., Simmons, Blake A., Singer, Steven W., Stapleton, James J. and VanderGheynst, Jean S. (2014). Characterization of bacterial communities in solarized soil amended with lignocellulosic organic matter. Applied Soil Ecology, 73, 97-104. doi: 10.1016/j.apsoil.2013.08.014
Eichorst, Stephanie A., Joshua, Chijioke, Sathitsuksanoh, Noppadon, Singh, Seema, Simmons, Blake A. and Singer, Steven W. (2014). Substrate-specific development of thermophilic bacterial consortia by using chemically pretreated switchgrass. Applied and Environmental Microbiology, 80 (23), 7423-7432. doi: 10.1128/AEM.02795-14
Simmons, Christopher W., Reddy, Amitha P., D'haeseleer, Patrik, Khudyakov, Jane, Billis, Konstantinos, Pati, Amrita, Simmons, Blake A., Singer, Steven W., Thelen, Michael P. and Vandergheynst, Jean S. (2014). Metatranscriptomic analysis of lignocellulolytic microbial communities involved in high-solids decomposition of rice straw. Biotechnology for Biofuels, 7 (1) 180. doi: 10.1186/s13068-014-0180-0
Simmons, Christopher W., Reddy, Amitha P., Vandergheynst, Jean S., Simmons, Blake A. and Singer, Steven W. (2014). Bacillus coagulans tolerance to 1-ethyl-3-methylimidazolium-based ionic liquids in aqueous and solid-state thermophilic culture. Biotechnology Progress, 30 (2), 311-316. doi: 10.1002/btpr.1859
Lupoi, Jason S., Singh, Seema, Simmons, Blake A. and Henry, Robert J. (2014). Assessment of lignocellulosic biomass using analytical spectroscopy: an evolution to high-throughput techniques. Bioenergy Research, 7 (1), 1-23. doi: 10.1007/s12155-013-9352-1
Chen, Zhiwei, Pereira, Jose H., Liu, Hanbin, Tran, Huu M., Hsu, Nathan S. Y., Dibble, Dean, Singh, Seema, Adams, Paul D., Sapra, Rajat, Hadi, Masood Z., Simmons, Blake A. and Sale, Kenneth L. (2013). Improved activity of a thermophilic cellulase, Cel5A, from Thermotoga maritima on ionic liquid pretreated switchgrass. PLoS ONE, 8 (11) e79725. doi: 10.1371/journal.pone.0079725
DeAngelis, Kristen M., Chivian, Dylan, Fortney, Julian L., Arkin, Adam P., Simmons, Blake, Hazen, Terry C. and Silver, Whendee L. (2013). Changes in microbial dynamics during long-term decomposition in tropical forests. Soil Biology and Biochemistry, 66, 60-68. doi: 10.1016/j.soilbio.2013.06.010
Li, Chenlin, Tanjore, Deepti, He, Wei, Wong, Jessica, Gardner, James L., Sale, Kenneth L., Simmons, Blake A. and Singh, Seema (2013). Scale-up and evaluation of high solid ionic liquid pretreatment and enzymatic hydrolysis of switchgrass. Biotechnology for Biofuels, 6 (1) 154. doi: 10.1186/1754-6834-6-154
DeAngelis, Kristen M., Sharma, Deepak, Varney, Rebecca, Simmons, Blake, Isern, Nancy G., Markilllie, Lye Meng, Nicora, Carrie, Norbeck, Angela D., Taylor, Ronald C., Aldrich, Joshua T. and Robinson, Errol W. (2013). Evidence supporting dissimilatory and assimilatory lignin degradation in Enterobacter lignolyticus SCF1. Frontiers in Microbiology, 4 (SEP). doi: 10.3389/fmicb.2013.00280
Shi, Jian, Gladden, John M., Sathitsuksanoh, Noppadon, Kambam, Pavan, Sandoval, Lucas, Mitra, Debjani, Zhang, Sonny, George, Anthe, Singer, Steven W., Simmons, Blake A. and Singh, Seema (2013). One-pot ionic liquid pretreatment and saccharification of switchgrass. Green Chemistry, 15 (9), 2579-2589. doi: 10.1039/c3gc40545a
Eichorst, Stephanie A., Varanasi, Patanjali, Stavila, Vatalie, Zemla, Marcin, Auer, Manfred, Singh, Seema, Simmons, Blake A. and Singer, Steven W. (2013). Community dynamics of cellulose-adapted thermophilic bacterial consortia. Environmental Microbiology, 15 (9), 2573-2587. doi: 10.1111/1462-2920.12159
Reyes-Ortiz, Vimalier, Heins, Richard A., Cheng, Gang, Kim, Edward Y., Vernon, Briana C., Elandt, Ryan B., Adams, Paul D., Sale, Kenneth L., Hadi, Masood Z., Simmons, Blake A., Kent, Michael S. and Tullman-Ercek, Danielle (2013). Addition of a carbohydrate-binding module enhances cellulase penetration into cellulose substrates. Biotechnology for Biofuels, 6 (1) 93. doi: 10.1186/1754-6834-6-93
D'haeseleer, Patrik, Gladden, John M., Allgaier, Martin, Chain, Patrik S. G., Tringe, Susannah G., Malfatti, Stephanie A., Aldrich, Joshua T., Nicora, Carrie D., Robinson, Errol W., Pasa-Tolic, Ljiljana, Hugenholtz, Philip, Simmons, Blake A. and Singer, Steven W. (2013). Proteogenomic Analysis of a Thermophilic Bacterial Consortium Adapted to Deconstruct Switchgrass. Plos One, 8 (7) e68465, e68465.1-e68465.11. doi: 10.1371/journal.pone.0068465
Singh, Seema, Varanasi, Patanjali, Singh, Priyanka, Adams, Paul D., Auer, Manfred and Simmons, Blake A. (2013). Understanding the impact of ionic liquid pretreatment on cellulose and lignin via thermochemical analysis. Biomass and Bioenergy, 54, 276-283. doi: 10.1016/j.biombioe.2013.02.035
McAndrew, Ryan P., Park, Joshua I., Heins, Richard A., Reindl, Wolfgang, Friedland, Gregory D., D'haeseleer, Patrik, Northen, Trent, Sale, Kenneth L., Simmons, Blake A. and Adams, Paul D. (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 (21), 14985-14992. doi: 10.1074/jbc.M113.458356
Groff, Dan, George, Anthe, Sun, Ning, Sathitsuksanoh, Noppadon, Bokinsky, Gregory, Simmons, Blake A., Holmes, Bradley M. and Keasling, Jay D. (2013). Acid enhanced ionic liquid pretreatment of biomass. Green Chemistry, 15 (5), 1264-1267. doi: 10.1039/c3gc37086k
Socha, Aaron M., Plummer, Samuel P., Stavila, Vitalie, Simmons, Blake A. and Singh, Seema (2013). Comparison of sugar content for ionic liquid pretreated Douglas-fir woodchips and forestry residues. Biotechnology for Biofuels, 6 (1) 61. doi: 10.1186/1754-6834-6-61
Cruz, Alejandro G., Scullin, Chessa, Mu, Chen, Cheng, Gang, Stavila, Vitalie, Varanasi, Patanjali, Xu, Dongyan, Mentel, Jeff, Chuang, Yi-De, Simmons, Blake A. and Singh, Seema (2013). Impact of high biomass loading on ionic liquid pretreatment. Biotechnology for Biofuels, 6 (52) 52. doi: 10.1186/1754-6834-6-52
Chiniquy, Dawn, Varanasi, Patanjali, Oh, Taeyun, Harholt, Jesper, Katnelson, Jacob, Singh, Seema, Auer, Manfred, Simmons, Blake, Adams, Paul D., Scheller, Henrik V. and Ronald, Pamela C. (2013). Three novel rice genes closely related to the Arabidopsis IRX9, IRX9L, and IRX14 genes and their roles in xylan biosynthesis. Frontiers in Plant Science, 4 (APR) 83. doi: 10.3389/fpls.2013.00083
Shi, Jian, Thompson, Vicki S., Yancey, Neal A., Stavila, Vitalie, Simmons, Blake A. and Singh, Seema (2013). Impact of mixed feedstocks and feedstock densification on ionic liquid pretreatment efficiency. Biofuels, 4 (1), 63-72. doi: 10.4155/bfs.12.82
De Angelis, Kristen M., D'Haeseleer, Patrik, Chivian, Dylan, Simmons, Blake, Arkin, Adam P., Mavromatis, Konstantinos, Malfatti, Stephanie, Tringe, Susannah and Hazen, Terry C. (2013). Metagenomes of tropical soil-derived anaerobic switchgrass-adapted consortia with and without iron. Standards in Genomic Sciences, 7 (3), 382-398. doi: 10.4056/sigs.3377516
Sun, Ning, Liu, Hanbin, Sathitsuksanoh, Noppadon, Stavila, Vitalie, Sawant, Manali, Bonito, Anaise, Tran, Kim, George, Anthe, Sale, Kenneth L., Singh, Seema, Simmons, Blake A. and Holmes, Bradley M. (2013). Production and extraction of sugars from switchgrass hydrolyzed in ionic liquids. Biotechnology for Biofuels, 6 (1) 39. doi: 10.1186/1754-6834-6-39
Li, Chenlin, Sun, Lan, Simmons, Blake A. and Singh, Seema (2013). Comparing the recalcitrance of eucalyptus, pine, and switchgrass using ionic liquid and dilute acid pretreatments. Bioenergy Research, 6 (1), 14-23. doi: 10.1007/s12155-012-9220-4
Sun, Lan, Li, Chenlin, Xue, Zhengjun, Simmons, Blake A. and Singh, Seema (2013). Unveiling high-resolution, tissue specific dynamic changes in corn stover during ionic liquid pretreatment. RSC Advances, 3 (6), 2017-2027. doi: 10.1039/c2ra20706k
Paap, Scott M., West, Todd H., Manley, Dawn K., Steen, Eric J., Beller, Harry R., Keasling, Jay D., Dibble, Dean C., Chang, Shiyan and Simmons, Blake A. (2013). Biochemical production of ethanol and fatty acid ethyl esters from switchgrass: a comparative analysis of environmental and economic performance. Biomass & Bioenergy, 49, 49-62. doi: 10.1016/j.biombioe.2012.11.029
Varanasi, Patanjali, Singh, Priyanka, Auer, Manfred, Adams, Paul D., Simmons, Blake A. and Singh, Seema (2013). Survey of renewable chemicals produced from lignocellulosic biomass during ionic liquid pretreatment. Biotechnology for Biofuels, 6 (1) 14. doi: 10.1186/1754-6834-6-14
Cheng, Xiaoliang, Hiras, Jennifer, Deng, Kai, Bowen, Benjamin, Simmons, Blake A., Adams, Paul D., Singer, Steven W. and Northen, Trent R. (2013). High throughput nanostructure-initiator mass spectrometry screening of microbial growth conditions for maximal β-glucosidase production. Frontiers in Microbiology, 4 (DEC). doi: 10.3389/fmicb.2013.00365
Perez-Pimienta, Jose A., Lopez-Ortega, Monica G., Varanasi, Patanjali, Stavila, Vitalie, Cheng, Gang, Singh, Seema and Simmons, Blake A. (2013). Comparison of the impact of ionic liquid pretreatment on recalcitrance of agave bagasse and switchgrass. Bioresource Technology, 127, 18-24. doi: 10.1016/j.biortech.2012.09.124
Cetinkol, Oezguel Persil, Smith-Moritz, Andreia M., Cheng, Gang, Lao, Jeemeng, George, Anthe, Hong, Kunlun, Henry, Robert, Simmons, Blake A., Heazlewood, Joshua L. and Holmes, Bradley M. (2012). Structural and chemical characterization of hardwood from tree species with applications as Bioenergy Feedstocks. PLoS One, 7 (12) e52820, e52820.1-e52820.11. doi: 10.1371/journal.pone.0052820
Cheng, Gang, Varanasi, Patanjali, Arora, Rohit, Stavila, Vitalie, Simmons, Blake A., Kent, Michael S. and Singh, Seema (2012). Impact of ionic liquid pretreatment conditions on cellulose crystalline structure using 1-ethyl-3-methylimidazolium acetate. Journal of Physical Chemistry B, 116 (33), 10049-10054. doi: 10.1021/jp304538v
Reddy, A. P., Simmons, C. W., Claypool, J., Jabusch, L., Burd, H., Hadi, M. Z., Simmons, B. A., Singer, S. W. and Vandergheynst, J. S. (2012). Thermophilic enrichment of microbial communities in the presence of the ionic liquid 1-ethyl-3-methylimidazolium acetate. Journal of Applied Microbiology, 113 (6), 1362-1370. doi: 10.1111/jam.12002
Cheng, Gang, Kent, Michael S., He, Lilin, Varanasi, Patanjali, Dibble, Dean, Arora, Rohit, Deng, Kai, Hong, Kunlun, Melnichenko, Yuri B., Simmons, Blake A. and Singh, Seema (2012). Effect of ionic liquid treatment on the structures of lignins in solutions: molecular subunits released from lignin. Langmuir, 28 (32), 11850-11857. doi: 10.1021/la300938b
Papa, G., Varanasi, P., Sun, L., Cheng, G., Stavila, V., Holmes, B., Simmons, B. A., Adani, F. and Singh, S. (2012). Exploring the effect of different plant lignin content and composition on ionic liquid pretreatment efficiency and enzymatic saccharification of Eucalyptus globulus L. mutants. Bioresource Technology, 117, 352-359. doi: 10.1016/j.biortech.2012.04.065
McClendon, Shara D., Batth, Tanveer, Petzold, Christopher J, Adams, Paul D., Simmons, Blake A. and Singer, Steven W. (2012). Thermoascus aurantiacus is a promising source of enzymes for biomass deconstruction under thermophilic conditions. Biotechnology for Biofuels, 5 (54) 54. doi: 10.1186/1754-6834-5-54
Chen, Zhiwei, Friedland, Gregory D., Pereira, Jose H., Reveco, Sonia A., Chan, Rosa, Park, Joshua I., Thelen, Michael P., Adams, Paul D., Arkin, Adam P., Keasling, Jay D., Blanch, Harvey W., Simmons, Blake A., Sale, Kenneth L., Chivian, Dylan and Chhabra, Swapnil R. (2012). Tracing determinants of dual substrate specificity in glycoside hydrolase family 5. Journal of Biological Chemistry, 287 (30), 25335-25343. doi: 10.1074/jbc.M112.362640
Liu, Hanbin, Cheng, Gang, Kent, Michael, Stavila, Vitalie, Simmons, Blake A., Sale, Kenneth L. and Singh, Seema (2012). Simulations reveal conformational changes of methylhydroxyl groups during dissolution of cellulose Iβ in ionic liquid 1-ethyl-3- methylimidazolium acetate. Journal of Physical Chemistry B, 116 (28), 8131-8138. doi: 10.1021/jp301673h
Dougherty, Michael J., D'haeseleer, Patrik, Hazen, Terry C., Simmons, Blake A., Adams, Paul D. and Hadi, Masood Z. (2012). Glycoside hydrolases from a targeted compost metagenome, activity-screening and functional characterization. BMC Biotechnology, 12 (1) 38. doi: 10.1186/1472-6750-12-38
Habermehl, S., Rodriguez, M. and Simmons, B. (2012). Formation of stress-controlled, highly textured, α-SiC thin films at 950 °c. Journal of Applied Physics, 112 (1) 013535, 013535. doi: 10.1063/1.4733967
Cheng, Gang, Datta, Supratim, Liu, Zelin, Wang, Chao, Murton, Jaclyn K., Brown, Page A., Jablin, Michael S., Dubey, Manish, Majewski, Jaroslaw, Halbert, Candice E., Browning, James F., Esker, Alan R., Watson, Brian J., Zhang, Haito, Hutcheson, Steven W., Huber, Dale L., Sale, Kenneth L., Simmons, Blake A. and Kent, Michael S. (2012). Interactions of endoglucanases with amorphous cellulose films resolved by neutron reflectometry and quartz crystal microbalance with dissipation monitoring. Langmuir, 28 (22), 8348-8358. doi: 10.1021/la300955q
Eudes, Aymerick, George, Anthe, Mukerjee, Purba, Kim, Jin S., Pollet, Brigitte, Benke, Peter I., Yang, Fan, Mitra, Prajakta, Sun, Lan, Çetinkol, Özgül P., Chabout, Salem, Mouille, Grégory, Soubigou-Taconnat, Ludivine, Balzergue, Sandrine, Singh, Seema, Holmes, Bradley M., Mukhopadhyay, Aindrila, Keasling, Jay D., Simmons, Blake A., Lapierre, Catherine, Ralph, John and Loqué, Dominique (2012). Biosynthesis and incorporation of side-chain-truncated lignin monomers to reduce lignin polymerization and enhance saccharification. Plant Biotechnology Journal, 10 (5), 609-620. doi: 10.1111/j.1467-7652.2012.00692.x
Park, Joshua I., Steen, Eric J., Burd, Helcio, Evans, Sophia S., Redding-Johnson, Alyssa M., Batth, Tanveer, Benke, Peter I., D'haeseleer, Patrik, Sun, Ning, Sale, Kenneth L., Keasling, Jay D., Lee, Taek Soon, Petzold, Christopher J., Mukhopadhyay, Aindrila, Singer, Steven W., Simmons, Blake A. and Gladden, John M. (2012). A thermophilic ionic liquid-tolerant cellulase cocktail for the production of cellulosic biofuels. PLoS One, 7 (5) e37010, e37010. doi: 10.1371/journal.pone.0037010
Gladden, John M., Eichorst, Stephanie A., Hazen, Terry C., Simmons, Blake A. and Singer, Steven W. (2012). Substrate perturbation alters the glycoside hydrolase activities and community composition of switchgrass-adapted bacterial consortia. Biotechnology and Bioengineering, 109 (5), 1140-1145. doi: 10.1002/bit.24388
Zendejas, Frank J., Benke, Peter I., Lane, Pamela D., Simmons, Blake A. and Lane, Todd W. (2012). Characterization of the acylglycerols and resulting biodiesel derived from vegetable oil and microalgae (Thalassiosira pseudonana and Phaeodactylum tricornutum). Biotechnology and Bioengineering, 109 (5), 1146-1154. doi: 10.1002/bit.24395
Klein-Marcuschamer, Daniel, Oleskowicz-Popiel, Piotr, Simmons, Blake A. and Blanch, Harvey W. (2012). The challenge of enzyme cost in the production of lignocellulosic biofuels. Biotechnology and Bioengineering, 109 (4), 1083-1087. doi: 10.1002/bit.24370
Torr, Kirk M., Love, Karen T., Etinkol, Özgül P., Donaldson, Lloyd A., George, Anthe, Holmes, Bradley M. and Simmons, Blake A. (2012). The impact of ionic liquid pretreatment on the chemistry and enzymatic digestibility of Pinus radiata compression wood. Green Chemistry, 14 (3), 778-787. doi: 10.1039/c2gc16362d
Sun, Lan, Varanasi, Patanjali, Yang, Fan, Loqué, Dominique, Simmons, Blake A. and Singh, Seema (2012). Rapid determination of syringyl: guaiacyl ratios using FT-Raman spectroscopy. Biotechnology and Bioengineering, 109 (3), 647-656. doi: 10.1002/bit.24348
Welz, Oliver, Zádor, Judit, Savee, John D., Ng, Martin Y., Meloni, Giovanni, Fernandes, Ravi X., Sheps, Leonid, Simmons, Blake A., Lee, Taek Soon, Osborn, David L. and Taatjes, Craig A. (2012). Low-temperature combustion chemistry of biofuels: pathways in the initial low-temperature (550 K-750 K) oxidation chemistry of isopentanol. Physical Chemistry Chemical Physics, 14 (9), 3112-3127. doi: 10.1039/c2cp23248k
Deangelis, Kristen M., Fortney, Julian L., Borglin, Sharon, Silver, Whendee L., Simmons, Blake A. and Hazen, Terry C. (2012). Anaerobic decomposition of switchgrass by tropical soil-derived feedstock-adapted consortia. mBio, 3 (1) e00249-11, 1-9. doi: 10.1128/mBio.00249-11
Chuck, George S., Tobias, Christian, Sun, Lan, Kraemer, Florian, Li, Chenlin, Dibble, Dean, Arora, Rohit, Bragg, Jennifer N., Vogel, John P., Singh, Seema, Simmons, Blake A., Pauly, Markus and Hake, Sarah (2012). Erratum: Overexpression of the maize Corngrass1 microRNA prevents flowering, improves digestibility, and increases starch content of switchgrass (Proceedings of the National Academy of Sciences of the United States of America (2011) 108, 42, (17550-17555) DOI: 10.1073/pnas.1113971108). Proceedings of the National Academy of Sciences of the United States of America, 109 (3), 995-995. doi: 10.1073/pnas.1120302109
Oleskowicz-Popiel, Piotr, Kádár, Zsófia, Heiske, Stefan, Klein-Marcuschamer, Daniel, Simmons, Blake A., Blanch, Harvey W. and Schmidt, Jens Ejbye (2012). Co-production of ethanol, biogas, protein fodder and natural fertilizer in organic farming - evaluation of a concept for a farm-scale biorefinery. Bioresource Technology, 104, 440-446. doi: 10.1016/j.biortech.2011.11.060
Bokinsky, Gregory, Peralta-Yahya, Pamela P., George, Anthe, Holmes, Bradley M., Steen, Eric J., Dietrich, Jeffrey, Lee, Taek Soon, Tullman-Ercek, Danielle, Voigt, Christopher A., Simmons, Blake A. and Keasling, Jay D. (2011). Synthesis of three advanced biofuels from ionic liquid-pretreated switchgrass using engineered Escherichia coli. Proceedings of the National Academy of Sciences of the United States of America, 108 (50), 19949-19954. doi: 10.1073/pnas.1106958108
George, Anthe, Tran, Kim, Morgan, Trevor J., Benke, Peter I., Berrueco, Cesar, Lorente, Esther, Wu, Ben C., Keasling, Jay D., Simmons, Blake A. and Holmes, Bradley M. (2011). The effect of ionic liquid cation and anion combinations on the macromolecular structure of lignins. Green Chemistry, 13 (12), 3375-3385. doi: 10.1039/c1gc15543a
Shepherd, Mervyn, Bartle, John, Lee, David J., Brawner, Jeremy, Bush, David, Turnbull, Paul, Macdonell, Paul, Brown, Troy R., Simmons, Blake and Henry, Robert (2011). Eucalypts as a biofuel feedstock. Biofuels, 2 (6), 639-657. doi: 10.4155/bfs.11.136
Deangelis, Kristen M., D'Haeseleer, Patrik, Chivian, Dylan, Fortney, Julian L., Khudyakov, Jane, Simmons, Blake, Woo, Hannah, Arkin, Adam P., Davenport, Karen Walston, Goodwin, Lynne, Chen, Amy, Ivanova, Natalia, Kyrpides, Nikos C., Mavromatis, Konstantinos, Woyke, Tanja and Hazen, Terry C. (2011). Complete genome sequence of "Enterobacter lignolyticus" SCF1. Standards in Genomic Sciences, 5 (1), 69-85. doi: 10.4056/sigs.2104875
Chuck, George S., Tobias, Christian, Sun, Lan, Kraemer, Florian, Li, Chenlin, Dibble, Dean, Arora, Rohit, Bragg, Jennifer N., Vogel, John P., Singh, Seema, Simmons, Blake A., Pauly, Markus and Hake, Sarah (2011). Overexpression of the maize Corngrass1 microRNA prevents flowering, improves digestibility, and increases starch content of switchgrass. Proceedings of the National Academy of Sciences of the United States of America, 108 (42), 17550-17555. doi: 10.1073/pnas.1113971108
Blanch, Harvey W., Simmons, Blake A. and Klein-Marcuschamer, Daniel (2011). Biomass deconstruction to sugars. Biotechnology Journal, 6 (9), 1086-1102. doi: 10.1002/biot.201000180
Reddy, Amitha P., Allgaier, Martin, Singer, Steven W., Hazen, Terry C., Simmons, Blake A., Hugenholtz, Philip and VanderGheynst, Jean S. (2011). Bioenergy feedstock-specific enrichment of microbial populations during high-solids thermophilic deconstruction. Biotechnology and Bioengineering, 108 (9), 2088-2098. doi: 10.1002/bit.23176
Gladden, John M., Allgaier, Martin, Miller, Christopher S., Hazen, Terry C., VanderGheynst, Jean S., Hugenholtz, Philip, Simmons, Blake A. and Singer, Steven W. (2011). Glycoside hydrolase activities of thermophilic bacterial consortia adapted to switchgrass. Applied and Environmental Microbiology, 77 (16), 5804-5812. doi: 10.1128/AEM.00032-11
Simmons, Blake (2011). Rethinking renewable energy in Japan. Biofuels, 2 (4), 365-367. doi: 10.4155/bfs.11.117
Li, Chenlin, Cheng, Gang, Balan, Venkatesh, Kent, Michael S., Ong, Markus, Chundawat, Shishir P.S., Sousa, Leonardo daCosta, Melnichenko, Yuri B., Dale, Bruce E., Simmons, Blake A. and Singh, Seema (2011). Influence of physico-chemical changes on enzymatic digestibility of ionic liquid and AFEX pretreated corn stover. Bioresource Technology, 102 (13), 6928-6936. doi: 10.1016/j.biortech.2011.04.005
Park, Joshua I., Kent, Michael S., Datta, Supratim, Holmes, Bradley M., Huang, Zhaohua, Simmons, Blake A., Sale, Kenneth L. and Sapra, Rajat (2011). Enzymatic hydrolysis of cellulose by the cellobiohydrolase domain of CelB from the hyperthermophilic bacterium Caldicellulosiruptor saccharolyticus. Bioresource Technology, 102 (10), 5988-5994. doi: 10.1016/j.biortech.2011.02.036
Cheng, Gang, Varanasi, Patanjali, Li, Chenlin, Liu, Hanbin, Melnichenko, Yuri B., Simmons, Blake A., Kent, Michael S. and Singh, Seema (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. doi: 10.1021/bm101240z
Deangelis, Kristen M., Allgaier, Martin, Chavarria, Yaucin, Fortney, Julian L., Hugenholtz, Philip, Simmons, Blake, Sublette, Kerry, Silver, Whendee L. and Hazen, Terry C. (2011). Characterization of trapped lignin-degrading microbes in tropical forest soil. Plos One, 6 (4) e19306, e19306.1-e19306.9. doi: 10.1371/journal.pone.0019306
Wu, Huawen, Volponi, Joanne V., Oliver, Ann E., Parikh, Atul N., Simmons, Blake A. and Singh, Seema (2011). In vivo lipidomics using single-cell Raman spectroscopy. Proceedings of the National Academy of Sciences of the United States of America, 108 (9), 3809-3814. doi: 10.1073/pnas.1009043108
Sun, Lan, Simmons, Blake A. and Singh, Seema (2011). Understanding tissue specific compositions of bioenergy feedstocks through hyperspectral Raman imaging. Biotechnology and Bioengineering, 108 (2), 286-295. doi: 10.1002/bit.22931
Dibble, Dean C., Li, Chenlin, Sun, Lan, George, Anthe, Cheng, Aurelia, Çetinkol, Özgül Persil, Benke, Peter, Holmes, Bradley M., Singh, Seema and Simmons, Blake A. (2011). A facile method for the recovery of ionic liquid and lignin from biomass pretreatment. Green Chemistry, 13 (11), 3255-3264. doi: 10.1039/c1gc15111h
Ouellet, Mario, Datta, Supratim, Dibble, Dean C., Tamrakar, Pramila R., Benke, Peter I., Li, Chenlin, Singh, Seema, Sale, Kenneth L., Adams, Paul D., Keasling, Jay D., Simmons, Blake A., Holmes, Bradley M. and Mukhopadhyay, Aindrila (2011). Impact of ionic liquid pretreated plant biomass on Saccharomyces cerevisiae growth and biofuel production. Green Chemistry, 13 (10), 2743-2749. doi: 10.1039/c1gc15327g
Zhang, Tao, Datta, Supratim, Eichler, Jerry, Ivanova, Natalia, Axen, Seth D., Kerfeld, Cheryl A., Chen, Feng, Kyrpides, Nikos, Hugenholtz, Philip, Cheng, Jan-Fang, Sale, Kenneth L., Simmons, Blake and Rubin, Eddy (2011). Identification of a haloalkaliphilic and thermostable cellulase with improved ionic liquid tolerance. Green Chemistry, 13 (8), 2083-2090. doi: 10.1039/c1gc15193b
Simmons, Blake A. (2011). Opportunities and challenges in advanced biofuel production: the importance of synthetic biology and combustion science. Biofuels, 2 (1), 5-7. doi: 10.4155/bfs.10.75
Bharadwaj, Rajiv, Wong, April, Knierim, Bernhard, Singh, Seema, Holmes, Bradley M., Auer, Manfred, Simmons, Blake A., Adams, Paul D. and Singh, Anup K. (2011). High-throughput enzymatic hydrolysis of lignocellulosic biomass via in-situ regeneration. Bioresource Technology, 102 (2), 1329-1337. doi: 10.1016/j.biortech.2010.08.108
Klein-Marcuschamer, Daniel, Oleskowicz-Popiel, Piotr, Simmons, Blake A. and Blanch, Harvey W. (2010). Technoeconomic analysis of biofuels: a wiki-based platform for lignocellulosic biorefineries. Biomass and Bioenergy, 34 (12), 1914-1921. doi: 10.1016/j.biombioe.2010.07.033
Achyuthan, Komandoor Elayavalli, Achyuthan, Ann Mary, Adams, Paul David, Dirk, Shawn Matthew, Harper, Jason Carl, Simmons, Blake Alexander and Singh, Anup Kumar (2010). Supramolecular self-assembled chaos: Polyphenolic lignin's barrier to cost-effective lignocellulosic biofuels. Molecules, 15 (12), 8641-8688. doi: 10.3390/molecules15118641
Yang, Yi, Dec, John, Dronniou, Nicolas and Simmons, Blake (2010). Characteristics of isopentanol as a fuel for HCCI engines. SAE International Journal of Fuels and Lubricants, 3 (2) 2010-01-2164, 725-741. doi: 10.4271/2010-01-2164
Liu, Hanbin, Pereira, Jose Henrique, Adams, Paul D., Sapra, Rajat, Simmons, Blake A. and Sale, Kenneth L. (2010). Molecular simulations provide new insights into the role of the accessory immunoglobulin-like domain of Cel9A. FEBS Letters, 584 (15), 3431-3435. doi: 10.1016/j.febslet.2010.06.041
Li, Chenlin, Knierim, Bernhard, Manisseri, Chithra, Arora, Rohit, Scheller, Henrik V., Auer, Manfred, Vogel, Kenneth P., Simmons, Blake A. and Singh, Seema (2010). Comparison of dilute acid and ionic liquid pretreatment of switchgrass: Biomass recalcitrance, delignification and enzymatic saccharification. Bioresource Technology, 101 (13), 4900-4906. doi: 10.1016/j.biortech.2009.10.066
DeAngelis, Kristen M., Gladden, John M., Allgaier, Martin, D'haeseleer, Patrik, Fortney, Julian L., Reddy, Amitha, Hugenholtz, Philip, Singer, Steven W., Vander Gheynst, Jean S., Silver, Whendee L., Simmons, Blake A. and Hazen, Terry C. (2010). Strategies for enhancing the effectiveness of metagenomic-based enzyme discovery in lignocellulolytic microbial communities. BioEnergy Research, 3 (2), 146-158. doi: 10.1007/s12155-010-9089-z
Arora, Rohit, Manisseri, Chithra, Li, Chenlin, Ong, Markus D., Scheller, Henrik Vibe, Vogel, Kenneth, Simmons, Blake A. and Singh, Seema (2010). Monitoring and analyzing process streams towards understanding ionic liquid pretreatment of switchgrass (Panicum virgatum L.). Bioenergy Research, 3 (2), 134-145. doi: 10.1007/s12155-010-9087-1
Achyuthan, Komandoor Elayavalli, Adams, Paul David, Datta, Supratim, Simmons, Blake Alexander and Singh, Anup Kumar (2010). Hitherto unrecognized fluorescence properties of coniferyl alcohol. Molecules, 15 (3), 1645-1667. doi: 10.3390/molecules15031645
Allagier, Martin, Reddy, Amitha, Park, Joshua I., Ivanova, Natalia, D'haeseleer, Patrik, Lowry, Steve, Sapra, Rajat, Hazen, Terry C., Simmons, Blake A., VanderGheynst, Jean S. and Hugenholtz, Philip (2010). Targeted discovery of glycoside hydrolases from a switchgrass-adapted compost community. PLoS One, 5 (1) e8812, e8812-1-e8812-9. doi: 10.1371/journal.pone.0008812
Çetinkol, Özgül Persil, Dibble, Dean C., Cheng, Gang, Kent, Michael S., Knierim, Bernhard, Auer, Manfred, Wemmer, David E., Pelton, Jeffrey G., Melnichenko, Yuri B., Ralph, John, Simmons, Blake A. and Holmes, Bradley M. (2010). Understanding the impact of ionic liquid pretreatment on eucalyptus. Biofuels, 1 (1), 33-46. doi: 10.4155/bfs.09.5
Wurtzel, Omri, Sapra, Rajat, Chen, Feng, Zhu, Yiwen, Simmons, Blake A. and Sorek, Rotem (2010). A single-base resolution map of an archaeal transcriptome. Genome Research, 20 (1), 133-141. doi: 10.1101/gr.100396.109
Achyuthan, Komandoor Elayavalli, Adams, Paul David, Simmons, Blake Alexander and Singh, Anup Kumar (2009). Spectroscopic analyses of the biofuels-critical phytochemical coniferyl alcohol and its enzyme-catalyzed oxidation products. Molecules, 14 (11), 4758-4778. doi: 10.3390/molecules14114758
Pereira, Jose Henrique, Sapra, Rajat, Volponi, Joanne V., Kozina, Carol L., Simmons, Blake and Adams, Paul D. (2009). Structure of endoglucanase Cel9A from the thermoacidophilic Alicyclobacillus acidocaldarius. Acta Crystallographica Section D: Biological Crystallography, 65 (8), 744-750. doi: 10.1107/S0907444909012773
Sabounchi, Poorya, Morales, Alfredo M., Ponce, Pierre, Lee, Luke P., Simmons, Blake A. and Davalos, Rafael V. (2008). Sample concentration and impedance detection on a microfluidic polymer chip. Biomedical Microdevices, 10 (5), 661-670. doi: 10.1007/s10544-008-9177-4
Simmons, Blake A., Loque, Dominique and Blanch, Harvey W. (2008). Next-generation biomass feedstocks for biofuel production. Genome Biology, 9 (12) 242, 1-6. doi: 10.1186/gb-2008-9-12-242
Wallow, Thomas I., Morales, Alfredo M., Simmons, Blake A., Hunter, Marion C., Krafcik, Karen Lee, Domeier, Linda A., Sickafoose, Shane M., Patel, Kamlesh D. and Gardea, Andy (2007). Low-distortion, high-strength bonding of thermoplastic microfluidic devices employing case-II diffusion-mediated permeant activation. Lab on a Chip, 7 (12), 1825-1831. doi: 10.1039/b710175a
Rucker, Victor C., Havenstrite, Karen L., Simmons, Blake A., Sickafoose, Shane M., Herr, Amy E. and Shediac, Renée (2005). Functional antibody immobilization on 3-dimensional polymeric surfaces generated by reactive ion etching. Langmuir, 21 (17), 7621-7625. doi: 10.1021/la050251r
Mela, Petra, van den Berg, Albert, Fintschenko, Yolanda, Cummings, Eric B., Simmons, Blake A. and Kirby, Brian J. (2005). The zeta potential of cyclo-olefin polymer microchannels and its effects on insulative (electrodeless) dielectrophoresis particle trapping devices. Electrophoresis, 26 (9), 1792-1799. doi: 10.1002/elps.200410153
Conference Papers
Varanasi, Patanjali, Singh, Priyanka, Arora, Rohit, Adams, Paul D., Auer, Manfred, Simmons, Blake A. and Singh, Seema (2012). Understanding changes in lignin of Panicum virgatum and Eucalyptus globulus as a function of ionic liquid pretreatment. Amsterdam, Netherlands: Elsevier. doi: 10.1016/j.biortech.2012.08.070
Greving, Matthew, Cheng, Xiaoliang, Reindl, Wolfgang, Bowen, Benjamin, Deng, Kai, Louie, Katherine, Nyman, Michael, Cohen, Joseph, Singh, Anup, Simmons, Blake, Adams, Paul, Siuzdak, Gary and Northen, Trent (2012). Acoustic deposition with NIMS as a high-throughput enzyme activity assay. 16th Conference on Solid State Analysis, Vienna, Austria, 4-6 July 2011. doi: 10.1007/s00216-012-5908-8
Liu, Hanbin, Datta, Supratim, Simmons, Blake A. and Sale, Kenneth (2011). Molecular dynamics studies of the structure and dynamics of an endoglucanase Cel9A in ionic liquid solutions. Engineering Sciences and Fundamentals - Core Programming Topic at the 2011 AIChE Annual Meeting, Minneapolis, MN, United States, 16-21 October 2011. New York, NY, United States: AIChE.
Li, Chenlin, Hu, Hongqiang, Liu, Hong, Vogel, Kenneth P., Simmons, Blake and Singh, Seema (2010). Ionic liquid pretreatment of lignocellulosic materials for enhanced sustainable biogas and electricity generation. 239th ACS National Meeting and Exposition, , , March 21, 2010-March 25, 2010.
Han, Ju, Singh, Seema, Sun, Lan, Simmons, Blake, Auer, Manfred and Parvin, Bahram (2010). Chemical profiling of the plant cell wall through Raman microspectroscopy. doi: 10.1109/ISBI.2010.5490228
Sabounchi, Poorya, Huber, David E., Kanouf, Michael P., Harris, Alison E. and Simmons, Blake A. (2008). Joule heating effects on insulatorbased dielectrophoresis. 12th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2008, , , October 12, 2008-October 16, 2008. Chemical and Biological Microsystems Society.
Sabounchi, Poorya, Morales, Alfredo M., Simmons, Blake A. and Davalos, Rafael V. (2008). Integrated microfluidic sample preconcentrator and impedance detection platform for pathogen monitoring. 12th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2008, , , October 12, 2008-October 16, 2008. Chemical and Biological Microsystems Society.
Morales, Alfrede M., Simmons, Blake A., Wallow, Thomas I., Campbell, K. Jeffery, Mani, Seethambal S., Mittal, Brita, Crocker, Robert W., Cummings, Eric B., Davalos, Rafael V., Domeier, Linda A., Hunter, Marion C., Krafcik, Karen L., McGraw, Gregory J., Mosier, Bruce P. and Sickafoose, Shane M. (2006). Injection molded microfluidic devices for biological sample separation and detection. doi: 10.1117/12.648135
Ezekial Smith, A., Hawkins, Benjamin G., Baldasaro, Nicholas G., Syed, Yusef A., Simmons, Blake A., Cummings, Eric B. and Kirby, Brian J. (2006). Dielectrophoretic particle manipulation in ridged microchannels. 2006 ASME International Mechanical Engineering Congress and Exposition, IMECE2006, , , November 5, 2006-November 10, 2006. American Society of Mechanical Engineers (ASME). doi: 10.1115/IMECE2006-14843
Skulan, Andrew J., Barrett, Louise M., Fiechtner, Gregory J., Kanouff, Mike, Singh, Anup K., Cummings, Eric B. and Simmons, Blake A. (2005). Opposing electrokinetic and hydrodynamic flows: Particle mixing and concentration devices. 9th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2005, , , October 9, 2005-October 13, 2005. Transducer Research Foundation.