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Simmons, Blake

TitleScientific Division Director
InstitutionLawrence Berkeley National Lab
DepartmentBiological Systems & Eng
Address1 Cyclotron Road
Berkeley CA 94720
Phone510/486-7808
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. Sun J, Liu D, Young RP, Cruz AG, Isern NG, Schuerg T, Cort JR, Simmons B, Singh S. Solubilization and Upgrading of High Polyethylene Terephthalate Loadings in a Low-Costing Bifunctional Ionic Liquid. ChemSusChem. 2018 Feb 22; 11(4):781-792. PMID: 29178551.
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    2. Liu D, Kim KH, Sun J, Simmons B, Singh S. Cascade Production of Lactic Acid from Universal Types of Sugars Catalyzed by Lanthanum Triflate. ChemSusChem. 2018 Feb 09; 11(3):598-604. PMID: 29178399.
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    3. Kjærbølling I, Vesth TC, Frisvad JC, Nybo JL, Theobald S, Kuo A, Bowyer P, Matsuda Y, Mondo S, Lyhne EK, Kogle ME, Clum A, Lipzen A, Salamov A, Ngan CY, Daum C, Chiniquy J, Barry K, LaButti K, Haridas S, Simmons B, Magnuson JK, Mortensen UH, Larsen TO, Grigoriev IV, Baker SE, Andersen MR. Linking secondary metabolites to gene clusters through genome sequencing of six diverse Aspergillus species. Proc Natl Acad Sci U S A. 2018 Jan 09. PMID: 29317534.
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    4. Reilly MC, Kim J, Lynn J, Simmons B, Gladden JM, Magnuson JK, Baker SE. Forward genetics screen coupled with whole-genome resequencing identifies novel gene targets for improving heterologous enzyme production in Aspergillus niger. Appl Microbiol Biotechnol. 2018 Feb; 102(4):1797-1807. PMID: 29305699.
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    5. Amaike Campen S, Lynn J, Sibert SJ, Srikrishnan S, Phatale P, Feldman T, Guenther JM, Hiras J, Tran YTA, Singer SW, Adams PD, Sale KL, Simmons B, Baker SE, Magnuson JK, Gladden JM. Expression of naturally ionic liquid-tolerant thermophilic cellulases in Aspergillus niger. PLoS One. 2017; 12(12):e0189604. PMID: 29281693.
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    6. To TQ, Procter K, Simmons B, Subashchandrabose S, Atkin R. Low cost ionic liquid-water mixtures for effective extraction of carbohydrate and lipid from algae. Faraday Discuss. 2017 Dec 14; 206:93-112. PMID: 28936499.
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    7. Mohamed ET, Wang S, Lennen RM, Herrgård MJ, Simmons B, Singer SW, Feist AM. Generation of a platform strain for ionic liquid tolerance using adaptive laboratory evolution. Microb Cell Fact. 2017 Nov 16; 16(1):204. PMID: 29145855.
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    8. Kolinko S, Wu YW, Tachea F, Denzel E, Hiras J, Gabriel R, Bäcker N, Chan LJG, Eichorst SA, Frey D, Chen Q, Azadi P, Adams PD, Pray TR, Tanjore D, Petzold CJ, Gladden JM, Simmons B, Singer SW. A bacterial pioneer produces cellulase complexes that persist through community succession. Nat Microbiol. 2018 Jan; 3(1):99-107. PMID: 29109478.
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    9. Yaegashi J, Kirby J, Ito M, Sun J, Dutta T, Mirsiaghi M, Sundstrom ER, Rodriguez A, Baidoo E, Tanjore D, Pray T, Sale K, Singh S, Keasling JD, Simmons B, Singer SW, Magnuson JK, Arkin AP, Skerker JM, Gladden JM. Rhodosporidium toruloides: a new platform organism for conversion of lignocellulose into terpene biofuels and bioproducts. Biotechnol Biofuels. 2017; 10:241. PMID: 29075325.
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    10. Sitepu IR, Garay LA, Enriquez L, Fry R, Butler JH, Lopez JM, Kanti A, Faulina SA, Nugroho AJ, Simmons B, Singer SW, Simmons CW, Boundy-Mills K. 1-Ethyl-3-methylimidazolium tolerance and intracellular lipid accumulation of 38 oleaginous yeast species. Appl Microbiol Biotechnol. 2017 Dec; 101(23-24):8621-8631. PMID: 29051987.
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    11. Mills MJL, Sale KL, Simmons B, Popelier PLA. Rhorix: An interface between quantum chemical topology and the 3D graphics program blender. J Comput Chem. 2017 Nov 05; 38(29):2538-2552. PMID: 28857244.
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    12. Narani A, Coffman P, Gardner J, Li C, Ray AE, Hartley DS, Stettler A, Konda NVSNM, Simmons B, Pray TR, Tanjore D. Predictive modeling to de-risk bio-based manufacturing by adapting to variability in lignocellulosic biomass supply. Bioresour Technol. 2017 Nov; 243:676-685. PMID: 28709073.
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    13. Sun J, Shi J, Murthy Konda NVSN, Campos D, Liu D, Nemser S, Shamshina J, Dutta T, Berton P, Gurau G, Rogers RD, Simmons B, Singh S. Efficient dehydration and recovery of ionic liquid after lignocellulosic processing using pervaporation. Biotechnol Biofuels. 2017; 10:154. PMID: 28638441.
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    14. d'Espaux L, Ghosh A, Runguphan W, Wehrs M, Xu F, Konzock O, Dev I, Nhan M, Gin J, Reider Apel A, Petzold CJ, Singh S, Simmons B, Mukhopadhyay A, García Martín H, Keasling JD. Engineering high-level production of fatty alcohols by Saccharomyces cerevisiae from lignocellulosic feedstocks. Metab Eng. 2017 Jul; 42:115-125. PMID: 28606738.
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    15. Eudes A, Dutta T, Deng K, Jacquet N, Sinha A, Benites VT, Baidoo EEK, Richel A, Sattler SE, Northen TR, Singh S, Simmons B, Loqué D. SbCOMT (Bmr12) is involved in the biosynthesis of tricin-lignin in sorghum. PLoS One. 2017; 12(6):e0178160. PMID: 28594846.
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    16. Papa G, Feldman T, Sale KL, Adani F, Singh S, Simmons B. Parametric study for the optimization of ionic liquid pretreatment of corn stover. Bioresour Technol. 2017 Oct; 241:627-637. PMID: 28605727.
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    17. Woo HL, DeAngelis KM, Teshima H, Davenport K, Daligault H, Erkkila T, Goodwin L, Gu W, Lo CC, Munk C, Scholz M, Xu Y, Chain P, Bruce D, Detter C, Tapia R, Han C, Simmons B, Hazen TC. High-Quality Draft Genome Sequences of Four Lignocellulose-Degrading Bacteria Isolated from Puerto Rican Forest Soil: Gordonia sp., Paenibacillus sp., Variovorax sp., and Vogesella sp. Genome Announc. 2017 May 04; 5(18). PMID: 28473393.
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    18. Kim KH, Dutta T, Ralph J, Mansfield SD, Simmons B, Singh S. Impact of lignin polymer backbone esters on ionic liquid pretreatment of poplar. Biotechnol Biofuels. 2017; 10:101. PMID: 28439294.
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    19. Kohler AC, Mills MJL, Adams PD, Simmons B, Sale KL. Structure of aryl O-demethylase offers molecular insight into a catalytic tyrosine-dependent mechanism. Proc Natl Acad Sci U S A. 2017 04 18; 114(16):E3205-E3214. PMID: 28373573.
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    20. Perez-Pimienta JA, Sathitsuksanoh N, Thompson VS, Tran K, Ponce-Noyola T, Stavila V, Singh S, Simmons B. Ternary ionic liquid-water pretreatment systems of an agave bagasse and municipal solid waste blend. Biotechnol Biofuels. 2017; 10:72. PMID: 28344647.
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    21. Kim KH, Brown RC, Daugaard T, Tivol WF, Auer M, Simmons B, Singh S. Strategy for Extending the Stability of Bio-oil-Derived Phenolic Oligomers by Mild Hydrotreatment with Ionic-Liquid-Stabilized Nanoparticles. ChemSusChem. 2017 03 09; 10(5):884-893. PMID: 27992678.
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    22. Yuan X, Duan Y, He L, Singh S, Simmons B, Cheng G. Characterization of white poplar and eucalyptus after ionic liquid pretreatment as a function of biomass loading using X-ray diffraction and small angle neutron scattering. Bioresour Technol. 2017 May; 232:113-118. PMID: 28214697.
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    23. Li C, Liang L, Sun N, Thompson VS, Xu F, Narani A, He Q, Tanjore D, Pray TR, Simmons B, Singh S. Scale-up and process integration of sugar production by acidolysis of municipal solid waste/corn stover blends in ionic liquids. Biotechnol Biofuels. 2017; 10:13. PMID: 28070222.
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    24. Wu YW, Higgins B, Yu C, Reddy AP, Ceballos S, Joh LD, Simmons B, Singer SW, VanderGheynst JS. Ionic Liquids Impact the Bioenergy Feedstock-Degrading Microbiome and Transcription of Enzymes Relevant to Polysaccharide Hydrolysis. mSystems. 2016 Nov-Dec; 1(6). PMID: 27981239.
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    25. McAndrew RP, Sathitsuksanoh N, Mbughuni MM, Heins RA, Pereira JH, George A, Sale KL, Fox BG, Simmons B, Adams PD. Structure and mechanism of NOV1, a resveratrol-cleaving dioxygenase. Proc Natl Acad Sci U S A. 2016 12 13; 113(50):14324-14329. PMID: 27911781.
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    26. Shi J, Wu D, Zhang L, Simmons B, Singh S, Yang B, Wyman CE. Dynamic changes of substrate reactivity and enzyme adsorption on partially hydrolyzed cellulose. Biotechnol Bioeng. 2017 03; 114(3):503-515. PMID: 27617791.
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    27. Healey AL, Lee DJ, Lupoi JS, Papa G, Guenther JM, Corno L, Adani F, Singh S, Simmons B, Henry RJ. Evaluation of Relationships between Growth Rate, Tree Size, Lignocellulose Composition, and Enzymatic Saccharification in Interspecific Corymbia Hybrids and Parental Taxa. Front Plant Sci. 2016; 7:1705. PMID: 27917179.
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    28. Yu C, Simmons B, Singer SW, Thelen MP, VanderGheynst JS. Ionic liquid-tolerant microorganisms and microbial communities for lignocellulose conversion to bioproducts. Appl Microbiol Biotechnol. 2016 Dec; 100(24):10237-10249. PMID: 27838839.
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    29. Hiras J, Wu YW, Deng K, Nicora CD, Aldrich JT, Frey D, Kolinko S, Robinson EW, Jacobs JM, Adams PD, Northen TR, Simmons B, Singer SW. Comparative Community Proteomics Demonstrates the Unexpected Importance of Actinobacterial Glycoside Hydrolase Family 12 Protein for Crystalline Cellulose Hydrolysis. MBio. 2016 08 23; 7(4). PMID: 27555310; PMCID: PMC4999548.
    30. Parthasarathi R, Sun J, Dutta T, Sun N, Pattathil S, Murthy Konda NV, Peralta AG, Simmons B, Singh S. Activation of lignocellulosic biomass for higher sugar yields using aqueous ionic liquid at low severity process conditions. Biotechnol Biofuels. 2016; 9:160. PMID: 27486479; PMCID: PMC4969646.
    31. Eudes A, Zhao N, Sathitsuksanoh N, Baidoo EE, Lao J, Wang G, Yogiswara S, Lee TS, Singh S, Mortimer JC, Keasling JD, Simmons B, Loqué D. Expression of S-adenosylmethionine Hydrolase in Tissues Synthesizing Secondary Cell Walls Alters Specific Methylated Cell Wall Fractions and Improves Biomass Digestibility. Front Bioeng Biotechnol. 2016; 4:58. PMID: 27486577; PMCID: PMC4949269.
    32. Pace S, Ceballos SJ, Harrold D, Stannard W, Simmons B, Singer SW, Thelen MP, VanderGheynst JS. Enrichment of microbial communities tolerant to the ionic liquids tetrabutylphosphonium chloride and tributylethylphosphonium diethylphosphate. Appl Microbiol Biotechnol. 2016 Jun; 100(12):5639-52. PMID: 27102129.
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    33. Perez-Pimienta JA, Flores-Gómez CA, Ruiz HA, Sathitsuksanoh N, Balan V, da Costa Sousa L, Dale BE, Singh S, Simmons B. Evaluation of agave bagasse recalcitrance using AFEX™, autohydrolysis, and ionic liquid pretreatments. Bioresour Technol. 2016 Jul; 211:216-23. PMID: 27017132.
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    34. Lupoi J, Simmons B, Henry R. Editorial: Biomass Modification, Characterization, and Process Monitoring Analytics to Support Biofuel and Biomaterial Production. Front Bioeng Biotechnol. 2016; 4:25. PMID: 27014688; PMCID: PMC4785235.
    35. Pereira JH, Heins RA, Gall DL, McAndrew RP, Deng K, Holland KC, Donohue TJ, Noguera DR, Simmons B, Sale KL, Ralph J, Adams PD. Structural and Biochemical Characterization of the Early and Late Enzymes in the Lignin ß-Aryl Ether Cleavage Pathway from Sphingobium sp. SYK-6. J Biol Chem. 2016 May 06; 291(19):10228-38. PMID: 26940872; PMCID: PMC4858972.
    36. Helmich KE, Pereira JH, Gall DL, Heins RA, McAndrew RP, Bingman C, Deng K, Holland KC, Noguera DR, Simmons B, Sale KL, Ralph J, Donohue TJ, Adams PD, Phillips GN. Structural Basis of Stereospecificity in the Bacterial Enzymatic Cleavage of ß-Aryl Ether Bonds in Lignin. J Biol Chem. 2016 Mar 04; 291(10):5234-46. PMID: 26637355; PMCID: PMC4777856.
    37. Yu C, Reddy AP, Simmons CW, Simmons B, Singer SW, VanderGheynst JS. Preservation of microbial communities enriched on lignocellulose under thermophilic and high-solid conditions. Biotechnol Biofuels. 2015; 8:206. PMID: 26633993; PMCID: PMC4667496.
    38. Healey AL, Lee DJ, Furtado A, Simmons B, Henry RJ. Efficient Eucalypt Cell Wall Deconstruction and Conversion for Sustainable Lignocellulosic Biofuels. Front Bioeng Biotechnol. 2015; 3:190. PMID: 26636077; PMCID: PMC4653827.
    39. Billings AF, Fortney JL, Hazen TC, Simmons B, Davenport KW, Goodwin L, Ivanova N, Kyrpides NC, Mavromatis K, Woyke T, DeAngelis KM. Genome sequence and description of the anaerobic lignin-degrading bacterium Tolumonas lignolytica sp. nov. Stand Genomic Sci. 2015; 10:106. PMID: 26594307; PMCID: PMC4653933.
    40. Hoang NV, Furtado A, Botha FC, Simmons B, Henry RJ. Potential for Genetic Improvement of Sugarcane as a Source of Biomass for Biofuels. Front Bioeng Biotechnol. 2015; 3:182. PMID: 26636072; PMCID: PMC4646955.
    41. Wu YW, Simmons B, Singer SW. MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets. Bioinformatics. 2016 Feb 15; 32(4):605-7. PMID: 26515820.
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    42. Hudson CM, Kirton E, Hutchinson MI, Redfern JL, Simmons B, Ackerman E, Singh S, Williams KP, Natvig DO, Powell AJ. Lignin-modifying processes in the rhizosphere of arid land grasses. Environ Microbiol. 2015 Dec; 17(12):4965-78. PMID: 26279186.
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    43. Deng K, Guenther JM, Gao J, Bowen BP, Tran H, Reyes-Ortiz V, Cheng X, Sathitsuksanoh N, Heins R, Takasuka TE, Bergeman LF, Geertz-Hansen H, Deutsch S, Loqué D, Sale KL, Simmons B, Adams PD, Singh AK, Fox BG, Northen TR. Development of a High Throughput Platform for Screening Glycoside Hydrolases Based on Oxime-NIMS. Front Bioeng Biotechnol. 2015; 3:153. PMID: 26528471; PMCID: PMC4603251.
    44. Parthasarathi R, Balamurugan K, Shi J, Subramanian V, Simmons B, Singh S. Theoretical Insights into the Role of Water in the Dissolution of Cellulose Using IL/Water Mixed Solvent Systems. J Phys Chem B. 2015 Nov 12; 119(45):14339-49. PMID: 26407132.
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    45. Torr KM, Love KT, Simmons B, Hill SJ. Structural features affecting the enzymatic digestibility of pine wood pretreated with ionic liquids. Biotechnol Bioeng. 2016 Mar; 113(3):540-9. PMID: 26369903.
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    46. Sun L, Singh S, Joo M, Vega-Sanchez M, Ronald P, Simmons B, Adams P, Auer M. Non-invasive imaging of cellulose microfibril orientation within plant cell walls by polarized Raman microspectroscopy. Biotechnol Bioeng. 2016 Jan; 113(1):82-90. PMID: 26137889.
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    47. Hiras J, Wu YW, Eichorst SA, Simmons B, Singer SW. Refining the phylum Chlorobi by resolving the phylogeny and metabolic potential of the representative of a deeply branching, uncultivated lineage. ISME J. 2016 Apr; 10(4):833-45. PMID: 26325358; PMCID: PMC4796922 [Available on 04/01/17].
    48. Lupoi JS, Smith-Moritz A, Singh S, McQualter R, Scheller HV, Simmons B, Henry RJ. Localization of polyhydroxybutyrate in sugarcane using Fourier-transform infrared microspectroscopy and multivariate imaging. Biotechnol Biofuels. 2015; 8:98. PMID: 26199643; PMCID: PMC4508826.
    49. Scullin C, Cruz AG, Chuang YD, Simmons B, Loque D, Singh S. Restricting lignin and enhancing sugar deposition in secondary cell walls enhances monomeric sugar release after low temperature ionic liquid pretreatment. Biotechnol Biofuels. 2015; 8:95. PMID: 26161139; PMCID: PMC4496950.
    50. Baker SE, Schackwitz W, Lipzen A, Martin J, Haridas S, LaButti K, Grigoriev IV, Simmons B, McCluskey K. Draft Genome Sequence of Neurospora crassa Strain FGSC 73. Genome Announc. 2015 Apr 02; 3(2). PMID: 25838471; PMCID: PMC4384475.
    51. Sun N, Xu F, Sathitsuksanoh N, Thompson VS, Cafferty K, Li C, Tanjore D, Narani A, Pray TR, Simmons B, Singh S. Blending municipal solid waste with corn stover for sugar production using ionic liquid process. Bioresour Technol. 2015 Jun; 186:200-206. PMID: 25817030.
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    52. Eudes A, Sathitsuksanoh N, Baidoo EE, George A, Liang Y, Yang F, Singh S, Keasling JD, Simmons B, Loqué D. Expression of a bacterial 3-dehydroshikimate dehydratase reduces lignin content and improves biomass saccharification efficiency. Plant Biotechnol J. 2015 Dec; 13(9):1241-50. PMID: 25583257.
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    53. Shih SC, Gach PC, Sustarich J, Simmons B, Adams PD, Singh S, Singh AK. A droplet-to-digital (D2D) microfluidic device for single cell assays. Lab Chip. 2015 Jan 07; 15(1):225-36. PMID: 25354549.
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    54. Simmons CW, Reddy AP, D'haeseleer P, Khudyakov J, Billis K, Pati A, Simmons B, Singer SW, Thelen MP, VanderGheynst JS. Metatranscriptomic analysis of lignocellulolytic microbial communities involved in high-solids decomposition of rice straw. Biotechnol Biofuels. 2014; 7(1):495. PMID: 25648696; PMCID: PMC4296540.
    55. Woo HL, Ballor NR, Hazen TC, Fortney JL, Simmons B, Davenport KW, Goodwin L, Ivanova N, Kyrpides NC, Mavromatis K, Woyke T, Jansson J, Kimbrel J, DeAngelis KM. Complete genome sequence of the lignin-degrading bacterium Klebsiella sp. strain BRL6-2. Stand Genomic Sci. 2014; 9:19. PMID: 25566348; PMCID: PMC4273726.
    56. Furtado A, Lupoi JS, Hoang NV, Healey A, Singh S, Simmons B, Henry RJ. Modifying plants for biofuel and biomaterial production. Plant Biotechnol J. 2014 Dec; 12(9):1246-58. PMID: 25431201.
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    57. Sitepu IR, Shi S, Simmons B, Singer SW, Boundy-Mills K, Simmons CW. Yeast tolerance to the ionic liquid 1-ethyl-3-methylimidazolium acetate. FEMS Yeast Res. 2014 Dec; 14(8):1286-94. PMID: 25348480.
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    58. Rotavera B, Zádor J, Welz O, Sheps L, Scheer AM, Savee JD, Akbar Ali M, Lee TS, Simmons B, Osborn DL, Violi A, Taatjes CA. Photoionization mass spectrometric measurements of initial reaction pathways in low-temperature oxidation of 2,5-dimethylhexane. J Phys Chem A. 2014 Nov 06; 118(44):10188-200. PMID: 25234586.
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    59. Scullin C, Stavila V, Skarstad A, Keasling JD, Simmons B, Singh S. Optimization of renewable pinene production from the conversion of macroalgae Saccharina latissima. Bioresour Technol. 2015 May; 184:415-420. PMID: 25318906.
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    60. Eichorst SA, Joshua C, Sathitsuksanoh N, Singh S, Simmons B, Singer SW. Substrate-Specific Development of Thermophilic Bacterial Consortia by Using Chemically Pretreated Switchgrass. Appl Environ Microbiol. 2014 Dec; 80(23):7423-32. PMID: 25261509; PMCID: PMC4249183.
    61. Parreiras LS, Breuer RJ, Avanasi Narasimhan R, Higbee AJ, La Reau A, Tremaine M, Qin L, Willis LB, Bice BD, Bonfert BL, Pinhancos RC, Balloon AJ, Uppugundla N, Liu T, Li C, Tanjore D, Ong IM, Li H, Pohlmann EL, Serate J, Withers ST, Simmons B, Hodge DB, Westphall MS, Coon JJ, Dale BE, Balan V, Keating DH, Zhang Y, Landick R, Gasch AP, Sato TK. 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. 2014; 9(9):e107499. PMID: 25222864; PMCID: PMC4164640.
    62. Socha AM, Parthasarathi R, Shi J, Pattathil S, Whyte D, Bergeron M, George A, Tran K, Stavila V, Venkatachalam S, Hahn MG, Simmons B, Singh S. Efficient biomass pretreatment using ionic liquids derived from lignin and hemicellulose. Proc Natl Acad Sci U S A. 2014 Sep 02; 111(35):E3587-95. PMID: 25136131; PMCID: PMC4156760.
    63. Wu YW, Tang YH, Tringe SG, Simmons B, Singer SW. MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm. Microbiome. 2014; 2:26. PMID: 25136443; PMCID: PMC4129434.
    64. Heins RA, Cheng X, Nath S, Deng K, Bowen BP, Chivian DC, Datta S, Friedland GD, D'Haeseleer P, Wu D, Tran-Gyamfi M, Scullin CS, Singh S, Shi W, Hamilton MG, Bendall ML, Sczyrba A, Thompson J, Feldman T, Guenther JM, Gladden JM, Cheng JF, Adams PD, Rubin EM, Simmons B, Sale KL, Northen TR, Deutsch S. Phylogenomically guided identification of industrially relevant GH1 ß-glucosidases through DNA synthesis and nanostructure-initiator mass spectrometry. ACS Chem Biol. 2014 Sep 19; 9(9):2082-91. PMID: 24984213; PMCID: PMC4168791.
    65. Frederix M, Hütter K, Leu J, Batth TS, Turner WJ, Rüegg TL, Blanch HW, Simmons B, Adams PD, Keasling JD, Thelen MP, Dunlop MJ, Petzold CJ, Mukhopadhyay A. Development of a native Escherichia coli induction system for ionic liquid tolerance. PLoS One. 2014; 9(7):e101115. PMID: 24983352; PMCID: PMC4077768.
    66. Woo HL, Utturkar S, Klingeman D, Simmons B, DeAngelis KM, Brown SD, Hazen TC. Draft Genome Sequence of the Lignin-Degrading Burkholderia sp. Strain LIG30, Isolated from Wet Tropical Forest Soil. Genome Announc. 2014 Jun 19; 2(3). PMID: 24948777; PMCID: PMC4064042.
    67. Lupoi JS, Singh S, Davis M, Lee DJ, Shepherd M, Simmons B, Henry RJ. High-throughput prediction of eucalypt lignin syringyl/guaiacyl content using multivariate analysis: a comparison between mid-infrared, near-infrared, and Raman spectroscopies for model development. Biotechnol Biofuels. 2014; 7:93. PMID: 24955114; PMCID: PMC4064109.
    68. Konda NM, Shi J, Singh S, Blanch HW, Simmons B, Klein-Marcuschamer D. Understanding cost drivers and economic potential of two variants of ionic liquid pretreatment for cellulosic biofuel production. Biotechnol Biofuels. 2014; 7:86. PMID: 24932217; PMCID: PMC4055852.
    69. Gao X, Kumar R, Singh S, Simmons B, Balan V, Dale BE, Wyman CE. Comparison of enzymatic reactivity of corn stover solids prepared by dilute acid, AFEX™, and ionic liquid pretreatments. Biotechnol Biofuels. 2014; 7:71. PMID: 24910713; PMCID: PMC4029885.
    70. Uppugundla N, da Costa Sousa L, Chundawat SP, Yu X, Simmons B, Singh S, Gao X, Kumar R, Wyman CE, Dale BE, Balan V. A comparative study of ethanol production using dilute acid, ionic liquid and AFEX™ pretreated corn stover. Biotechnol Biofuels. 2014; 7:72. PMID: 24917886; PMCID: PMC4050221.
    71. Deng K, Takasuka TE, Heins R, Cheng X, Bergeman LF, Shi J, Aschenbrener R, Deutsch S, Singh S, Sale KL, Simmons B, Adams PD, Singh AK, Fox BG, Northen TR. Rapid kinetic characterization of glycosyl hydrolases based on oxime derivatization and nanostructure-initiator mass spectrometry (NIMS). ACS Chem Biol. 2014 Jul 18; 9(7):1470-9. PMID: 24819174.
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    72. Ruegg TL, Kim EM, Simmons B, Keasling JD, Singer SW, Lee TS, Thelen MP. An auto-inducible mechanism for ionic liquid resistance in microbial biofuel production. Nat Commun. 2014 Mar 26; 5:3490. PMID: 24667370.
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    73. Oleskowicz-Popiel P, Klein-Marcuschamer D, Simmons B, Blanch HW. Lignocellulosic ethanol production without enzymes--technoeconomic analysis of ionic liquid pretreatment followed by acidolysis. Bioresour Technol. 2014 Apr; 158:294-9. PMID: 24632406.
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    74. Gladden JM, Park JI, Bergmann J, Reyes-Ortiz V, D'haeseleer P, Quirino BF, Sale KL, Simmons B, Singer SW. Discovery and characterization of ionic liquid-tolerant thermophilic cellulases from a switchgrass-adapted microbial community. Biotechnol Biofuels. 2014 Jan 29; 7(1):15. PMID: 24479406; PMCID: PMC3923250.
    75. Simmons CW, Reddy AP, Vandergheynst JS, Simmons B, Singer SW. Bacillus coagulans tolerance to 1-ethyl-3-methylimidazolium-based ionic liquids in aqueous and solid-state thermophilic culture. Biotechnol Prog. 2014 Mar-Apr; 30(2):311-6. PMID: 24376258.
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    76. Bergmann JC, Costa OY, Gladden JM, Singer S, Heins R, D'haeseleer P, Simmons B, Quirino BF. Discovery of two novel ß-glucosidases from an Amazon soil metagenomic library. FEMS Microbiol Lett. 2014 Feb; 351(2):147-55. PMID: 24236615.
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    77. Cheng X, Hiras J, Deng K, Bowen B, Simmons B, Adams PD, Singer SW, Northen TR. High throughput nanostructure-initiator mass spectrometry screening of microbial growth conditions for maximal ß-glucosidase production. Front Microbiol. 2013; 4:365. PMID: 24367356; PMCID: PMC3854461.
    78. Chen Z, Pereira JH, Liu H, Tran HM, Hsu NS, Dibble D, Singh S, Adams PD, Sapra R, Hadi MZ, Simmons B, Sale KL. Improved activity of a thermophilic cellulase, Cel5A, from Thermotoga maritima on ionic liquid pretreated switchgrass. PLoS One. 2013; 8(11):e79725. PMID: 24244549; PMCID: PMC3828181.
    79. Woo HL, Hazen TC, Simmons B, DeAngelis KM. Enzyme activities of aerobic lignocellulolytic bacteria isolated from wet tropical forest soils. Syst Appl Microbiol. 2014 Feb; 37(1):60-7. PMID: 24238986.
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    80. Li C, Tanjore D, He W, Wong J, Gardner JL, Sale KL, Simmons B, Singh S. Scale-up and evaluation of high solid ionic liquid pretreatment and enzymatic hydrolysis of switchgrass. Biotechnol Biofuels. 2013 Oct 25; 6(1):154. PMID: 24160440; PMCID: PMC3817576.
    81. Reddy AP, Simmons CW, D'haeseleer P, Khudyakov J, Burd H, Hadi M, Simmons B, Singer SW, Thelen MP, Vandergheynst JS. Discovery of microorganisms and enzymes involved in high-solids decomposition of rice straw using metagenomic analyses. PLoS One. 2013; 8(10):e77985. PMID: 24205054; PMCID: PMC3808287.
    82. Deangelis KM, Sharma D, Varney R, Simmons B, Isern NG, Markilllie LM, Nicora C, Norbeck AD, Taylor RC, Aldrich JT, Robinson EW. Evidence supporting dissimilatory and assimilatory lignin degradation in Enterobacter lignolyticus SCF1. Front Microbiol. 2013; 4:280. PMID: 24065962; PMCID: PMC3777014.
    83. D'haeseleer P, Gladden JM, Allgaier M, Chain PS, Tringe SG, Malfatti SA, Aldrich JT, Nicora CD, Robinson EW, Paša-Tolic L, Hugenholtz P, Simmons B, Singer SW. Proteogenomic analysis of a thermophilic bacterial consortium adapted to deconstruct switchgrass. PLoS One. 2013; 8(7):e68465. PMID: 23894306.
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    84. Reyes-Ortiz V, Heins RA, Cheng G, Kim EY, Vernon BC, Elandt RB, Adams PD, Sale KL, Hadi MZ, Simmons B, Kent MS, Tullman-Ercek D. Addition of a carbohydrate-binding module enhances cellulase penetration into cellulose substrates. Biotechnol Biofuels. 2013 Jul 03; 6(1):93. PMID: 23819686; PMCID: PMC3716932.
    85. Eichorst SA, Varanasi P, Stavila V, Zemla M, Auer M, Singh S, Simmons B, Singer SW. Community dynamics of cellulose-adapted thermophilic bacterial consortia. Environ Microbiol. 2013 Sep; 15(9):2573-87. PMID: 23763762.
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    86. Socha AM, Plummer SP, Stavila V, Simmons B, Singh S. Comparison of sugar content for ionic liquid pretreated Douglas-fir woodchips and forestry residues. Biotechnol Biofuels. 2013 May 01; 6(1):61. PMID: 23635001; PMCID: PMC3672072.
    87. McAndrew RP, Park JI, Heins RA, Reindl W, Friedland GD, D'haeseleer P, Northen T, Sale KL, Simmons B, Adams PD. From soil to structure, a novel dimeric ß-glucosidase belonging to glycoside hydrolase family 3 isolated from compost using metagenomic analysis. J Biol Chem. 2013 May 24; 288(21):14985-92. PMID: 23580647; PMCID: PMC3663519.
    88. Cruz AG, Scullin C, Mu C, Cheng G, Stavila V, Varanasi P, Xu D, Mentel J, Chuang YD, Simmons B, Singh S. Impact of high biomass loading on ionic liquid pretreatment. Biotechnol Biofuels. 2013 Apr 11; 6(1):52. PMID: 23578017; PMCID: PMC3646703.
    89. Chiniquy D, Varanasi P, Oh T, Harholt J, Katnelson J, Singh S, Auer M, Simmons B, Adams PD, Scheller HV, Ronald PC. Three Novel Rice Genes Closely Related to the Arabidopsis IRX9, IRX9L, and IRX14 Genes and Their Roles in Xylan Biosynthesis. Front Plant Sci. 2013; 4:83. PMID: 23596448; PMCID: PMC3622038.
    90. Sun N, Liu H, Sathitsuksanoh N, Stavila V, Sawant M, Bonito A, Tran K, George A, Sale KL, Singh S, Simmons B, Holmes BM. Production and extraction of sugars from switchgrass hydrolyzed in ionic liquids. Biotechnol Biofuels. 2013 Mar 20; 6(1):39. PMID: 23514699; PMCID: PMC3621597.
    91. Deangelis KM, D'Haeseleer P, Chivian D, Simmons B, Arkin AP, Mavromatis K, Malfatti S, Tringe S, Hazen TC. Metagenomes of tropical soil-derived anaerobic switchgrass-adapted consortia with and without iron. Stand Genomic Sci. 2013; 7(3):382-98. PMID: 24019987; PMCID: PMC3764933.
    92. Varanasi P, Singh P, Auer M, Adams PD, Simmons B, Singh S. Survey of renewable chemicals produced from lignocellulosic biomass during ionic liquid pretreatment. Biotechnol Biofuels. 2013 Jan 28; 6(1):14. PMID: 23356589; PMCID: PMC3579681.
    93. Cetinkol ÖP, Smith-Moritz AM, Cheng G, Lao J, George A, Hong K, Henry R, Simmons B, Heazlewood JL, Holmes BM. Structural and chemical characterization of hardwood from tree species with applications as bioenergy feedstocks. PLoS One. 2012; 7(12):e52820. PMID: 23300786.
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    94. Perez-Pimienta JA, Lopez-Ortega MG, Varanasi P, Stavila V, Cheng G, Singh S, Simmons B. Comparison of the impact of ionic liquid pretreatment on recalcitrance of agave bagasse and switchgrass. Bioresour Technol. 2013 Jan; 127:18-24. PMID: 23131619.
      View in: PubMed
    95. Varanasi P, Singh P, Arora R, Adams PD, Auer M, Simmons B, Singh S. Understanding changes in lignin of Panicum virgatum and Eucalyptus globulus as a function of ionic liquid pretreatment. Bioresour Technol. 2012 Dec; 126:156-61. PMID: 23073103.
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    96. Cheng G, Varanasi P, Arora R, Stavila V, Simmons B, Kent MS, Singh S. Impact of ionic liquid pretreatment conditions on cellulose crystalline structure using 1-ethyl-3-methylimidazolium acetate. J Phys Chem B. 2012 Aug 23; 116(33):10049-54. PMID: 22823503.
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    97. Cheng G, Kent MS, He L, Varanasi P, Dibble D, Arora R, Deng K, Hong K, Melnichenko YB, Simmons B, Singh S. Effect of ionic liquid treatment on the structures of lignins in solutions: molecular subunits released from lignin. Langmuir. 2012 Aug 14; 28(32):11850-7. PMID: 22738225.
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    98. McClendon SD, Batth T, Petzold CJ, Adams PD, Simmons B, Singer SW. Thermoascus aurantiacus is a promising source of enzymes for biomass deconstruction under thermophilic conditions. Biotechnol Biofuels. 2012 Jul 28; 5(1):54. PMID: 22839529; PMCID: PMC3507748.
    99. Liu H, Cheng G, Kent M, Stavila V, Simmons B, Sale KL, Singh S. Simulations reveal conformational changes of methylhydroxyl groups during dissolution of cellulose Iß in ionic liquid 1-ethyl-3-methylimidazolium acetate. J Phys Chem B. 2012 Jul 19; 116(28):8131-8. PMID: 22574852.
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    100. Dougherty MJ, D'haeseleer P, Hazen TC, Simmons B, Adams PD, Hadi MZ. Glycoside hydrolases from a targeted compost metagenome, activity-screening and functional characterization. BMC Biotechnol. 2012 Jul 03; 12:38. PMID: 22759983; PMCID: PMC3477009.
    101. Chen Z, Friedland GD, Pereira JH, Reveco SA, Chan R, Park JI, Thelen MP, Adams PD, Arkin AP, Keasling JD, Blanch HW, Simmons B, Sale KL, Chivian D, Chhabra SR. Tracing determinants of dual substrate specificity in glycoside hydrolase family 5. J Biol Chem. 2012 Jul 20; 287(30):25335-43. PMID: 22645145; PMCID: PMC3408205.
    102. Park JI, Steen EJ, Burd H, Evans SS, Redding-Johnson AM, Batth T, Benke PI, D'haeseleer P, Sun N, Sale KL, Keasling JD, Lee TS, Petzold CJ, Mukhopadhyay A, Singer SW, Simmons B, Gladden JM. A thermophilic ionic liquid-tolerant cellulase cocktail for the production of cellulosic biofuels. PLoS One. 2012; 7(5):e37010. PMID: 22649505; PMCID: PMC3359315.
    103. Cheng G, Datta S, Liu Z, Wang C, Murton JK, Brown PA, Jablin MS, Dubey M, Majewski J, Halbert CE, Browning JF, Esker AR, Watson BJ, Zhang H, Hutcheson SW, Huber DL, Sale KL, Simmons B, Kent MS. Interactions of endoglucanases with amorphous cellulose films resolved by neutron reflectometry and quartz crystal microbalance with dissipation monitoring. Langmuir. 2012 Jun 05; 28(22):8348-58. PMID: 22554348.
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    104. Khudyakov JI, D'haeseleer P, Borglin SE, Deangelis KM, Woo H, Lindquist EA, Hazen TC, Simmons B, Thelen MP. Global transcriptome response to ionic liquid by a tropical rain forest soil bacterium, Enterobacter lignolyticus. Proc Natl Acad Sci U S A. 2012 Aug 07; 109(32):E2173-82. PMID: 22586090; PMCID: PMC3420158.
    105. Eudes A, George A, Mukerjee P, Kim JS, Pollet B, Benke PI, Yang F, Mitra P, Sun L, Cetinkol OP, Chabout S, Mouille G, Soubigou-Taconnat L, Balzergue S, Singh S, Holmes BM, Mukhopadhyay A, Keasling JD, Simmons B, Lapierre C, Ralph J, Loqué D. Biosynthesis and incorporation of side-chain-truncated lignin monomers to reduce lignin polymerization and enhance saccharification. Plant Biotechnol J. 2012 Jun; 10(5):609-20. PMID: 22458713.
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    106. Greving M, Cheng X, Reindl W, Bowen B, Deng K, Louie K, Nyman M, Cohen J, Singh A, Simmons B, Adams P, Siuzdak G, Northen T. Acoustic deposition with NIMS as a high-throughput enzyme activity assay. Anal Bioanal Chem. 2012 May; 403(3):707-11. PMID: 22407334.
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    107. DeAngelis KM, Fortney JL, Borglin S, Silver WL, Simmons B, Hazen TC. Anaerobic decomposition of switchgrass by tropical soil-derived feedstock-adapted consortia. MBio. 2012; 3(1). PMID: 22354956; PMCID: PMC3374387.
    108. Welz O, Zádor J, Savee JD, Ng MY, Meloni G, Fernandes RX, Sheps L, Simmons B, Lee TS, Osborn DL, Taatjes CA. Low-temperature combustion chemistry of biofuels: pathways in the initial low-temperature (550 K-750 K) oxidation chemistry of isopentanol. Phys Chem Chem Phys. 2012 Mar 07; 14(9):3112-27. PMID: 22286869.
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    109. Zendejas FJ, Benke PI, Lane PD, Simmons B, Lane TW. Characterization of the acylglycerols and resulting biodiesel derived from vegetable oil and microalgae (Thalassiosira pseudonana and Phaeodactylum tricornutum). Biotechnol Bioeng. 2012 May; 109(5):1146-54. PMID: 22161571.
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    110. Gladden JM, Eichorst SA, Hazen TC, Simmons B, Singer SW. Substrate perturbation alters the glycoside hydrolase activities and community composition of switchgrass-adapted bacterial consortia. Biotechnol Bioeng. 2012 May; 109(5):1140-5. PMID: 22125273.
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    111. Bokinsky G, Peralta-Yahya PP, George A, Holmes BM, Steen EJ, Dietrich J, Lee TS, Tullman-Ercek D, Voigt CA, Simmons B, Keasling JD. Synthesis of three advanced biofuels from ionic liquid-pretreated switchgrass using engineered Escherichia coli. Proc Natl Acad Sci U S A. 2011 Dec 13; 108(50):19949-54. PMID: 22123987; PMCID: PMC3250153.
    112. Oleskowicz-Popiel P, Kádár Z, Heiske S, Klein-Marcuschamer D, Simmons B, Blanch HW, Schmidt JE. Co-production of ethanol, biogas, protein fodder and natural fertilizer in organic farming--evaluation of a concept for a farm-scale biorefinery. Bioresour Technol. 2012 Jan; 104:440-6. PMID: 22154299.
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    113. Klein-Marcuschamer D, Oleskowicz-Popiel P, Simmons B, Blanch HW. The challenge of enzyme cost in the production of lignocellulosic biofuels. Biotechnol Bioeng. 2012 Apr; 109(4):1083-7. PMID: 22095526.
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    114. Sun L, Varanasi P, Yang F, Loqué D, Simmons B, Singh S. Rapid determination of syringyl: guaiacyl ratios using FT-Raman spectroscopy. Biotechnol Bioeng. 2012 Mar; 109(3):647-56. PMID: 22012706.
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    115. Chuck GS, Tobias C, Sun L, Kraemer F, Li C, Dibble D, Arora R, Bragg JN, Vogel JP, Singh S, Simmons B, Pauly M, Hake S. Overexpression of the maize Corngrass1 microRNA prevents flowering, improves digestibility, and increases starch content of switchgrass. Proc Natl Acad Sci U S A. 2011 Oct 18; 108(42):17550-5. PMID: 21987797; PMCID: PMC3198312.
    116. Deangelis KM, D'Haeseleer P, Chivian D, Fortney JL, Khudyakov J, Simmons B, Woo H, Arkin AP, Davenport KW, Goodwin L, Chen A, Ivanova N, Kyrpides NC, Mavromatis K, Woyke T, Hazen TC. Complete genome sequence of "Enterobacter lignolyticus" SCF1. Stand Genomic Sci. 2011 Oct 15; 5(1):69-85. PMID: 22180812; PMCID: PMC3236048.
    117. Blanch HW, Simmons B, Klein-Marcuschamer D. Biomass deconstruction to sugars. Biotechnol J. 2011 Sep; 6(9):1086-102. PMID: 21834132.
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    118. Liu H, Sale KL, Simmons B, Singh S. Molecular dynamics study of polysaccharides in binary solvent mixtures of an ionic liquid and water. J Phys Chem B. 2011 Sep 01; 115(34):10251-8. PMID: 21827163.
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    119. Gladden JM, Allgaier M, Miller CS, Hazen TC, VanderGheynst JS, Hugenholtz P, Simmons B, Singer SW. Glycoside hydrolase activities of thermophilic bacterial consortia adapted to switchgrass. Appl Environ Microbiol. 2011 Aug 15; 77(16):5804-12. PMID: 21724886; PMCID: PMC3165268.
    120. Cheng G, Liu Z, Murton JK, Jablin M, Dubey M, Majewski J, Halbert C, Browning J, Ankner J, Akgun B, Wang C, Esker AR, Sale KL, Simmons B, Kent MS. Neutron reflectometry and QCM-D study of the interaction of cellulases with films of amorphous cellulose. Biomacromolecules. 2011 Jun 13; 12(6):2216-24. PMID: 21553874.
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    121. Reddy AP, Allgaier M, Singer SW, Hazen TC, Simmons B, Hugenholtz P, VanderGheynst JS. Bioenergy feedstock-specific enrichment of microbial populations during high-solids thermophilic deconstruction. Biotechnol Bioeng. 2011 Sep; 108(9):2088-98. PMID: 21520015.
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    122. DeAngelis KM, Allgaier M, Chavarria Y, Fortney JL, Hugenholtz P, Simmons B, Sublette K, Silver WL, Hazen TC. Characterization of trapped lignin-degrading microbes in tropical forest soil. PLoS One. 2011 Apr 29; 6(4):e19306. PMID: 21559391; PMCID: PMC3084812.
    123. Li C, Cheng G, Balan V, Kent MS, Ong M, Chundawat SP, Sousa Ld, Melnichenko YB, Dale BE, Simmons B, Singh S. Influence of physico-chemical changes on enzymatic digestibility of ionic liquid and AFEX pretreated corn stover. Bioresour Technol. 2011 Jul; 102(13):6928-36. PMID: 21531133.
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    124. Cheng G, Varanasi P, Li C, Liu H, Melnichenko YB, Simmons B, Kent MS, Singh S. Transition of cellulose crystalline structure and surface morphology of biomass as a function of ionic liquid pretreatment and its relation to enzymatic hydrolysis. Biomacromolecules. 2011 Apr 11; 12(4):933-41. PMID: 21361369.
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    125. Park JI, Kent MS, Datta S, Holmes BM, Huang Z, Simmons B, Sale KL, Sapra R. Enzymatic hydrolysis of cellulose by the cellobiohydrolase domain of CelB from the hyperthermophilic bacterium Caldicellulosiruptor saccharolyticus. Bioresour Technol. 2011 May; 102(10):5988-94. PMID: 21421309.
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    126. Wu H, Volponi JV, Oliver AE, Parikh AN, Simmons B, Singh S. In vivo lipidomics using single-cell Raman spectroscopy. Proc Natl Acad Sci U S A. 2011 Mar 01; 108(9):3809-14. PMID: 21310969; PMCID: PMC3048102.
    127. Sun L, Simmons B, Singh S. Understanding tissue specific compositions of bioenergy feedstocks through hyperspectral Raman imaging. Biotechnol Bioeng. 2011 Feb; 108(2):286-95. PMID: 20824689.
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    128. Achyuthan KE, Achyuthan AM, Adams PD, Dirk SM, Harper JC, Simmons B, Singh AK. Supramolecular self-assembled chaos: polyphenolic lignin's barrier to cost-effective lignocellulosic biofuels. Molecules. 2010 Nov 29; 15(12):8641-88. PMID: 21116223.
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    129. Bharadwaj R, Chen Z, Datta S, Holmes BM, Sapra R, Simmons B, Adams PD, Singh AK. Microfluidic glycosyl hydrolase screening for biomass-to-biofuel conversion. Anal Chem. 2010 Nov 15; 82(22):9513-20. PMID: 20964411.
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    130. Bharadwaj R, Wong A, Knierim B, Singh S, Holmes BM, Auer M, Simmons B, Adams PD, Singh AK. High-throughput enzymatic hydrolysis of lignocellulosic biomass via in-situ regeneration. Bioresour Technol. 2011 Jan; 102(2):1329-37. PMID: 20884206.
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    131. Liu H, Pereira JH, Adams PD, Sapra R, Simmons B, Sale KL. Molecular simulations provide new insights into the role of the accessory immunoglobulin-like domain of Cel9A. FEBS Lett. 2010 Aug 04; 584(15):3431-5. PMID: 20609364.
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    132. Pereira JH, Chen Z, McAndrew RP, Sapra R, Chhabra SR, Sale KL, Simmons B, Adams PD. Biochemical characterization and crystal structure of endoglucanase Cel5A from the hyperthermophilic Thermotoga maritima. J Struct Biol. 2010 Dec; 172(3):372-9. PMID: 20599513.
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    133. Liu H, Sale KL, Holmes BM, Simmons B, Singh S. Understanding the interactions of cellulose with ionic liquids: a molecular dynamics study. J Phys Chem B. 2010 Apr 01; 114(12):4293-301. PMID: 20218725.
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    134. Simmons B, Loqué D, Ralph J. Advances in modifying lignin for enhanced biofuel production. Curr Opin Plant Biol. 2010 Jun; 13(3):313-20. PMID: 20359939.
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    135. Achyuthan KE, Adams PD, Datta S, Simmons B, Singh AK. Hitherto unrecognized fluorescence properties of coniferyl alcohol. Molecules. 2010 Mar 11; 15(3):1645-67. PMID: 20336005.
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    136. Allgaier M, Reddy A, Park JI, Ivanova N, D'haeseleer P, Lowry S, Sapra R, Hazen TC, Simmons B, VanderGheynst JS, Hugenholtz P. Targeted discovery of glycoside hydrolases from a switchgrass-adapted compost community. PLoS One. 2010 Jan 21; 5(1):e8812. PMID: 20098679; PMCID: PMC2809096.
    137. Li C, Knierim B, Manisseri C, Arora R, Scheller HV, Auer M, Vogel KP, Simmons B, Singh S. Comparison of dilute acid and ionic liquid pretreatment of switchgrass: Biomass recalcitrance, delignification and enzymatic saccharification. Bioresour Technol. 2010 Jul; 101(13):4900-6. PMID: 19945861.
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    138. Achyuthan KE, Adams PD, Simmons B, Singh AK. Spectroscopic analyses of the biofuels-critical phytochemical coniferyl alcohol and its enzyme-catalyzed oxidation products. Molecules. 2009 Nov 23; 14(11):4758-78. PMID: 19935474.
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    139. Wurtzel O, Sapra R, Chen F, Zhu Y, Simmons B, Sorek R. A single-base resolution map of an archaeal transcriptome. Genome Res. 2010 Jan; 20(1):133-41. PMID: 19884261; PMCID: PMC2798825.
    140. Singh S, Simmons B, Vogel KP. Visualization of biomass solubilization and cellulose regeneration during ionic liquid pretreatment of switchgrass. Biotechnol Bioeng. 2009 Sep 01; 104(1):68-75. PMID: 19489027.
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    141. Pereira JH, Sapra R, Volponi JV, Kozina CL, Simmons B, Adams PD. Structure of endoglucanase Cel9A from the thermoacidophilic Alicyclobacillus acidocaldarius. Acta Crystallogr D Biol Crystallogr. 2009 Aug; 65(Pt 8):744-50. PMID: 19622857; PMCID: PMC2714717.
    142. Kent MS, Murton JK, Zendejas FJ, Tran H, Simmons B, Satija S, Kuzmenko I. Nanosilica formation at lipid membranes induced by the parent sequence of a silaffin peptide. Langmuir. 2009 Jan 06; 25(1):305-10. PMID: 19035672.
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    143. Simmons B, Loque D, Blanch HW. Next-generation biomass feedstocks for biofuel production. Genome Biol. 2008; 9(12):242. PMID: 19133109; PMCID: PMC2646290.
    144. Sabounchi P, Morales AM, Ponce P, Lee LP, Simmons B, Davalos RV. Sample concentration and impedance detection on a microfluidic polymer chip. Biomed Microdevices. 2008 Oct; 10(5):661-70. PMID: 18484178.
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    145. Blanch HW, Adams PD, Andrews-Cramer KM, Frommer WB, Simmons B, Keasling JD. Addressing the need for alternative transportation fuels: the Joint BioEnergy Institute. ACS Chem Biol. 2008 Jan 18; 3(1):17-20. PMID: 18205287.
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    146. Wallow TI, Morales AM, Simmons B, Hunter MC, Krafcik KL, Domeier LA, Sickafoose SM, Patel KD, Gardea A. Low-distortion, high-strength bonding of thermoplastic microfluidic devices employing case-II diffusion-mediated permeant activation. Lab Chip. 2007 Dec; 7(12):1825-31. PMID: 18030407.
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    147. Bauer CA, Timofeeva TV, Settersten TB, Patterson BD, Liu VH, Simmons B, Allendorf MD. Influence of connectivity and porosity on ligand-based luminescence in zinc metal-organic frameworks. J Am Chem Soc. 2007 Jun 06; 129(22):7136-44. PMID: 17503820.
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    148. Bauer CA, Robinson DB, Simmons B. Silica particle formation in confined environments via bioinspired polyamine catalysis at near-neutral pH. Small. 2007 Jan; 3(1):58-62. PMID: 17294469.
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    149. Dentinger PM, Simmons B, Cruz E, Sprague M. DNA-mediated delivery of lipophilic molecules via hybridization to DNA-based vesicular aggregates. Langmuir. 2006 Mar 28; 22(7):2935-7. PMID: 16548535.
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    150. Lee ES, Robinson D, Rognlien JL, Harnett CK, Simmons B, Bowe Ellis CR, Davalos RV. Microfluidic electroporation of robust 10-microm vesicles for manipulation of picoliter volumes. Bioelectrochemistry. 2006 Sep; 69(1):117-25. PMID: 16483852.
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    151. Long TM, Simmons B, McElhanon JR, Kline SR, Wheeler DR, Loy DA, Rahimian K, Zifer T, Jamison GM. Metathesis depolymerization for removable surfactant templates. Langmuir. 2005 Sep 27; 21(20):9365-73. PMID: 16171375.
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    152. Lapizco-Encinas BH, Davalos RV, Simmons B, Cummings EB, Fintschenko Y. An insulator-based (electrodeless) dielectrophoretic concentrator for microbes in water. J Microbiol Methods. 2005 Sep; 62(3):317-26. PMID: 15941604.
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    153. Rucker VC, Havenstrite KL, Simmons B, Sickafoose SM, Herr AE, Shediac R. Functional antibody immobilization on 3-dimensional polymeric surfaces generated by reactive ion etching. Langmuir. 2005 Aug 16; 21(17):7621-5. PMID: 16089360.
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    154. McElhanon JR, Zifer T, Kline SR, Wheeler DR, Loy DA, Jamison GM, Long TM, Rahimian K, Simmons B. Thermally cleavable surfactants based on furan-maleimide Diels-Alder adducts. Langmuir. 2005 Apr 12; 21(8):3259-66. PMID: 15807562.
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    155. Lapizco-Encinas BH, Simmons B, Cummings EB, Fintschenko Y. Insulator-based dielectrophoresis for the selective concentration and separation of live bacteria in water. Electrophoresis. 2004 Jun; 25(10-11):1695-704. PMID: 15188259.
      View in: PubMed
    156. Lapizco-Encinas BH, Simmons B, Cummings EB, Fintschenko Y. Dielectrophoretic concentration and separation of live and dead bacteria in an array of insulators. Anal Chem. 2004 Mar 15; 76(6):1571-9. PMID: 15018553.
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