Publications

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596 Records as of 04/21/2014

Publication Date Author Title Journal/Book Volume/Issue Focus Area DOI
11/01/2011 Abraham Defining the Boundaries and Characterizing the Landscape of Functional Genome Expression in Vascular Tissues of Populus using Shotgun Proteomics

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Journal of Proteome Research Abraham, P., Adams, R., Giannone, R.J., Kalluri, U., Ranjan, P., Erickson, B., Shah, M., Tuskan, G.A., Hettich, R.L. "Defining the Boundaries and Characterizing the Landscape of Functional Genome Expression in Vascular Tissues of Populus using Shotgun Proteomics." Journal of Proteome Research 11:449–460, 2012. Research Area: Characterization and Modeling 10.1021/pr200851y
10/16/2012 Abraham Putting the pieces together: high-performance LC-MS/MS provides network-pathway-, and protein-level perspectives in Populus

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Molecular and Cellular Proteomics Abraham, P., Giannone, R.J., Adams, R.M., Kalluri, U., Tuskan, G.A., Hettich, R.L., Putting the pieces together: high-performance LC-MS/MS provides network-, pathway-, and protein-level perspectives in Populus, Molecular and Cellular Proteomics, 12(1):106-19, 2013. Research Area: Biomass Formation and Modification 10.1074/mcp.M112.022996 mcp.M112.022996
07/01/2013 Abraham Moving away from the reference genome: evaluating a peptide sequencing tagging approach for single amino acid polymorphism identifications in the genus Populus

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Journal of Proteome Research Abraham, P., Adams, R.M., Tuskan, G.A., Hettich, R.L., Moving away from the reference genome: evaluating a peptide sequencing tagging approach for single amino acid polymorphism identifications in the genus Populus, 12(8):3642-51, 2013. Research Area: Biomass Formation and Modification 10.1021/pr400192r
03/01/2010 Abulencia Accessing Microbial Communities Relevant to Biofuels Production Manual of Industrial Microbiology and Biotechnology Abulencia, C. B., Wells, S. M., Gray, K. A., Keller, M., Kreps, J.A., Accessing microbial communities relevant to biofuels production. in: R. H.Baltz, J. E.Davies, A. L.Demain (Eds.), Industrial Microbiology and Biotechnology, 3rd Edn, ASM press, Washington DC 2010, pp. 565–576. Research Area: Biomass Deconstruction and Conversion ISBN 155581512X
07/01/2010 Alahuhta Structure of a fibronectin type III-like module from Chostridium thermocellum

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Acta Crystallographica - Section F Alahuhta, Markus, Xu Qi, Brunecky, Roman, Adney, William S., Ding, Shi You, Himmel Michael E, Lunin, Vladimir V., Structure of a fibronectin type III-like module from Chostridium thermocellum, Structural Biology and Crystallization Communications, Volume 66, Issue Pt 8, Pages 878-80, 2010. Research Area: Biomass Deconstruction and Conversion 10.1107/S1744309110022529
01/01/2011 Alahuhta Structure of CBM4 from Clostridium thermodellum cellulase K

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Acta Crystallographica - Section F Alahuhta, M., Luo, Y., Ding, S-Y, Himmel, M.E., Lunin, V.V., Structure of CBM4 from Clostridium thermocellum cellulase K, Acta Crystallographica, 2011, F67, 527-530. Research Area: Biomass Deconstruction and Conversion ISSN 1744-3091
07/01/2010 Alahuhta The Unique Binding Mode of Cellulosomal CBM4 from Clostridium thermocellum Cellobiohydrolase A

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Journal of Microbiology Alahuhta, M., Xu, Q., Bomble, Y.J., Brunecky, R., Adney, W.S., Ding, S-Y., Himmel, M.E, Lunin, V.V., The Unique Binding Mode of Cellulosomal CBM4 from Clostridium thermocellum Cellobiohydrolase A, Journal of Microbiology,Volume 402, Issue 2, pp 374-387, 2010. Research Area: Biomass Deconstruction and Conversion 10.1016/j.jmb.2010.07.028
11/30/2013 Alahuhta Structure of Acidothermus cellulolyticus family 74 glycoside hydrolase at 1.82 A resolution

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Acta Crystallographica Section F Structural Biology and Crystallization Communications Alahuhta, M., Adney, W.S., Himmel, M.E., Lunin, V.V., Structure of Acidothermus cellulolyticus family 74 glycoside hydrolase at 1.82 A resolution, Acta Crystallographica Section F Structural Biology and Crystallization Communications, F69, 1335-1338, 2013. Research Area: Biomass Deconstruction and Conversion 10.1107/S1744309113030005
03/01/2013 Alahuhta The structure and mode of action of Caldicellulosiruptor bescii family 3 pectate lyase in biomass deconstruction

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Acta Crystallographica - Section D Alahuhta, M., Brunecky, R., Chandrayan, P., Kataeva, I., Adams, M.W.W., Himmel, M.E., Lunin, V.V., The structure and mode of action of Caldicellulosiruptor bescii family 3 pectate lyase in biomass deconstruction, Acta Crystallographica Section D, D69, 534-539, 2013. Research Area: Biomass Deconstruction and Conversion 10.1107/S0907444912050512
11/01/2011 Alahuhta A 1.5 A resolution X-ray structure of the catalytic module of Caldicellulosiruptor bescii family 3 pectate lyase

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Acta Crystallographica - Section F Alahuhta, M., Chandrayan, P., Kataeva, I., Adams, M. W. W., Himmel, M. E. and Lunin, V. V. (2011). “A 1.5 Å resolution X-ray structure of the catalytic module of Caldicellulosiruptor bescii family 3 pectate lyase.” Acta Crystallographica Section F, 67: 1498–1500 Research Area: Biomass Formation and Modification 10.1107/S1744309111038449
07/01/2010 Andrews Part I: characterization of the extracellular proteome of the extreme thermophile Caldicellulosiruptor saccharolyticus by GeLC-MS2

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Annuals of Bioanalytical Chemistry Muddiman, David, Andrews, Genna, Lewis, Derrick, Notey, Jaspreet, Kelly, Robert, Part I: characterization of the extracellular proteome of the extreme thermophile Caldicellulosiruptor scccharolyticus by GeLC-MS2, Annuals of Bioanalytical Chemistry, 398:377–389, 2010. Research Area: Biomass Deconstruction and Conversion 10.1007/s00216-010-3955-6
07/01/2010 Andrews Part II: defining and quantifying individual and co-cultured intracellular proteomes of two thermophilic microorganisms by GeLC-MS2 and spectral counting

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Annnuals of Bioanalytical Chemistry Muddiman, David, Andrews, Genna, Lewis, Derrick, Notey, Jaspreet, Kelly, Robert, Part II: defining and quantifying individual and co-cultured intracellular proteomes of two thermophilic microorganisms by GeLC-MS2 and spectral counting, Annuals of Bioanalytical Chemistry, 398:1, 391-404, 2010. Research Area: Biomass Deconstruction and Conversion 10.1007/s00216-010-3929-8
07/19/2012 Archambault-Leger Integrated analysis of hydrothermal flowthrough pretreatment

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Biotechnology for Biofuels Archambault-Leger, V., Show, X., Lynd, L.R., Integrated analysis of hydrothermal flowthroughpretreatment, Biotechnology for Biofuels, 5:49, 2012. Research Area: Biomass Deconstruction and Conversion 10.1186/1754-6834-5-49
01/12/2014 Archambault-Leger Fluid mechanics relevant to flow through pretreatment of cellulosic biomass

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Bioresource Technology Archambault-Leger, V., Lynd, L.R., Fluid mechanics relevant to flow through pretreatment of cellulosic biomass, Bioresource Technology, 157; (278-283) 2014. Research Area: Biomass Deconstruction and Conversion 10.1016/j.biortech.2014.01.035
09/30/2011 Argyros High Ethanol Titers from Cellulose using Metabolically Engineered Thermophilic, Anaerobic Microbes

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Applied Environmental Microbiology Argyrosa, D.A., Tripathia, S.A., Barretta, T.F., Rogers, S.R., Feinberg, L.F., Olson, D.G., Fodena, J.M., Miller, B.B., Lynd, L.R., Hogsett, D.A., Caiazza, N.C., High Ethanol Titers from Cellulose using Metabolically Engineered Thermophilic, Anaerobic Microbes, Applied Environmental Microbiology, 77:8288-8294, 2011 Research Area: Biomass Deconstruction and Conversion 10.1128/AEM.00646-11
06/15/2013 Atalla Irreversible transformations of native celluloses, upon exposure to elevated temperatures

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Carbohydrate Polymers Atalla, R.S., Crowley, M.F., Himmel, M.E., Atalla, R.H., Irreversible transformations of native celluloses, upon exposure to elevated temperatures, Carbohydrate Polymers, 100, 2-8, 2013. Research Area: Biomass Deconstruction and Conversion 10.1016/j.carbpol.2013.06.007,
05/08/2013 Atmodjo Evolving views of pectin biosynthesis

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Annual Review of Plant Biology Atmodjo, M.A., Hao, Z., Mohnen, D., Evolving views of pectin biosynthesis, Annual Review of Plant Biology, 64:, 747-779, 2013. Research Area: Biomass Formation and Modification 10.1146/annurev-arplant-042811-105534
11/21/2011 Atmodjo Galacturonosyltransferase (GAUT)1 and GAUT7 are the core of a plant cell wall pectin biosynthetic homogalacturonan–galacturonosyltransferase complex

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PNAS Atmodjo, M.A., Sakuragi, Y., Zhu, X., Burrell, A.J., Mohanty, S.S., Atwood III, J.A., Orlando, R., Scheller, H.V., Mohnen, D., Galacturonosyltransferase (GAUT)1 and GAUT7 are the core of a plant cell wall pectin biosynthetic homogalacturonan–galacturonosyltransferase complex, PNAS, 108(50):20225-30, 2011. Research Area: Biomass Formation and Modification 10.1073/pnas.1112816108/-/DCSupplemental.
12/21/2010 Atsumi Evolution, genomic analysis, and reconstruction of isobutanol tolerance in Escherichia coli

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Molecular Systems Biology Atsumi, S., Wu, T. Y., Machado, I. M. P., Huang, W. C., Chen, P. Y., Pellegrini, M., Liao, J. C., 2010, Evolution, genomic analysis, and reconstruction of isobutanol tolerance in Escherichia coli, Molecular Systems, Volume 6, pp 11. Research Area: Biomass Deconstruction and Conversion 10.1038/msb.2010.98
03/01/2011 Bar-Peled Plant Nucleotide Sugar Formation, Interconversion, and Salvage by Sugar Recycling

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Annual Review of Plant Biology Bar-Peled, Maor, O'Neill, Malcolm A., Plant Nucleotide Sugar Formation, Interconversion, and Salvage by Sugar Recycling, Annual Review of Plant Biology, 62:127-55, 2011. Research Area: Biomass Formation and Modification 10.1146/annurev-arplant-042110-103918
05/11/2012 Bar-Peled The Synthesis and Origin of the Pectic Polysaccharide Rhamnogalacturonan II - Insights from Nucleotide Sugar Formation and Diversity

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Frontiers in Plant Science Bar-Peled, M., Urbanowicz, B.R., O'Neill, M.A., The Synthesis and Origin of the Pectic Polysaccharide Rhamnogalacturonan II - Insights from Nucleotide Sugar Formation and Diversity, 3:92, 2012. Research Area: Biomass Formation and Modification 10.3389/fpls.2012.00092
02/01/2013 Bartley Overexpression of a BAHD Acyltransferase, OsAt10, alters rice cell wall hydroxycinnamic acid content and saccharification

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Plant Physiology Bartley, L.E., et. al., Overexpression of a BAHD Acyltransferase, OsAt10, alters rice cell wall hydroxycinnamic acid content and saccharification, Plant Physiology, 161 (4), pp1615-1633, 2012. Research Area: Characterization and Modeling 10.1104/pp.112.208694
11/20/2013 Basen Degradation of high loads of crystalline cellulose and of unpretreated plant biomass by the thermophilic bacterium Caldicellulosiruptor bescii

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Bioresource Technology Basen, M., Rhaesa, A.M., Kataeva, I., Prybol, C.J., Scott, I.M., Pools, F.L., Adams, M.W.W., Degradation of high loads of crystalline cellulose and of unpretreated plant biomass by the thermophililic bacterium Caldicellulosiruptor bescii, Bioresource Technology, 152 (384-392) 2013. Research Area: Biomass Deconstruction and Conversion 10.1016/j.biortech.2013.11.024
04/27/2012 Basen Engineering a Hyperthermophilic Archaeon for Temperature-Dependent Product Formation

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mBio Basen, M., Sun, J., Adams, M.W.W., Engineering a Hyperthermophilic Archaeon for Temperature-Dependent Product Formation, mBio, 3(2), 2012. Research Area: Biomass Deconstruction and Conversion 10.1128/mBio.00053-12
11/01/2013 Baxter Effects of altered lignin biosynthesis on phenylpropanoid metabolism and plant stress

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Biofuels Baxter, H.L., Stewart Jr., C.N., Effects of altered lignin biosynthesis on phenylpropanoid metabolism and plant stress, Biofuels, 4(6), 635-667, 2013. Research Area: Biomass Formation and Modification 10.4155/bfs.13.56
12/01/2010 Beckham Application of computational science for understanding enzymatic deconstruction of cellulose

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Current Opinion in Biotechnology Beckham, Gregg T., Bomble, Yannick J., Bayer, Edward A., Himmel, Michael E., 2011, Applications of computational science for understanding enzymatic deconstruction of cellulose, Current Opinion in Biotechnology, Volume 22, pp 1-8. Research Area: Biomass Deconstruction and Conversion 10.1016/j.copbio.2010.11.005
05/15/2012 Bennetzen Reference genome sequence of the model plant Setaria

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Nature Biotechnology Bennetzen, J.L., et. al., Reference genome sequence of the model plant Setaria, Nature Biotechnology, 30,555–561, 2012. Research Area: Biomass Formation and Modification 10.1038/nbt.2196
10/01/2010 Bergenstrahle Simulation studies of the insolubility of cellulose

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Carbohydrate Research Bergenstrahle, M.,Wohlert, J., Himmel, M. E., Brady, J. W., Simulation studies of the insolubility of cellulose, Carbohydrate Research, Volume 345, Issue 14, pages 2060-2066, 2010. Research Area: Biomass Deconstruction and Conversion 10.1016/j.carres.2010.06.017
03/01/2013 Bhandiwad Metabolic engineering of thermoanaerobacterium thermosaccharolyticum for increased n-butanol production

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Advances in Microbiology Bhandiwad, A., Guseva, A., Lynd, L. R., Metabolic engineering of thermoanaerobacterium thermosaccharolyticum for increased n-butanol production, 3, 46-51, 2013. Research Area: Biomass Deconstruction and Conversion 10.4236/aim.2013.31007
09/27/2011 Biagioni Orthogonal projection to latent structures solution properties for chemometrics and systems biology data

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Journal of Chemometrics Biagioni, D.J., Astling, D.P., Graf, P., Davis, M.F., Orthogonal projection to latent structures solution properties for chemometrics and systems biology data, Journal of Chemometrics, 25;9, 2011. Research Area: Characterization and Modeling 10.1002/cem.1398
01/07/2014 Biswal Aspen pectate lyase PtxtPl1-27 mobilizes matrix plysaccharides from woody tissues and improves saccharification yield

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Biotechnology for Biofuels Biswal, A.K., Soeno, K., Gandla, M.L., Immerzeel, P., Pattathil, S., Lucenius, J., Serimaa, R., Hahn, M.G., Moritz, T. Jonsson, L.J., Isralelsson-Nordstrom, M., Mellerowica, E.J., Aspen pectate lyase PtxtPl1-27 mobilizes matrix plysaccharides from woody tissues and improves saccharification yield, Biotechnology for Biofuels, 7:11, 2014. Research Area: Characterization and Modeling 10.1186/1754-6834-7-11
02/07/2014 Biswas Increase in ethanol yield via elimination of lactate production in an ethanol-tolerant mutant of clostridium thermocellum

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Plos One Biswas, R., Prabhu, S., Lynd, L.R., Guss, A. M., Increase in ethanol yield via elimination of lactate production in an ethanol-tolerant mutant of clostridium thermocellum, Plos One, 9(2), 2014. Research Area: Biomass Deconstruction and Conversion 10.1371/journal.pone.0086389
03/01/2014 Biswas Elimination of hydrogenase active site assembly blocks H2 production and increases ethanol yield in Clostridium thermocellum PNAS Biswas, R., Wilson, C.M., Zheng, T., Giannone, R. J., Klingeman, D.M., Hettich, R. L., Olson, D.G., Lynd, L.R., Brown, S.D., Guss, A.M., Elimination of hydrogenase active site assembly blocks H2 production and increases ethanol yield in Clostridium thermocellum, PNAS, 2014 Research Area: Biomass Deconstruction and Conversion
08/01/2013 Blumer-Schuette Thermophilic lignocellulose deconstruction FEMS Microbiology Review Blumer-Schuette, S.E., Sander, K.E., Bayer, E.A., Zurawski, J.V., Conway, J.M., Adams, M.W.W., Kelly, R.M., Paradigms for thermophilic lignocellulose deconstruction, FEMS Microbial Review, 2013 Research Area: Biomass Deconstruction and Conversion 10.1111/1574-6976.12044
05/25/2012 Blumer-Schuette Caldicellulosiruptor core and pan genomes reveal determinants for non-cellulosomal thermophilic deconstruction of plant biomass

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Journal of Bacteriology Blumer-Schuette, S.E., Giannone, R.J., Zurawski, J.V., Ozdemir, I., Ma, Q., Yin, Y., Xu, Y., Kataeva, I., Poole II, F.L., Adams, M.W.W., Hamilton-Brehm, S.D., Elkins, J.G., Larimer, F.W., Land, M.L., Hauser, L., Cottingham, R.W., Hettich, R.L., Kelly, R.M., Caldicellulosiruptor core and pan genomes reveal determinants for non-cellulosomal thermophilic deconstruction of plant biomass, Journal of Bacteriology, 194(15):4015-28, 2012. Research Area: Biomass Deconstruction and Conversion 10.1128/​JB.00266-12
01/01/2011 Blumer-Schuette Complete Genome Sequences for the Anaerobic, Extremely Thermophilic Plant Biomass-Degrading Bacteria Caldicellulosiruptor hydrothermalis, Caldicellulosiruptor kristjannonii, Caldicellulosiruptor kronotskyensis, Caldicellulosiruptor lactoaceticus

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Journal of Bacteriology Blumer-Schuette, S.E., Ozdemir, I., Mistry, D., Lucas, S., Lapidus, A., Cheng, J.F., Goodwin, L.A., Pitluck, S., Land, M.L., Hauser, L.J., Woyke, T., Mikhailova, N., Pati, A., Kyrpides, D., Ivanova, N., Detter, J.C., Walston-Davenport, K., Han, S., Adams, M.W.W., Kelly, R.M., Complete Genome Sequences for the Anaerobic, Extremely Thermophilic Plant Biomass-Degrading Bacteria Caldicellulosiruptor hydrothermalis, Caldicellulosiruptor kristjanssonii, Caldicellulosiruptor kronotskyensis, Caldicellulosiruptor owensensis, and Caldicellulosiruptor lactoaceticus, Journal of Bacteriology, 193:6;1483-1484, 2011. Research Area: Biomass Deconstruction and Conversion 10.1128/​JB.01515-10
06/01/2008 Blumer-Schuette Extremely thermophilic microorganisms for biomass conversion: status and prospects

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Current Opinion in Biotechnology Blumer-Schuette, Sara E., Kataeva, Irina, Westpheling, Janet, Adams, Michael W.W., Kelly, Robert M., 2008, Extremely thermophilic microorganisms for biomass conversion; status and prospects, Current Opinion in Biotechnology, 19(3), 210-217, 2008. Research Area: Biomass Deconstruction and Conversion 10.1016/j.copbio.2008.04.007
10/22/2010 Blumer-Schuette Phylogenetic, microbiological and glycoside hydrolase diversity within the extremely thermophilic, plant biomass-degrading genus Caldicellulosiruptor

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Applied Environmental Microbiology Blumer-Schuette, S.E., Lewis, D.L., Kelly, R.M., Phylogenetic, microbiological and glycoside hydrolase diversity within the extremely thermophilic, plant biomass-degrading genus Caldicellulosiruptor, Applied Environmental Microbiology, 2010 Dec;76(24):8084-92 Research Area: Biomass Deconstruction and Conversion 10.1128/AEM.01400-10
12/11/2009 Bochner Phenotype MicroArray Profiling of Zymomonas mobilis ZM4

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Applied Biochemistry and Biotechnology Bochner, Barry, Gomez, Vanessa, Ziman, Michael, Yang, Shihui, Brown, Steven D., Phenotype MicroArray Profiling of Zymomonas mobilis AM4, Applied Biochemistry and Biotechnology, May 2010; pp 116-123 Research Area: Biomass Deconstruction and Conversion 10.1007/s12010-009-8842-2
06/01/2011 Bomble Modeling the Self-assembly of the Celluosome Enzyme Complex

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The Journal of Biological Chemistry Bomble, Y.J., Beckham, G.T., Matthews, J.F., Nimlos, M.R., Himmel, M.E., Crowley, M.F., Modeling the Selt-asembly of the Celluosome Enzyme Complex, The Journal of Biological Chemistry, volume 286(7), pp. 5614-5623, 2011. Research Area: Biomass Deconstruction and Conversion 10.1074/jbc.M110.186031
07/19/2010 Bomble Modeling the Cellulosome Using Multiscale Methods

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ACS Symposium Series - Computational Modeling in Lignocellulosic Biofuel Production Bomble, Yannick J., Crowley, Michael F., Xu, Q.I., Himmel, Michael E., Computational Modeling in Lignocellulosic Biofuel Production, Modeling the Cellulosome Using Multiscale Models, chapter 4, pp 75-98 Research Area: Biomass Deconstruction and Conversion 10.1021/bk-2010-1052.ch004
06/12/2008 Bordner Comprehensive inventory of protein complexes in the Protein Data Bank from consistent classification of interfaces

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BMC Bioinformatics Bordner, Andrew J., Gorin, AndreyA., Comprehensive inventory of protein complexes in the Protein Data Band from consistent classification of interfaces, BMC Bioinformatics, 2008, 9:234. Research Area: Characterization and Modeling 10.1186/1471-2105-9-234
11/01/2011 Broach Biosynthesis of UDP-glucuronic acid and UDP-galacturonic acid in Bacillus cereus subsp. Cytotoxis NVH 391-98

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The FEBS Journal Broach, B., Gu, X., Bar-Peled, M., Biosynthesis of UDP-glucuronic acid and UDP-galacturonic acid in Bacillus cereus subsp. Cytotoxis NVH 391-98, The FEBS Journal, 279; 1, 2012. Research Area: Biomass Formation and Modification 10.1111/j.1742-4658.2011.08402.x
07/01/2012 Brosse Miscanthus: a fast-growing crop for biofuels and chemicals production

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Biofuels, Biproducts & Biorefining Brosse, N., Dufour, A., Meng, X., Sun, Q., Ragauskas, A., Miscanthus: a fast-growning crop for biofuels and chemicals production, Biofuels, Bioproducts & Biorefining, Volume 6, Issue 5, pages 580–598, 2012. Research Area: Characterization and Modeling 10.1002/bbb.1353
05/25/2012 Brown Draft Genome Sequences for Clostridium thermocellum Wild-Type Strain YS and Derived Cellulose Adhesion-Defective Mutant Strain AD2

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Journal of Bacteriology Brown, S.D., Lamed, R., Morag, E., Borovok, I., Shoham, Y., Klingeman, D.M., Johnson, C.M., Yang, Z., Land, M.L., Utturkar, S.M., Keller, M., Bayer, E.A., Draft Genome Sequences for Clostridium thermocellum Wild-Type Strain YS and Derived Cellulose Adhesion-Defective Mutant Strain AD2, Journal of Bacteriology, 194 (12) pp 3290-3291, 2012. Research Area: Biomass Deconstruction and Conversion 10.1128/JB.00473-12
06/01/2013 Brown Genome sequences of industrially relevant saccharomyces cerevisiae strain M3707, isolated from a sample of distillers yeast and four haploid derivatives

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Genome Announcements Brown, S.D., Klingeman, D.M., Johnson, C.M., Clum, A., Aerts, A., Salamov, A., Sharma, A., Zane, M., Barry, K., Grigoriev, I.V., Davison, B.D., Lynd, L.R., Gilna, P., Hau, H., Hogsett, D.A., Froehlich, A.C., Genome sequences of industrially relevant Saccharomyces cerevisiae Strain M3707, isolated from a sample of distillers yeast and four haploid derivatives, Genome Announcements, vol. 1 no. 3, 2013. Research Area: Biomass Deconstruction and Conversion 10.1128/genomeA.00323-13
07/14/2011 Brown Complete Genome Sequence of the Haloalkaliphilic, Hydrogen Producing Halanaerobium hydrogenoformans

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Journal of Bacteriology Brown, S.D., Begemann, M.B., Mormile, M.R., Wall, J.D., Han, C.S., Goodwin, L.A., Pitluck, S., Land, M.L., Hauser, L.J., Elias, D.A., Complete Genome Sequence of the Haloalkaliphilic, Hydrogen Producing Halanaerobium hydrogenoformans, Journal of Bacteriology, Volume 193, No. 4, 2011. Research Area: Biomass Deconstruction and Conversion 10.1128/JB.05209-11
08/16/2011 Brown Mutant alcohol dehydrogenase leads to improved ethanol tolerance in Clostridium thermocellum

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PNAS Brown, S.D., Shao, X., Guss, A.M., Bhandiwad, A., Karpinets, T.V., Parks, J.M., Smolin, N., Yang, S., Land, M.L., Klingemen, D.M., Rodriguez Jr., M., Raman, B., Zhu, M., Mielenz, J.R., Smith, J.C., Tschaplinski, T.J., Engle, N.L., Giannone, R.J., Hettich, R.L., Keller, M., Lynd, L.R., Mutant alcohol dehydrogenase leads to improved ethanol tolerance in Clostridium thermocellum, PNAS, 108(33):13752-13757, 2011. Research Area: Biomass Deconstruction and Conversion 10.1073/pnas.1102444108
03/21/2014 Brown Comparison of single-molecule sequencing and hybrid approaches for finishing the genome of Clostridium autoethanogenum and analysis of CRISPR systems in industrial relevant Clostridia Biotechnology for Biofuels Brown, S.D., Nagaraju, S., Utturkar, S., De Tissera, S., Segovia, S., Mitchell, W., Land, M.L., Dassanayake, A., Kopke, M., Comparison of single-molecule sequencing and hybrid approaches for finishing the genome of Clostridium autoethanogenum and analysis of CRISPER systems in industrial relevant Clostridia, BioTechnology for Biofuels, 7:40, 2014. Research Area: Characterization and Modeling 10.1186/1754-6834-7-40
01/01/2014 Brunecky Basic biological research relevant to feedstock conversion

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Compendium of Bioenergy Plants: Corn Brunecky, R., Donohoe, B.S., Selig, M.H., Wei, H., Resch, M., Himmel, M.E., Basic Biological Research Relevant to Feestock Conversion, Compendium of Bioenergy Plants: Corn, Chapter 2, pp 33-69, 2014. Research Area: Biomass Deconstruction and Conversion
12/20/2013 Brunecky Revealing nature's cellulase diversity: the digestion mechanism of caldicellulosiruptor bescii celA

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Science Brunecky, R., Alahuhta, M., Xu, Q., Donohoe, B.S., Crowley, M.F., Kataeva, I.A., Yang, S.J., Resch, M. G., Adams, M.W.W., Lunin, V.V., Himmel, M.E., Bomble, Y.J., Revealing nature's cellulase diversity: the digestion mechanism of caldicellulosiruptor bescii celA, Science, 342 (6165): 1513-1516, 2013. Research Area: Biomass Deconstruction and Conversion 10.1126/science.1244273
08/01/2012 Brunecky Analysis of Transgenic Glycoside Hydrolases Expressed in Plants: T. reesei CBH I and A. celluloyticus EI Methods in Molecular Biology Biomass Conversion: Methods and Protocols Brunecky, R., Baker, J.O., Wei, H., Taylor, L.E., Himmel, M.E., Decker, S.R., Analysis of Transgenic Glycoside Hydrolases Expressed in Plants: T. reesei CBH I and A. celluloyticus EI, Methods in Molecular Biology Biomass Conversion: Methods and Protocols, 908:197-211, 2012. Research Area: Biomass Deconstruction and Conversion 10.1007/978-1-61779-956-3_18
03/01/2012 Brunecky Structure and function of the Clostridium thermocellum cellobiohydrolase A X1-module repeat: enhancement through stabilization of the CbhA complex

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Acta Crystallographica - Section D Brunecky, R., M. Alahuhta, et al. (2012). "Structure and function of the Clostridium thermocellum cellobiohydrolase A X1-module repeat: enhancement through stabilization of the CbhA complex." Acta Crystallographica Section D 68(3): 292-299. Research Area: Biomass Deconstruction and Conversion 10.1107/S0907444912001680
01/01/2009 Burris An improved tissue culture system for embyrogenic callus production and plant regeneration in switchgrass (Panicum virgatum L.) BER-130R1

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Bioenergy Research Burris, Jason N., Mann, David G.J., Joyce, Blake, Stewart, C. Neal, 2009, BioEnergy Research, An improved tissue culture system for embyrogenic callus production and plant regeneration in switchgrass, Volume 2, Number 4, December 2009. Research Area: Biomass Formation and Modification 10.1007/s12155-009-9048-8
09/11/2009 Caffall Arabidopsis thaliana T-DNA Mutants Implicate GAUT Genes in the Biosynthe sis of Pectin and Xylan in Cell Walls and Seed Testa

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Molecular Plant Caffall, Kerry H., Pattathil, Sivakumar, Phillips, Sarah E., Hahn, Michael G., Mohnen, Debra, Arabidopsis thaliana T-DNA Mutants Implicate GAUT Genes in the Biosynthe sis of Pectin and Xylan in Cell Walls and Seed Testa, Molecular Plant, Volume 2, Number 5, pp 1000 - 1014 Research Area: Biomass Formation and Modification 10.1093/mp/ssp062
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Carbohydrate Research Caffall KH, Mohnen D., The structure, function, and biosynthesis of plant cell wall pectic polysaccharides., Carbohydrate Research 2009;344(14):1879-1900. Research Area: Biomass Formation and Modification 10.1016/j.carres.2009.05.021
03/18/2011 Cai MicroSyn: A user friendly tool for detection of microsynteny in a gene family

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BMC Bioinformatics Cai, Bin, Yang, Xiaohan, Yang, Tuskan, Gerald A., Cheng, Zong-Ming, MicroSyn: A user friendly tool for detection of microsynteny in a gene family, BMC Bioinformatics, 12:79, 2011. Research Area: Biomass Formation and Modification 10.1186/1471-2105-12-79
09/01/2012 Cao Chemical transformations of Populus trichocarpa during dilute acid pretreatment

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RCS Advances Cao, S., Pu, Y., Studer, M., Wyman, C., Ragauskas, A., Chemical transformations of Populus trichocarpa during dilute acid pretreatment, RCS Advances, 2, 10925-10936, 2012. Research Area: Characterization and Modeling 10.1039/C2RA22045H
02/16/2011 Cartmell The structure and function of an arabinan-specific a-1,2- arabinofuranosidase identified from screening the activities of bacterial GH43 glycoside hydrolases

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Journal of Biological Chemistry Cartmell, A., McKee, Lauren S., Pena, Maria J., Larsbring, Johan, Brumer, Harry, Kaneko, Satoshi, Ichinose, Hitomi, Lewis, Richard J., Vikso-Nielson, Anders, Gilbert, Harry J., Marles-Wright, Jon, The Structure and Function of an Arabinan-specific α-1,2-Arabinofuranosidase Identified from Screening the Activities of Bacterial GH43 Glycoside Hydrolases , The Journal of Biological Chemistry, 2011 286: 15483-15495. Research Area: Biomass Formation and Modification 10.1074/jbc.M110.215962
11/01/2011 Casler The Switchgrass Genome: Tools and Strategies

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The Plant Genome Casler, M.D., Tobias, C.M., Kaeppler, S.M., Buell, C.R., Wang, Z.Y., Cao, P., Schmutz, J., Ronald, Pa., The Switchgrass Genome: Tools and Strategies, The Plant Genome. 4(3): 273-282, 2011. Research Area: Biomass Formation and Modification 10.3835/plantgenome2011.10.0026
10/01/2013 Cha Isolation and bioinformatic analysis of a novel transposable element, ISCbe4, from the hyperthermophilic bacterium, caldicellulosiruptor bescii

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Microbiology and Biotechnology Cha, M., Wang, H., Chung, D., Bennetzen, J.L., Westpheling, J., Isolation and bioinformatic analysis of a novel transposable element, ISCbe4, from the hyperthermophilic bacterium, caldicellulosiruptor bescii, Journal of Industrial Microbiology and Biotechnology, 40, (12) p. 1443-8, 2013. Research Area: Biomass Deconstruction and Conversion
06/01/2013 Cha Metabolic engineering of Caldicellulosiruptor bescii yields increased hydrogen production from lignocellulosic biomass

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Biotechnology for Biofuels Cha, M., Chung, D., Elkins, J.G., Guss, A.M., Westpheling, J., Metabolic engineering of Caldicellulosiruptor bescii yields increased hydrogen production from lignocellulosic biomass, Biotechnology for Biofuels, 6:85, 2013. Research Area: Biomass Deconstruction and Conversion 10.1186/1754-6834-6-85
01/29/2014 Chen Experimental and modeling studies of an unusual water-filled pore structure with possible mechanistic implications in family 48 cellulases The Journals of Physical Chemistry B Chen, M., Kostylev, M., Bomble, Y.J., Crowley, M.F., Himmel, M.E., Wilson, D.B., Brady, J.W., Experimental and modeling studies of an unusual water-filled pore structure with possible mechanistic implications in family 48 cellulases, The Journal of Physical Chemistry B, 2014 Research Area: Biomass Deconstruction and Conversion 0.1021/jp408767j
12/08/2011 Chen Molecular dynamics simulations of the interaction of glucose with imidazole in aqueous solution

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Carbohydrate Research Chen, M., Y. J. Bomble,t al. (2012). "Molecular dynamics simulations of the interaction of glucose with imidazole in aqueous solution." Carbohydrate Research 349:73–77. Research Area: Biomass Deconstruction and Conversion 10.1016/j.carres.2011.12.008
01/17/2012 Chen A polymer of caffeyl alcohol in plant seeds

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PNAS Chen, F., Y. Tobimatsu, et al. (2012). "A polymer of caffeyl alcohol in plant seeds." Proceedings of the National Academy of Sciences 109 (5): 1772-1777. Research Area: Biomass Formation and Modification 10.1073/pnas.1120992109
08/01/2012 Chen Lignin-Degrading Enzyme Activities Methods in Molecular Biology Biomass Conversion: Methods and Protocols Chen, Y.R., Sarkanen, S., Wang, Y.Y., Lignin-Degrading Enzyme Activities, Methods in Molecular Biology Biomass Conversion: Methods and Protocols, 908:251-268, 2012. Research Area: Biomass Deconstruction and Conversion 10.1007/978-1-61779-956-3_21
09/07/2012 Chen Novel seed coat lignins in the Cactaceae: structure, distribution and implications for the evolution of lignin diversity

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The Plant Journal Chen, F., Tobimatsu, Y., Jackson, L., Ralph, J., Dixon, R.A., Novel seed coat lignins in the Cactaceae: structure, districution and implications for the evolution of lignin diversity, The Plant Journal, 2012. Research Area: Biomass Formation and Modification 10.1111/tpj.12012
03/01/2010 Chen Macromolecular replication during lignin biosynthesis

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Phytochemistry Chen, Y., Sarkanen, S., Macromolecular replication during lignin biosynthesis, Phytochemistry, Volume 71, Issue 4, March 2010, Pages 453-462 Research Area: Biomass Deconstruction and Conversion 10.1016/j.phytochem.2009.11.012
01/01/2011 Chen The family of terpene synthases in plants: a mid-size family of genes for specialized metabolism that is highly diversified throughout the kingdom

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The Plant Journal Chen, F., Tholl, D., Bohlmann, J., Pichersky, E., The family of terpene synthases in plants: a mid-size family of genes for specialized metabolism that is highly diversified throughout the kingdom, The Plant Journal, 66, 212-229, 2011. Research Area: Biomass Formation and Modification 10.1111/j.1365-313X.2011.04520.x
05/01/2010 Chen A High - Throughput Transient Gene Expression System for Switchgrass (Panicum virgatum L.) Seedlings

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Biotechnology for Biofuels A High - Throughput Transient Gene Expression System for Switchgrass (Panicum virgatum L.) Seedlings, Biotechnology for Biofuels, 7;3:9, 2010 Research Area: Biomass Formation and Modification 10.1186/1754-6834-3-9
01/01/2011 Chen Genome-wide discovery of missing genes in biological pathways of prokaryotes

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BMC Bioinformatics Chen, Y., Mao, F., Li, G., Xu, Y., Genome-wide discovery of missing genes in biological pathways of prokaryotes, BMC Bioinformatics, 12 (suppl 1):S1, 2011. Research Area: Characterization and Modeling 10.1186/1471-2105-12-S1-S1
09/01/2009 Chen Genomics of Secondary Metabolism in Populus: Interactions with Biotic and Abiotic Environments

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Critical Reviews in Plant Sciences Chen, F., Liu, C.J., Tschaplinski, T.J., Zhao, N.,Genomics of Secondary Metabolism in Populus: Interactions with Biotic and Abiotic Environments, Critical Reviews in Plant Sciences, 28:375-392, 2009. Research Area: Biomass Formation and Modification 10.1080/07352680903241279
09/05/2009 Cheng Populus community mega-genomics: coming of age

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Critical Reviews in Plant Sciences Zong-Ming Cheng and Gerald A. Tuskan. 2009 Populus community mega-genomics: coming of age. Critical Reviews in Plant Sciences. 28(5):282-284. Research Area: Biomass Formation and Modification 10.1080/07352680903240933
08/23/2010 Chou GolgiP: prediction of Golgi resident proteins in plants

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Bioinformatics Chou, W.C., Yin, Y., Xu, Y., GolgiP: prediction of Golgi resident proteins in plants, Bioinformatics, Volume 26, Issue 19, pages 2464-2465 Research Area: Characterization and Modeling 10.1093/bioinformatics/btq446
06/01/2009 Chou Recent developments in parameter estimation and structure identification of biochemical and genomic systems

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Mathematical Biosciences Chou, I. C., Voit, E. O., Recent Developments in parameter estimation and structure identification of biochemical and genomic systems, Mathematical Biosciences, Volume 219, Issue 2, pp 57-83, 2009 Research Area: Characterization and Modeling 10.1016/j.mbs.2009.03.002
08/09/2012 Chou Estimation of dynamic flux profiles from metabolic time series data

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BMC Systems Biology Chou, I.C., Voit, E.O., Estimation of dynamic flux profiles from metabolic time series data, BMC Systems Biology, 6:84, 2012. Research Area: Characterization and Modeling 10.1186/1752-0509-6-84
03/01/2014 Chou Analysis of strand-specific RNA-seq data using machine learning reveals the structures of transcription units in Clostridium thermocellum Nucleic Acids Research Chou, W.C., Ma, Q., Yang, S., Cao, Klingeman, D.M., Brown, S.D., Xu, Y., Analysis of strand-specific RNA-seq data using machine learning reveals the structures of transcription units in Clostridium thermocellum, Nucleic Acids Research, 2014 Research Area: Characterization and Modeling
02/04/2011 Chundawat Deconstruction of Lignocellulosic Biomass to Fuels and Chemicals

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The Annual Review of Chemical and Biomolecular Engineering Chundawat, Shishir P.S., Beckham, Gregg T., Himmel, Michael E., Dale, Bruce E., Deconstruction of Lignocellulosic Biomass to Fuels and Chemicals, The Annual Review of Chemical and Biomolecular Engineering, 2: 121-145, 2011. Research Area: Biomass Deconstruction and Conversion 10.1146/annurev-chembioeng-061010-114205
05/22/2011 Chung Identification and characterization of CbeI, a novel thermostable restriction enzyme from Caldicellulosiruptor bescii DSM 6725 and a member of a new subfamily of HaeIII-like enzymes

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Journal of Industrial Microbiology and Biotechnology Chung, D.H., Huddleston, J.R., Farkas, J., Westpheling, J., Identification and characterization of CbeI, a novel thermostable restriction enzyme from Caldicellulosiruptor bescii DSM 6725 and a member of a new subfamily of HaeIII-like enzymes, Journal of Industrial Microbiology and Biotechnology, 38(11): 1867-1877, 2011. Research Area: Biomass Deconstruction and Conversion 10.1007/s10295-011-0976-x
08/22/2012 Chung Methylation by a Unique alpha-class N4-Cytosine Methyltransferase Is Required for DNA Transformation of Caldicellulosiruptor bescii DSM6725

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PLoS One Chung, D., Farkas, J., Huddleston, J., Olivar, E., Westpheling, J., Methylation by a unique α-class N4-Cytosine Methyltransferase is Required for DNA Transformation of Caldicellulosiruptor bescii DSM6725, PLoS One, 7(8): e43844, 2012. Research Area: Biomass Deconstruction and Conversion 10.1371/journal.pone.0043844
06/01/2013 Chung Overcoming restriction as a barrier to DNA transformation in Caldicellulosiruptor species results in efficient marker replacement

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Biotechnology for Biofuels Chung, D., Farkas, J., Westpheling, J., Overcoming restriction as a barrier to DNA transformation in Caldicellulosiruptor species results in efficient marker replacement, Biotechnology for Biofuels, 6:82, 2013. Research Area: Biomass Deconstruction and Conversion 10.1186/1754-6834-6-82
04/03/2013 Chung Construction of a stable replicating shuttle vector for Caldicellulosiruptor species: use for extending genetic methodologies to other members of this genus

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PLoS One Chung, D., Cha, M., Farkas, J., Westpheling, J., Construction of a stable replicating shuttle vector for Caldicellulosiruptor species: use for extending genetic methodologies to other members of this genus, PLoS ONE, 8(5): e62881, 2013. Research Area: Biomass Deconstruction and Conversion 10.1371/journal.pone.0062881
11/01/2008 Cole Possible impacts of the US EPA Notice of Proposed Rulemaking on the biofuels industry

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Industrial Biotechnology Possible impacts of the US EPA Notice of Proposed Rulemaking on the biofuels industry, Industrial Biotechnology, Volume 4, No:4; pages 322-333, 2008. Research Area: Characterization and Modeling 10.1089/ind.2008.4.322
08/01/2012 Corea Laser Microdissection and Genetic Manipulation Technologies to Probe Lignin Heterogeneity and Configuration in Plant Cell Walls Methods in Molecular Biology Biomass Conversion: Methods and Protocols Corea, O.R.A., Ki, C., Cardenas, C.L., Davin, L.B., Lewis, N.G., Laser Microdissection and Genetic Manipulation Technologies to Probe Lignin Heterogeneity and Configuration in Plant Cell Walls, Methods in Molecular Biology Biomass Conversion: Methods and Protocols, 908:229-250, 2012. Research Area: Biomass Deconstruction and Conversion 10.1007/978-1-61779-956-3_20
05/20/2011 Correia The structure and function of an arabinoxylan-specific xylanase

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Journal of Biological Chemistry Correia, Marcia A., Mazumder, K., Bras, J.L., Firbank, S.J., Zhu, Y., Lewis, R.J., York, W.S., Fontes, C.M., Gilbert, H.J., The structure and function of an arabinoxylan-specific xylanase, Journal of Biological Chemistry, 286: 22510-22520, 2011. Research Area: Biomass Formation and Modification 10.1074/jbc.M110.217315 jbc.M110.217315
05/14/2012 Cui Enzymatic Digestibility of Corn Stover Fractions in Response to Fungal Pretreatment

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Industrial & Engineering Chemistry Research Cui, Z., Wan, C., Shi, J., Sykes, R.W., Li, Y., Enzymatic Digestibility of Corn Stover Fractions in Response to Fungal Pretreatment, Industrial and Engineering Chemistry Research, 51 (21), pp 7153–7159, 2012. Research Area: Biomass Deconstruction and Conversion 10.1021/ie300487z
02/01/2013 Currie Functional heterologous expression of an engineered full length CipA from Clostridium thermocellum in Thermoanaerobacterium saccharolytim

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Biotechnology for Biofuels Currie, D.H., Herring, C.D., Guss, A.M., Olson, D.G., Hogsett, D.A., Lynd, L.R., Functional heterologous expression of an engineered full length CipA from Clostridium thermocellum in Thermoanaerobacterium saccharolytim, Biotechnology for Biofuels, 6:32, 2013. Research Area: Biomass Deconstruction and Conversion 10.1186/1754-6834-6-32
10/29/2012 Czarnecki Evidence for a contribution of ALA synthesis to plastid-to-nucleus signaling

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Frontiers in Plant Science Czamecki, O., Glaber, C., Chen, J.G., Mayer, K.F.X., Grimm, Evidence for a contribution of ALA synthesis to plastid-to-nucleus signaling, Frontiers in Plant Science, 3:236, 2012. Research Area: Biomass Formation and Modification 10.3389/fpls.2012.00236
12/04/2010 Dagel In Situ Imaging of Single Carbohydrate-Binding Modules on Cellulose Microfibrils

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Journal of Physical Chemistry B Dagel, D. J., Liu, Y. S., Zhong, L. L., Luo, Y. H., Himmel, M. E., Xu, Q., Zeng, Y. N., Ding, S. Y., Smith, S., In Situ Imaging of Single Carbohydrate-Binding Modules on Cellulose Microfibrils, Journal of Physical Chemistry B, Volume 115, Issue 4, 635-641, 2011. Research Area: Characterization and Modeling 10.1021/jp109798p
08/01/2011 Dagel DOPI and PALM Imaging of Single Carbohydrate Binding Modules Bound to Cellulose Nanocrystals

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SPIE Proc. Proc Dagel, D.J., Liu, Y.S., Zong, L., Luo, Y., Zeng, Y., Himmel, M., Ding, S.Y., Smith, S., DOPI and PALM Imaging of Single Carbohydrate Binding Modules Bound to Cellulose Nanocrystals, SPIE 7905, 79050P, 2011. Research Area: Biomass Deconstruction and Conversion 10.1117/12.875285
01/20/2011 Dam Insights into plant biomass conversion from the genome of the anaerobic thermophilic bacterium Caldicellulosiruptor bescii DSM 6725

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Nucleic Acids Research Advance Dam, Phuongan, Kataeva, Irina, Yang, Sung-Jae, Zhou, Fengfeng, Yin, Chou, Wenchi, Poole II, Farris L., Westpheling, Janet , Hettich, Robert, Giannone, Richard Giannone, Lewis, Derrick L., Kelly, Robert, Gilbert, Harry J., Henrissat, Bernard, Xu, Ying, Adams, Michael W. W, Insights into plant biomass conversion from the genome of the anaerobic thermophilic bacterium Caldicellulosiruptor bescii DSM 6725, Nucleic Acids Research, 2011, 1-15. Research Area: Biomass Deconstruction and Conversion 10.1093/nar/gkq1281
04/01/2010 Darvill Plant Cell Walls Plant Cell Walls Albersheim, P., Darvill, A., Roberts, K., Sederoff, R., Staehelin, A., Plant Cell Walls,, Plant Cell Walls, 2010. Research Area: Biomass Formation and Modification ISBN: 978-0-8153-1996-2
07/01/2010 David Switchgrass as an energy crop for biofuel production: A review of its ligno-cellulosic chemical properties

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Energy and Environmental Science Kasi, David, Ragauskas, A.J., Switchgrass as an energy crop for biofuel production: A review of its ligno-cellulosic chemical properties, Energy and Environmental Science, Volume 3, Issue 9, pp 1182-1190, 2010. Research Area: Characterization and Modeling 10.1039/b926617h
12/01/2009 Davison The goals and research of the BioEnergy Sciences Center (BESC): Developing cost-effective and sustainable means of producing biofuels by overcoming biomass recalcitrance

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Bioenergy Research Davison, Brian H., Fowler, V. Suzy, The goals and research of the BioEnergy Sciences Center (BESC): Developing cost-effective and sustainable means of producing biofuels by overcoming biomass recalcitrance, Bioenergy Research, Volume 2, Number 4 / December, 2009. Research Area: Characterization and Modeling 10.1007/s12155-009-9057-7
09/01/2011 Davison Plant Cell Walls: Basics of Structure, Chemistry, Accessibility and the Influence on Conversion

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Aqueous Pretreatment of Plant Biomass for Biological and Davison, B.H., Parks, J., Davis, M.F., Donohoe, B.,Sannigrahi, P., Ragauskas, A.J., Fundamentals of biomass pretreatment by fractionation, Aqueous Pretreatment of Plant Biomass for Biological and Chemical Conversion to Fuels and Chemicals, (ed Wyman, C.E.), chapter 3, pp 23-36, 2013. Research Area: Characterization and Modeling
07/31/2012 Davison The Increasing Importance and Capabilities of Biomass Characterization

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Industrial Biotechnology Davison, Brian H., The Increasing Importance and Capabilities of Biomass Characterization, Industrial Biotechnology, 8:4, 2012. Research Area: Characterization and Modeling 10.1089/ind.2012.1527
11/06/2012 De Souza Composition and Structure of Sugarcane cell wall polysaccharides: implications for second-generation bioethanol production

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Bioenergy Research de Souza, A.P., Leite, D.C.C., Pattathil, S., Hahn, M.G., Buckeridge, M.S., Composition and structure of sugarcane cell wall polysaccharides: implications for second-generation bioethanol production, BioEnergy Research, Volume 6, Issue 2, pp 564-579, 2012. Research Area: Biomass Formation and Modification 10.1007/s12155-012-9268-1
08/01/2012 Decker Reducing the Effect of Variable Starch Levels in Biomass Recalcitrance Screening Methods in Molecular Biology Biomass Conversion: Methods and Protocols Decker, S.R., Carlile, M., Selig, M.J., Doeppke, C., Davis, M., Sykes, R., Turner, G., Ziebell, A., Reducing the Effect of Variable Starch Levels in Biomass Recalcitrance Screening, Methods in Molecular Biology Biomass Conversion: Methods and Protocols, 908;181-198, 2012. Research Area: Characterization and Modeling 10.1007/978-1-61779-956-3_17
12/01/2009 Decker High-Throughput Screening Techniques for Biomass Conversion

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Bioenergy Research Decker, Stephen R., Brunecky, Roman, Tucker, Melvin, P., Himmel, Michael E., Selig, Michael J., High-throughput screening techniques for biomass conversion, Bioenergy Research, Volume 2, Number 4 / December, 2009. Research Area: Biomass Deconstruction and Conversion 10.1007/s12155-009-9051-0
09/06/2011 DeMartini Application of monoclonal antibodies to investigate plant cell wall deconstruction for biofuels production

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Energy and Environmental Science DeMartini, J.D., Pattathil, S., Uvci, U., Szekalski, K., Mazumder, K., Hahn, M.G., Wyman, C.E., Application of monoclonal antibodies to investigate plant cell wall deconstruction for biofuels production, Energy and Environmental Science, 4, 4332-4339, 2011. Research Area: Characterization and Modeling 10.1039/C1EE02112E
10/01/2010 DeMartini Changes in composition and sugar release across the annual rings of Populus wood and implications on recalcitrance

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Bioresource Technology DeMartini, J. D., Wyman, C. E., Changes in composition and sugar release across the annual rings of Populus wood and implications on recalcitrance, Bioresource Technology, Volume 12, Issue 2, pp 1352-1358, 2011. Research Area: Characterization and Modeling 10.1016/j.biortech.2010.08.123
09/01/2010 DeMartini Small scale and automatable high-throughput compositional analysis of biomass

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Biotechnology and Bioengineering DeMartini, J. D., Studer, M. H., Wyman, C. E., Small-Scale and Automatable High-Throughput Compsitional Analysis of Biomass, Biotechnology and Bioengineering, Volume 108, Issue 2, pp 306-312, 2011. Research Area: Characterization and Modeling 10.1002/bit.22937
11/15/2011 DeMartini Composition and hydrothermal pretreatment and enzymatic saccharification performance of grasses and legumes from a mixed species prarie

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Biotechnology for Biofuels DeMartini, J.D., Wyman, C. E., Composition and hydrothermal pretreatment and enzymatic saccharification performance of grasses and legumes from a mixed species prairie, Biotechnology for Biofuels, 4:52, 2011 Research Area: Characterization and Modeling 10.1186/1754-6834-4-52
01/08/2013 DeMartini Investigating plant cell wall components that affect biomass recalcitrance in poplar and switchgrass

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Energy & Environmental Science DeMartini, J.D., Pattathil, S., Miller, J.S., Li, H., Hahn, M.G., Wyman, C.E., Investigating plant cell wall components that affect biomass recalcitrance in poplar and switchgrass, 6, 898-909,2012. Research Area: Characterization and Modeling 10.1039/C3EE23801F
05/01/2013 DeMartini High-throughput pretreatment and hydrolysis systems for screening biomass species in aqueous pretreatment of plant biomass

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Aqueous Pretreatment of Plant Biomass for Biological and Chemical Conversion to Fuels and Chemicals Demartini, J., Wyman, C.E., High-throughput pretreatment and hydrolysis systems for screening biomass species in aqueous pretreatment of plant biomass, Aqueous Pretreatment of Plant Biomass for Biological and Chemical Conversion to Fuels and Chemicals, (ed Wyman, C.E.), chapter 22, pp 471-486, 2013. Research Area: Characterization and Modeling 10.1002/9780470975831.ch22
12/01/2012 Deng Redirecting carbon flux through exogenous pyruvate kinase to achieve high ethanol yields in Clostridium thermocellum

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Metabolic Engineering Deng, Y., Olson, D.G., Zhou, J., Herring, C.D., Shaw, A., Lynd, L.R., Redirecting carbon Flux through exogenous pyruvate kinase to achive high ethanol yields in Clostridium thermocellum, Metabolic Engineering, 15:151-8, 2012. Research Area: Biomass Deconstruction and Conversion
05/01/2011 Deshpande Plant Genetics for Study of the Roles of Root Exudates and Microbes in the Soil

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Root Genomics Deshpande, A., Pontaroli, A.C., Chaluvadi, S.R., Lu, F., Bennetzen, J.L., Plant Genetics for Study of the Roles of Root Exudates and Microbes in the Soil, Root Genomics, Chapter 4, p. 99-111, 2011. Research Area: Biomass Formation and Modification 10.1007/978-3-540-85546-0_4
01/01/2009 Desikan Nanomechanical Methods to Study Single Cells

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Accessing Uncultivated Microorganisms Desikan, Ramya, Laurene Tetard, Ali Passian, Ram Datar, and Thomas Thundat , Nanomechanical Methods to Study Single Cells, Accessing Uncultivated Microorganisms, book ed. By Karsten Zengler, ASM Press, 2009. Research Area: Characterization and Modeling ISBM 1555814069
05/01/2011 DiFazio Populus: A premier pioneer system for plant genomics

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Genetics, Genomics and Breeding of Crop Plants DiFazio S.P., G.T. Slavov, and C.S. Joshi, Populus: A premier pioneer system for plant genomics, In Joshi, C.P., and S.P. DiFazio (eds). Poplar. Science Publishers, Enfield, New Hampshire, chapter 1, pp 1-28, 2011. Research Area: Biomass Formation and Modification 10.1201/b10819-2
09/30/2010 DiFazio The Populus Genome Project

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Principles and Practices of Plant Genomics Volume 3 In Kole, C., and A. Albert (eds). Vol. 3: Advanced Genomics. Science Publishers, Enfield, New Hampshire (accepted) Research Area: Biomass Formation and Modification ISBN: 978-1-57808-683-2
06/01/2008 Ding A Biophysical Perspective of the Cellulosome: New Opportunities for Biomass Conversion

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Current Opinion in Biotechnology Ding, Shi-You, Qi Xu, Michael Crowley, Yining Zeng, Mark Nimlos, Raphael Lamed, Edward A. Bayer, and Michael E. Himmel , A Biophysical Perspective of the Cellulosome: New Opportunities for Biomass Conversion , Current Opinion Biotechnology, 19(3), 218-227, 2008 Research Area: Characterization and Modeling 10.1016/j.copbio.2008.04.008; 2008
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11/18/2013 Ding Overview of Lignocellulose: Structure and Chemistry

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Biological Concerstion of Biomass for Fuels and Chemicals: Exploration from Natural Utilization Systems Ding, S.Y., Overview of Lignocellulose: Structure and Chemistry, Biological Concerstion of Biomass for Fuels and Chemicals: Exploration from Natural Utilization Systems, 10 (2), 14-25, 2013. Research Area: Biomass Deconstruction and Conversion
01/01/2008 Ding Identify Molecular Structural Features of Biomass Recalcitrance Using Nondestructive Microscopy and Spectroscopy

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Microcopy and Microanalysis Ding, S.Y., Himmel, M., Xie, X.S., Identify Molecular Structural Features of Biomass Recalcitrance Using Nondestructive Microscopy and Spectroscopy, Microcopy and Microanalysis, 14:1494-1495, 2008. Research Area: Characterization and Modeling 10.1017/S1431927608088582
08/01/2012 Ding Imaging Cellulose Using Atomic Force Microscopy Methods in Molecular Biology Biomass Conversion: Methods and Protocols Ding, S.Y., Liu, Y.S., Imaging Cellulose Using Atomic Force Microscopy, Methods in Molecular Biology Biomass Conversion: Methods and Protocols, 908:23-30, 2012. Research Area: Biomass Deconstruction and Conversion 10.1007/978-1-61779-956-3_3
11/23/2012 Ding How Does Plant Cell Wall Nanoscale Architecture Correlate With Enzymatic Digestibility?

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Science Ding, S.Y., Liu, Y.S., Zeng, Y., Himmel, M.E., Baker, J.O., Bayer, E.A., How Does Plant Cell Wall Nanoscale Architecture Correlate With Enzymatic Digestibility?, Science, 338 (6110), 1055-1060, 2012. Research Area: Biomass Deconstruction and Conversion 10.1126/science.1227491
12/01/2009 Dixon DOE Bioenergy Center Special Issue. The Bioenergy Sciences Center (BESC)

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BioEnergy Research Dixon, Richard, DOE BioEnergy Center Special Issue, The BioEnergy Sciences Center (BESC), Bioenergy Research, Volume 2, Number 4 / December, 2009 Research Area: Biomass Formation and Modification 10.1007/s12155-009-9059-5
06/01/2009 Drost A Microarray-Based Genotyping and Genetic Mapping Approach for Highly Heterozygous Outcrossing Species Localizes a Large Fraction of the Unassembled Populus trichocarpa Genome Sequence

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Plant Journal Drost, D., Novaes, E., Boaventura-Novaes, C., Benedict, C., Brown, R., Yin, T., Tuskan, G., A Microarray-Based Genotyping and Genetic Mapping Approach for Highly Heterozygous Outcrossing Species Localizes a large fraction of the unassembles populus trichocarpa, genome sequence, Plant Journal, March 2009; 58, 1054-1067. Research Area: Biomass Formation and Modification 10.111/j.1365-313X.2009.038258.x
05/09/2012 Duceppe Assessment of Genetic Variability of Cell Wall Degradability for the Selection of Alfalfa with Improved Saccharification Efficiency

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BioEnergy Research Duceppe, M.O., Bertrand, A., Pattathil, S., Miller, J., Castonguay, Y., Hahn, M.G., Michaud, R., Dube, M.P., Assessment of Genetic Variability of Cell Wall Degradability for the Selection of Alfalfa with Improved Saccharification Efficiency, BioEnergy Research, 2012 Research Area: Biomass Formation and Modification 10.1007/s12155-012-9204-4
11/29/2013 Dumitrache Tracking the cellulolytic activity of clositridium thermocellum biofilms Biotechnology for Biofuels Dumitrache, A., Wolfaardt, G.M., Allen, D.G., Liss, S.N., Lynd, L.R., Tracking the cellulolytic activity of clostridium thermocellum biofilms, Biotechnology for Biofuels, 2013 Research Area: Biomass Deconstruction and Conversion 10.1186/1754-6834-6-175
Dykstra Development of a multi-point quantitation method of simultaneously measure enzymatic and structural components of the Clostridium thermocellum Cellulosome protein complex Journal of Proteome Research Dykstra, A., St. Brice, L., Rodriguez Jr., M., Raman, B., Izquierdo, J., Cook, K.D., Lynd, L.R., Hettich, R.L., Development of a multi-point quantitation method to simultaneously measure enzymatic and structural components of the Clostridium thermocellum Cellulosome protein complex, Journal of Proteome Research, 2013 Research Area: Biomass Deconstruction and Conversion
03/01/2014 Edwards Replacing a suite of commercial pectinases with a single enzyme, pectate lyase B, in Saccharomyces cerevisiae fermentations of cull peaches

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Journal of Microbiology and Biotechnology Edwards, M.C., Williams, T., Pattathil, S., Hahn, M.G., Peterson-Doran, J., Replacing a suite of commercial pectinases with a single enzyme, pectate lyase B, in Saccharomyces cerevisiae fermentations of cull peaches, Journal of Microbiology and Biotechnology, 41:679-686, 2014. Research Area: Characterization and Modeling 10.1007/s10295-013-1394-z
04/11/2013 Elkins Complete genome sequence of the hyperthermophilic sulfate-reducing bacterium thermodesulfobacterium geofontis OPF15

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Genome Announcements Elkins, J.G., Hamilton-Brehm, S.D., Lucas, S., Han, J., Lapidus, A., Cheng, J.F., Goodwin, L.A., Pitluck, S., Peters, L., Mikhailova, N., Davenport, K.W., Detter, J.C., Han, C.S., Tapia, R., Land, M.L., Hauser, L., Kyrpides, N.C., Ivanova, N.N., Pagani, I., Bruce, D., Woyke, T., Cottingham, R.W., Complete genome sequence of the hyperthermophilic sulfate-reducing bacterium thermodesulfobacterium geofontis OPF15, Genome Announcements, 1(2); e00162-13, 2013. Research Area: Characterization and Modeling 10.1128/genomeA.00162-13
10/01/2010 Elkins Complete Genome Sequence of the Cellulolytic Thermophile Caldicellulosiruptor obsidiansis OB47T

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Journal of Bacteriology Elkins, J.G., Lochner, A., Hamilton-Brehm, S.D., Davenport, K.W., Podar, M., Brown, S.D., Land, M.L., Hauser, L.J., Klingeman, D.M., Raman, B., Goodwin, L.A., Tapia, R., Meincke, L.J., Detter, J.C., Bruce, D.C., Han, C.S., Palumbo, A.V., Cottingham, R.W., Keller, M., Graham, D.E., Complete Genome Sequence of the Cellulolytic Thermophile Caldicellulosiruptor obsidiansis OB47, Journal of Bacteriology, 192:22, pp 6099-6100, 2010. Research Area: Biomass Deconstruction and Conversion 10.1128/JB.00950-10
06/01/2010 Elkins Engineered microbial systems for enhanced conversion of lignocellulosic biomass

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Current Opinion in Biotechnology Elkins, J. G., Raman, B., Keller, M., Engineered microbial systems for enhanced conversion of lignocellulosic biomass, Current Opinion in Biotechnology, Volume 21, Issue 5, pp 657-662, 2010. Research Area: Biomass Deconstruction and Conversion 10.1016/j.copbio.2010.05.008
10/01/2011 Ellis Closing the Carbon Balance for Fermentation by Clostridium thermocellum (ATCC 27405)

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Bioresource Technology Ellis, L.D., Holwerda, E.K., Hogsett, D., Rogers, S., Shao, X., Tschaplinski, T., Thorne, P., Lynd, L.R., Closing the Carbon Balance for Fermentation by Clostridium thermocellum (ATCC 27405), Bioresource Technology, 103(1):293-299, 2011 Research Area: Biomass Deconstruction and Conversion 10.1016/j.biortech.2011.09.128
Escamilla-Trevino Early lignin pathway enzymes and routes to chlorogenic acid in switchgrass (Panicum virgatum L.)

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Plant Molecular Biology Escamilla-Trevino, L.L., Shen, H., Hernandez, T., Yin, Y., Xu, Y., Dixon, R.A., Early lignin pathway enzymes and routes to chlorogenic acid in switchgrass (Panicum virgatum L.), Plant Molecular Biology, 2013 Research Area: Biomass Formation and Modification
10/14/2011 Escamilla-Treviño Potential of Plants from the Genus Agave as Bioenergy Crops

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BioEnergy Research Escamilla-Trevino, L.. (2011) "Potential of Plants from the Genus Agave as Bioenergy Crops." Bioenergy Research. (published online doi:10.1007/s12155-011-9159-x) Research Area: Biomass Formation and Modification 10.1007/s12155-011-9159-x
01/01/2010 Escamilla-Treviño Switchgrass (Panicum virgatum L.) possesses a divergent family of cinnamoyl CoA reductases with distinct biochemical properties

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New Phytologist Escamilla-Treviño Luis L., Hui Shen, Srinivasa Rao Uppalapati, Tui Ray, Yuhong Tang, Timothy Hernandez, Yanbin Yin, Ying Xu, and Richard A. Dixon, Switchgrass (Panicum virgatum L.) possesses a divergent family of cinnamoyl CoA reductases with distinct biochemical properties, New Phytologist, Volume 185 Issue 1, Pages 143 - 155, 2009. Research Area: Biomass Formation and Modification 10.1111/j.1469-8137.2009.03018
07/22/2011 Farkas Defining Components of the Chromosomal Origin of Replication of the Hyperthermophilic Archaeon, Pyrococcus furiosus, needed for construction of a stable replicating shuttle vector

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Applied Environmental Microbiology Farkas, J., Chung D., DeBarry, M., Adams, Michael W.W., Westpheling, J., Defining Components of the Chromosomal Origin of Replication of the Hyperthermophilic Archaeon, Pyrococcus furiosus, needed for construction of a stable replicating shuttle vector, Applied Environmental Microbiology, 77;18, pp 6343-6349, July 2011. Research Area: Biomass Deconstruction and Conversion 10.1128/AEM.05057-11
04/01/2012 Farkas The Recombinogenic Properties of the Pyrococcus furiosus COM1 Strain Enable Rapid Selection of Targeted Mutants

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Applied Environmental Microbiology Farkas, J., Stirrett, K., Lipscomb, G.L., Nixon, W., Scott, R.A., Adams, M.W.W., Westpheling, J., The Recombinogenic Properties of the Pyrococcus furiosus COM1 Strain Enable Rapid Selection of Targeted Mutants, Applied Environmental Microbiology, 2012. Research Area: Biomass Deconstruction and Conversion 10.1128/AEM.00936-12
09/19/2012 Farkas Improved growth media and culture techniques for genetic analysis and assessment of biomass utilization by Caldicellulosiruptor bescii

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Journal of Industrial Microbiology and Biotechnology Farkas, J., Chung, D., Cha, M., Copeland, J., Grayeski, P., Westpheling, J., Improved growth media and culture techniques for genetic analysis and assessment of biomass utilization by Caldicellulosiruptor bescii, Journal of Industrial Microbiology and Biotechnology, 40(1):41-9., 2012. Research Area: Biomass Deconstruction and Conversion 10.1007/s10295-012-1202-1
12/12/2013 Fineran Draft genome sequence of Serratia sp. Strain ATCC 39006, a model bacterium for analysis of the biosynthesis and regulation of prodigiosin, a carbapenem, and gas vesicles

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Genome Announcements Fineran, P.C., Cans Igleslas, M.C., Ramsay, J.P., Wilf, N.M., Cossyleon, D., McNeil, M.B., Williamson, N.R., Monson, R.E., Becher, S.A., Stanton, J.L., Brugger, K., Brown, S.D., Salmond, G.P.C., Draft genome sequence of Serratia sp. Strain ATCC 39006, a model bacterium for analysis of the biosynthesis and regulation of prodigiosin, a carbapenem, and gas vesicles, 2013 Research Area: Characterization and Modeling 10.1128/genomeA.01039-13.
04/24/2013 Flowers SMET: Systematic multiple enzyme targeting - a method to rationally design optimal strains for target chemical overproduction Biotechnology Journal Flowers, D., Thompson R.A., Bridwell, D., Wang, T., Trihn, C.T., SMET: Systematic multiple enzyme targeting - a method to rationally design optimal strains for target chemical overproduction, Biotechnology Journal, 8(5):605-18, .2013 Research Area: Characterization and Modeling
09/14/2012 Foston NMR a critical tool to study the production of carbon fiber from carbon

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Carbon NMR a critical tool to study the production of carbon fiber from lignin, Carbon, 52 p 65-73, 2012. Research Area: Characterization and Modeling 10.1016/j.carbon.2012.09.006
05/29/2012 Foston C cell wall enrichment and ionic liquid NMR analysis: progress towards a high-throughput detailed chemical analysis of the whole plant cell wall

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Analyst Foston, M., Samuel, S., Ragauskas, A.J., C cell wall enrichment and ionic liquid NMR analysis: progress towards a high-throughput detailed chemical analysis of the whole plant cell wall, Analyst, 2012. Research Area: Characterization and Modeling 10.1039/c2an35344j
08/16/2012 Foston Biomass Characterization: Recent Progress in Understanding Biomass Recalcitrance

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Industrial Biotechnology Foston, M., Ragauskas, A.J., Biomass Characterization: Recent Progress in Understanding Biomass Recalcitrance, 8(4); 191-208, 2012. Research Area: Characterization and Modeling 10.1089/ind.2012.0015
10/20/2011 Foston Chemical, ultrastructural and supermolecular analysis of tension wood in Populus tremula x alba as a model substrate for reduced recalcitrance

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Energy and Environmental Science Foston, M., Hubbell, C.A., Samuel, R., Jung, S., Fan, H., Ding, S.Y., Zeng, Y., Jawdy, S., Davis, M., Sykes, R., Gjersing, E., Tuskan, G.A., Kalluri, U., Ragauskas, A.J., Chemical, ultrastructural and supra molecular analysis of tension wood in Populus tremula x alba as a model substrate for reduced recalcitrance, Energy and Environmental Science, 4: 4962-4971, 2011 Research Area: Characterization and Modeling 10.1039/c1ee02073k
12/01/2009 Foston Variations in Cellulosic Ultrastructure of Poplar BER-123R1

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BioEnergy Research Foston, M., Hubbell, C. A., Davis, M., Ragauskas, A. J., Variations in Cellulosic Ultrastructure of Poplar, Bioenergy Research, Volume 2, Number 4, pp 193-197, December,2;4, pp 193-197, 2009. Research Area: Characterization and Modeling 10.1007/s12155-009-9050-1
02/01/2012 Foston Solid-State Selective 13C Excitation and Spin Diffusion NMR To Resolve Spatial Dimensions in Plant Cell Walls

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Journal of Agricultural and Food Chemistry Foston, M., R. Katahira, et al. (2012). "Solid-State Selective 13C Excitation and Spin Diffusion NMR To Resolve Spatial Dimensions in Plant Cell Walls." Journal of Agricultural and Food Chemistry 60 (6):1419–1427. Research Area: Characterization and Modeling 10.1021/jf204853b
07/01/2010 Foston Changes In Lignocellulosic Supramolecular And Ultrastructure During Dilute Acid Pretreatment Of Populus And Switchgrass

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Biomass and Bioenergy Foston, M., Ragauskas, A. J., Changes in lignocellulosic supramolecular and ultrastructure during dilute acid pretreatment of Populus and switchgrass, Biomass and Bioenergy, Volume 34, Issue 12, pp 1885-1895, 2010. Research Area: Characterization and Modeling 10.1016/j.biombioe.2010.07.023
09/30/2010 Foston Changes in the Structure of the Cellulose Fiber Wall during Dilute Acid Pretreatment in Populus Studied by 1H and 2H NMR

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Energy and Fuels Foston, Marcus, Ragauskas, Arthur J., Changes in the Structure of the Cellulose Fiber Wall during Dilute Acid Pretreatment in Populus studies by 1H and 2H NMR, Energy Fuels, 2010, 24, 5677-5685. Research Area: Characterization and Modeling 10.1021/ef100882t
02/01/2013 Fried Self-assembly and application of cellulosomal components Bionanotechnology: Biological Self-assembly and its Applications Fried, D.B., Morais, S., Xu, Q., Ding, S.Y., Baker, J.O., Bomble, Y.J., Himmel, M.E., Bayer, E.A., Self-assembly and application of cellulosomal components, Bionanotechnology: Biological Self-assembly and its Applications, Chapter 2, 2013. Research Area: Biomass Deconstruction and Conversion
07/25/2012 Frock Extreme thermophiles: moving beyond single-enzyme biocatalysis

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Current Opinion in Chemical Engineering Frock, A.D., Kelly, R.M., Extreme thermophiles: moving beyond single-enzyme biocatalysis, Current Opinion in Chemical Engineering, 1;4, pp 363-372, 2012. Research Area: Biomass Deconstruction and Conversion 10.1016/j.coche.2012.07.003
01/12/2012 Fu Overexpression of miR156 in switchgrass (Panicum virgatum L.) results in various morphological alterations and leads to improved biomass production

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Plant Biotechnology Journal Fu, C., R. Sunkar, et al. (2012). "Overexpression of miR156 in switchgrass (Panicum virgatum L.) results in various morphological alterations and leads to improved biomass production." Plant Biotechnology Journal, 10(4), 2012. Research Area: Biomass Formation and Modification 10.1111/j.1467-7652.2011.00677.x
01/07/2011 Fu Downregulation of Cinnamyl Alcohol Dehydrogenase (CAD) Leads to Improved Saccharification Efficiency in Switchgrass

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BioEnergy Research Chunxiang Fu, Xirong Xiao, Yajun Xi, Yaxin Ge, Fang Chen, Joseph Bouton, Richard A. Dixon and Zeng-Yu Wang Downregulation of Cinnamyl Alcohol Dehydrogenase (CAD) Leads to Improved Saccharification Efficiency in Switchgrass, Bioenergy Research, 4;3, pp 153-164, 2011. Research Area: Biomass Formation and Modification 10.1007/s12155-010-9109-z
03/01/2011 Fu Genetic manipulation of lignin reduces recalcitrance and improves ethanol production from switchgrass

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PNAS Fu, Chunxiang, Mielenz, Jonathan R., Xiao, Xirong, Ge, Yaxin, Hamilton, Choo Y., Rodriguez, Jr., Miguel, Chen, Fang, Foston, Marcus, Ragauskas, Arthur, Bouton, Joseph, Dixon, Richard A., Wang, Zeng-Yu, Genetic manipulation of lignin reduces recalcitrance and improves ethanol production from switchgrass, PNAS, 108(9): 3803-3808, 2011. Research Area: Biomass Deconstruction and Conversion 10.1073/pnas.1100310108
09/11/2011 Gallego-Giraldo Salicylic acid mediates the reduced growth of lignin down-regulated plants

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PNAS Gallego-Giraldo, L., Escamilla-Trevino, L., Jackson, L.A., Dixon, R.A. "Salicylic acid mediates the reduced growth of lignin down-regulated plant." PNAS. (Published online before print November 28, 2011, doi: 10.1073/pnas.1117873108) Research Area: Biomass Formation and Modification 10.1073/pnas.1117873108
11/01/2012 Gao Application of High Throughput Pretreatment and Co-Hydrolysis System to Thermochemical Pretreatment - Part 1: Dilute Acid

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Biotechnology and Bioengineering Gao, X., Kumar, R., DeMartini, J.D., Li, H., Wyman, C.E., Application of High Throughput Pretreatment and Co-Hydrolysis System to Thermochemical Pretreatment - Part 1: Dilute Acid, Biotechnology and Bioengineering, 110(3):754-62, 2012. Research Area: Characterization and Modeling 10.1002/bit.24751
12/17/2013 Gao Fast hemicellulose quantification via a simple one-step acid hydrolysis Biotechnology and Bioengineering Gao, X., Kumar, R., Wyman, C.E., Fast hemicellulose quantification via a simple one-step acid hydrolysis, Biotechnology and Bioengineering, 2013 Research Area: Characterization and Modeling 10.1002/bit.25174
Gao Comparison of enzymatic reactivity of corn stover solids prepared by dilute acid, AFEXtm, and ionic liquid pretreatments Biotechnology for Biofuels Gao, X., Kumar, R., Singh, S., Simmons, B.A., Balan, V., Dale, B.E., Wyman, C.E., Comparison of Enzymatic reactivity of corn stover solids prepared by dilute acid, AFEXtm, and ionic liquid pretreatments, Biotechnology for Biofuels, 2014 Research Area: Characterization and Modeling
08/11/2011 Ge Pollen Viability and Longevity of Switchgrass (Panicum virgatum L.)

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Crop Science Ge, Y., Fu, C., Bhandari, H., Bouton, J., Brummer, E.C., Wang, Z.Y., Pollen Viability and Longevity of Switchgrass (Panicum virgatum L.), Crop Science, volume 51, 2011. Research Area: Biomass Formation and Modification 10.2135/cropsci2011.01.0057
09/04/2013 GhattyVenkataKrishna Dynamics of water in the amphiphilic pore of amyloid beta fibrils

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Chemical Physics Letters GhattyVenkataKrishna, P.K., Mostofian, B., Dynamics of water in the amphiphilic pore of amyloid b fibrils, Chemical Physics Letters, 582, 1-5, 2013. Research Area: Characterization and Modeling 10.1016/j.cplett.2013.07.026
07/08/2013 GhattyVenkataKrishna Effect of the amyloid B hairpin's structure on the handedness of helices formed by its aggregates

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FEBS Letters GhattyVankataKrishna, P., Uberbacher, E.C., Cheng, X., Effect of the amyloid B hairpin's structure on the handedness of helices formed by its aggregates, FEBS Letters, 587(16), 2649-2655, 2013. Research Area: Characterization and Modeling 10.1016/j.febslet.2013.06.050
02/01/2013 GhattyVenkataKrishna Initial Recognition of a Cellodextrin Chain in the Cellulose-Binding Tunnel may affect cellobiohydrolase directional specificity

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Biophysical Journal GhattyVenkataKrishna, P.K., Alekozai, E.M., Beckham, G.T., Schulz, R., Crowley, M.F., Uberbacher, E.C., Cheng, X., Initial recognition of a cellodextrin chain in the cellulose-binding tunnel may affect cellobiohydrolase directional specificity, Biophysical Journal, 104, 904-912, 2013. Research Area: Characterization and Modeling 10.1016/j.bpj.2012.12.052
08/12/2011 Ghimire Enhancement of Switchgrass (Panicum virgatum L.) Biomass Production under Drought Conditions by the Ectomycorrihizal Fungus Sebacina vermifera

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Applied and Environmental Microbiology Ghimire, S.R., Craven, K.D.,The Ectomycorrhizal Fungus Sebacina vermifera, Enhances Biomass Production of Switchgrass (Panicum virgatum L.) Under Drought Conditions, Applied Microbiology and Biotechnology, 77(19):7063-7067, 2011 Research Area: Biomass Formation and Modification 10.1128/AEM.05225-11
06/01/2009 Ghimire The mycorrhizal fungus, Sebacina vermifera, enhances seed germination and biomass production in switchgrass (Panicum virgatum L)

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BioEnergy Research Ghimire, S. R, Charlton, N., and Craven, K. D. (2009). The mycorrhizal fungus, Sebacina vermifera, enhances seed germination and biomass production in switchgrass (Panicum virgatum L). Bioenergy Research 2: 51‐58, Volume 2, Numbers 1-2 / June, 2009 Research Area: Biomass Formation and Modification 10.1007/s12155-009-9033-2
11/01/2010 Ghimire Biodiversity of fungal endophyte communities inhabiting switchgrass (Panicum virgatum L.) growing in the native tallgrass prairie of northern Oklahoma

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Fungal Diversity Ghimire, S.R., Charlton, N.D., Bell, J.D., Krishnamurthy, Y.L. Craven, K.D., Biodiversity of fungal endophyte communities inhabiting switchgrass (Panicum virgatum L.) growing in the native tallgrass prairie of northern Oklahoma, Fungal Diversity, 47;1, pp 19-27, 2010. Research Area: Biomass Formation and Modification 10.1007/s13225-010-0085-6
08/01/2012 Gilbert Bioprospecting Metagenomics for New Glycoside Hydrolases Methods in Molecular Biology Biomass Conversion: Methods and Protocols Gilbert, J., Li, Luen-Luen, Taghavi, S., McCorkle, S.M., Tringe, S., van der Lelie, D., Bioprospecting Metagenomics for New Glycoside Hydrolases, Methods in Molecular Biology Biomass Conversion: Methods and Protocols, 908;141-151, 2012. Research Area: Biomass Deconstruction and Conversion 10.1007/978-1-61779-956-3_14
10/18/2012 Gjersing Rapid determination of sugar content in biomass hydrolysates using nuclear magentic resonance spectroscopy

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Biotechnology and Bioengineering Gjersing, E., Happs, R.M., Sykes, R.W., Doeppke, C., Davis, M.F., Rapid determination of sugar content in biomass hydrolysates using nuclear magnetic resonance spectroscopy, Biotechnology and Bioengineering, 110(3); 721-8, 2012. Research Area: Characterization and Modeling 10.1002/bit.24741
08/01/2008 Goel System estimation from metabolic time-series data sys

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Bioinformatics Goel, Gautam, I-Chun Chou and Eberhard O. Voit , System estimation from metabolic time-series data sys, Bioinformatics, 24(21), 2505-2511, 2008. Research Area: Characterization and Modeling 10.1093/bioinformatics/ btn470
06/07/2010 Gu Biosynthesis of a new UDP-sugar, UDP-2-Acetamido-2-deoxy-xylose, in the human pathogen Bacillus cereus subsp. cytotoxis NVH 391-98.

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Journal of Biological Chemistry Gu X, Glushka J, Lee SG, Bar-Peled M. (2010) Biosynthesis of a new UDP-sugar, UDP-2-acetamido-2-deoxyxylose, in the human pathogen Bacillus cereus subspecies cytotoxis NVH 391-98. J Biol Chem. 285(32):24825-33. Research Area: Biomass Formation and Modification 10.1074/jbc.M110.125872
09/16/2010 Gu Biosynthesis of UDP-xylose and UDP-arabinose in Sinorhizobium meliloti 1021: first characterization of a bacterial UDP-xylose synthase, and UDP-xylose-4-epimerase

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Microbiology Gu, X. G., Lee, S. G., Bar-Peled, M., Biosynthesis of UDP-xylose and UDP-arabinose in Sinorhizobium meliloti 1021: first characterization of a bacterial UDP-xylose synthase, and UDP-xylose 4-epimerase, Microbiology, Volume 157, pp 260-269, 2011. Research Area: Biomass Formation and Modification 10.1099/mic.0.040758-0
03/19/2010 Gu Identification of a bifunctional UDP-4-keto-pentose/UDP-xylose synthase in the plant pathogenic bacterium Ralstonia solanacearum strain GMI1000, a distinct member of the 4,6-dehydratase and decarboxylase family

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Journal of Biological Chemistry Gu X, Glushka J, Yin Y, Xu Y, Denny T, Smith J, Jiang Y, Bar-Peled M.(2010) Identification of a bifunctional UDP-4-keto-pentose/UDP-xylose synthase in the plant pathogenic bacterium Ralstonia solanacearum strain GMI1000, a distinct member of the 4,6-dehydratase and decarboxylase family. J Biol Chem. 2010 285(12):9030-40. Research Area: Biomass Formation and Modification 10.1074/jbc.M109.066803
06/15/2009 Gu Enzymatic characterization and comparison of various Poaceae UDP-GlcA 4-Epimerase Isoforms

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Journal of Biochemistry Gu X, Wages CJ, Davis KE, Guyett PJ, Bar-Peled M. (2009) Enzymatic characterization and comparison of various poaceae UDP-GlcA 4-epimerase isoforms. J Biochem. 146(4):527-34. Research Area: Biomass Formation and Modification 10.1093/jb/mvp099
05/06/2012 Guss Dcm methylation is detrimental to plasmid transformation in Clostridium thermocellum

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Biotechnology for Biofuels Guss, A.M., Olson, D.G., Caiazza, N.C., Lynd, L.R., Dcm methylation is detrimental to plasmid transformation in Clostridium thermocellum, Biotechnology for Biofuels, 5:30, 2012. Research Area: Biomass Deconstruction and Conversion 10.1186/1754-6834-5-30
03/27/2009 Guyett Real-time NMR monitoring of intermediates and labile products of the bifunctional enzyme UDP-apiose/UDP-xylose synthase

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Carbohydrate Research Guyett P, Glushka J, Gu X, Bar-Peled M. (2009) Real-time NMR monitoring of intermediates and labile products of the bifunctional enzyme UDP-apiose/UDP-xylose synthase. Carbohydr Res. 344(9):1072-8. Research Area: Biomass Formation and Modification PMID: 19375693
12/18/2009 Hamilton-Brehm Caldicellulosiruptor obsidiansis sp. nov., an anaerobic, extremely thermophilic, cellulolytic bacterium isolated from Obsidian Pool, Yellowstone National Park

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Applied and Environmental Microbiology Hamilton-Brehm, S.D., Mosher, J.J., Vishnivetskaya, T., Podar, M., Carroll, S., Allman, S., Phelps, T.J., Keller, M., Elkins, J.G., Caldicellulosiruptor obsidiansis sp. nov., an anaerobic, extremely thermophilic, cellulolytic bacterium isolated from Obsidian Pool, Applied and Environmental Microbiology, 76:1014-1020. 2010. Research Area: Biomass Deconstruction and Conversion 10.1128/AEM.01903-09
08/01/2012 Hamilton-Brehm Anaerobic High-Throughput Cultivation Method for Isolation of Thermophiles Using Biomass-Derived Substrates Methods in Molecular Biology Biomass Conversion: Methods and Protocols Hamilton-Brehm, S.D., Vishnivetskaya, T.A., Allman, S.L., Mielenz, J.R., Elkins, J.G., Anaerobic High-Throughput Cultivation Method for Isolation of Thermophiles Using Biomass-Derived Substrates, Methods in Molecular Biology Biomass Conversion: Methods and Protocols, 908;153-168, 2012. Research Area: Biomass Deconstruction and Conversion 10.1007/978-1-61779-956-3_15
01/04/2013 Hamilton-Brehm Thermodesulfobacterium geofontis sp. Nov., a hyperthermophilic, sulfate-reducing bacterium isolated from Obsidian Pool, Yellowstone National Park

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Extremophiles Hamilton-Brehm, S.D., Gibson, R.A., Green, S.J., Hopmans, E.C., Schouten, S., van der Meer, M.T.J., Shields, J.P., Damste, J.S.S., Elkins, J.G., Thermodesulfobacterium geofontis sp. Nov., a hyperthermophilic, sulfate-reducing bacterium isolated from Obsidian Pool, Yellowstone National Park, Extremophiles, 17(2):251-63, 2013. Research Area: Biomass Deconstruction and Conversion 10.1007/s00792-013-0512-1)
03/03/2014 Hao A review of xylan and lignin biosynthesis: foundation for studying Arabidopsis irregular eylem mutants with pleiotropic phenotypes Critical Reviews in Biochemistry and Molecular Biology Hao, Z., Mohnen, D., A review of xylan and lignin biosynthesis: foundation for studying Arabidopsis irregular xylem mutants with pleiotropic phenotypes, Critical Reviews in Biochemistry and Molecular Biology, 2014 Research Area: Biomass Formation and Modification 10.3109/10409238.2014.889651
01/17/2013 Hardin Standardization of Switchgrass Sample Collection for cell wall and biomass trait analysis

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Bioenergy Research Hardin, C.F., Fu, C., Hisano, H., Xiao, X., Shen, H., Stewart Jr. C.N., Parrott, W., Dixon, R.A., Wang, Z-Y., Standardization of switchgrass sample collection for cell wall and biomass trait analysis, Bioenergy Research, 6 (2), 755-762, 2013. Research Area: Biomass Formation and Modification 10.1007/s12155-012-9292-1
04/01/2011 Higashide Metabolic Engineering of Clostridium cellulolyticum for Isobutanol Production from Cellulose

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Applied and Environmental Microbiology Higashide, Wendy, Li, Yongchao, Yang, Yunfeng, Liao, James C., Metabolic engineering of Clostridium cellulolyticum for isobutanol production from cellulose, Applied Environmental Microbiology, 77(8): 2727-2733, 2011. Research Area: Biomass Deconstruction and Conversion 10.1128/AEM.02454-10
03/01/2010 Himmel Microbial enzyme systems for biomass conversion: emerging paradigms

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Biofuels Himmel, Michael E., Xu, Qi, Luo, Yonghua, Ding, Shi-You, Lamed, Raphael, Bayer, Edward A., Microbial enzyme systems for biomass conversion: emerging paradigms, Biofuels, March 2010, Vol. 1, No. 2, Pages 323-341, 2010. Research Area: Biomass Deconstruction and Conversion 10.1021/cm903135
08/01/2012 Himmel Challenges for Assessing the Performance of Biomass Degrading Biocatalysts Methods in Molecular Biology Biomass Conversion: Methods and Protocols Himmel, M.E., Decker, S.R., Johnson, D.K., Challenges for Assessing the Performance of Biomass Degrading Biocatalysts, Methods in Molecular Biology Biomass Conversion: Methods and Protocols, 908:1-8, 2012. Research Area: Biomass Deconstruction and Conversion 10.1007/978-1-61779-956-3_1
03/13/2009 Hisano Genetic modification of lignin biosynthesis for improved biofuel production

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Journal of In Vitro Cellular and Developmental Biology – Plant Hisano, H., Nandakumar, R., Wang, Z.Y., Genetic modification of lignin biosynthesis for improved biofuel production, Journal of In Vitro Cellular and Developmental Biology - Plant, 344;9, pp 1072-1078, 2009. Research Area: Biomass Formation and Modification 10.1007/s11627-009-9219-5
02/14/2012 Holwerda A defined growth medium with very low background carbon for culturing Clostridium thermocellum

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Journal of Industrial Microbiology and Biotechnology Holwerda, E., K. Hirst, et al. (2012). "A defined growth medium with very low background carbon for culturing Clostridium thermocellum." Journal of Industrial Microbiology and Biotechnology. (published ahead of print doi:10.1007/s10295-012-1091-3) Research Area: Biomass Deconstruction and Conversion 10.1007/s10295-012-1091-3
04/11/2013 Holwerda Testing alternative kinetic models for utilization of crystalline cellulose (Avicel) by batch cultures of Clostridium thermocellum

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Biotechnology and Bioengineering Holwerda, E.K., Lynd, L.R., Testing alternative kinetic models for utilization of crystalline cellulose (Avicel) by batch cultures of Clostridium thermocellum, Biotechnology and Bioengineering, 110(9):2389-94, 2013. Research Area: Biomass Deconstruction and Conversion 10.1002/bit.24914
04/11/2013 Holwerda Development and evaluation of methods to infer biosynthesis and substrate consumption in cultures of cellulolytic microorganisms

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Biotechnology and Bioengineering Holwerda, E.K., Ellis, L.D., Lynd, L.R., Development and evaluation of methods to infer biosynthesis and substrate consumption in cultures of cellulolytic microorganisms, Biotechnology and Bioengineering, 110(9):2380-8, 2013. Research Area: Biomass Deconstruction and Conversion 10.1002/bit.24915
07/01/2008 Hong Bioseparation of recombinant cellulose binding module-protein by affinity adsorption on an ultra-high-capacity cellulosic adsorbent

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Analytica Chimica Acta Hong, Jiong, Xinhao Ye, Yiran Wang and Y.-H. Percival Zhang Bioseparation of recombinant cellulose binding module-protein by affinity adsorption on an ultra-high-capacity cellulosic adsorbent, Analytica Chimica Acta, 621:193-199, 2008. Research Area: Biomass Deconstruction and Conversion 10.1016/j.aca.2008.05.041
06/20/2008 Hong Simple protein purification through affinity adsorption on regenerated amorphous cellulose followed by intein self-cleavage

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Journal of Chromatography Hong, Jiong, Yiran Wang, Xinhao Ye and Y.-H. Percival Zhang , Simple protein purification through affinity adsorption on regenerated amorphous cellulose followed by intein self-cleavage, Journal of Chromatography, A Volume 1194, Issue 2, 20, Pages 150-154, June 2008. Research Area: Biomass Deconstruction and Conversion 10.1016/j.chroma.2008.04.048
03/28/2012 Hoover Eliminating the scattering ambiguity in multifocal, multimodal, multiphoton imaging systems Journal of Biophotonics Hoover, E. E., J. J. Field, et al. (2012). "Eliminating the scattering ambiguity in multifocal, multimodal, multiphoton imaging systems." Journal of Biophotonics. Research Area: Characterization and Modeling 10.1002/jbio.2011001390
09/25/2012 Hu Impact of Pseudolignin versus Dilute Acid-Pretreated Lignin on Enzymatic Hydrolysis of Cellulose

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ACS Sustainable Chemistry and Engineering Hu, F., Jung, S., Ragauskas, A., Impact of Pseudolignin versus Dilute Acid-Pretreated Lignin on Enzymatic Hydrolysis of Cellulose, ACS Sustainable Chemistry & Engineering, 1(1); 62-65, 2013. Research Area: Characterization and Modeling 10.1021/sc300032j
04/01/2012 Hu Pseudo-lignin formation and its impact on enzymatic hydrolysis

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Bioresource Technology Hu, F., Jung, S., Ragauskas, A., Pseudo-lignin formation and its impact on enzymatic hydrolysis, Bioresource Technology, 117, 7-12, 2012. Research Area: Biomass Deconstruction and Conversion 10.1016/j.biortech.2012.04.037
05/25/2012 Hu Pretreatment and Lignocellulosic Chemistry BioEnergy Research Hu, F., Ragauskas, A., Pretreatment and Lignocellulosic Chemistry, BioEnergy Research, 5:2, 2012. Research Area: Characterization and Modeling 10.1007/s12155-012-9208-0
12/16/2013 Hu Supression of pseudo-lignin formation under dilute acid pretreatment conditions

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RCS Advances Hu, F., Ragauskas, A., Suppression of pseudo-lignin formation under dilute acid pretreatment conditions, RCS Advances, 4, 4317-4323, 2014. Research Area: Characterization and Modeling 10.1039/C3RA42841A
05/01/2010 Hu Chemical Profiles of Switchgrass

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Bioresource Technology Hu, Z., R. Sykes, M.F. Davis, E.C. Brummer, and A.J. Ragauskas, Chemical profiles of switchgrass. Bioresource Technology.101:3253-3257.2009, May 2010. Research Area: Characterization and Modeling 10.1016/j.biortech.2009.12.033
12/01/2010 Huang Analysis of biofuels production from sugar based on three criteria: Thermodynamics, bioenergetics, and product separation

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Energy and Environmental Science Huang, W. D., Zhang, Y. H. P., Analysis of biofuels production from sugar based on three criteria: Thermodynamics, bioenergetics, and product separation, Energy and Environmental Science, Vol 4, Issue 3, pp 784, 2011. Research Area: Biomass Deconstruction and Conversion 10.1039/c0ee0069h
07/01/2011 Huang Energy Efficiency Analysis: Biomass-to-Wheel Efficiency Related with Biofuels Production, Fuel Distribution, and Powertrain System

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PloS One Huang, W.D., Zhang, Y-H.P., Energy Efficiency Analysis: Biomass-to-Wheel Efficiency Related with Biofuels Production, Fuel Distribution, and Powertrain Systems. PLoS ONE 6(7): e22113, 2011. Research Area: Biomass Deconstruction and Conversion 10.1371/journal.pone.0022113
05/14/2010 Hubbell Effect of acid-chlorite delignification on cellulose degree of polymerization

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Bioresource Technology Hubbell, Christopher A., Ragauskas, Arthur J., Effect of acid-chlorite delignification on cellulose degree of polymerization, Bioresource Technology, 101, 7410-7415, 2010. Research Area: Characterization and Modeling 10.1016/j.biortech.2010.04.029
07/12/2012 Hyatt Gene and Translation Initiation Site Prediction in Metagenomic Sequences

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Bioinformatics Hyatt, D., LoCascio, P.F., Hauser, L.J., Uberbacher, E.C., Gene and Translation Initiation Site Prediction in Metagenomic Sequences, Bioinformatics, 2012 Research Area: Characterization and Modeling 10.1093/bioinformatics/bts429
03/08/2012 Induri Identification of quantitative trait loci and candidate genes for cadmium tolerance in Populus

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Tree Physiology Iduri, B.R., Ellis, D.R., Slavov, G.T., Yin, T., Zhang, X., Muchero, W., Tuskan, G.A., DiFazio, S.P., Identification of quantitative trait loci and candidate genes for cadmium tolerance in Populus, Tree Physiology, 00, 1-13, 2012. Research Area: Biomass Formation and Modification 10.1093/treephys/tps032
11/20/2013 Iwata Coarse but efficient identification of metabolic pathway systems

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International Journal of Systems Biology Iwata, M., Shiraishi, F., Voit, E.O., Coarse but efficient identification of metabolic pathway systems, International Journal of Systems Biology, 4 (1), 57-72, 2013. Research Area: Characterization and Modeling 0975-2900 & E-ISSN: 0975-9204,
03/12/2012 Izquierdo Complete Genome Sequence of Clostridium clariflavum DSM 19732

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Standards In Genomic Sciences Izquierdo, J. A., L. Goodwin, et al. (2012). Complete Genome Sequence of Clostridium clariflavum DSM 19732. Standards In Genomic Sciences: 6(1). Research Area: Biomass Deconstruction and Conversion 10.4056/sigs.2535732
06/01/2010 Izquierdo Diversity of bacteria and glycosyl hydrolase family 48 genes in cellulolytic consortia enriched from thermophilic biocompost

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Applied and Environmental Microbiology Izquierdo, J. A., Sizova, M. V., Lynd, L. R., Diversity of Bacteria and Glycosyl Hydrolase Family 48 Genes in Cellulolytic Consortia Enriched from Thermophilic Biocompost, Applied and Environmental Microbiology, Volume 76, Issue 11, pp 3545-3553, 2010. Research Area: Biomass Deconstruction and Conversion 10.1128/AEM.02689-09
10/01/2010 Jiang Rapid determination of lignin content via direct dissolution and 1H NMR analysis of the plant cell walls

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ChemSusChem Jiang, N., Pu, Y. Q., Ragauskas, A. J., Rapid Determination of Lignin Content via Direct Dissolution and H-1 NMR Analysis of Plant Cell Walls, Chemsuschem, Volume 3, Issue 11, pp 1285-1289, 2010. Research Area: Characterization and Modeling 10.1002/cssc.201000120
10/01/2010 Jiang Time-Resolved NMR: Extracting the Topology of Complex Enzyme Networks

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Biophysical Journal Jiang, Yingnan, McKinnon, Tyler, Varatharajan, Janani, Glushka, John, Prestegard, James H., Sornborger, Andrew T., Schuttler, Heiza-Berd, Bar-Peled, Maor, Time-Resolved NMR: Extracting the Topology of Complex Enzyme Networks, Biophysical Journal, 99(7):2318-26, 2010. Research Area: Biomass Formation and Modification 10.1016/j.bpj.2010.08.014
01/01/2009 Jiang Perdeuterated pyridinium molten salt (ionic liquid) for direct dissolution and NMR analysis of the plant cell walls

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Green Chemistry Jiang, N., Pu, Y., Ragauskas, R.J., Perdeuterated pyridinium molten salt (ionic liquid) for direct dissolution and NMR analysis of the plant cell walls, Green Chemistry, 11, 1762 - 1766, 2009. Research Area: Characterization and Modeling 10.1039/b913609f
08/12/2011 Joyce Designing the perfect plant feedstock for biofuel production: using the whole buffalo to diversify fuels and products

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Biotechnology Advances Joyce, B.L., Stewart Jr., C.N. (2011) "Designing the perfect plant feedstock for biofuel production: Using the whole buffalo to diversify fuels and products." Biotechnology Advance (published ahead of print doi:10.1016/j.biotechadv.2011.08.006 Research Area: Biomass Formation and Modification 10.1016/j.biotechadv.2011.08.006
11/30/2010 Jung Direct analysis of cellulose in poplar stem by matrix-assisted laser desorption/ionization imaging mass spectrometry

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Rapid Communications in Mass Spectrometry Jung, S., Chen Y., Sullards, M.C., Ragauskas, A.J, Direct analysis of cellulose in poplar stem by matrix-assisted laser desorption/ionization imaging mass spectrometry, Rapid Communications in Mass Spectrometry, volume 24, Issue 22, pp 3230-3236, 2010. Research Area: Characterization and Modeling 10.1002/rcm.4757
01/11/2010 Jung Surface Characterization of Dilute Acid Pretreated Populus deltoides by ToF-SIMS

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Energy and Fuels Seokwon Jung, Marcus Foston, M. Cameron Sullards, and Art J. Ragauska, Surface Characterization of Dilute Acid Pretreated Populus deltoides by ToF-SIMS, Energy and Fuels, 24 (2), pp 1347-1357, 2011. Research Area: Characterization and Modeling 10.1021/ef901062p
09/28/2012 Jung 3D Chemical Image using TOF-SIMS Revealing the Biopolymer Component Spatial and Lateral Distributions in Biomass

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Angewandte Chemie Jung, S., Foston,k M., Kalluri, U., Tuskan, G.A., Ragauskas, A.J., 3D Image using TOF-SIMS Revealing the Biopolymer Component Spatial and Lateral Distribution in Biomass,m Angewandte Chemiek. 51 (48):12005-8, 2012. Research Area: Characterization and Modeling 10.1002/anie.201205243
11/01/2009 Kalluri Shotgun proteome profile of Populus developing xylem

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Proteomics Kalluri, U, Hurst G, Lankford P, Ranjan P and Pelletier D, Shotgun proteome profile of Populus developing xylem, Proteomics, Volume 9, Issue 21, 2009. Pages: 4871-4880, 2009. Research Area: Biomass Formation and Modification
06/11/2010 Kalluri Bioenergy Research: A new paradigm in multidisciplinary research

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Journal of the Royal Society Interface Kalluri U.C and Keller M, “Bioenergy Research: A new paradigm in multidisciplinary research” (2010) Journal of the Royal Society Interface. 7 (51):1391‐1401, 2010. Research Area: Biomass Formation and Modification 10.1098/rsif.2009.0564.
04/11/2010 Kang Transgenic hybrid aspen overexpressing the Atwbc19 gene encoding an ATP-binding cassette transporter confers resistance to four aminoglycoside antibiotics

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Plant Cell Reports Kang, B.G., Xia, Y., Osburn, L.D., Stewart Jr., C.N., Cheng, Z.M., Transgenic hybrid aspen overexpressing the Atwbc19 gene encoding an ATP-binding cassette transporter confers resistance to four aminoglycoside antibiotics, Plant Cell Reports, 2010, 29:643-650, 2010. Research Area: Biomass Formation and Modification 10.1007/s00299-010-0850-8
12/01/2009 Kang Micropropagation of Populus trichocarpa 'Nisqually-1': The genotype deriving the Populus reference genome

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Plant Cell, Tissue and Organ Culture (PCTOC) - Journal of Plant Biotechnology Kang, B.G., Osburn, Lori, Kopsell, Dean, Tuskan, G.A., Cheng, Z.M., Micropropagation of Populus trichocarpa 'Nisqually-1': The genotype deriving the Populus reference genome, Journal of Plant Biotechnology, 99(3):251-257, 2009. Research Area: Biomass Formation and Modification 10.1007/s11240-009-9596-9
02/26/2009 Karpinets Phenotype fingerprinting suggests the involvement of single-genotype consortia in degradation of aromatic compounds by Rhodopseudomonas palustris

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PLoS One Karpinets, T., Pelletier, D, Pan, C., Uberbacher, E.C., Melnichenko, G.V., Hettich, R.L., Samatove, N.F., Phenotype fingerprinting suggests the imvolvement of single-genotype consortia in degradation of aromatic compounds by Rhodopseudomonas palustris, PLoS ONE, 4(2):e4615, 2009. Research Area: Characterization and Modeling
05/25/2012 Karpinets Analyzing large biological datasets with associated networks

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Nucleic Acids Research Karpinets, T.V., Park, B.H., Uberbacher, Analyzing large biological datasets with association networks, Nucleic Acids Research, 1-8, 2012. Research Area: Characterization and Modeling 10.1093/nar/gks403
03/01/2014 Karpinets Metabolic environments and genomic features associated with pathogenic and mutualistic interactions between bacteria and plants Molecular Plant-Microbe Interactions Karpinets, T.V., Park, B.H., Syed, M.H., Klotz, M.G., Uberbacher, E.C., Metabolic environments and genomic features associated with pathogenic and mutualistic interactions between bacteria and plants, Molecular Plant-Microbe Interactions, 2014 Research Area: Characterization and Modeling 10.1094/MPMI-12-13-0368-R
05/01/2013 Kataeva Carbohydrate and lignin are simultaneously solubilized from unpretreated switchgrass by microbial action at high temperature

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Energy and Environmental Science Kataeva, I., Foston, M.B., Yang, S., Pattathil, S., Biswal, A.K., Poole, F.L., Basen, M., Rhaesa, A.M., Thomas, T.P., Azadi, P., Olman, V., Safford, T.D., Mohler, K.E., Lewis, D.L., Doeppke, C., Zeng, Y., Tschaplinski, T.J., York, W., Davis, M., Mohnen, D., Xu, Y., Ragauskas, A.J., Ding, S.Y., Kelly, R.M., Hahn, M.G., Adams, W.W.M., Carbohydrate and lignin are simultaneously solubilized from unpretreated switchgrass by microbial action at high temperature, Energy and Environmental Science, (7), 2013 Research Area: Biomass Formation and Modification 10.1039/C3EE40932E
06/01/2009 Kataeva Genome Sequence of the Anaerobic, Thermophilic and Cellulolytic Bacterium Anaerocellum thermophilum DSM 6725

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Journal of Bacteriology Kataeva IA, Yang SJ, Dam P, Poole FL, Yin Y, Zhou F, Chou WC, Xu Y, Goodwin L, Sims DR, Detter JC, Hauser LJ, Westpheling J, Adams WW, Genome Sequence of the Anaerobic, Thermophilic and Celluloytic Bacterium Anaerocellum thermophilum, Journal of Bacteriology, Jun;191(11):3760-1, 2009. Research Area: Biomass Deconstruction and Conversion 10.1128/JB.00256-09
08/01/2010 Kausch Genetic modification in dedicated bioenergy crops and strategies for gene confinement.

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Biotechnology in Agriculture and Forestry Kausch A.P., J. Hague, M. Oliver, Y. Li, H. Daniell, P.Mascia, C.N. Stewart, Jr. 2010. Genetic modification in dedicated bioenergy crops and strategies for gene confinement. Pp. 299-315. In: Widholm, J. and T. Nagata (Eds) Biotechnology in Agriculture and Forestry; P.N Maschia, J. Scheffran, and J. Widholm (Eds), 66. Plant Biotechnology for Sustainable Production of Energy and Co-products. Springer Verlag, Heidelberg.. Research Area: Biomass Formation and Modification 10.1007/978-3-642-13440-1_11
08/01/2010 Kausch Gene flow in genetically engineered perennial grasses: lessons for modification of dedicated bioenergy crops

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Biotechnology in Agriculture and Forestry Kausch, A.P., J. Hague, M. Oliver, L . S . Watrud, C. Mallory-Smith, V. Meier, A. Snow, and C. N. Stewart, Jr. 2010. Gene flow in genetically engineered perennial grasses: lessons for modification of dedicated bioenergy crops. Pp. 285-298, In: Widholm, J. and T. Nagata (Eds) Biotechnology in Agriculture and Forestry; P.N Maschia, J. Scheffran, and J. Widholm (Eds), 66. Plant Biotechnology for Sustainable Production of Energy and Co-products. Springer Verlag, Heidelberg Research Area: Biomass Formation and Modification 10.1007/978-3-642-13440-1_10
01/01/2010 Kausch Transgenic perennial biofuel feedstocks and strategies for bioconfinement

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Biofuels Kausch, A.P., J. Hague, M. Oliver, Y. Li, H. Daniell, P. Maschia, L.S. Watrud, and C.N.Stewart, Jr., Transgenic perennial biofuel feedstocks and strategies for bioconfinement, Biofuels, Vol 1; Issue 1; p. 163-176, 2010. Research Area: Biomass Formation and Modification 10.4155/BFS.09.11
01/01/2009 Keller Single-Cell Genomics Accessing Uncultivated Microorganisms Keller, M., Schadt, C.W., Palumbo, A.V., Environment to Organisms and Genomes and Backed. Karsten Zengler, (2009), ASM Press. Research Area: Biomass Deconstruction and Conversion
01/07/2008 Keller Microbial goods from single cells and metagenomes

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Current Opinion in Microbiology Keller, Martin, Ramos, Juan L., 2008, Microbial goods from single cells and metagenomes, Current Opinion in Microbiology, 11(3), 195-197, 2008. Research Area: Biomass Deconstruction and Conversion 10.1016/j.mib.2008.05.003
03/09/2009 Keller Environmental Proteomics: a Paradigm Shift in Characterizing Microbial Activities at the Molecular Level

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Microbiology and Molecular Biology Reviews Keller, Martin, Hettich, Robert, Environmental Proteomics: a Paradigm Shift in Characterizing Microbial Activities at the Molecular Level, Microbiology and Molecular Biology Reviews, March 2009, p. 62-70, Vol. 73, No. 1 Research Area: Biomass Deconstruction and Conversion 10.1128/MMBR.00028-08
12/21/2009 Kim Piezoresistive cantilever array sensor for consolidated bioprocess monitoring

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Scanning Kim, S., Rahman, T., Senesac, L.R., Davison, B.H., Thundat, T., Piezoresistive cantilever array sensor for consolidated bioprocess monitoring, Scanning, Volume 31 Issue 5; Pages 204-210 epub Research Area: Characterization and Modeling 10.1002/sca.20159
11/01/2013 King Biolistic transformation of elite genotypes of switchgrass (Panicum virgatum L.)

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Plant Cell Reports King, Z.R., Bray, A.L., LaFayette, P.R., Parrott, W.A., Biolistic transformation of elite genotypes of switchgrass (Panicum virgatum L.), Plant Cell Reports, 2013 Research Area: Biomass Formation and Modification 10.1007/s00299-013-1531-1
09/01/2009 Kong Two Poplar Glycosyltransferase Genes, PdGATL1.1 and PdGATL1.2, Are Functional Orthologs to PARVUS/AtGATL1 in Arabidopsis

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Molecular Plant Yingzhen Konga, Gongke Zhoua, Utku Avcia, Xiaogang Gua, Chelsea Jonesa, Yanbin Yin, Ying Xu, and Michael G. Hahn, Two Poplar Glycosyltransferase Genes, PdGATL1.1 and PdGATL1.2, Are Functional Orthologs to PARVUS/AtGATL1 in Arabidopsis, Molecular Plant, Volume 2, Number 5, Pages 1040–1050, 2009 Research Area: Biomass Formation and Modification 10.1093/mp/ssp068
01/01/2012 Kostylev Synergistic interactions in cellulose hydrolysis

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Biofuels Kostylev, M. and D. Wilson (2011). "Synergistic interactions in cellulose hydrolysis." Biofuels 3(1): 61-70. Research Area: Biomass Deconstruction and Conversion 10.4155/bfs.11.150
07/09/2013 Kostylev Two-parameter kinetic model based on a time-dependent activity coefficient accurately describes enzymatic cellulose digestion

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Biochemistry Kostylev, M., Wilson, D., Two-parameter kinetic model based on a time-dependent activity coefficient accurately describes enzymatic cellulose digestion, Biochemistry, 52 (33), pp 5656–5664, 2013. Research Area: Biomass Deconstruction and Conversion 10.1021/bi400358v
07/15/2011 Kostylev Determination of the catalytic base in family 48 glycosyl hydrolases

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Applied Environmental Microbiology Kostylev, M., Wilson, D.B., Determination of the catalytic base in family 48 glycosyl hydrolases, Applied Environmental Microbiology, 77;17, pp 6274-6276, 2011. Research Area: Biomass Deconstruction and Conversion 10.1128/AEM.05532-11
11/02/2011 Kulkarni The ability of land plants to synthesize glucuronoxylans predates the evolution of tracheophytes

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Glycobiology Kulkarni, A., M. J. Peña, et al. (2012). "The ability of land plants to synthesize glucuronoxylans predates the evolution of tracheophytes." Glycobiology 22 (3): 439-451. Research Area: Biomass Formation and Modification 10.1093/glycob/cwr117
08/01/2012 Kulkarni Comparison of Arabinoxylan Structure in Bioenergy and Model Grasses

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Industrial Biotechnology Kulkarni, A.R., Pattathil, S., Hah, M.G., York, W.S., O'Neill, M.A., Comparison of Arabinoxylan Structure in Bioenergy and Model Grasses, Industrial Biotechnology, 2012 Research Area: Biomass Formation and Modification 10.1089/ind.2012.0014
04/01/2014 Kumagai Simultaneous saccharification and fermentation and a consolidated bioprocessing for Hinoki cypress and Eucalyptus after fibrillation by steam and subsequent wet-disk milling Bioresource Technology Kumagai, A., Kawamura, S., Lee, S.H., Endo, T., Rodriguez Jr., M., Mielenz, J. R., Simultaneous saccharification and fermentation and a consolidated bioprocessing for Hinoki cypress and Eucalyptus after fibrillation by steam and subsequent wet-disk milling, Bioresource Technology, 2014 Research Area: Characterization and Modeling 10.1016/j.biortech.2014.03.110
02/12/2014 Kumar Strong cellulase inhibition by mannan polysaccharides in cellulose conversion to sugars Biotechnology and Bioengineering Kumar, R., Wyman, C.E., Strong cellulase inhibition by mannan polysaccharides in cellulose conversion to sugars, Biotechnology and bioengineering, 2014 Research Area: Characterization and Modeling 10.1002/bit.25218
05/01/2013 Kumar Physical and chemical features of pretreated biomass that influence macro-micro-accessibility and biological processing

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Aqueous Pretreatment of Plant Biomass for Biological and Chemical Conversion to Fuels and Chemicals Kumar, R., Wyman, C.E., Physical and chemical features of pretreated biomass that influence macro-micro-accessibility and biological processing, Aqueous Pretreatment of Plant Biomass for Biological and Chemical Conversion to Fuels and Chemicals, (ed Wyman, C.E.), chapter 14, pp 281-296, 2013. Research Area: Characterization and Modeling 10.1002/9780470975831.ch14
10/01/2012 Kumar Carbohydrate Derived-Pseudo-Lignin can retard cellulose biological conversion

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Biotechnology and Bioengineering Kumar, R., Hu. F., Sannigrahi, P., Jung, S., Ragauskas, A.J., Wyman, C.E., Carbohydrate Derived-Pseudo-Lignin Can Retard Cellulose Biological Conversion, Biotechnology and Bioengineering, 110(3):737-53, 2012. Research Area: Characterization and Modeling 10.1002/bit.24744
12/05/2012 Kumar Comparison of Laboratory Delignification Methods, their selectivity, and impacts on physiochemical characteristics of cellulosic biomass

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Bioresource Technology Kumar, R., Hu, F., Hubbell, C.A., Ragauskas, A.J., Wyman, C.E., Comparison of Laboratory delignification methods, their selectivity, and impacts on physiochemical characteristics of cellulosic biomass, Bioresource Technology, 130: 372-381, 2012. Research Area: Characterization and Modeling 10.1016/j.biortech.2012.12.028
01/01/2012 Kwit Gene flow matters in switchgrass (Panicum virgatum L.,) a potential widespread biofuel feedstock

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Ecological Applications Kwit, C., Stewart, C. N. (2012). Gene flow matters in switchgrass (Panicum virgatum L.), a potential widespread biofuel feedstock, Ecological Applications 22(1):3-7. Research Area: Biomass Formation and Modification 10.1890/11-1516.1
03/14/2014 Kwit Switchgrass (Panicum virgatum L.) as a bioenergy crop: advantages concerns, and future prospects Compendium of Bioenergy Plants: Switchgrass Kwit, C., Nageswara-Rao, M., Stewart Jr., C.N., Switchgrass (Panicum virgatum L.) as a bioenergy crop: advantages, concerns, and future prospects, Compendium of Bioenergy Plants: Switchgrass, 14, 403-420, 2014. Research Area: Biomass Formation and Modification
06/30/2010 Lacayo Imaging Cell Wall Architecture in Single Zinnia elegans Tracheary Elements

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Plant Physiology Lacayo, C.I., Malkin, A.J., Holman, H.Y.N., Chen, L., Ding, S.Y., Hwang, M.S., Thelen, M.P., Imaging Cell Wall Architecture in Single Zinnia elegans Tracheary Elements, Plant Physiology, Volume 154, Issue 1, Pages 121-133, 2010. Research Area: Characterization and Modeling 10.1104/pp.110.155242
05/16/2011 Lee Integrative Analysis of Transgenic Alfalfa (Medicago sative L.) Suggests New Metabolic Control Mechanisms for Monolignol Biosynthesis

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PloS Computational Biology Lee, Y., Chen, F., Gallego-Giraldo, L., Dixon, Richard A., Voit, E.O., Integrative Analysis of Transgenic Alfalfa (Medicago sative L.) Suggests New Metabolic Control Mechanisms for Monolignol Biosynthesis, PLoS Computational Biology, Volume 7, Issue 5, 2011. Research Area: Characterization and Modeling 10.1371/journal.pcbi.1002047
09/01/2010 Lee Mathematical modeling of monolignol biosynthesis in Populus xylem

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Mathematical Biosciences Lee, Y., Voit, E.O., Mathematical modeling of monolignol biosysthesis in Populus xylem, Mathematical Bioscience, Volume 228, Issue 1, pp 78-89, 2010. Research Area: Characterization and Modeling 10.1016/j.mbs.2010.08.009
07/27/2009 Lee Effects of gold patterning on the bending profile and frequency response of a microcantilever

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Journal of Applied Physics Lee D, Kim S, Jung N, Thundat T, Jeon S. Effects of gold patterning on the bending profile and frequency response of a microcantilever. Journal of Applied Physics 2009;106(2):7, 2009. Research Area: Characterization and Modeling 10.1063/1.3177326
02/01/2011 Lee Analysis of Operating Principles with S-system Models

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Mathematical Biosciences Lee, Y., Chen, Po-Wei, Voit, Eberhard O., 2011, Analysis of Operating Principles with S-system Models, Mathematical Biosciences, 231(1): 49-60, 2011. Research Area: Characterization and Modeling 10.1016/j.mbs.2011.03.001
02/08/2012 Lee Biological conversion assay using Clostridium phytofermentans to estimate plant feedstock quality

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Biotechnology for Biofuels Lee, S., T. Warnick, et al. (2012). "Biological conversion assay using Clostridium phytofermentans to estimate plant feedstock quality." Biotechnology for Biofuels 5(1): 5. Research Area: Biomass Formation and Modification 10.1186/1754-6834-5-5
11/08/2012 Lee Functional Analysis of Metabolic Channeling and Regulation in Lignin Biosynthesis: A Computational Approach

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PLOS Computational Biology Lee, Y., Escamilla-Trevino, L., Dixon, R.A., Voit, E.O., Functional Analysis of Metabolic Channeling and Regulation in Lignin Biosynthesis: A Computational Approach, PLOS Computational Biology, 8:11, 2012. Research Area: Characterization and Modeling 10.1371/journal.pcbi.1002769
05/30/2012 Leuze Binding Motifs in Bacterial Gene Promoters Modulate Transcriptional Effects of Global Regulators CRP and ArcA

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Gene Regulation and Systems Biology Leuze, M.R., Karpinets, T.V., Syed, M.H., Beliaev, A.S., Uberbacher, E.C., Binding Motifs in Bacterial Gene Promoters Modulate Transcriptional Effects of Global Regulators CRP and ArcA, Gene Regulation and Systems Biology, 6 93-107, 2012. Research Area: Characterization and Modeling 10.4137/GRSB.S9357
06/06/2012 Li Structural characterization of alkaline hydrogen peroxide pretreated grasses exhibiting diverse lignin phenotypes

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Biotechnology for Biofuels Li, M., Foster, C., Kelkar, S., Pu, Y., Holmes, D., Ragauskas, A., Saffron, C., Hodge, D.B., Structural characterization of alkaline hydrogen peroxide pretreated grasses exhibiting diverse lignin phenotypes, Biotechnology for Biofuels, 5:38, 2012. Research Area: Characterization and Modeling 10.1186/1754-6834-5-38
03/29/2012 Li Chemical Composition and Characterization of Cellulose for Agave as a Fast Growing, Drought Tolerant Biofuels Feedstock

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RSC Advances Li, H., M. B. Foston, et al. Chemical Composition and Characterization of Cellulose for Agave as a Fast Growing, Drought Tolerant Biofuels Feedstock, RSC Advances, 2, 4951-4958, 2012. Research Area: Characterization and Modeling 10.1039/C2RA20557B
09/29/2011 Li Integration of sequence-similarity and functional association information can overcome intrinsic problems in orthology mapping across bacterial genomes

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Nucleic Acids Research Li, G., Q. Ma, et al. (2011). "Integration of sequence-similarity and functional association information can overcome intrinsic problems in orthology mapping across bacterial genomes." Nucleic Acids Research 39(22): e150 Research Area: Characterization and Modeling 10.1093/nar/gkr766
01/04/2012 Li Combined inactivation of the Clostridium cellulolyticum lactate and malate dehydrogenase genes substantially increases ethanol yield from cellulose and switchgrass fermentations

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Biotechnology for Biofuels Yongchao Li, Timothy J Tschaplinski, Nancy L Engle, Choo Y Hamilton, Miguel Rodriguez, James C Liao, Christopher W Schadt, Adam M Guss, Yunfeng Yang and David E Graham. (2012). "Combined inactivation of the Clostridium cellulolyticum lactate and malate dehydrogenase genes substantially increases ethanol yield from cellulose and switchgrass fermentations." Biotechnology for Biofuels 5:2. Research Area: Biomass Deconstruction and Conversion 10.1186/1754-6834-5-2
12/01/2012 Li Complete genome sequence of Clostridium sp. Strain BNL1100, a cellulolytic mesophile isolated from corn stover

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Journal of Bacteriology Li, L.L., Taghavi, S., Izquierdo, J.A., van der Lelie, D., Complete genome sequence of Clostridium sp. Strain BNL1100, a cellulolytic mesophile isolated from corn stover, Journal of Bacteriology, 194(24), p 69820-6983, 2012. Research Area: Biomass Deconstruction and Conversion 10.1128/JB.01908-12
05/01/2013 Li Application of high throughput pretreatment and co-hydrolysis system to thermochemical pretreatment. Part 2: dilute alkali

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Biotechnology and Bioengineering Li, H., Gao, X., DeMartini, J.D., Kumar, R., Wyman, C.E., Application of high throughput pretreatment and co-hydrolysis system to thermochemical pretreatment. Part 2: dilute alkali, Biotechnology and Bioengineering, 2013 Research Area: Characterization and Modeling 10.1002/bit.24951
03/19/2013 Li Chromatographic determination of 1, 4-b-xylooligosaccharides of different chain lengths to follow xylan deconstruction in biomass conversion

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Journal of Industrial Microbiology & Biotechnology Li, H., Qing, Q., Kumar, R., Wyman, C.E., Chromatographic determination of 1, 4-b-xylooligosaccharides of different chain lengths to follow xylan deconstruction in biomass conversion, Journal of Industrial Microbiology Biotechnology, 40:551-559, 2013. Research Area: Characterization and Modeling 10.1007/s10295-013-1254-x
Li Investigation of lignin deposition on cellulose during hydrothermal pretreatment, its effect on cellulose hydrolysis, and underlying mechanisms Biotechnology and Bioengineering Li, H., Pu, Y., Kumar, R., Ragauskas, A.J., Wyman, C.E., Investigation of lignin deposition on cellulose during hydrothermal pretreatment, its effect on cellulose hydrolysis, and underlying mechanisms, 2013 Research Area: Characterization and Modeling 10.1002/bit.25108
09/29/2010 Li A new framework for identifying cis-regulatory motifs in prokaryotes

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Nucleic Acids Research Li, G., Liu, B.Q., Ma, Q., Xu, Y., A new framework for identifying cis-regulatory motifs in prokaryotes, Nucleic Acids Research, v 39, no. 7, 2011. Research Area: Characterization and Modeling 10.1093/nar/gkq948
02/01/2009 Li Bioprospecting metagenomes: Glycosyl hydrolases for converting biomass

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Biotechnology for Biofuels Li, L. L., McCorkle, S. R., Monchy, S., Taghavi, S., van der Lelie, D., Bioprospecting metagenomes: glycosyl hydrolases for converting biomass, Biotechnology for Biofuels, Volume 2, pp 11, 4:23, 2009. Research Area: Biomass Deconstruction and Conversion 10.1186/1754-6834-2-10
08/04/2011 Li Bioprospecting metagenomics of decaying wood: mining for new glycoside hydrolases

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Biotechnology for Biofuels Li, L.L., Taghavi, S., McCorkle, S.M., Zhang, Y.B., Blewitt, M.G., Bruneck, R., Adney, W.S., Himmel, M.E., Brumm, P., Drinkwater, C., Mead, D.A., Tringe, S.G., van der Lelie, D., Bioprospecting metagenomics of decaying wood: mining for new glycoside hydrolases, Biotechnology for Biofuels, 4:23, 2011. Research Area: Biomass Deconstruction and Conversion 10.1186/1754-6834-4-23
04/01/2010 Li Increased Crystalline Cellulose Activity via Combinations of Amino Acid Changes in the Family 9 Catalytic Domain and Family 3c Cellulose Binding Module of Thermobifida fusca Cel9A

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Applied and Environmental Microbiology Li, Y., Irvin, D.C., Wilson, D.B., Increased Crystalline Cellulose Activity via Combinations of Amino Acid Changes in the Family 9 Catalytic Domain and Family 3c Cellulose Binding Module of Thermobifida fusca Cel9A, Applied and Environmental Microbiology, Volume 76, Issue 8, pp 2582-2588, 2010. Research Area: Biomass Deconstruction and Conversion 10.1128/AEM.02735-09
04/04/2014 Li Agave proves to be a low recalcitrant lignocellulosic feedstock for biofuels production on semi-arid lands

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Biotechnology for Biofuels Li, H., Pattathil, S., Foston, M.B., Ding, S.Y., Kumar, R., Gao, X., Mittal, A., Yarbrough, J.M., Himmel, M.E., Ragauskas, A.J., Hahn, M.G., Wyman, C.E., Agave proves to be a low recalcitrant lignocellulosic feedstock for biofuels production on semi-arid lands, Biotechnology for Biofuels, 7:50, 2014 Research Area: Characterization and Modeling 10.1186/1754-6834-7-50
Li Identification of features associated with plant cell wall recalcitrance to pretreatment by alkaline hydrogen peroxide in diverse bioenergy feedstocks using glycome profiling RSC Advances Li, M., Pattathil, S., Hahn, M.G., Hodge, D., Identification of features associated with plant cell wall recalcitrance to pretreatment by alkaline hydrogen peroxide in diverse bioenergy feedstocks using glycome profiling, RSC Advances, 2014 Research Area: Characterization and Modeling 10.1039/C4RA00824C
08/01/2013 Lian Catalytic mechanism and origin of high activity of cellulase TmCel12A at high temperature: a quantum mechanical/molecular mechanical study

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Cellulose Lian, P., Guo, H.B., Smith, J.C., Wei, D.Q., Gui, H, Catalytic mechanism and origin of high activity of cellulase TmCel12A at high temperature: a quantum mechanical/molecular mechanical study, Cellulose, 2013 Research Area: Characterization and Modeling 10.1007/s10570-013-0011-7
07/16/2011 Liao One-step purification and immobilization of thermophilic polyphosphate glucokinase from Thermobifida fusca YX: glucose-6-phosphate generation without ATP

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Applied Microbiology and Biotechnology Liao, H.H., Myung, Suwan, Zhang, Y-HP., One-step purification and immobilization of thermophilic polyphosphate glucokinase from Thermobifida fusca YX: glucose-6-phosphate generation without ATP, Applied Microbiology and Biotechnology, 93:1109-1117. Research Area: Biomass Deconstruction and Conversion 10.1007/s00253-011-3458-1
07/01/2011 Liao A minimal set of bacterial cellulases for consolidated bioprocessing of lignocelluloses

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Biotechnology Journal Liao, H.H., Zhang, X.Z., Rollin, J.A., Zhang, Y-H.P, A minimal set of bacterial cellulases for consilodated bioprocessing of lignocelluloses, Biotechnology Journals, 6(11):1409-1418, 2011. Research Area: Biomass Deconstruction and Conversion 10.1002/biot.201100157
01/01/2010 Lindedam Near Infrared Spectroscopy as a Screening Tool for Sugar Release and Chemical Composition of Wheat Straw

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Journal of Biobased Materials and Bioenergy Lindedam, J., Bruun, S., DeMartini, J., Jorgensen, H. Felby, C., Yang, B., Wyman C.E., Magid, J., Near Infrared Spectroscopy as a Screening Tool for Sugar Release and Chemical Composition of Wheat Straw, Journal of Biobased Materials and Bioenergy, 4, 1-6, 2010. Research Area: Characterization and Modeling 10.1166/jbmb.2010.1104
12/29/2011 Lindedam Cultivar variation and selection potential relevant to the production of cellulosic ethanol from wheat straw

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Biomass and Bioenergy Lindedam, J., S. B. Andersee, et al. (2012). "Cultivar variation and selection potential relevant to the production of cellulosic ethanol from wheat straw." Biomass and Bioenergy 37:221–228. Research Area: Characterization and Modeling 10.1016/j.biombioe.2011.12.009
03/21/2014 Lindedam Evaluation of high throughput screening methods in picking up differences between cultivars of lignocellulosic biomass for ethanol production Biomass and Bioenergy Lindedam, J., Bruun, S., Jorgensen, H., Decker, S.R., Turner, G.B., DeMartini, J.D., Wyman, C.E., Felby, C., Evaluation of high throughput screening methods in picking up differences between cultivars of lignocellulosic biomass for ethanol production, Biomass and Bioenergy, 2014 Research Area: Characterization and Modeling 10.1016/j.biombioe.2014.03.006
08/20/2013 Linville Kinetic modeling of batch fermentation for Populus hydrolysate tolerant mutant and wild type strains of Clostridium thermocellum Bioresource Technology Linville, J.L., Rodiguez Jr., M., Mielenz, J. R., Cox, C.D., Kinetic modeline of batch fermentation for Populus hydrolysate tolerant mutant and wild type strains of Clostridium thermocellum, Bioresource Technology, 147, pp 605-613, 2013. Research Area: Characterization and Modeling 10.1016/j.biortech.2013.08.086
10/21/2013 Linville Industrial robustness: understanding the mechanism of tolerance for the populus hydrolysate-tolerant mutant strain of clostridium thermocellum Plos One Linville, J.L., Rodriguez Jr., M., Land, M., Syed, M., Engle, N.L., Tschaplinski, T.J., Mielenz, J.R., Cox, C.D., Industrial robustness: understanding the mechanism of tolerance for the populus hydrolysate-tolerant mutant strain of clostridium thermocellum, Plos One, 8(10): e78829, 2013. Research Area: Characterization and Modeling 10.1371/journal.pone.0078829
11/26/2013 Liu Advanced genetic tools for plant biotechnology

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Nature Reviews Genetics Liu, W., Yuan, J.S., Stewart J., C.N., Advanced genetic tools for plant biotechnology, Nature Reviews, Volume 14, 781, 2013. Research Area: Biomass Formation and Modification 10.1038/nrg3583
11/18/2013 Liu Advances in the measurement and characterization of biomass structure and processing

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Biological Concerstion of Biomass for Fuels and Chemicals: Exploration from Natural Utilization Systems Liu, Y.S., Ding, S.Y., Advances in the measurement and characterization of biomass structure and processing, Biological Concerstion of Biomass for Fuels and Chemicals: Explorations from Natural Utilization Systems, 10 (3), 26-36, 2013. Research Area: Characterization and Modeling
08/01/2012 Liu Single-Molecule Tracking of Carbohydrate-Binding Modules on Cellulose Using Fluorescence Microscopy Methods in Molecular Biology Biomass Conversion: Methods and Protocols Liu, Y.S., Ding, S.Y., Himmel, M.E., Single-Molecule Tracking of Carbohydrate-Binding Modules on Cellulose Using Fluorescence Microscopy, Methods in Molecular Biology Biomass Conversion: Methods and Protocols, 908;129-140, 2012. Research Area: Biomass Deconstruction and Conversion 10.1007/978-1-61779-956-3_13
09/01/2009 Liu The family 1 glycoside hydrolase from Clostridium cellulolyticum H10 is a cellodextrin glucohydrolase.

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Applied Biochemistry and Biotechnology Liu W, Bevan DR, Zhang Y-HP,The family 1 glycoside hydrolase from Clostridium cellulolyticum H10 is a cellodextrin glucohydrolase, Applied Biochemistry and Biotechnology, 161:1-8, 2009. Research Area: Biomass Deconstruction and Conversion 10.1007/s12010-009-8782-x
12/01/2009 Liu A single molecule study of cellulase hydrolysis of crystalline cellulose

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Spie-Int Soc Optical Engineering Liu, Y. S., Luo, Y. H., Baker, J. O., Zeng, Y. N., Himmel, M. E., Smith, S., Ding, S. Y., A single molecule study of cellulase hydrolysis of crystalline cellulose, Spie-Int Soc Optical Engineering, Volume 7571; 757103; 2010 Research Area: Characterization and Modeling 10.1117/12.840975
02/01/2011 Liu Cellobiohydrolase Hydrolyzes Crystalline Cellulose on Hydrophobic Faces

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Journal of Biological Chemistry Liu, Yu-San, Baker, John O., Zeng, Yining, Himmel, Michael E., Haas, Thomas, Ding, Shi-You, Cellobiohydrolase Hydrolyzes Crystalline Cellulose on Hydrophobic Faces, Journal of Biological Chemistry, 286:11195-11201, 2011. Research Area: Characterization and Modeling
06/19/2009 Liu Does the Cellulose-Binding Module Move on the Cellulose Surface?

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Cellulose Liu, Yu-San, Yining Zeng, Yonghua Luo, Qi Xu, Michael E. Himmel, Steve J. Smith, and Shi-You Ding , Does the Cellulose-Binding Module Move on the Cellulose Surface?, Cellulose, 2009, 16(4):587-597, 2009. Research Area: Characterization and Modeling 10.1007/s10570-009-9306-0
06/01/2010 Liu Engineering of Clostridium phytofermentans endoglucanase Cel5A for improved thermostability

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Applied and Environmental Microbiology Liu, W.J., Zhang, X.A., Zhang, Z.M., Zhang, Y.H.P., Engineering of Clostridium phytofermentans Endoglucanase Cel5A for Improved Thermostability, Applied and Environmental Microbiology, Volume 76, Issue 14, pp 4914-4917, 2010. Research Area: Biomass Deconstruction and Conversion 10.1128/AEM.00958-10
04/01/2009 Liu Fast identification of thermostable beta-glucosidase mutants on cellobiose by a novel combinatorial selection/screening approach

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Biotechnology and Bioengineering Liu, W.J., Hong, J., Bevan, D.R., Zhang, Y.H.P., Fast Identification of Thermostable Beta-Blucosidase Mutants on Cellobiose by a Novel Combinatorial Selection/Screening Approach, Biotechnology and Bioengineering, Volume 103 Issue 6, Pages 1087 - 1094, 2009. Research Area: Biomass Deconstruction and Conversion 10.1002/bit.22340
Liu Coupling alkaline pre-extraction with alkaline-oxidative post-treatment of corn stover to enhance enzymatic hydrolysis and fermentability Biotechnology for Biofuels Liu, T., Williams, D.L., Pattathil, S., Hahn, M.G., Li, M., Hodge, D.B., Coupling alkaline pre-extraction with alkaline-oxidative post-treatment of corn stover to enhance enzymatic hydrolysis and fermentability, Biotechnology for Biofuels, 2014 Research Area: Characterization and Modeling
04/01/2008 Ljungdahl Contribution of domain interactions and calcium binding to the stability of carbohydrate-Active enzymes

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Bioenergy Ljungdaho, L.G., Kataeva, I.A., Uversky, V.V., Contribution of domain interactions and calcium binding to the stability of carbohydrate-Active enzymes, Bioenergy, Judy D. Wall, Caroline S. Harwood and Arnold Demain eds., ASM Press, washington, DC, p.115-127, 2008. Research Area: Biomass Deconstruction and Conversion ISBN-13: 9781555814786
04/15/2011 Lochner Label-free quantitative proteomics distinguish the secreted cellulolytic systems of Caldicellulosiruptor bescii and Caldicellulosiruptor obsidiansis

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Applied Environmental Microbiology Lochner, Adriane, Giannone, Richard J., Rodriquez Jr., Miguel, Shah, Manesh, B., Mielenz, Jonathan R., Keller, Martin, Antranikian, Garabed, Graham, David E., Hettich, Roberts L., 2011, Label-free quantitative proteomics distinguish the secreted cellulolytic systems of Caldicellulosiruptor bescii and Caldicellulosiruptor obsidiansis, Applied Environmental Microbiology, 77(12): 4042-4054, 2011. Research Area: Biomass Deconstruction and Conversion 10.1128/AEM.02811-10
10/11/2011 Lochner Label-free Quantitative Proteomics for the Extremely Thermophilic Bacterium Caldicellulsiruptor obsidiansis Reveal Distinct Abundance Patterns upon Growth on Cellobiose, Crystalline Cellulose, and Switchgrass

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Journal of Proteome Research Lochner, A., Giannone, R.J., Keller, M., Antranikian, G., Graham, D.E., Hettich, R.L., Label-free Quantitative Proteomics for the Extremely Thermophilic Bacterium Caldicellulosiruptor obsidiansis Reveal Distinct Abundance Patterns upon Growth on Cellobiose, Crystalline Cellulose, and Switchgrass, Journal of Proteome Research, 10(12), 5302-5314, 2011. Research Area: Biomass Deconstruction and Conversion 10.1021/pr200536j
05/01/2013 Lynd Cellulosic Biofuels: Importance, Recalcitrance, and Pretreatment

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Aqueous Pretreatment of Plant Biomass for Biological and Chemical Conversion to Fuels and Chemicals Lynd, L., Laser, M., Cellulosic Biofuels: Importance, Recalcitrance, and Pretreatment, Aqueous Pretreatment of Plant Biomass for Biological and Chemical Conversion to Fuels and Chemicals, (ed Wyman, C.E.), chapter 2, pp 17-21, 2013. Research Area: Biomass Deconstruction and Conversion 10.1002/9780470975831.ch2
02/01/2008 Lynd How biotech can transform biofuels

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Nature Biotechnology Lynd, L. R., Laser, M. S., Brandsby, D., Dale, B. E., Davison, B., Hamilton, R., Himmel, M., Keller, M., McMillan, J. D., Sheehan, J., Wyman, C. E., How Biotech can transform biofuels, Nature Biotechnology, 26(2), 169-172, 2008. Research Area: Biomass Deconstruction and Conversion 10.1038/nbt0208-169
04/17/2013 Ma Computational analyses of transcriptomic data reveal the dynamic organization of the Escherichia coli chromosome under different conditions

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Nucleic Acids Research Ma, Q., Yin, Y., Schell, M.A., Zhang, H., Li, G., Xu, Y. ,Computational analyses of transcriptomic data reveal the dynamic organization of the Escherichia coli chromosome under different conditions, Nucleic Acids Research, 41(11):5594-603, 2013. Research Area: Characterization and Modeling 10.1093/nar/gkt261
01/25/2013 Ma Global genomic arrangement of bacterial genes is closely tied with the total transcriptional efficiency

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Genomics, Proteomics & Bioinformatics Ma, Q., Xu, Y., Global genomic arrangement of bacterial genes is closely tied with the total transcriptional efficiency, Genomics, Proteomics & Bioinformatics, 11(1), 66-71, 2012. Research Area: Characterization and Modeling 10.1016/j.gpb.2013.01.004
07/10/2013 Ma An integrated toolkit for accurate prediction and analysis of cis regulatory motifs at a genome scale

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Bioinformatics Ma, Q., Liu, B., Zhou, C., Yin , Y., Li, G., Xu, Y., An integrated toolkit for accurate prediction and analysis of cis regulatory motifs at a genome scale, Bioinformatics, 29 (18) pp 2261-2268, 2013. Research Area: Characterization and Modeling 10.1093/bioinformatics/btt397
Ma DMINDA: an integrated web server for DNA motif indentification and analysis Nucleic Acids Research Ma, Q., Zhang, H., Mao, X., Zhou, C., Liu, B., Chen, X., Xu, Y., DMINDA: An integrated web server for DNA motif identification and analyses, Nucleic Acids Research, 2014 Research Area: Characterization and Modeling
12/01/2009 Machina Automated piecewise power-law modeling of biological systems

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Journal of Biotechnology Machina, A., Ponosovb, Ar., Voit, E.O., Automated piecewise power-law modeling of biological systems, Journal of Biotechnology, Volume 149, Issue 3, Special Issue SI, pp 154-165, 2009. Research Area: Characterization and Modeling 10.1016/j.jbiotec.2009.12.016
01/01/2011 Mann pANIC: A versatile set of Gateway-compatible vectors for gene overexpression and RNAi-mediated down-regulation in monocots

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Plant Transformation Technologies Mann, D.G.J, P.R. LaFayette, L.G Abercrombie, W.A. Parrott, C.N. Stewart, Jr. , pANIC: A versatile set of Gateway-compatible vectors for gene overexpression and RNAi-mediated down-regulation in monocots, Plant Transformation Technologies, pp 161-168. 2011. Research Area: Biomass Formation and Modification ISBN: 978-0-8138-2195-5
07/11/2011 Mann Switchgrass (Panicum virgatum L.) ubiquitin gene (PvUbi1 and PvUbi2) promoters for use in plant transformation

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BMC Biotechnology Mann, D.G., King, Z.R., Liu, W., Joyce, B.L., Percifield, R.J., Hawkins, J.S., LaFayette, Peter R., Artelt, B.J., Burris, J.N., Mazarei, M., Bennetzen, J.L., Parrott, W.A., Stewart Jr., C. Neal, Switchgrass (Panicum virgatum L.) ubiquitin gene (PvUbi1 and PvUbi2) promoters for use in plant transformation, BMC Biotechnology, 11:74,2011. Research Area: Biomass Formation and Modification 10.1186/1472-6750-11-74
12/01/2009 Mann Rapid assessment of lignin content and structure in switchgrass (Panicum virgatum L.) grown under different environmental conditions

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BioEnergy Research David G.J. Mann, Nicole Labbé, Robert W. Sykes, Kristen Gracom, Lindsey Kline, Isabella M. Swamidoss, Jason N. Burris, Mark Davis, C. Neal Stewart, Jr., Rapid assessment of lignin content and structure in switchgrass (Panicum virgatum L.) grown under different environmental conditions, Bioenergy Research, Volume 2, Number 4 / December, 2009 Research Area: Biomass Formation and Modification 10.1007/s12155-009-9054-x
09/28/2011 Mann Gateway-compatible vectors for high-throughput gene functional analysis in switchgrass (Panicum virgatum L.) and other monocot species

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Plant Biotechnology Journal Mann, G.J., LaFayette, P.R., Abercrombie, L.L., King, Z.R., Mazarei, M., Halter, M.C., Poovaiah, C.R., Baxter, H., Shen, H., Dixon, R.A., Parrott, W.A., Stewart Jr., C.N. (2012) "Gateway-compatible vectors for high-throughput gene functional analysis in switchgrass (Panicum virgatum L.)." Plant Biotechnology Journal 10(2):226–236. Research Area: Biomass Formation and Modification 10.1111/j.1467-7652.2011.00658.x
04/03/2012 Mann Very bright orange fluorescent plant: endoplasmic reticulum targeting of orange fluorescent proteins as visual reporters in transgenic plants

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BMC Biotechnology Mann, D.G.J., Abercrombie, L.L., Rudis, M.R., Milwood, R.J., Dunlap, J.R., Stewart, C.N., Very bright orange fluorescent plants: endoplasmic reticulum targeting of orange fluorescent proteins as visual reporters in transgenic plants, BMC Biotechnology, 12:17, 2012. Research Area: Biomass Formation and Modification 10.1186/1472-6750-12-17
06/26/2012 Mao The percentage of bacterial genes on leading versus lagging strands is influenced by multiple balancing forces

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Nucleic Acids Research Mao, X, Zhang, H., Yin, Y., Xu, X., The percentage of bacterial genes on leading versus lagging strands is influenced by multiple balancing forces, Nucleic Acids Research, 1-9, 2012. Research Area: Characterization and Modeling 10.1093/nar/gks605
11/07/2013 Mao DOOR 2.0: presenting operons and their functions through dynamic and integrated views

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Nucleic Acids Research Mao, X., Ma, Q., Zhou, C., Chen, X., Zhang, H., Yang, J., Mao, F., Lai, W., Xu, Y., DOOR 2.0: presenging operons and their functions through dynamic and integrated views, Nucleic Acids Research, 1-6, 2013. Research Area: Characterization and Modeling 10.1093/nar/gkt1048
02/15/2013 Mao Barcode Server: A visualization-based genome analysis system

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PLoS ONE Mao, F., Olman, V., Wang, Y., Xu, Y., Barcode Server: A visualization-based genome analysis system, PLoS ONE, 8(2): e56726, 2013. Research Area: Characterization and Modeling 10.1371/ journal.pone.0056726
12/07/2012 Mao CINPER: An interactive web system for pathway predition for prokaryotes

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PLOSOne Mao, Z., Chen, X., Zhang, Y., Pangle, S., Xu, Y., CINPER: an interactive web system for pathway prediction for prokaryotes, PLOS One, 7(12); e51252, 2012. Research Area: Characterization and Modeling 10.1371/journal.pone.0051252
07/22/2011 Mao SEAS: A system for SEED-Based Pathway Enrichment Analysis

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PloS One Mao, X., Zhang, Y., Xu, Y., SEAS: A system for SEED-Based Pathway Enrichment Analysis, Plos One, 6 (7), e22556, 2011. Research Area: Characterization and Modeling 10.1371/journal.pone.0022556
09/01/2009 Mao pDAWG: an Integrated Database for Plant Cell-Wall Genes

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BioEnergy Research Fenglou Mao, Yanbin Yan, Fengfeng Zhou, Wen-Chi Chou, Chan Zhou, Huiling Chen and Ying Xu, pDAWG: an Integrated Database for Plant Cell-Wall Genes, Bioenergy Research, Volume 2, Number 4 / December, 2009 Research Area: Characterization and Modeling 10.1007/s12155-009-9052-z
10/06/2008 Mao DOOR: a database for prokaryotic operons

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Nucleic Acids Research Mao, Fenglou, Phuongan Dam, Jacky Chou, Victor Olman, and Ying Xu , DOOR: a database for prokaryotic operons, 37, Nucleic Acids Research, Database Issue 37, D459-D463, 2009. Research Area: Characterization and Modeling 10.1093/nar/gkn757
03/19/2013 Martin del Campo High-Yield Production of Dihydrogen from Xylose by Using a Synthetic Enzyme Cascade in a Cell-Free System

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Angewandte Chemie Martin del Camp, J.S., Rollin, J., Myung, S., Chun, Y., Chandrayan, S., Patino, R., Adams, M.W.W., Zhang, Y.H., High-yield production of dihydrogen from xylose by using a synthetic enzyme cascade in a cell-free system, Angewandte Chemie, 52, 1-5, 2013. Research Area: Biomass Deconstruction and Conversion 10.1002/anie.201300766
01/06/2012 Martinez Biosynthesis of UDP-4-keto-6-deoxyglucose and UDP-rhamnose in Pathogenic Fungi Magnaporthe grisea and Botryotinia fuckeliana

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The Journal of Biological Chemistry Martinez, V., Ingwers, M., Smith, J., Glushka, J., Yang, T., Bar-Peled, M., Biosynthesis of UDP-4-keto-6-deoxyglucose and UDP-rhamnose in Pathogenic Fungi Magnaporthe grisea and Botryotinia fuckeliana, The Journal of Biological Chemistry, 287: 879-892, 2012. Research Area: Biomass Formation and Modification 10.1074/jbc.M111.287367
01/01/2009 Mazarei Protoplast isolation and transient gene expression in switchgrass, Panicum virgatum L.

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Biotechnology Journal Mazarei, Mitra, Al-Ahmad, Hani, Rudis, Mary R., Stewart, Jr., C. Neal, Protoplast isolation and transient gene expression in switchgrass, Panicum virgatum L., Biotechnology Journal,3, 354-359, 2008. Research Area: Biomass Formation and Modification 10.1002/biot.200700189
05/01/2011 Mazarei Switchgrass (Panicum virgatum L.) cell suspension cultures: Establishment, characterization, and application

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Plant Science Mazarei, Mitra, Al-Ahmad, Hani, Rudis, Mary R., Joyce, Blake J., Stewart Jr., C. Neal, Switchgrass (Panicum virgatum L.) cell suspension cultures: Establishment, characterization, and application, Plant Science, 18(6): 712-715, 2011. Research Area: Biomass Formation and Modification 10.1016/j.plantsci.2010.12.010
07/01/2010 Mazumder Structural analysis of arabinoxylans isolated from ball milled switchgrass biomass

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Carbohydrate Research Mazumder, K., York, W.S., Structural analysis of arabinoxylans isolated from ball-milled switchgrass biomass, Carbohydrate Research, Volume 345, Issue 15, pp 2183-2193, 2010. Research Area: Biomass Formation and Modification 10.1016/j.carres.2010.07.034
08/01/2012 Mazumder Structural Characterization of the Heteroxylans from Poplar and Switchgrass Methods in Molecular Biology Biomass Conversion: Methods and Protocols Mazumder, K., Pena, M.J., O'Neill, M.A., York, W.S., Structural Characterization of the Heteroxylans from Poplar and Switchgrass, Methods in Molecular Biology Biomass Conversion: Methods and Protocols, 908;215-228, 2012. Research Area: Biomass Formation and Modification 10.1007/978-1-61779-956-3_19
04/24/2012 McKee Introducing endo-xylanase activity into an exo-acting arabinofuranosidase that targets side chains

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PNAS McKee, L.S., Pena, M.J., Rogowski, A., Jackson, A., Lewis, York, W.S., Krogh, K.B.R.M., Vikse-Nielsen, A., Skjot, M., Gilbert, H.J., Marles-Wright, J., Introducing endo-xylanase activity into an exo-acting arabinofuranosidase that targets side chains, PNAS, 109(17), 6537-6542, 2012. Research Area: Biomass Formation and Modification 10.1073/pnas.1117686109
08/16/2012 Mearls Formation and characterization of non-growth states in Clostridium thermocellum: spores and L-forms

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BMC Microbiology Mearls, E.B., Izquierdo, J.A., Lynd, L.E., Formation and characterization of non-growth states in Clostridium thermocellum: spores and L-forms, BMC Microbiology, 12:180, 2012. Research Area: Biomass Deconstruction and Conversion 10.1186/1471-2180-12-180
07/08/2013 Meng Determination of porosity of lignocellulosic biomass before and after pretreatment by using Simons' stain and NMR techniques

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Bioresource Technology Meng, X., Foston, M., Leisen, J., DeMartini, J., Wyman, C.E., Ragauskas, A.J., Determination of porosity of lignocellulosic biomass before and after pretreatment by using Simons' stain and NMR techniques, Bioresource Technology, 144:467-76, 2013. Research Area: Characterization and Modeling 10.1016/j.biortech.2013.06.091
02/01/2014 Meng Recent advances in understanding the role of cellulose accessibility in enzymatic hydrolysis of lignocellulosic substrates Current Opinion in Biotechnology Meng, X., Ragauskas, A.J., Recent advances in understanding the role of cellulose accessibility in enzymatic hydrolysis of lignocellulosic substrates, Current Opinion in Biotechnology, 27, 150-158, 2014. Research Area: Characterization and Modeling 10.1016/j.copbio.2014.01.014
03/01/2010 Mielenz Improving microbial robustness using systems biology

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Manual of Industrial Microbiology and Biotechnology Mielenz, J.R., Hogsett, D.A., Improving microbial robutsness using systems biology, Manual of Industrial Microbiology and Biotechnology, 3rd Edition, p. 605-620, 2010. Research Area: Biomass Deconstruction and Conversion ISBN 978-1-55581-512-7
12/01/2009 Mielenz Fermentation of soybean hulls to ethanol while preserving protein value

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Bioresource Technology Mielenz, J.R., Bardsley, J.S., Wyman, C.E., Fermentation of soybean hulls to ethanol while preserving protein value, Bioresource Technology, Jul;100(14):3532-9, 2009. Research Area: Biomass Deconstruction and Conversion 10.1016/j.biortech.2009.02.044
06/01/2009 Miller The DOE BioEnergy Science Center - a U.S. Department of Energy Bioenergy Research Center

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Journal of In Vitro Cellular and Developmental Biology – Plant Keller, Martin, Miller, Russ, 2009, The DOE BioEnergy Science Center - a U.S. Department of Energy Bioenergy Research Center, In Vitro Cell Development Biology, Volume 45, Number 3 / June, 2009. Research Area: Characterization and Modeling
06/01/2008 Mohnen Pectin Structure and Biosynthesis

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Current Opinion Plant Biology Mohnen, D., Pectin structure and biosysthesis, Current Opinion in Plant Biology, Vol. 11(3), 266- 277, 2008. Research Area: Biomass Formation and Modification 10.1016/j.pbi.2008.03.006
06/17/2011 Mohnen Plants Get Hyp to O-Glycosylation

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Science Mohnen, D., Tierney, Mary L., Plants Get Hyp to O-Glycosylation, Science, 332:1393-1394, 2011. Research Area: Biomass Formation and Modification 10.1126/science.1208641
01/01/2008 Mohnen Cell wall polysaccharide synthesis

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Biomass Recalcitrance Mohnen, Debra, Maor Bar-Peled, and Chris Somerville , Cell wall polysaccharide synthesis, Biomass Recalcitrance, Ed. Michael Himmel, Chapter 5, 94-187, Oxford: Blackwell Publishing, 2008. Research Area: Biomass Formation and Modification
07/22/2010 Moinuddin Insights into lignin primary structure and deconstruction from Arabidopsis thaliana COMP (caffeic acid O-methyl transferase mutant Atomt1

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Organic and Biomolecular Chemistry Moinuddin, Syed G.A., Jourdes, M., Laskas, D.D., Ki, C., Cardenas, C.L., Kim, K.W., Zhang, D., Davin, L. B., Lewis, N.G., Insights into lignin primary structure and deconstruction from Arabidopsis thaliana COMP (caffeic acid O-methyl transferase mutant Atomt1, Organic and Biomolecular Chemistry, 2010, 8, pp 3928-3946, 2010. Research Area: Biomass Deconstruction and Conversion 10.1039/c004817h
05/29/2010 Moon Sustainable Use of Biotechnology for Bioenergy Feedstocks

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Environmental Management Moon, H.S., Abercrombie, J.M., Kausch, A.P., Stewart, C. Neal, Jr., Sustainable Use of Biotechnology for Bioenergy Feedstocks, Environmental Management, volume 46, issue 4, pp 531-538, 2010. Research Area: Biomass Formation and Modification 10.1007/s00267-010-9503-5
08/01/2013 Mostofian Simulation of a cellulose fiber in ionic liquid suggests a synergistic approach to dissolution

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Cellulose Mostofian, B., Smith, J.C., Cheng, X., Simulation of a cellulose fiber in ionic liquid suggests a synergistic approach to dissolution, 2013 Research Area: Characterization and Modeling 10.1007/s10570-013-0018-0
08/01/2008 Moxley Efficient Sugar Release by the Cellulose Solvent-Based Lignocellulose Fractionation Technology and Enzymatic Cellulose Hydrolysis

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Journal of Agricultural and Food Chemistry Moxley, Geoffrey, Zhiguang Zhu, and Y.-H. Percival Zhang ,Efficient Sugar Release by the Cellulose Solvent-Based Lignocellulose Fractionation Technology and Enzymatic Cellulose Hydrolysis , Journal of Agricultural and Food Chemistry, 56 (17), 7885–7890, 2008 Research Area: Biomass Deconstruction and Conversion 10.1021/jf801303f
12/01/2013 Muchero Genome resequencing in Populus: revealing large-scale genome variation and implications on specialized-trait genomics

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Challenges and Opportunities for the World's Forests in the 21st Century Muchero, W., Labbe, J., Ranjan, P., DiFazio, S., Tuskan, G.A., Genome resequencing in Populus: revealing large-scale genome variation and implications on specialized-trait genomics, Challenges and Opportunities for the World's Forests in the 21st Century Forestry Sciences, Volume 81, pp 587-595, 2013. Research Area: Biomass Formation and Modification 10.1007/978-94-007-7076-8_25
01/29/2013 Muchero Genome anchored QTLs for biomass productivity in hybrid populus grown under contrasting environments

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PLOS ONE Muchero, W., Sewell, M.M., Ranjan P., Gunter, L.E., Tschaplinski, T.J., Yin, T., Tuskan, G.A., Genome anchored QTLs for biomass productivity in hybrid populus grown under contrasting environments, PLOS ONE, 8(1): e54468, 2013. Research Area: Biomass Formation and Modification 10.1371/journal.pone.0014021
03/21/2011 Myung Ultra-stable phosphoglucose isomerase through immobilization of cellulosebinding module-tagged thermophilic enzyme on low-cost high-capacity cellulosic adsorbent

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Biotechnology Progress Myung, Suwan, Zhang, Xiao-Zhou, Zhang, Y.H. Percival, Ultra-stable phosphoglucose isomerase through immobilization of cellulose-binding module-tagged thermophilic enzyme on low-cost high-capacity cellulosic adsorbent, Biotechnology Progress, 27(4): 969-975, 2011. Research Area: Biomass Deconstruction and Conversion 10.1002/btpr.606
04/01/2010 Myung Fructose-1,6-bisphosphatase from a hyper-thermophilic bacterium Thermotoga maritime: Characterization, metabolite stability, and its implications

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Process Biochemistry Myung, S., Wang, Y. R., Zhang, Y. H. P., Fructose-1,6-bisphosphatase from a hyper-thermophilic bacterium Thermotoga maritima: Characterization, metabolite stability, and its implications, Process Biochemistry, Volume 45, Issue 12, pp 1882-1887, 2010. Research Area: Biomass Deconstruction and Conversion 10.1016/j.procbio.2010.03.017
02/09/2012 Nag Enhancing a Pathway-Genome Database (PGDB) to capture subcellular localization of metabolites and enzymes: the nucleotide-sugar biosynthetic pathways of Populus trichocarpa

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Database Nag, A., T. V. Karpinets, Chang, C.H., Bar-Peled, M., "Enhancing a Pathway-Genome Database (PGDB) to capture subcellular localization of metabolites and enzymes: the nucleotide-sugar biosynthetic pathways of Populus trichocarpa." Database Vol. 2012: Article ID bas013, 2012. Research Area: Biomass Formation and Modification 10.1093/database/bas013
08/16/2012 Nageswara-Rao Genetic diversity and structure of natural and agronomic switchgrass (Panicum virgatum L.) populations

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Genetic Resources and Crop Evolution Nageswara-Rao, M., Stewart Jr., C.N., Kwit, C., Genetic diversity and structure of natural and agronomic switchgrass (Panicum virgatum L.) populations, Genetic Resources and Crop Evolution, 60: 1057-1068, 2012. Research Area: Biomass Formation and Modification 10.1007/s10722-012-9903-x
05/01/2013 Nageswara-Rao Advances in biotechnology and genomics of switchgrass

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Biotechnology for Biofuels Nageswara-Rao, M., Soneji, J.R., Kwit, C., Stewart Jr., C.N., Advances in biotechnology and genomics of switchgrass, Biotechnology for Biofuels, 6:77, 2013. Research Area: Biomass Formation and Modification 10.1186/1754-6834-6-77
12/01/2012 Olson The role of the CipA scaffoldin protein in cellulose solubilization as determined by targeted gene deletion and complementation in Clostridium thermocellum

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Journal of Bacteriology Olson, D.G., Giannone, R.J., Hettich, R.L., Lynd, L.R., The role of the CipA scaffoldin protein in cellulose solubilization as determined by targeted gene deletion and complementation in Clostridium thermocellum, Journal of Bacteriology, 195(4):733-9, 2012. Research Area: Biomass Deconstruction and Conversion 10.1128/​JB.02014-12
05/11/2012 Olson Computational design and characterization of a temperature-sensitive plasmid replicon for gram positive thermophiles

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Journal of Biological Engineering Olson, D., Lynd, L.R., Computational design and characterization of a temperature-sensitive plasmid replicon for gram positive thermophiles, Journal of Biological Engineering, 6:5, 2012. Research Area: Biomass Deconstruction and Conversion 10.1186/1754-1611-6-5
05/17/2012 Olson Transformation of Clostridium Thermocellum by Electroporation

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Methods in Enzymology Olson, D.G., Lynd, L.R., Transformation of Clostridium Thermocellum by Electroporation, Methods in Enzymology, 510, p 317-330, 2012. Research Area: Biomass Deconstruction and Conversion 10.1016/B978-0-12-415931-0.00017-3
12/14/2011 Olson Recent progress in consolidated bioprocessing

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Current Opinion in Biotechnology Olson, D. G., J. E. McBride, et al. (2011). "Recent progress in consolidated bioprocessing." Current Opinion in Biotechnology. (published ahead of print doi:10.1016/j.copbio.2011.11.026) Research Area: Biomass Deconstruction and Conversion 10.1016/j.copbio.2011.11.026
08/16/2010 Olson Deletion of Cel48S from Clostridium thermocellum

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PNAS Olson, Daniel G., Tripathi, Shital A., Giannone, Richard J., Lo, Jonathan, Caiazza, Nicky C., Hogsett, David A.,Hettich, Robert, Guss, Adam M., Dubrovsky, Genia, Lynd, Lee R., Deletion of Cel48S from Clostridium thermocellum, PNAS, Volume 107, Issue 41, pp 17727-17732, 2010. Research Area: Biomass Deconstruction and Conversion 10.1073/pnas.1003584107
11/19/2011 Ozdemir S-layer homology (SLH) domain proteins Csac_0678 and Csac_2722 implicated in plant polysaccharide deconstruction by the extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus

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Applied and Environmental Microbiology Ozdemir, I., S. E. Blumer-Schuette, et al. (2012). "S-layer homology (SLH) domain proteins Csac_0678 and Csac_2722 implicated in plant polysaccharide deconstruction by the extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus." Applied and Environmental Microbiology 78(3):768-777. Research Area: Biomass Deconstruction and Conversion 10.1128/AEM.07031-11
12/01/2010 Park CAZymes Analysis Toolkit (CAT): Web service for searching and analyzing carbohydrate-active enzymes in a newly sequenced organism using CAZy database

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Glycobiology Park, Byung H., Karpinets, Tatiana V., Syey, Mustafa, H., Leuze, Michael R., Uberbacher, Edward C., CAZymes Analysis Toolkit (CAT): Web service for searching and analyzing carbohydrate-active enzymes in a newly sequenced organism using CAZy database, Glycobiology, 20:12, 1574-1584, 2010. Research Area: Characterization and Modeling 10.1093/glycob/cwq106
04/04/2013 Passian Comments on the paper 'A comprehensive modeling and vibration analysis of AFM microcantilevers subjected to nonlinear tip-sample interaction forces'

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Ultramicroscopy Passian, A., Tetard, L., Thundat, T., Comments on the paper 'A comprehensive modeling and vibration analysis of AFM microcantilevers subjected to nonlinear tip-sample interaction forces, Ultramicroscopy, 131:92-93, 2013. Research Area: Characterization and Modeling 10.1016/j.ultramic.2013.03.016
07/31/2012 Pattathil Changes in Cell Wall Carbohydrate Extractability Are Correlated with Reduced Recalcitrance of HCT Downregulated Alfalfa Biomass

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Industrial Biotechnology Pattathil, S., Saffold, T., Gallego-Giraldo, L., O'Neill, M., York, W.S., Dixon, R.A., Hahn, M.G., Changes in Cell Wall Carbohydrate Extractability Are Correlated with Reduced Recalcitrance of HCT Downregulated Alfalfa Biomass, Industrial Biotechnology, 8:4, 2012. Research Area: Biomass Formation and Modification 10.1089/ind.2012.0013
08/01/2012 Pattathil Immunological Approaches to Plant Cell Wall and Biomass Characterization: Glycome Profiling Methods in Molecular Biology Biomass Conversion: Methods and Protocols Pattathil, S., Avci, U., Miller, J.S., Hahn, M.G., Immunological Approaches to Plant Cell Wall and Biomass Characterization: Glycome Profiling, Methods in Molecular Biology Biomass Conversion: Methods and Protocols, 908:61-72, 2012. Research Area: Biomass Deconstruction and Conversion 10.1007/978-1-61779-956-3_6
10/22/2009 Patten Probing native lignin macromolecular configuration in Arabidopsis thaliana in specific cell wall types: Further insights into limited substrate degeneracy and assembly of the lignins of ref8, fah 1–2 and C4H::F5H lines

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Molecular BioSystems Patten A.M., Jourdes, M., Cardenas, C.L., Laskas, D.D., Nakazawa, Y., Chung, B.Y., Franceschi, V.R., Davin, L.B., Lewis, N.G., Probing native lignin macromolecular configuration in Arabidopsis thaliana in specific cell wall types: Further insights into limited substrate degeneracy and assembly of the lignins of ref8, fah 1–2 and C4H::F5H lines, Molecular BioSystems, 6:3:pp 425-604, 2010. Research Area: Biomass Deconstruction and Conversion 10.1039/b819206e
05/17/2012 Pena Methods for Structural Characterization of the Products of Cellulose - and Xyloglucan-Hydrolyzing Enzymes

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Methods in Enzymology Pena, Maria J., Tuomivaara, S.T., Urbanowicz, B.R., O'Neill, M.A., York, W.S., Methods for Structural Characterization of the Products of Cellulose - and Xyloglucan-hydrolyzing Enzymes, Methods in Enzymology, 510, p 121-139, 2012. Research Area: Biomass Formation and Modification 10.1016/B978-0-12-415931-0.00007-0
01/30/2014 Penning Validation of PyMBMS as a high-throughput screen for lignin abundance in lignocellulosic biomass of grasses

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Bioenergy Research Penning, B.W., Sykes, R.W., Babcock, N.C., Dugard, C.K., Klimek, J.F., Gamblin, D., Davis, M., Filley, T.R., Mosier, N.S., Weil, C.F., McCann, M.C., Carpita, N.C., Validation of PyMBMS as a high-throughput screen for lignin abundance in lignocellulosic biomass of grasses, Bioenergy Research, 2014 Research Area: Characterization and Modeling 10.1007/s12155-014-9410-3
12/01/2008 Petridis Cellulosic ethanol: progress towards a simulation model of lignocellulosic biomass

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Journal of Physics L Petridis and J C Smith, Cellulosic ethanol: progress towards a simulation model of lingnocellulosic biomass, Journal of Physics, Conference Series, Vol. 125, pp 012055, 2008. Research Area: Characterization and Modeling 10.1088/1742-6596/125/1/012055
04/01/2011 Petridis Atomistic Simulation of Lignocellulosic Biomass and Associated Cellulosomal Protein Complexes

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ACS Symposium Series - Computational Modeling in Lignocellulosic Biofuel Production Petridis, L. and Xu, J. and Crowley, M. F. and Smith, J. C. and Cheng, X. Atomistic Simulation of Lignocellulosic Biomass and Associated Cellulosomal Protein Complexes. 2010. In book "ACS Symposium Series - Computational Modeling in Lignocellulosic Biofuel Production", (editors: Mark R. Nimlos and Michael F. Crowley), publisher ACS, Chapter 3, pp. 55-73. Research Area: Characterization and Modeling 10.1021/bk-2010-1052.ch003
03/12/2010 Petridis A Molecular Mechanics Force Field for Lignin

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Journal of Computational Chemistry Petridis, L., Smith, J.C., A Molecular Mechanics Force Field for Lignin, Journal of Computational Chemistry, 30(3), pp 457-67, 2009. Research Area: Characterization and Modeling
10/01/2009 Podar Single Cell Whole Genome Amplification of Uncultivated Organisms

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Uncultivated Microorganisms Microbiology Monographs Podar, Mircea, Keller, Martin, Hugenholtz, Philip, 2009, Singel Cell Whole Genome Amplification of Uncultivated Organisms, Microbial Monogr, Series; Volume 10/2009. Research Area: Biomass Deconstruction and Conversion 10.1007/7171_2008_10
12/29/2010 Podkaminer Enzyme inactivation by ethanol and development of a kinetic model for thermophilic simultaneous saccharification and fermentation at 50°C with Thermoanaerobacterium saccharolyticum ALK2

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Biotechnology and Bioengineering Podkaminer, Kara K., Hogsett, David A., Shao, Xiongjun, Lynd, Lee R., Enzyme inactivation by ethanol and development of a kinetic model for thermophilic simultaneous saccharification and fermentation at 50°C with Thermoanaerobacterium saccharolyticum ALK2, Biofuels and Environmental Biotechnology, 108(6), 2011. Research Area: Biomass Deconstruction and Conversion 10.1002/bit.23050
06/15/2012 Podkaminer Ethanol and anaerobic conditions reversibly inhibit commercial cellulase activity in thermophilic simultaneous saccharification and fermentation (tSSF)

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Biotechnology for Biofuels Podkaminer, K.K., Kenealy, W.R., Herring, C.D., Hogsett, D.A., Lynd, L.R., Ethanol and anaerobic conditions reversibly inhibit commercial cellulase activity in thermophilic simultaneous saccharification and fermentation (tSSF), Biotechnology for Biofuels, 5:43, 2012. Research Area: Biomass Deconstruction and Conversion 10.1186/1754-6834-5-43
09/28/2012 Podkaminer Characterization of xylan utilization and discovery of a new endoxylanase in Thermoanaerobacterium saccharolyticum through targeted gene deletions

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Applied and Environmental Microbiology Podkaminer, K.K., Guss, A.M., Trajano, H.L., Hogsett, D.A., Lynd, L.R., Characterization of xylan utilization and discovery of a new endoxylanase in Thermoanaerobacterium saccharolyticum through targeted gene deletions, Applied and Environmental Microbiology, 78:8441-7, 2012 Research Area: Biomass Deconstruction and Conversion 10.1128/AEM.02130-12
12/20/2012 Porth Populus trichocarpa cell wall chemistry and ultrastructure trait variation, genetic control and genetic correleations

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New Phytologist Porth, I., Klapste, J., Skyba, O., Lai, B.S.K., Geraldes, A., Muchero, W., Tuskan, G.A., Douglas, C.J., El-Kassaby, Y.A., Mansfield, S.D., Populus trichocarpa cell wall chemistry and ultrastructure trait variation, genetic control and genetic correleations, New Phytologist, 197: 777–790, 2012. Research Area: Biomass Formation and Modification 10.1111/nph.12014
01/28/2013 Pu Assessing the molecular structure basis for biomass recalcitrance during dilute acid and hydrothermal pretreatments

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Biotechnology for Biofuels Pu, Y., Hu, F., Huang, F., Davison, B.H., Ragauskas, A.J., Accessing the molecular structure basis for biomass recalcitrance furing dilute acid and hydrothermal pretreatments, Biotechnology for Biofuels, 6:15, 2013. Research Area: Characterization and Modeling 10.1186/1754-6834-6-15
05/01/2013 Pu Plant biomass characterization: application of solution- and solid-state NMR spectroscopy

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Aqueous Pretreatment of Plant Biomass for Biological and Chemical Conversion to Fuels and Chemicals Pu, Y., Hallac, B., Ragauskas, A.J., Plant biomass characterization: application of solution- and solid-state NMR spectroscopy, Aqueous Pretreatment of Plant Biomass for Biological and Chemical Conversion to Fuels and Chemicals, (ed Wyman, C.E.), chapter 18, pp 369-387, 2013. Research Area: Characterization and Modeling 10.1002/9780470975831.ch18
05/01/2011 Pu Application of quantitative P31 NMR in biomass lignin and biofuel precursors characterization

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Energy and Environmental Science Pu, Y., Cao, S., Ragauskas, A.J., Application of quantitative 31P NMR in biomass lignin and biofuel precursors characterization, Energy and Environmental Science, 4, pp 3154-3166, Jun 2011. Research Area: Characterization and Modeling 10.1039/c1ee01201k
09/01/2011 Pu Challenges of the utilization of wood polymers: how can they be overcome?

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Applied Microbiology and Biotechnology Pu, Y., Kosa, M., Kalluri, U.C., Tuskan, G.A., Ragauskas, A.J., Challenges of the utilization of wood polymers: how can they be overcome?, Applied Microbiology and Biotechnology, 91(6): 1525-1536, 2011. Research Area: Biomass Formation and Modification 10.1007/s00253-011-3350-z
12/01/2009 Pu NMR Characterization of C3H and HCT Down-regulated Alfalfa Lignin

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BioEnergy Research Yunqiao Pu, Fang Chen, Angela Ziebell, Brian H. Davison and Arthur J. Ragauskas, NMR Characterization of C3H and HCT Down-regulated Alfalfa Lignin, Bioenergy Research, Volume 2, Number 4 / December, 2009 2:198-208 Research Area: Characterization and Modeling 10.1007/s12155-009-9056-8
05/01/2013 Qing Xylooligosaccharides production, quantification, and characterization in context of lignocellulosic biomass pretreatment

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Aqueous Pretreatment of Plant Biomass for Biological and Chemical Conversion to Fuels and Chemicals Qing, Q., Li, H., Kumar, R., Wyman, C.E., Xylooligosaccharides production, quantification, and characterization in context of lignocellulosic biomass pretreatment, Aqueous Pretreatment of Plant Biomass for Biological and Chemical Conversion to Fuels and Chemicals, (ed Wyman, C.E.), chapter 19, pp 391-410, 2013. Research Area: Characterization and Modeling 10.1002/9780470975831.ch19
05/01/2013 Ragauskas When to accept no … to yesterday's solutions

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Biofuels, Bioproducts and Biorefining Ragauskas, A.J., When to accept no … to yesterday's solutions, Biofuels, Bioproducts and Biorefining, 7(3), 2013. Research Area: Characterization and Modeling 10.1002/bbb.1414
04/22/2009 Raman Impact of pretreated switchgrass and biomass carbohydrates on Clostridium thermocellum ATCC 27405 cellulosome composition: a quantitative proteomic analysis

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PLoS One Raman, B., Pan, C., Hurst, G. B., Rodriguez, M., McKeown, C. K., Lankford, Samatova, N. F., Mielenz, J. R., Impact of Pretreated Switchgrass and Biomass Carbohydrates on Clostridium thermocellum ATCC 27405 Cellulosome Composition: A Quantitative Proteomic Analysis, Plos One, 4(4): e5271 (2009) Research Area: Biomass Deconstruction and Conversion 10.1371/journal.pone.0005271
06/14/2011 Raman Transcriptomic analysis of Clostridium thermocellum ATCC 27405 cellulose fermentation

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BMC Microbiology Raman, B., McKeown, Catherine K., Rodriguez Jr, M., Brown, Steven D., Mielenz, Jonathan R., Transcriptomic analysis of Clostridium thermocellum ATCC 27405 cellulose fermentation, BMC Microbiology, 11:134, 2011. Research Area: Biomass Deconstruction and Conversion 10.1186/1471-2180-11-134
01/01/2013 Ramanna Rationale for developing new virus vectors to analyze gene function in grasses through virus-induced gene silencing Methods and Protocols Series; Methods in Molecular Biology, Volume 975 Ramanna, H., Ding, X.S., Nelson, R.S., Rationale for developing new virus vectors to analyze gene function in grasses through virus-induced gene silencing, Methods in Molecular Biology, 975, 15-32, 2013. Research Area: Biomass Formation and Modification 10.1007/978-1-62703-278-0_2.
11/01/2009 Ranjan Bioinformatics-Based Identification of Candidate Genes from QTLs Associated with Cell Wall Traits in Populus

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BioEnergy Research Ranjan P, Yin T, Zhang X, Kalluri U.C, Yang X, Jawdy S, Tuskan G A, Bioinformatics‐based identification of candidate genes from QTLs associated with cell wall traits in Populus, BioEnergy Research,3;2, pp 172-182, 2009. Research Area: Biomass Formation and Modification 10.1007/s12155-009-9060-z
10/01/2013 Ratnaparkhe Analyses using cell wall glycan-directed monoclonal antibodies reveal xylan-degration by two microbial glycosyl hydrolases in cell walls from poplar and switchgrass biomass

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Bioremediation & Biodegradation Ratnaparkhe, S., Venkatachalam, S., Hah, M.G., Pattathil, S., Analyses using cell wall glycan-directed monoclonal antibodies reveal xylan-degration by two microbial glycosyl hydrolases in cell walls from poplar and switchgrass biomass, Bioremediation & Biodegradation, s4, 2013. Research Area: Characterization and Modeling 10.4172/2155-6199.S4-004
12/12/2013 Reed Cellulose fermentation by C. thermocellum and a mixed consortium in an automated repetitive batch reactor Bioresource Technology Reed, P.T., Izquierdo, J.A., Lynd, L.R., Cellulose fermentation by C. thermocellum and a mixed consortium in an automated repetitive batch reactor, Bioresource Technology, 2013 Research Area: Biomass Deconstruction and Conversion 10.1016/j.biortech.2013.12.051
04/08/2013 Resch Fungal cellulases and complexed cellulosomal enzymes exhibit synergistic mechanisms in cellulose deconstruction

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Energy and Environmental Science Resch, M.G., Donohoe, B.S., Baker, J.O., Decker, S.R., Bayer, E.A., Beckham, G.T., Himmel, M.E., Fungal cellulases and complexed cellulosomal enzymes exhibit synergistic mechanisms in cellulose deconstruction, Energy and Environmental Science, 6; 1858-1867, 2013. Research Area: Biomass Deconstruction and Conversion 10.1039/C3EE00019B
03/18/2014 Reyes-Hernandez The root indeterminacy-to-determinacy developmental switch is operated through a folate-dependent pathway in Arabidopsis thaliana

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New Phytologist Reyes-Hernandez, B.J., Srivastava, A.C., Ugartechea-Chirino, Y., Shishkova, S., Ramos-Parra, P.A., Lira-Ruan, V., Diaz de la Garza, R.I., Dong, G., Moon, J.C., Blancaflor, E.B. Dubrovsky, J. G., The root indeterminacy-to-determinacy developmental switch is operated through a folate-dependent pathway in Arabidopsis thaliana, New Phytologist, 2014 Research Area: Biomass Formation and Modification 10.1111/nph.12757
03/01/2014 Robinson Farming for Fuels

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Dimensions Robinson, W., “Farming for Fuels”, Dimensions, 16(2) 46-48, 2014 Research Area: Characterization and Modeling
09/10/2013 Rodgers-Melnick Predicting whole genome protein interaction networks from primary sequence data in model and non-model organisms using ENTS BMC Genomics Rodgers-Melnick, E., Culp, M., DiFazio, S.P., Predicting whole genome protein interaction networks from primary sequence data in model and non-model organisms using ENTS, BMC Genomics, 14:608, 2013. Research Area: Biomass Formation and Modification 10.1186/1471-2164-14-608
10/05/2011 Rodgers-Melnick Contrasting Patterns of Evolution Following Whole Genome versus Tandem Duplication Events in Populus

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Genome Research Rodgers-Melnick, E., Mane, S.P., Dharmawardhana, P., Slavov, G.T., Crasta, O.R., Strauss, S.H., Brunner, A.M., DiFazio, S.P. (2011) "Contrasting Patterns of Evolution Following Whole Genome versus Tandem Duplication Events in Populus," Genome Research, 22:95-105. Research Area: Biomass Formation and Modification 10.1101/gr.125146.111
08/30/2010 Rollin Increasing cellulose accessibility is more important than removing lignin: A comparison of cellulose solvent-based lignocellulose fractionation and soaking in aqueous ammonia

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Biotechnology and Bioengineering Rollin, J. A., Zhu, Z. G., Sathitsuksanoh, N., Zhang, Y. H. P., Increasing Cellulose Accessibility Is More Important Than Removing Lignin: A Comparison of Cellulose Solvent-Based Lignocellulose Fractionation and Soaking in Aqueous Ammonia, Biotechnology and Bioengineering, Volume 108, Issue 1, pp 22-30, 2011 Research Area: Biomass Deconstruction and Conversion 10.1002/bit.22919
06/29/2010 Saar Label-free, real-time monitoring of biomass processing with stimulated Raman scattering microscopy

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Angewandte Chemie Saar, B.G., Zeng, Y., Freudiger, C.W., Liu, Y.S., Himmel, M.E., Xie, S.X., Ding, S.Y., Label-free, real-time monitoring of biomass processing with stimulated Raman scattering microscopy, Angewandte Chemie, Volume 49, Issue 32, pp 5476-5479, 2011. Research Area: Characterization and Modeling 10.1002/ange.201000900
04/09/2013 Saha Self-rescue of an EXTENSIN mutant reveals alternative gene expression programs and candidate proteins for new cell wall assembly in Arabidopsis

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The Plant Journal Saha, P., Ray, T., Tang, Y., Dutta, I., Evangelous, N.R., Kieliszewski, M.J., Chen, Y., Cannon, M.C., Self-rescue of an EXTENSIN mutant reveals alternative gene expression programs and candidate proteins for new cell wall assembly in Arabidopsis, The Plant Journal, 75(1):104-16, 2013. Research Area: Biomass Formation and Modification 10.111/tpj.12204
10/12/2010 Saharay Catalytic Mechanism of Cellulose Degradation by a Cellobiohydrolase, CelS

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PloS One Saharay, M., Guo, H., Smith, J.C., Catalytic Mechanism of Cellulose Degradation by a Cellobiohydrolase, CelS, Plos One, 5(10), e12947, 2010. Research Area: Characterization and Modeling 10.1371/ journal.pone.0012947
04/11/2011 Samuel HSQC (heteronuclear single quantum coherence) 13C–1H correlation spectra of whole biomass in perdeuterated pyridinium chloride–DMSO system: An effective tool for evaluating pretreatment

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Fuel Samuel, R., Foston, M., Jaing, N., Cao, S., Allison, L., Studer, M., Wyman, C., Ragauskas, A.J., HSQC (heteronuclear single quantum coherence) 13C–1H correlation spectra of whole biomass in perdeuterated pyridinium chloride–DMSO system: An effective tool for evaluating pretreatment, Fuel, 90(9): 2836-2842, 2011. Research Area: Characterization and Modeling 10.1016/j.fuel.2011.04.021
08/25/2011 Samuel Structural Changes in switchgrass lignin and hemicelluloses during pretreatments by NMR analysis

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Polymer Degradation and Stability Samuel, R., Foston, M., Jiang, N., Allison, L., Ragauskas, A.J., Structural Changes in Switchgrass Lignin and Hemicelluloses during Pretreatments by NMR Analysis Polymer Degradation and Stability, Polymer Degradation and Stability, 96(11):2002-2009, 2011. Research Area: Biomass Deconstruction and Conversion 10.1016/j.polymdegradstab.2011.08.015
08/24/2009 Samuel Structural characterization and comparison of switchgrass ball milled lignin before and after dilute acid pretreatment

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Applied Biochemistry and Biotechnology Samuel,R., Pu, Y., Babu, R., Ragauskas, A.J.Structural Characterizations and comparison of switchgrass lignin before and after dilute acid pretreatment A. Applied Biochemistry and Biotechnology, 162 (1), 62-74, 2010. Research Area: Characterization and Modeling 10.1007/s12010-009-8749-y
01/01/2010 Samuel Solid-state NMR characterization of switchgrass cellulose after dilute acid pretreatment

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Biofuels Samuel, R., Pu, Y., Foston, M., Ragauskas, A.J., Solid-state NMR characterization of switchgrass cellulose after dilute acid pretreatment, Biofuels, 1:1, pp 89-90, 2010. Research Area: Characterization and Modeling 10.4155/bfs.09.17
02/04/2013 Samuel Investigation of the fate of poplar lignin during autohydrolysis pretreatment to understand the biomass recalcitrance

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RCS Advances Samuel, R., Cao, S., Das, B.K., Hu, F., Pu, Y., Ragauskas, A.J., Investigation of the fate of poplar lignin during autohydrolysis pretreatment to understand the biomass recalcitrance, RCS Adv., , 3 (16), 5305 - 5309, 2013. Research Area: Characterization and Modeling 10.1039/C3RA40578H
01/20/2014 Samuel Structural characterization of lignin in wild-type versus COMT down-regulated switchgrass

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Frontiers in Energy Research Samuel, R., Pu, Y., Jiang, N., Fu, C., Wang, Z.Y., Ragauskas, A., Structural characterization of lignin in wild-type versus COMT down-regulated switchgrass, Frontiers in Energy Research, 14;1, 2014. Research Area: Characterization and Modeling 10.3389/fenrg.2013.00014
12/30/2013 Sangha Chemical Factors that control lignin polymerization

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The Journal of Physical Chemistry B Sangha, A.K., Davison, B.H., Standaert, R.F., Davis, M.F., Smith, J.C., Parks, J.M., Chemical factors that control lignin polymerization, The Journal of Physical Chemistry B, 118 (1), pp 164-170, 2014. Research Area: Characterization and Modeling 10.1021/jp411998t
12/30/2011 Sangha Molecular simulation as a tool for studying lignin

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Environmental Progress and Sustainable Energy Sangha, A. K., L. Petridis, et al. (2012). Molecular simulation as a tool for studying lignin. Environmental Progress and Sustainable Energy 31(1): 47-54. Research Area: Characterization and Modeling 10.1002/ep.10628
04/04/2012 Sangha Radical Coupling Reactions in Lignin Synthesis: A Density Functional Theory study

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The Journal of Physical Chemistry B Sangha, A.K., Parks, J.M., Standaert, R.F., Ziebell, A., Davis, M.F., Smith, J.C., Radical Coupling Reactions in Lignin Synthesis: A DFT study, The Journal of Physical Chemistry B, 2012 Research Area: Characterization and Modeling 10.1021/jp2122449
12/01/2011 Sannigrahi Characterization of Fermentation Residues from the Production of Bio-Ethanol from Lignocellulosic Feedstocks

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Journal of Biobased Materials and Bioenergy Sannigrahi, P. and A. J. Ragauskas (2011). "Characterization of Fermentation Residues from the Production of Bio-Ethanol from Lignocellulosic Feedstocks." Journal of Biobased Materials and Bioenergy 5(4): 514-519. Research Area: Characterization and Modeling 10.1166/jbmb.2011.1170
05/01/2013 Sannigrahi Fundamentals of biomass pretreatment by fractionation

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Aqueous Pretreatment of Plant Biomass for Biological and Chemical Conversion to Fuels and Chemicals Sannigrahi, P., Ragauskas, A.J., Fundamentals of biomass pretreatment by fractionation, Aqueous Pretreatment of Plant Biomass for Biological and Chemical Conversion to Fuels and Chemicals, (ed Wyman, C.E.), chapter 10, pp 201-219, 2013. Research Area: Characterization and Modeling 10.1002/9780470975831.ch10
12/01/2010 Sannigrahi Pseudo-lignin and pretreatment chemistry

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Energy and Environmental Science Sannigrahi, P., Kim, Dong Ho., Seokwon, Jung, Ragauskas, Arthur, Pseudo-lignin and pretreatment chemistry, Energy and Environmental Science, 4:4:1306-1310, 2011. Research Area: Characterization and Modeling 10.1039/c0ee00378f
03/01/2010 Sannigrahi Poplar as a feedstock for biofuels: A review of compositional characteristics

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Biofuels, Bioproducts and Biorefining (Biofpr) Sannigrahi, P., Ragauskas, A.J., Tuskan, G.A., Poplar as a feedstock for biofuels: A review of compositional characteristics, Biofuels Bioproducts and Biorefining-Biofpr, Volume 4, Issue2, pp 209-226 2010. Research Area: Biomass Formation and Modification 10.1002/bbb.206
05/28/2009 Sathitsuksanoh Saccharification of a potential bioenergy crop, Phragmites australis (common reed), by lignocellulose fractionation followed by enzymatic hydrolysis at decreased cellulase loadings

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Industrial & Engineering Chemistry Research Sathitsuksanoh, N., Zhu, Z. G., Templeton, N., Rollin, J. A., Harvey, S. P., Zhang, Y. H. P., Saccharification of a Potential Bioenergy Crop, Phragmites australis (Common Reed), by Lignocellulose Fractionation Followed by Enzymatic Hydrolysis at Decreased Cellulase Loadings, Industrial and Engineering Chemistry Research, Volume 48; Issue 13; pp 6441-6447; July 1, 2009. Research Area: Biomass Deconstruction and Conversion 10.1021/ie900291s
11/12/2010 Sathitsuksanoh Cellulose solvent-based pretreatment breaks highly ordered hydrogen bonds in cellulose fibers of switchgrass

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Biotechnology and Bioengineering Sathitsuksanoh, Noppadon, Zhu, Zhiguang, Wi, Sungsool, Zhang, Y.H-P, Cellulose Solvent-Based Biomass Pretreatment Breaks Highly Ordered Hydrogen Bonds in Cellulose Fibers of Switchgrass, Biotechnology and Bioengineering, 2011;108: 521-529, 2010. Research Area: Biomass Deconstruction and Conversion 10.1002/bit.22964
09/25/2009 Sathitsuksanoh Bamboo saccharification through cellulose solvent-based biomass pretreatment followed by enzymatic hydrolysis at ultra-low cellulase loadings

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Bioresource Technology Sathitsuksanoh N, Zhu ZG, Ho T-J, Bai M-D, Zhang Y-HP,Bamboo saccharification through cellulose solvent-based biomass pretreatment followed by enzymatic hydrolysis at ultra-low cellulase loadings Volume 101, Issue 13, July 2010, Pages 4926-4929, 2009. Research Area: Biomass Deconstruction and Conversion 10.1016/j.biortech.2009.09.081
11/30/2012 Sathitsuksanoh New lignocellulose pretreatments using cellulose solvents: a review

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Journal of Chemical Technology and Biotechnology Sathitsuksanoh, N., George, A., Zhang, Y-H P., New lignocellulose pretreatments using cellulose solvents: a review, Journal of Chemical Technology and Biotechnology, 88 (2), 169-180, 2012. Research Area: Biomass Deconstruction and Conversion 10.1002/jctb.3959
09/27/2013 Sathitsuksanoh Overcoming biomass recalcitrance by combining genetically modified switchgrass and cellulose solvent-based lignocellulose pretreatment

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Plos One Sathitsuksanoh, N., Xu, B., Zhao, B., Zhang, Y.-H. P., Overcoming biomass recalcitrance by combining genetically modified switchgrass and cellulose solvent-based lignocellulose pretreatment, Plos One, 8(9): e73523, 2013. Research Area: Biomass Deconstruction and Conversion 10.1371/journal.pone.0073523
04/01/2012 Sathitsuksanoh Cellulose solvent-based pretreatment for corn stove rand avicel: concentrated phosphoric acid versus ionic liquid [BMIM]C1

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Cellulose Sathitsuksanoh, N., Zhu, Z., Zhang, Y.H.P., Cellulose solvent-based pretreatment for corn stove rand avicel: concentrated phosphoric acid versus ionic liquid [BMIM]C1, Cellulose, 2012. Research Area: Biomass Deconstruction and Conversion 10.1007/s10570-012-9719-z
04/21/2012 Sathitsuksanoh Cellulose solvent - and organic solvent-based lignocellulose fractionation enabled efficient sugar release from a variety of lignocellulosic feedstocks

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Bioresource Technology Sathitsuksanoh, N., Zhu, Z., Zhang, Y-H.P., Cellulose solvent - and organic solvent-based lignocellulose fractionation enabled efficient sugar release from a variety of lignocellulosic feedstocks, Bioresource Technology, 2012. Research Area: Biomass Deconstruction and Conversion 10.1016/j.biotech.2012.04.088
10/01/2009 Schulz Scaling of Multimillion-Atom Biological Molecular Dynamics Simulation on a Petascale Supercomputer

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Journal of Chemical Theory and Computation Roland Schulz, Benjamin Lindner, Loukas Petridis, and Jeremy C. Smith, Scaling of Multimillion-Atom Biological Molecular Dynamics Simulation on a Petascale Supercomputer, Journal of Chemical Theory and Computation2009, 5, 2798-2808, 2009. Research Area: Characterization and Modeling 10.1021/cr900292r
04/01/2010 Selig Lignocellulose recalcitrance screening by integrated high- throughput hydrothermal pretreatment and enzymatic

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Industrial Biotechnology Selig, Michael J., Tucker, Melvin P., Sykes, R., Reichel, D., Brunecky, R., Himmel, M.E., Davis, M.F., Decker, S.R., Biomass Recalcitrance Screening by Integrated High Throughput Hydrothermal Pretreatment and Enzymatic Saccharification, Industrial Biotechnology , Volume 6 (2) Apr 1, 2010. Research Area: Biomass Deconstruction and Conversion
02/02/2011 Selig High-Throughput Determination of Glucan and Xylan Fractions in Lignocelluloses

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Biotechnology Letters Selig, Michael J., Tucker, Melvin P., Law, Cody, Doeppke, Crissa, Himmel, Michael E., Decker, Stephen R., High throughput determination of glucan and xylan fractions in lignocelluloses, Biotechnology Letters, 33(5): 961-975, 2011. Research Area: Biomass Deconstruction and Conversion 10.1007/s10529-011-0526-7
03/24/2013 Serba Linkage maps of lowland and upland tetraploid switchgrass ecotypes

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Bioenergy Research Serba, D., Wu, L., Daverdin, G., Bahri, B.A., Wang, X., Kilian, A., Bouton, J.H., Brummer, E.C., Saha, M.C., Devos, K.M., Linkage maps of lowland and upland tetraploid switchgrass ecotypes, Bioenergy Research, 6 (3), 953-965, 2013. Research Area: Biomass Formation and Modification 10.1007/s12155-013-9315-6
12/10/2012 Shao Kinetic modeling of xylan hydrolysis in co- and countercurrent liquid hot water flow-through pretreatments Bioresource Technology Shao, X., Lynd, L., Kinetic modeling of xylan hydrolysis in co- and countercurrent liquid hot water flow-through pretreatments, Bioresource Technology, 130, pp 117-124, 2012. Research Area: Biomass Deconstruction and Conversion 10.1016/j.biortech.2012.11.109
06/01/2011 Shao Conversion for Avicel and AFEX pretreated corn stover by Clostridium thermocellum and simultaneous saccharification and fermentation: Insights into microbial conversion of pretreated cellulosic biomass

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Bioresource Technology Shao, X., Jin, M., Guseva, A., Liu, C., Balan, V., Hogsett, D., Dale, B.E., Lynd, L, Conversion for Avicel and AFEX pretreated corn stover by Clostridium thermocellum and simultaneous saccharification and fermentation: Insights into microbial conversion of pretreated cellulosic biomass, Bioresource Technology, 102(17): 8040-8045, 2011. Research Area: Biomass Deconstruction and Conversion 10.1016/j.biortech.2011.05.021
08/27/2011 Shao Mutant selection and phenotypic and genetic characterization of ethanol-tolerant strains of Clostridium thermocellum

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Applied Microbiology and Biotechnology Shao, X., Raman, B., Zhu, M., Mielenz, J.R., Brown, S.D., Guss, A.M., Lynd, L.R., Mutant selection and phenotypic and genetic characterization of ethanol-tolerant strains of Clostridium thermocellum, Applied Microbiology and Biotechnology, 92(3):641-652, 2011 Research Area: Biomass Deconstruction and Conversion 10.1007/s00253-011-3492-z
05/01/2010 Shaw Natural Competence in Thermoanaerobacter and Thermoanaerobacterium Species

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Applied and Environmental Microbiology Shaw, A., Joe, Hogsett, David A., Lynd, Lee R., Natural Competence in Thermoanaerobacter and Thermoanaerobacterium Species, Applied and Environmental Microbiology, Volume 76, Issue 14, pp 4713-4719, July 2010. Research Area: Biomass Deconstruction and Conversion 10.1128/AEM.00402-10
10/20/2009 Shen Developmental control of lignification in stems of lowland switchgrass variety Alamo and the effects on saccharification efficiency

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BioEnergy Research Shen H, Fu C, Xiao X, Ray T, Tang Y, Wang Z. and Chen F. (2009) Developmental Control of Lignification in Stems of Lowland Switchgrass Variety Alamo and the Effects on Saccharification Efficiency. Bioenerg. Res. 2:233–245, Volume 2, Number 4 / December, 2009, pp 233-245 Research Area: Biomass Formation and Modification 10.1007/s12155-009-9058-6
10/11/2011 Shen Functional characterization of the switchgrass (Panicum virgatum) R2R3-MYB transcription factor PvMYB4 for improvement of lignocellulosic feedstocks

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New Phytologist Shen, H., He, X., Poovaiah, C.R., Wuddineh, W.A., Ma, J., Mann, D.G.J., Abercrombie, L.A., Wang, H., Jackson, L., Tang, Y., Stewart, C.N. Jr., Chen, F. and Dixon, R.A, Functional characterization of the switchgrass (Panicum virgatum) R2R3-MYB transcription factor PvMYB4 for improvement of lignocellulosic feedstocks, New Phytologist, 2012 Jan;193(1):121-36. Research Area: Biomass Formation and Modification 10.1111/j.1469-8137.2011.03922
10/16/2009 Shen A Bioinformatic Analysis of NAC Genes for Plant Cell Wall Development in Relation to Lignocellulosic Bioenergy Production BER-120R1

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BioEnergy Research Shen H, Yin Y, Chen F, Xu Y and Dixon RA (2010) A Bioinformatic Analysis of NAC Genes for Plant Cell Wall Development in Relation to Lignocellulosic Bioenergy Production. Bioenergy Research, Volume 2, Number 4 / December, 2009, pp 217-232 Research Area: Biomass Formation and Modification 10.1007/s12155-009-9047-9
04/01/2013 Shen Enhanced characteristics of genetically modified switchgrass (Panicum virgatum L.) for high biofuel production

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Biotechnology for Biofuels Shen, H., Pooviah, C.R., Ziebell, A., Tschaplinski, T.J., Pattathil, S., Gjersing, E., Engle, N.L., Katahira, R., Pu, Y., Sykes, R., Chen, F., Ragauskas, A.J., Mielenz, J.R., Hahn, M.G., Davis, M., Stewart, Jr., N., Dixon, R.A., Enhanced characteristics of genetically modified switchgrass (Panicum virgatum L.) for high biofuel production, Biotechnology for Biofuels, 5:71, 2013. Research Area: Biomass Formation and Modification 10.1186/1754-6834-6-71
11/30/2013 Shen A genomics approach to deciphering lignin biosynthesis in swithgrass

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Plant Cell Shen, H., Hisano, H., Hardin, F., Mazarei, M., Fu, C., Escamilla-Trevino, L.L., Xiao, X., Rudi, M.R., Tang, Y., Jackson, L.A., Li, G., Hernandez, T., Nandakumar, R., Che, R., Stewart Jr., C.N., Wang, Z,.-Y., Dixon, R.A., Research Area: Biomass Formation and Modification 10.1105/tpc.113.118828
02/01/2014 Shields_Menard Draft genome sequence of Rhodococcus rhodochrous Strain ATCC 21198

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Genome Announcements Shields-Menard, S.A., Brown, S.D., Klingeman, D.M., Indest, K., Hancock, D., Wewalwela, J.J., French, W.T., Donaldson, J.R., Draft genome sequence of Rhodococcus rhodochrous Strain ATCC 21198, Genome Announcements, 2(1), 2014. Research Area: Characterization and Modeling 10.1128/genomeA.00054-14.
02/11/2011 Sizova Cellulose and Xylan-Degrading Thermophilic Anaerobic Bacteria from Biocompost

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Applied and Environmental Microbiology Sizova, M. V., Izquierdo, J. A., Panikow, N. S., Lynd, L. R., Thermophilic A naerobic Bacteria from Biocompost Able to Degrade Cellulose and Xylan, Applied and Environmental Microbiology, 77(7): 2282-2291, 2011. Research Area: Biomass Deconstruction and Conversion 10.1128/AEM.01219-10
01/01/2010 Slavov Salient Biological Features, Systematics, and Genetic Variation of Populus

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Genetics and Genomics of Populus Slavov, G.T., Zhelev, P., Salient Biological Features, Systematics, and Genetic Variation of Populus, Genetics and Genomics of Populus, 8, Volume 8, pp 15-38 2010. Research Area: Biomass Formation and Modification 10.1007/978-1-4419-1541-2_2
05/05/2010 Slavov Population substructure in continuous and fragmented stands of Populus trichocarpa

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Heredity Slavov, G.T., Leonardi, S., Adams, W.T., Strauss, S.H., DiFazio, S.P., Population substructure in continuous and fragmented stands of Populus trichocarpa, Heredity, 1-10, 2010. Research Area: Biomass Formation and Modification
01/01/2009 Slavov Extensive pollen flow in two ecologically contrasting populations of Populus trichocarpa

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Molecular Ecology Slavov, G.T., Leonardi, S., Burczyk, J., Adams, W.T., Strauss, S.H., Difazio, S.P., Extensive pollen flow in two ecologically contrasting populations of Populus trichocarpa, Molecular Ecology, 18(2): pp 357-373, 2009. Research Area: Biomass Formation and Modification 10.1111/j.1365-294X.2008.04016.x
08/01/2012 Slavov Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa

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New Phytologist Slavov, G.T., DiFazio, S.P., Martin, J., Schackwitz, W., Muchero, W., Rodgers-Melnick, E., Lipphardt, M.F., Pennacchio, C.P., Hellsten, U., Pennacchio, L.A., Gunter, L.W., Ranjan, P., Vining, K., Pomraning, K.R., Wilhelm, L.J., Pellegrini, M., Mockler, T.C., Freitag, M., Geraldes, Ar., El-Kassaby, Y.A., Mansfield, S.D., Crong, Q.C.B., Douglas, C.J., Strauss, S.H., Rokhsar, D., Tuskan, G.A., Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa, New Phytologist, 196(3):713–725, 2012. Research Area: Biomass Formation and Modification 10.1111/j.1469-8137.2012.04258
12/01/2009 Smith Supercomputers Tackle BIOFUEL Production Problems

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SciDAC Review Jeremy C. Smith, Mark Nimlos, Mike Himmel, Mike Crowley, John Brady, Supercomputers Tackle BIOFUEL Production Problems, SciDAC, 2009. Research Area: Biomass Deconstruction and Conversion
03/01/2011 Srivastava The plastidial folylpolyglutamate synthetase and root apical meristem maintenance

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Plant Signaling and Behavior Srivastava, Avinach C., Tang, Yuhong, Diaz de la Garza, Rocio I., Blancaflor, Elison B., The plastidial folylpolyglutamate synthetase and root apical meristem maintenance, Plant Signaling and Behavior, 155(3): 1237-1251, 2011. Research Area: Biomass Formation and Modification 10.1104/pp.110.168278
01/13/2011 Srivastava The Folylpolyglutamate Synthetase Plastidial Isoform is Required for Postembryonic Root Development in Arabidopsis

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Plant Physiology Srivastava, Avinash C., Ramos-Parra, Perla A., Bedair, Mohamed, Robledo-Hernández, Ana L., Tang, Yuhong, Sumner, Lloyd W., Díaz de la Garza, Rocío I., Blancaflor, Elison B., The Folylpolyglutamate Synthetase Plastidial Isoform is Required for Postembryonic Root Development in Arabidopsis, Plant Physiology, Plant Physiology 155 (3):1237-1251, 2011. Research Area: Biomass Formation and Modification 10.1104/pp.110.168278
05/01/2011 Srivastava Collection and analysis of expressed sequence tags derived from laser capture microdissected switchgrass (Panicum virgatum L. Alamo) vascular tissues

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BioEnergy Research Srivastava, A.C., Palanichelvam, K., Ma, J.Y., Steele, J., Blancaflor, E.B., Tang, Y.H., Ceollection and Analysis of Expressed Sequence Tage Derived from Laser Capture Microdissected Switchgrass (Panicum virgatum L. Alamo) Vascular Tissues, BioEnergy Research, 3;3, pp 278-294, 2010. Research Area: Biomass Formation and Modification 10.1007/s12155-010-9080-8
01/01/2010 Stewart China-U.S. Workshop on Biotechnology of Bioenergy Plants

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Ecotoxicology Stewar, C. Neal, Jr., Shugart, Lee, Liu, Gong-She, Zhuang, Jie, Ma Yongqing, Tuskan, Gerald A., Meilan, Richard, Gentry, Randall W., Sayler, Gary S., China-U.S. Workshop on Biotechnology of bioenergy plants, Exotoxicology, Volume 19, Number 1 / January 2010. Research Area: Biomass Formation and Modification 10.1007/s10646-009-0448-5
09/05/2011 Stewart Bioenergy plants in the United States and China

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Plant Science Stewart Jr., C. N., Liu, G.S., Bioenergy plants in the United States and China, Plant Science, 181:6, pp 621-622, 2011. Research Area: Biomass Formation and Modification 10.1016/j.plantsci.2011.09.001
07/12/2011 Studer Co-hydrolysis of hydrothermal and dilute acid pretreated Populus slurries to support development of a high-throughput pretreatment system

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Biotechnology for Biofuels Studer, M.H., Brethauer, S., DeMartini, J.D., McKenzie, H.L., Wyman, C.E., Co-hydrolysis of hydrothermal and dilute acid pretreated Populus slurries to support development of a high-throughput pretreatment system, Biotechnology for Biofuels, 2011, 4:19. Research Area: Characterization and Modeling 10.1186/1754-6834-4-19
02/01/2010 Studer Engineering of a High-Throughput Screening System to Identify Cellulosic Biomass, Pretreatments, and Enzyme Formulations that Enhance Sugar Release.

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Biotechnology and Bioengineering Studer, M.H., DeMartini, J.D., Brethauer, S., McKenzie, H.L., Wyman, C.E., Engineering of a High-Throughput Screening System to Identify Cellulosic Biomass, Pretreatments, and Enzyme Formulations That Enhance Sugar Release, Biotechnology and Bioenginjeering, Volume 105, Issue 2, pp 231-238, 2010. Research Area: Characterization and Modeling 10.1002/bit.22527
03/01/2011 Studer Lignin content in natural Populus variants affects sugar release

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PNAS Studer, Michael E., DeMartini, Jaclyn D., Davis, Mark F., Sykes, Robert W., Davison, Brian H., Keller, Martin, Tuskan, Gerald A., Wyman, Charles E., Lignin content in natural Populus variants affects sugar release, PNAS, 108(15): 6300-6305, 2011. Research Area: Characterization and Modeling 10.1073/pnas.1009252108
05/01/2011 Sukharnikov Cellulases: ambiguous nonhomologous enzymes in a genomic perspective

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Trends in Biotechnology Sukharnikov, Leonid O., Cantwell, Brian J., Podar, Mircea, Zhulin, Igor B., Cellulases: ambiguous nonhomologous enzymes in a genomic perspective, Trends in Biotechnology, 29(10): 473-479, 2011. Research Area: Characterization and Modeling 10.1016/j.tibtech.2011.04.008
10/10/2012 Sukharnikov Sequence, Structure, and Evolution of cellulases in the glycoside Hydrolase Family 48

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The Journal of Biological Chemistry Sukharnikov, L, Alahuhta, M., Brunecky, R., Upadhyay, A., Himmel, M., Lunin, Zhulin, I, Sequence , Structure, and Evolution of Cellulases in the Glycoside Hydrolase Family 48, The Journal of Biological Chenistry, 287(49):41068-77, 2012. Research Area: Characterization and Modeling 10.1074/jbc.M112.405720 jbc.M112.405720
02/08/2012 Sun Thermophilic Thermotoga maritima ribose-5 phosphate isomerase RpiB: Optimized heat treatment purification and basic characterization

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Protein Expression and Purification Sun, F., Zhang, X.Z., Myung, S., Zhang, Y.-H.P, Thermophilic Thermotoga maritima ribose-5 phosphate isomerase RpiB: Optimized heat treatment purification and basic characterization, Protein Expression and Purification, 2012 Feb 8;82(2):302-307. Research Area: Biomass Deconstruction and Conversion 10.1016/j.pep.2012.01.017
03/28/2012 Sun MicroRNA Expression Analysis in the Cellulosic Biofuel Crop Switchgrass (Panicum virgatum) under Abiotic Stress

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PLoS One Sun, G., C. N. Stewart, Jr., et al. (2012). "MicroRNA Expression Analysis in the Cellulosic Biofuel Crop Switchgrass (Panicum virgatum) under Abiotic Stress." PLoS ONE 7(3): e32017. Research Area: Biomass Formation and Modification 10.1371/journal.pone.0032017
01/11/2012 Syed BESC knowledgebase public portal

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Bioinformatics Syed, M.H., Karpinets, T.V., Parang, M., Leuze, M.R., Park, B.H., Hyatt, D., Brown, S.D., Moulton, S., Galloway, M.D., Uberbacher, E.C., BESC knowledgebase public portal, Bioinformatics., volume 28, number 5, pp 750-751, 2012. Research Area: Characterization and Modeling 10.1093/bioinformatics/bts016
12/01/2008 Sykes Within tree variability of lignin composition in Populus

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Wood Science and Technology Sykes, Robert, Bob Kodrzycki, Gerald Tuskan, Kirk Foutz and Mark Davis , Within tree variability of lignin composition in Populus, Wood Science and Technology, 17 June 2008 epub Research Area: Biomass Formation and Modification
09/18/2009 Sykes High Throughput Screening of Plant Cell Wall Composition Using Pyrolysis Molecular Beam Mass Spectroscopy

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Biofuels: Methods and Protocols Sykes, R., Yung, M., Novaes, E., Kirst, M., Peter, G., Davis, M., High Throughput Screening of Plant Cell Wall Composition Using Pyrolysis Molecular Beam Mass Spectroscopy, Biofuels, Methods and Protocols Series: , Vol. 581, pp 169-183, Mielenz, Jonathan R. (Ed.) 2009. Research Area: Characterization and Modeling 10.1007/978-1-60761-214-8_12
08/08/2013 Taghavi Complete Genome Sequence of Clostridium sp. Strain DL-VIII, a novel solventogenic Clostridium species isolated from anaerobic sludge

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Genome Announcements Taghavi, S., Izquierdo, J.A., van der Lelie, D., Complete Genome Sequence of Clostridium sp. Strain DL-VIII, a Novel Solventogenic Clostridium Species Isolated from Anaerobic Sludge, Genome Announcements, 1 (4), 2013. Research Area: Biomass Deconstruction and Conversion 10.1128/genomeA.00605-13.
01/01/2013 Tan An Arabidopsis cell wall proteoglycan consists of pectin and arabinoxylan covalently linked to an arabinogalactan protein

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The Plant Cell Tan, L., Eberhard, S., Pattathil, S., Warder, C., Glushka, J., Yuan, C., Hao, Z., Zhu, X., Avci, U., Miller, J.S., Baldwin, D., Pham, C., Orlando, R., Darvill, A., Hahn, M.G., Kieliszewski, M.J., Mohnen, D., An Arabidopsis cell wall proteoglycan consists of pectin and arabinoxylan covalently linked to an arabinogalactan protein, The Plant Cell, 25(1):270-287, 2012. Research Area: Biomass Formation and Modification
09/05/2011 Tetard Nanometrology of delignified Populus using mode synthesizing atomic force microscopy

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Nanotechnology Tetard, L., Passian, A., Farahi, R.H., Davison, B.H., Jung, S., Ragauskas, A.J., Lereu, A.L., Thundat, T. (2011) "Nanometrology of delignified Populus using mode synthesizing atomic force microscopy." Nanotechnology 22:465702 . Research Area: Characterization and Modeling 10.1088/0957-4484/22/46/465702
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03/01/2011 Tsai Poplar Genome Microarrays Genetics, Genomics and Breeding of Crop Plants: Poplar Tsai, C.J., Ranjan, P., DiFazio, S.P., Tuskan, G.A., Johnson, V.E., Poplar Genome Microarrays, Genetics, Genomics and Breeding of Popular, chapter 5, 112-127, 2011. Research Area: Biomass Formation and Modification 10.1201/b10819-6
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BioEnergy Research Xi, Y. J., Fu, C. X., Ge, Y. X., Nandakumar, R., Hisano, H., Bouton, J., Wang, Z. Y., Agrobacterium-Mediated Transformation of Switchgrass and Inheritance of the Transgenes, Bioenergy Research, Volume 2, Number 4, pp 275-283, December, 2009 Research Area: Biomass Formation and Modification 10.1007/s12155-009-9049-7
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11/28/2013 Xie High-throughput deep sequencing shows that microRNAs play important roles in switchgrass responses to drought and salinity stress Plant Biotechnology Journal Xie, F., Stewart Jr., C.N., Taki, F.A., He, Q., Liu, H., Zhang, B., High-throughput deep sequencing shows that microRNAs play important roles in switchgrass responses to drought and salinity stress, Plant Biotechnology Journal, 2013 Research Area: Biomass Formation and Modification 10.1111/pbi.12142
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PlosOne Xu, B., Sathitsuksanoh, N., Tang, Y., Udvardi, M.K., Zhang, J.Y., Shen, Z., Balota, M., Harich, K., Zhang, P.Y.H., Zhao, B., Overexpression of AtLOV1 in Switchgrass alters plant architecture, lignin content, and flowering time, PLOSONE, 7(12), e47399, 2012. Research Area: Biomass Formation and Modification 10.1371/journal.pone.0047399
08/05/2011 Xu Multifunctional Enzyme Systems for Plant Cell Wall Degradation Comprehensive Biotechnology (Second Edition) Xu, Q., Y. Luo, et al. (2011). 3.03 - Multifunctional Enzyme Systems for Plant Cell Wall Degradation. Comprehensive Biotechnology (Second Edition). M.-Y. Editor-in-Chief: Murray. Burlington, Academic Press: 15-25. Research Area: Biomass Deconstruction and Conversion 10.1016/B978-0-08-088504-9.00167-7
07/25/2011 Xu Silencing of 4-coumarate:coenzyme A ligase in switchgrass leads to reduced lignin content and improved fermentable sugar yields for biofuel production

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New Phytologist Xu, B., Escamilla-Trevino, L.L., Sathitsuksanoh, N., Shen, Z., Shen, H., Zhang, Y.H.P, Dixon, R.A., Zhao, B., Silencing of 4-coumarate:coenzyme A ligase in switchgrass leads to reduced lignin content and improved fermentable sugar yields for biofuel production, New Phytologist, 192(3):611-625, 2011. Research Area: Biomass Deconstruction and Conversion 10.1111/j.1469-8137.2011.03830.x
08/03/2010 Xu Probing the mechanism of cellulosome attachment to the Clostridium thermocellum cell surface: computer simulation of the Type II cohesin–dockerin complex and its variants

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Protein Engineering, Design and Selection Xu, J., Smith, J.C., Probing the mechanism of cellulosome attachment to the Clostridium thermocellum cell surface: computer simulation of the Type II cohesin–dockerin complex and its variants, Protein Engineering, Design and Selection, Vol. 23, no. 10, pp 759-768, 2010. Research Area: Characterization and Modeling 10.1093/protein/gzq049
05/01/2009 Xu Building a Foundation for Structure-Based Cellulosome Design for Cellulosic Ethanol: Insight into Cohesin-Dockerin Complexation from Computer Simulation

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Protein Science Xu, J.C., Crowley, M.F., Smith, J.C., Building a Foundation for Structure-Based Cellulosome Design for Cellulosic Ethanol: Insight into Cohesin-Dockerin Complexation from Computer Simulation, Protein Science, 18;5, pp 949 - 959, 2009 Research Area: Biomass Deconstruction and Conversion
10/09/2009 Xu Comparative genome analysis of lignin biosynthesis gene families across the plant kingdom

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BMC Bioinformatics Xu, Zhanyou, Zhang, Dandan, Hu, Jun, Zhou, Xin, Ye, Xia, Reichel, Kristen L., Stewart, Nathan R., Syrenne, Ryan D., Yang, Xiaohan, Gao, Peng, Shi, Weibing, Doeppke, Crissa, Sykes, Robert W., Burris, Jason N., Bozell, Joseph J., Cheng, Max Zong-Ming, Hayes, Douglas G., Labbe, Nicole, Davis, Mark, Stewart, C. Neal, Jr., Yuan, Joshua S., Comparative genome analysis of lignin biosynthesis gene families across the plant kingdom, BMC Bioinformatics, 2009, 10(Suppl ii):S3. Research Area: Biomass Formation and Modification 10.1186/1471-2105-10-S11-S3
01/01/2010 Xu Computational Challenges in Deciphering Genomic Structures of Bacteria

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Journal of Computer Science and Technology Xu, Y., Computational Challenges in Deciphering Genomic Structures of Bacteria, Journal of Computer Science and Technology, 25;1, pp 53-70, 2010. Research Area: Characterization and Modeling
12/01/2009 Yang Classification of 'Anaerocellum thermophilum' strain DSM 6725 as Caldicellulosiruptor bescii sp. nov.

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International Journal of Systematic and Evolutionary Microbiology Sung-Jae Yang, Irina Kataeva, Juergen Wiegel, Yanbin Yin, Phuongan Dam, Ying Xu, Janet Westpheling and Michael W. W. Adams, Classification of 'Anaerocellum thermophilum' strain DSM 6725 as Caldicellulosiruptor bescii sp. Nov., International Journal of Systematic and Evolutionary, Microbiology, Volume 60, Part 9, pp 2011-2015 Research Area: Biomass Deconstruction and Conversion 10.1099/ijs.0.017731-0
01/01/2012 Yang Ethanol-tolerant Gene Identification in Clostridium thermocellum using Pyro-resequencing for Metabolic Engineering Microbial Metabolic Engineering: Methods and Protocols Yang, S., Klingeman, D, Brown, S.D., Ethanol-tolerant Gene Identification in Clostridium thermocellum using Pyro-resequencing for Metabolic Engineering, Methods in Molecular Biology, Vol. 834 Cheng, Qiong, 1st Edition, 2012;834:111-36. Research Area: Biomass Deconstruction and Conversion 10.1007/978-1-61779-483-4_9
08/31/2010 Yang Genomic aspects of research involving polyploid plants

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Plant Cell, Tissue and Organ Culture (PCTOC) Yang, Xiaohan, Ye, Chu-Yu, Cheng, Zong-Ming, Tschaplinski, Timothy J., Wullschleger, Stan D., Yin, Weilun, Xia, Xinli, Tuskan, Gerald A., Genomic aspects of research involving polyploid plants, Plant Cell Tissue and Organ Culture, 2011, 104:387-397. Research Area: Biomass Formation and Modification 10.1007/s11240-010-9826-1
06/01/2010 Yang Identification of a novel UDP-sugar Pyrophosphorylase with a broad substrate specificity In Trypanosoma cruzi

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Biochemical Journal Yang T, Bar-Peled M. (2010) Identification of a novel UDP-sugar pyrophosphorylase with a broad substrate specificity in Trypanosoma cruzi. Biochem J.;429(3):533-43. Research Area: Biomass Formation and Modification 10.1042/BJ20100238
02/17/2011 Yang Identification of candidate genes in Arabidopsis and Populus cell wall biosynthesis using text-mining, co-expression network analysis and comparative genomics

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Plant Science Yang, Xiaohan, Ye, Chu-Yu, Bisaria, Anjali, Tuskan, Gerald A., Kalluri, Udaya C., Identification of candidate genes in Arabidopsis and Populus cell wall biosynthesis using text-mining, co-expression network analysis and comparatie genomics, Plant Science, 181(6): 675-687, 2011. Research Area: Biomass Formation and Modification 10.1016/J.plantsci.2011.01.020
08/07/2009 Yang Identification of galacturonic acid-1-P kinase: a new member of the GHMP kinase super family in plants and comparison with galactose-1-P kinase

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Journal of Biological Chemistry Yang T, Bar-Peled L, Gebhart L, Lee SG, Bar-Peled M. (2009)Identification of galacturonic acid-1-phosphate kinase, a new member of the GHMP kinase superfamily in plants, and comparison with galactose-1-phosphate kinase. J Biol Chem. 284(32):21526-35. Research Area: Biomass Formation and Modification
05/01/2009 Yang Efficient degradation of lignocellulosic plant biomass without pretreatment by the thermophilic anaerobe, Anaerocellum thermophilum DSM 6725

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Applied and Environmental Microbiology Yang, S.J., Kataeva, I., Hamilton-Brehm, S., Engle, N.D., Tschaplinski, T.J., Doeppke, Cr., Davis, M., Westpheling, J., Adams, M.W.W., Efficient degradation of lignocellulosic plant biomass without pretreatment by the thermophilic anaerobe, Anaerocellum thermophilium, Applied and Environmental Microbiology, Volume 75, Issue 14, pp 4762-4769 Research Area: Biomass Deconstruction and Conversion 10.1128/AEM.00236-09
03/02/2011 Yang Discovery and annotation of small proteins using genomics, proteomics, and computational approaches

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Genome Research Yang, Xiaohan, Tschaplinski, Timothy J., Hurst, Gregory B., Jawdy, Sara, Abraham, Paul E., Lankford, Patricia K., Adams, Rachel M., Shah, Manesh B., Hettich, Robert L., Lindquist, Erika, Kalluri, Udaya C., Gunter, Lee E., Pennacchio, Christa, Tuskan, Gerald A., Discovery and annotation of small proteins using genomics, proteomics, and computational approaches, Genome Research, 21: 634-641, 2011. Research Area: Biomass Formation and Modification 10.1101/gr.109280.110
04/07/2010 Yang The Zymomonas mobilis regulator Hfq and related Saccharomyces cerevisiae proteins contribute to tolerance against multiple lignocellulosic pretreatment inhibitors

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BMC Microbiology Yang, S.H., Pelletier, D.A., Lu, T.Y.S, Brown, S.D., The Zymomonas mobilis regulator Hfq and related Saccharomyces cerevisiae proteins contribute to tolerance against multiple lignocellulosic pretreatment inhibitors, BMC Microbiology, 10;135, 2010. Research Area: Biomass Deconstruction and Conversion 10.1186/1471-2180-10-135
01/20/2009 Yang Transcriptomic and metabolomic profiling of Zymomonas mobilis during aerobic and anaerobic fermentations

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BMC Genomics Yang, S.H., Tschaplinski, T.J., Engle, N.L., Carroll, S.L., Martin, S.L., Davison, B.H., Palumbo, A.V., Rodriguez, M., Brown, S.D., Transcriptomic and metabolomic profiling of Zymomonas mobilis during aerobic and anaerobic fermentations, BMC Genomics, 10;34; 2009. Research Area: Biomass Deconstruction and Conversion 10.1186/1471-2164-10-34
04/01/2010 Yang Paradigm for industrial strain improvement identifies sodium acetate tolerance loci in Zymomonas mobilis and Saccharomyces cerevisiae

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PNAS Yang, S.H., Land, M.L., Klingeman, D.M., Pelletier, D.A., Lu, T.Y.S., Martin, S.L., Guo, H.B., Smith, J.C., Brown, S.D., Paradigm for industrial strain improvement identifies sodium acetate tolerance loci in Zymomonas mobilis and Saccharomyces cerevisiae, PNAS, 107;23, pp 10398-10400, 2012. Research Area: Biomass Deconstruction and Conversion 10.1073/pnas.0914506107
10/14/2009 Yang Natural variation for nutrient-use and remobilization efficiencies in switchgrass BER-124R1

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BioEnergy Research Yang J, E Worley, M Wang, B Lahner, D E Salt, M Saha, M Udvardi (2009) Natural Variation for Nutrient Use and Remobilization Efficiencies in Switchgrass. Bioenergy Res. 2:257–266. Research Area: Biomass Formation and Modification 10.1007/s12155-009-9055-9
01/01/2009 Yang Poplar genomics: State of the science

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Critical Reviews in Plant Sciences Yang XH, Kalluri UC, DiFazio SP, Wullschleger SD, Tschaplinski TJ, Cheng ZM, Tuskan GA. Poplar Genomics: State of the Science. Critical Reviews in Plant Sciences 2009;Volume 28, Issue 5, pp 285-308, 2009 Research Area: Biomass Formation and Modification 10.1080/07352680903241014
07/05/2011 Yang Innovative Biological Solutions to Challenges in Sustainable Biofuels Production

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Biofuel Production-Recent Developments and Prospects Xiaohan Yang, Ting Li, David Weston, Abhijit Karve, Jessy L. Labbe, Lee E. Gunter, Poornima Sukumar, Anne Borland, Jin-Gui Chen, Stan D. Wullschleger, Timothy J. Tschaplinski and Gerald A. Tuskan. Innovative Biological Solutions to Challenges in Sustainable Biofuels Production. 2011. In book "Biofuel Production-Recent Developments and Prospects", ( ed. Marco Aurélio dos Santos Bernardes), InTech, Chapter 15, p. 375-414. Research Area: Biomass Formation and Modification ISBN: 978-953-307-478-8
10/01/2009 Yang Improved genome annotation for Zymomonas mobilis

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Nature Biotechnology Yang, S.H., Pappas, K.M., Hauser, L.J., Land, M.L., Chen, G.L., Hurst, G.B., Pan, C.L., Kouvelis, V.N., Typas, M.A., Pelletier, D.A., Klingeman, D.M., Chang, Y.J., Samatova, N.F., Brown, S.D., Improved genome annotation for Zymomonas mobilis, Nature Biotechnology, 27;10, pp 893 - 894, 2009. Research Area: Biomass Deconstruction and Conversion 10.1038/nbt1009-893
06/17/2010 Yang Identification and characterization of a strict and a promiscuous N-acetylglucosamine-1-P uridylyltransferase in Arabidopsis

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Biochemical Journal Yang T, Echols M, Martin A, Bar-Peled M. (2010) Identification and characterization of a strict and a promiscuous N-acetylglucosamine-1-P uridylyltransferase in Arabidopsis. Biochem J. 430(2):275-84. Research Area: Biomass Formation and Modification :10.1042/BJ20100315
07/01/2011 Yang Enzymatic hydrolysis of cellulosic biomass

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Biofuels Yang, B., Z. Dai, et al. (2011). "Enzymatic hydrolysis of cellulosic biomass." Biofuels 2(4): 421-450. Research Area: Characterization and Modeling 10.4155/bfs.11.116
01/01/2012 Yang Genomics on Pretreatment Inhibitor Tolerance of Zymomonas mobilis

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Microbial Stress Tolerance for Biofuel (book chapter) Yang, S., Keller, M., Brown, S.D., Microbial Stress Tolerance for Biofuels, Microbiology Monographs, 2012, Volume 22/2012, 161-175. Research Area: Biomass Deconstruction and Conversion 10.1007/978-3-642-21467-7_7
12/20/2011 Yang In-microbe formation of nucleotide sugars in engineered Escherichia coli

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Analytical Biochemistry Yang, T., Y. Bar-Peled, et al. (2012). "In-microbe formation of nucleotide sugars in engineered Escherichia coli." Analytical Biochemistry 421(2): 691-698. Research Area: Biomass Formation and Modification 10.1016/j.ab.2011.12.028
07/23/2012 Yang Clostridium thermocellum ATCC27405 transcriptomic, metabolomic and proteomic profiles after ethanol stress

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BMC Genomics Yang, S., Giannone, R.J., Dice, L., Yang, Z.K., Engle, N.L., Tschaplinski, T.J., Hettich, R.L., Brown, S.D., Clostridium thermocellum ATCC27405 transcriptomic, metabolomic and proteomic profiles after ethanol stress, BMC Genomics, 13:336, 2012. Research Area: Biomass Deconstruction and Conversion 10.1186/1471-2164-13-336
07/16/2013 Yang Systems biology analysis of zymomonas mobilis ZM4 ethanol stress responses

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Plos One Yang, S., Pan, C., Tschaplinski, T.J., Hurst, G.B., Engle, N.L., Zhou, W., Dam, P., Xu, Y., Rodriguez Jr. M., Dice, L., Johnson, C.M., Davison, B.H., Brown, S.D., Systems biology analysis of zymomonas mobilis ZM4 ethanol stress responses, Plos One, 7(8), 2013. Research Area: Characterization and Modeling 10.1371/journal.pone.0068886
12/17/2010 Yao QM/MM Free Energy Simulations of Salicylic Acid Methyltransferase: Effects of Stabilization of TS-like Structures on Substrate Specificity

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Journal of Physical Chemistry B Yao, Jianzhuang, Xu, Qin, Chen, Feng, Guo, Hong, QM/MM Free Energy Simulations of Salicylic Acid Methyltransferase: Effects of Stabilization of TS-like Structures on Substrate Specificity, The Journal of Physical Chemistry B, 115, 389-396, 2011. Research Area: Biomass Formation and Modification 10.1021/jp1086812
01/01/2009 Ye Spontaneous high-yield production of hydrogen from cellulosic materials and water catalyzed by enzyme cocktails

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ChemSusChem Ye, Xinhao, Yiran Wang, Robert C. Hopkins, Michael W. W. Adams, Barbara R. Evans, Jonathan R. Mielenz, Y.-H. Percival Zhang, Spontaneous high-yield production of hydrogen from cellulosic materials and water catalyzed by enzyme cocktails , ChemSusChem, (2009), 2(2), 149-52, 2009 Research Area: Biomass Deconstruction and Conversion 10.1002/cssc.200900017
09/12/2011 Ye Transgenic Populus trees for forest products, bioenergy, and functional genomics

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Critical Reviews in Plant Sciences Ye, Xia., Busov, V., Zhao, N., Meilan, R., McDonnell, L.M., Coleman, H.D., Mansfield, S.D., Chen, F., Li, Y., Cheng, Z.M., Transgenic Populus Trees for Forest Products, Bioenergy, and Functional Genomics, Critical Reviews in Plant Science, 30:415-434, 2011. Research Area: Biomass Formation and Modification 10.1080/07352689.2011.605737
03/01/2010 Ye Thermophilic alpha-glucan phosphorylase from Clostridium thermocellum: Cloning, characterization and enhanced thermostability

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Journal of Molecular Catalysis B: Enzymatic Ye, X., Rollin, J., Zhang, Y.H.P., Thermophilic α-glucan phosphorylase from Clostridium thermocellum: Cloning, characterization and enhanced thermostability, Journal of Molecular Catalysis B: Enzymatic, Volume 65, Issue 1-4, pp 110-116 Research Area: Biomass Deconstruction and Conversion 10.1016/j.molcatb.2010.1001.1015
06/01/2009 Ye Identification of the Flavin-dependent Monooxygenase-encoding YUCCA Gene Family in Populus trichocarpa and Their Expression in Vegetative Tissues and in Response to Hormone and Environmental Stresses

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Plant Cell, Tissue and Organ Culture (PCTOC) - Journal of Plant Biotechnology Ye, X., B-g Kang, L. D. Osburn, and Z.-M. Cheng. 2009 Identification of the Flavindependent Monooxygenase-encoding YUCCA Gene Family in Populus trichocarpa and Their Expression in Vegetative Tissues and in Response to Hormone and Environmental Stresses. PCTOC: J. of Plant Biotechnology 97:271–283(2009). Research Area: Biomass Formation and Modification 10.1007/s11240-009-9526-x
08/18/2011 Ye Evolution and divergence in the coding and promoter regions of the Populus gene family encoding xyloglucan endotransglycosylase / hydrolases

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Tree Genetics and Genomes Ye, X., Yuan, S., Guo, H., Chen, F., Tuskan, G.A., Cheng, Z.M. (2012) "Evolution and divergence in the coding and promoter regions of the Populus gene family encoding exyloglucan endotransglycosylase/ hydrolases." Tree Genetics and Genomes 8:177–194. Research Area: Biomass Formation and Modification 10.1007/s11295-011-0431-1
05/03/2011 Ye Fusion of a family 9 cellulose-binding module improves catalytic potential of Clostridium thermocellum cellodextrin phosphorylase on insoluble cellulose

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Applied Microbiology and Biotechnology Ye, X., Zhu, Z., Zhang, C., Zhang, Y.H.P., Fusion of a family 9 cellulose-binding module improves catalytic potential of Clostridium thermocellum cellodextrin phosphorylase on insoluble cellulose, Applied Microbiology and Biotechnology, 92(3): 551-560, 2011 Research Area: Biomass Deconstruction and Conversion 10.1007/s00253-011-3346-8
05/01/2011 Ye Comparative analysis of GT14/GT14-like gene family in Arabidopsis, Oryza, Populus, Sorghum and Vitis

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Plant Science Ye, Chu-Yu, Li, Ting, Tuskan, Gerald A., Tschaplinski, Timothy J., Yang, Xiaohan, Comparative analysis of GT14/GT14-like gene family in Arabidopsis, Oryza, Populus, Sorghum and Vitis, Plant Science, 181(6): 688-695, 2011. Research Area: Biomass Formation and Modification 10.1016/j.plantsci.2011.01.021
11/04/2012 Ye Evolutionary analyses of non-family genes in plants

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The Plant Journal Ye, C-Y., Li, T., Yin, H., Weston, D.J., Tuskan, G.A., Tschaplinski, T.J., Yang, X., Evolutionary analyses of non-family genes in plants, The Plant Journal, 73(5): 788-97, 2013. Research Area: Biomass Formation and Modification 10.1111/tpj.12073
04/01/2012 Ye Engineering a large protein by combined rational and random approaches: stabilizing the Clostridium thermocellum cellobiose phosphorylase

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Molecular BioSystems Ye, X., Zhang, C., Zhang, Y-H.P., Engineering a large protein by combined rational and random approaches: stabilizing the Clostridium thermocellum cellobiose phosphorylase, Molecular BioSystems, 2012. Research Area: Biomass Deconstruction and Conversion 10.1039/c2mb05492b
11/12/2012 Yee Evaluation of the bioconversion of genetically modified switchgrass using simultaneous saccharification and fermentation and a consolidated bioprocessing approach

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Biotechnology for Biofuels Yee, K.L., Rodriguez Jr. M., Tschaplinski, T.J., Engle, N.L., Martin, M.Z., Fu, C., Wang, Z.Y., Hamilton-Brehm, S.D., Mielenz, J.R., Evaluation of the bioconversion of genetically modified switchgrass using simultaneous saccharification and fermentation and a consolidated bioprocessing approach, Biotechnology for Biofuels, 5:81, 2012. Research Area: Characterization and Modeling 10.1186/1754-6834-5-81
05/29/2012 Yin dbCAN: a web resource for automated carbohydrate-active enzyme annotation

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Nucleic Acids Research Yin, Y., Mao, X., Yang, J., Chen, X., Mao, F., Xu, Y., dbCAN: a web resource for automated carbohydrate-active enzyme annotation, Nucleic Acids Research, 1-7, 2012. Research Area: Characterization and Modeling 10.1093/nar/gks479
11/18/2011 Yin Evolution of Plant Nucleotide-Sugar Interconversion Enzymes

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PloS One Yin, Y., Huang, J., Gu, X., Bar-Peled, M., Xu, Y. (2011) "Evolution of Plant Nucleotide-Sugar Interconversion Enzymes." Plos one, 6(11):e27995. Research Area: Characterization and Modeling 10.1371/ journal.pone.0027995
03/01/2010 Yin Evolution and function of the plant cell wall synthesis-related glycosyltransferase family 8

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Plant Physiology Yin, Y.B., Chen, H.L., Hahn, M.G., Mohnen, D., Xu, Y., Evolution and Function of the Plant Cell Wall Synthesis-Related Glycosyltransferase Family 8, Plant Physiology, Volume 153, Issue 4, pp 1729-1746, 2010. Research Area: Biomass Formation and Modification 10.1104/pp.110.154229
03/22/2010 Yin Genomic arrangement of bacterial operons is constrained by biological pathways encoded in the genome

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PNAS Yin, Y.B., Zhang, H., Olman, V., Xu, Y., Genomic arrangement of bacterial operons is constrained by biological pathways encoded in the genome, PNAS, 107 (14):6310-5, 2010. Research Area: Biomass Formation and Modification
12/22/2010 Yin Glycosyltransferases of the GT8 Family Annual Plant Reviews, Plant Polysaccharides, Biosynthesis and Bioengineering Yin, Y., Mohnen, D., Gelineo-Albersheim, I., Xu, Y. and Hahn, M. G., Glycosyltransferases of the GT8 Family, in Annual Plant Reviews: Plant Polysaccharides, Biosynthesis and Bioengineering, Volume 41 (ed P. Ulvskov), Wiley-Blackwell, Oxford, UK, 2010. Research Area: Biomass Formation and Modification 10.1002/9781444391015.ch6
11/22/2010 Yin Differential Detection of Genetic Loci Underlying Stem and Root Lignin Content in Populus

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PloS One Yin, T., Zhang, X., Gunter, L., Priya, R., Sykes, R., Davis, M., Wullschleger, S.D., Tuskan, G.A.,Differential Detection of Genetic Loci Underlying Stem and Root Lignin Content in Populus, Plos One, 5(11): e14021, 2010. Research Area: Biomass Formation and Modification 10.1371/journal.pone.0014021
07/31/2009 Yin The cellulose synthase superfamily in fully sequenced plants and algae

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BMC Plant Biology Yin, Y.B., Huang, J.L., Xu, Y., The cellulose synthase superfamily in fully sequenced plants and algae, BMC Plant Biology, 9;99, 2009. Research Area: Characterization and Modeling 10.1186/1471-2229-9-99
01/01/2009 Yin Microsatellite primer resource for Populus developed from the mapped sequence scaffolds of the Nisqually-1 genome

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New Phytologist Yin, T. M., Zhang, X. Y. Gunter, L. E., Li, S. X., Wullschleger, S. D., Huang, M. R., Tuskan, G., A. Microsatellite primer resource for Populus developed from the mapped sequence scaffolds of the Nisqually-1 genome, New Phytologist, Volume 181, Number 2, January 2009 , pp. 498-503(6) Research Area: Biomass Formation and Modification 10.1111/j.1469-8137.2008.02663.x
03/07/2014 Yin Functional genomics of drought tolerance in bioenergy crops

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Critical Reviews in Plant Sciences Yin, H., Chen, C.J., Yang, J., Weston, D.J., Chen, J.G., Muchero, W., Ye, N., Tschaplinski, T.J., Wullschleger, S.D., Cheng, Z.M., Tuskan, G.A., Yang, X., Functional genomics of drought tolerance in bioenergy crops, Critical Reviews in Plant Sciences, Volume 33, Issue 2-3, 2014. Research Area: Biomass Formation and Modification 10.1080/07352689.2014.870417
06/01/2008 York Biochemical control of xylan biosynthesis — which end is up?

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Current Opinion Plant Biology York WS, O'Neill MA. 2008. Biochemical control of xylan biosynthesis - which end is up? Current Opinion in Plant Biology 11(3):258-265. Research Area: Biomass Formation and Modification 2008
12/01/2011 You Enhanced microbial cellulose utilization of recalcitrant cellulose by an ex vivo cellulosome-microbe complex

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Applied and Environmental Microbiology You, C., Zhang, X.Z., Sathitsuksanon, N., Lynd, L.R., Zhang, Y.H.P (2011) Enhanced microbial cellulose utilization of recalcitrant cellulose by an ex vivo cellulosome-microbe complex, Applied and Environmental Microbiology, 2011. Research Area: Biomass Deconstruction and Conversion 10.1128/AEM.07138-11
12/01/2011 You Simple Cloning via direct transformation of PCR product (DNA multimer) to Escherichia coli and Bacillus subtilis

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Applied and Environmental Microbiology You, C., Zhang, X.Z., Zhang, Y.H.P., Simple Cloning: direct transformation of PCR product (DNA multimer) to Escherichia coli and Bacillus subtilis, Applied and Environmental Microbiology, 78;5, pp 1593-1595, 2012. Research Area: Biomass Deconstruction and Conversion 10.1128/AEM07105-11
02/15/2012 You Mini-scaffoldin enhanced mini-cellulosome hydrolysis performance on low-accessibility cellulose (Avicel) more than on high-acccessibility amorphous cellulose

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Biochemical Engineering Journal You, C., Zhang, X.Z., Zhang, Zhang, Y.H.P., Mini-scaffoldin enhanced mini-cellulosome hydrolysis performance on low -accessibility cellulose (Avicel) more than on high-accessibility amorphous cellulose, Biochemical Engineering Journal, 2012. Research Area: Biomass Deconstruction and Conversion 10.1016/j.bej.2012.01.011
05/22/2012 You Easy preparation of a large-size random gene mutagenesis library in Escherichia coli

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Analytical Biochemistry You, C., Zhang, Y.H.P, Easy preparation of a large-size random gene mutagenesis library in Escherichia coli, Analytical Biochemistry, 2012 Research Area: Biomass Deconstruction and Conversion 10.1016/j.ab.2012.05.022
07/23/2012 You Facilitated Substrate Channeling in a Self-Assembled Trifunctional Enzyme Complex

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Angewandte Chemie You, C., Myung, S., Zhang, Y.-H. P., Facilitated Sustrate Channeling in a Self-Assembled Trifunctional Enzyme Complex, Angewandte Chemie International Edition, 51, 1-5, 2012. Research Area: Biomass Deconstruction and Conversion 10.1002/anie.201202441
04/01/2013 You Enzymatic transformation of nonfood biomass to starch

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PNAS You, C., Chen, H., Myung, S., Sathitsuksanoh, N., Ma. H., Zhang, X.Z., Li, J., Zhang, Y.-H.P., Enzymatic transformation of nonfood biomass to starch, PNAS, 110 no. 18 7182-7187 2013. Research Area: Biomass Deconstruction and Conversion 10.1073/pnas.1302420110
01/01/2014 You Simple Cloning and DNA Assembly in Escherichia coli by Prolonged Overlap Extension PCR DNA Cloning and Assembly Methods - Methods in Molecular Biolology You, C., Zhang, Y.-H. P., Simple Cloning and DNA Assembly in Escherichia coli by Prolonged Overlap Extension PCR, DNA Cloning and Assembly Methods Methods in Molecular Biology, Volume 1116, 2014, pp 183-192. Research Area: Biomass Deconstruction and Conversion 978-1-62703-764-8
09/01/2011 Yuan US-China collaborative biofuel research: towards a global solution for petroleum replacement

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Biofuels Yuan, J.A., Qu, Y., Li, S., Stewart Jr., C.N., US-China collaborative biofuel research: towards a global solution for petroleum replacement, Biofuels, 2:5, 487-789, 2011. Research Area: Biomass Formation and Modification 10.4155/BFS.11.130
09/01/2011 Yuan Biomass feedstock: diversity as a solution

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Biofuels Yuan, J.S., Wang, X., Stewart Jr., C.N., Biomass feedstock: diversity as a solution, Biofuels, 2:5, 491-493, 2011. Research Area: Biomass Formation and Modification 10.4155/BFS.11.135
08/01/2008 Yuan Plants to power: bioenergy to fuel the future

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Trends in Plant Science Yuan, Joshua S., Kelly H. Tiller, Hani Al-Ahmad, Nathan R. Stewart, C. Neal Stewart, Jr., Plants to power: bioenergy to fuel the future, Trends in Plant Science, Vol. 13(8), 421-429, 2008 Research Area: Biomass Deconstruction and Conversion 10.1016/j.tplants.2008.06.001
02/25/2010 Zeng Imaging Lignin-Downregulated Alfalfa Using Coherent Anti-Stokes Raman Scattering Microscopy

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BioEnergy Research Zeng Y, Saar BG, Friedrich MG, Chen F, Liu Y, Dixon RA, Himmel ME, Xie XS and Ding S (2010), Imaging Lignin‐Downregulated Alfalfa Using Coherent Anti‐Stokes Raman Scattering Microscopy, Bioenerg. Res. 3:272–277, Volume 3, Issue 3, pp 272-277 Research Area: Characterization and Modeling 10.1007/s12155-010-9079-1
08/01/2012 Zeng Coherent Raman Microscopy Analysis of Plant Cell Walls Methods in Molecular Biology Biomass Conversion: Methods and Protocols Zeng, Y., Himmel, M.E., Ding, S.Y., Coherent Raman Microscopy Analysis of Plant Cell Walls, Methods in Molecular Biology Biomass Conversion: Methods and Protocols, 908:49-60, 2012. Research Area: Biomass Deconstruction and Conversion 10.1007/978-1-61779-956-3_5
06/01/2013 Zeng Lignin plays a negative role in the biochemical process for producing lignocellulosic biofuels

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Current Opinion in Biotechnology Zeng, Y., Zhao, S., Yang, S., Ding, S., Lignin plays a negative role in the biochemical process for producing lignocellulosic biofuels, Current Opinion in Biotechnology, 27 (38-45), 2013. Research Area: Characterization and Modeling 10.1016/j.copbio.2013.09.008
07/12/2013 Zhang Cellulases: Characteristics, sources, production, and applications

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Bioprocessing Technologies in Biorefinery for Sustainable Production of Fuels, Chemicals, and Polymers Zhang, X.Z., Zhang, Y.H.P., Cellulases: Characteristics, sources, production, and applications, Bioprocessing Technologies in Biorefinery for Sustainable Production of Fuels, Chemicals, and Polymers, Chapter 8, pp 131- 146, 2014. Research Area: Biomass Deconstruction and Conversion 10.1002/9781118642047.ch8
01/05/2013 Zhang Development of an integrated transcript sequence database and a gene expression atlas for gene discovery and analysis in switchgrass (Panicum virgatum L.)

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The Plant Journal Zhang, J.Y., Lee, Y.C., Torres-Jerez, I., Wang, M., Yin, Y., Chou, W.C., He, J., Shen, H., Srivastava, A.C., Pennacchio, C., Lindquist, E., Grimwod, J., Schmutz, J., Xu, Y., Sharma, M., Sharma, R., Bartley, L.E., Ronald, P.C., Saha, M.C., Dixon, R.A., Tang, Y., Udvardi, M.K., Development of an integrated transcript sequence database and a gene expression atlas for gene discovery and analysis in switchgrass (Panicum virgatum L.), The Plant Journal, 74(1):160-73, 2012. Research Area: Biomass Formation and Modification 10.1111/tpj.12104
01/03/2012 Zhang Genomic Arrangement of Regulons in Bacterial Genomes

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PLoS One Zhang, H., Y. Yin, et al. (2012). "Genomic Arrangement of Regulons in Bacterial Genomes." PLoS ONE 7(1): e29496. Research Area: Characterization and Modeling 10.1371/journal.pone.0029496.g001
06/07/2011 Zhang Substrate channeling and enzyme complexes for biotechnological applications

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Biotechnology Advances Zhang, Y.-H.P. (2011). Substrate channeling and enzyme complexes for biotechnological applications. Biotechnology Advances 29:715-725. Research Area: Biomass Deconstruction and Conversion 10.1016/j.biotechadv.2011.05.020
03/03/2012 Zhang A new high-energy density hydrogen carrier—carbohydrate—might be better than methanol

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International Journal of Energy Research Percival Zhang, Y.-H., J.-H. Xu, et al. (2012). "A new high-energy density hydrogen carrier—carbohydrate—might be better than methanol." International Journal of Energy Research. (published online ahead of print doi:10.1002/er.2897) Research Area: Biomass Deconstruction and Conversion 10.1002/er.2897
08/12/2011 Zhang Natural Hybrids and Gene Flow between Upland and Lowland Switchgrass

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Crop Science Zhang, Y., Zalapa, J.E., Jakubowski, A.R., Price, D.L., Acharya, A., Wei, Y., Brummer, E.C., Kaeppler, S.M., Casler, M.D, Natural Hybrids and Gene Flow between Upland and Lowland Switchgrass, Crop Science, 51, 2011. Research Area: Biomass Formation and Modification 10.2135/cropsci2011.02.0104
08/02/2010 Zhang One-step production of biocommodities from lignocellulosic biomass by recombinant cellulolytic Bacillus subtilis: Opportunities and challenges

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Engineering in Life Sciences Zhang, X. Z., Zhang, Y. H. P., One-step production of biocommodities from lignocellulosic biomass by recombinant cellulolytic Bacillus subtilis: Opportunities and challenges, Engineering in Life Science, Volume 10, Issue 5, pp 398-406, 2010. Research Area: Biomass Deconstruction and Conversion 10.1002/elsc.201000011
05/03/2011 Zhang One-step production of lactate from cellulose as the sole carbon source without any other organic nutrient by recombinant cellulolytic Bacillus subtillis

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Metabolic Engineering Zhang, Xiao-Zhou, Sathitsuksanoh, Noppadon, Zhu, Zhiguang, Zhang, Y.H. Percival, One-step production of lactate from cellulose as the sole carbon source without any other organic nutrient by recombinant cellulolytic Bacillus subtilis, Metabolic Engineering, 13(4): 364-372, 2011. Research Area: Biomass Deconstruction and Conversion 10.1016/j.ymben.2011.04.003
03/01/2010 Zhang The non-cellulosomal family 48 cellobiohydrolase from Clostridium phytofermentans ISDg: Heterologous expression, characterization, and processivity.

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Applied Microbiology and Biotechnology Zhang, Z.Z., Zhang, Z., Zhu, Z., Sathitsuksanoh, N., Yang, Y., Zhang, Y.H.P., The noncellulosomal family 48 cellobiohydrolase from Clostridium phytofermentans ISDg: heterologous expression, characterization, and processivity, Applied Microbiology Biotechnology, 2010, Volume 86, Number 2; p 525-533 Research Area: Biomass Deconstruction and Conversion http://dx.doi.org/10.1007/s00253-009-2231-1
07/04/2011 Zhang Toward low-cost biomanufacturing through in vitro synthetic biology: bottom-up design

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Journal of Materials Chemistry Zhang, Y.H. Percival, Myung, Suwan, You, Chun, Zhu, Zhiguang, Rollin, J.A., Toward low-cost biomanufacturing through invitro synthetic biology: bottom-up design, Journal of Materials Chemistry, 21(47):18877-18886, 2011. Research Area: Biomass Deconstruction and Conversion 10.1039/c1jm12078f
01/04/2011 Zhang Simple, fast and high-efficiency transformation system for directed evolution of cellulase in Bacillus subtilis

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Microbial Biotechnology Zhang, Xiao-Zhou, Zhang, Y.H. Percival, Simple, fast and high-efficiency transformation system for directed evolution of cellulase in Bacillus subtilis, Microbial Biotechnology, 4: 98-105, 2011. Research Area: Biomass Deconstruction and Conversion 10.1111/j.1751-7915.2010.00230.x
07/01/2011 Zhang Simpler Is Better: High-Yield and Potential Low-Cost Biofuels Production through Cell-Free Synthetic Pathway Biotransformation (SyPaB)

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ACS Catalysis Zhang, Y.H. Percival, Simpler Is Better: High-Yield and Potential Low-Cost Biofuels Production through Cell-Free Synthetic Pathway Biotransformation (SyPaB), ACS Catalysis, 1: 998-1009, 2011. Research Area: Biomass Deconstruction and Conversion 10.1021/cs200218f
11/01/2009 Zhang Production of biocommodities and bioelectricity by cell-free synthetic enzymatic pathway biotransformations (SyPaB): Challenges and opportunities

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Biotechnology and Bioengineering Zhang YHP. Production of Biocommodities and Bioelectricity by Cell-Free Synthetic Enzymatic Pathway Biotransformations: Challenges and Opportunities. Biotechnology and Bioengineering 2010;105(4):663-677. Research Area: Biomass Deconstruction and Conversion 10.1002/bit.22630
07/23/2011 Zhang Post-glacial evolution of Panicum virgatum: centers of diversity and gene pools revealed by SSR markers and cpDNA sequences

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Genetica Zhang, Y., Zalapa, J.E., Jakubowski, A.R., Price, D.L., Acharya, A., Wei, Y., Brummer, E.C., Kaeppler, S.M., Casler, M.D.,Post-glacial evolution of Panicum virgatum: centers of diversity and gene pools revealed by SSR markers and cpDNA sequences, Genetica, 139:933-948, 2011. Research Area: Biomass Formation and Modification 10.1007/s10709-011-9597-6
07/01/2010 Zhang Renewable carbohydrates are a potential high-density hydrogen carrier

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International Journal of Hydrogen Energy Zhang, Y.H.P., Renewable carbohydrates are a potential high-density hydrogen carrier, International Journal of Hydrogen Energy, Volume 35, Issue 19, pp 10334-10342, 2010. Research Area: Biomass Deconstruction and Conversion doi:10.1016/j.ijhydene.2010.07.132
01/31/2011 Zhang Renewable Hydrogen Carrier — Carbohydrate: Constructing the Carbon-Neutral Carbohydrate Economy

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Energies Zhang, Y-H Percival, Mielenz, Jonathan R., Renewable Hydrogen Carrier -- Carbohydrate: Constructing the Carbon-Neutral Carbohydrate Economy, energies, 4, 254-275, 2011. Research Area: Biomass Deconstruction and Conversion 10.3390/en4020254
06/01/2010 Zhang Biofuel production by in vitro synthetic pathway biotransformation

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Current Opinion in Biotechnology Zhang, Y. H. P., Sun, J. B., Zhong, J. J., Biofuel production by in vitro synthetic enzymatic pathway biotransformation, Current Opinion in Biotechnology, Volume 21, Issue 5, pp 663-669, 2010. Research Area: Biomass Deconstruction and Conversion 10.1016/j.copbio.2010.05.005
01/01/2009 Zhang A sweet and out-of-the-box solution for the hydrogen economy: Is sugar-powered car science fiction?

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Energy and Environmental Science Zhang YHP. A sweet out-of-the-box solution to the hydrogen economy: is the sugar-powered car science fiction? Energy and Environmental Science 2009;2(3):272-282. Research Area: Biomass Deconstruction and Conversion 10.1039/ b818694d
01/01/2009 Zhang Advances in cellulose solvent- and organic solvent-based lignocellulose fractionation (COSLIF) ACS Symposium Series Zhang Y-HP, Zhu Z, Rollin J, Sathisuksanoh N. 2010. Chapter 20. Advances in cellulose solvent- and organic solvent-based lignocellulose fractionation (COSLIF). ACS Symposium Series 1033: 365-379 (Cellulose solvents: For analysis, shaping and chemical modification), Oxford University Press, UK, ISBN13: 9780841200067. Research Area: Biomass Deconstruction and Conversion 10.1021/bk-2010-1033.ch020.
08/01/2011 Zhang What is vital (and not vital) to advance economically-competitive biofuels production

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Process Biochemistry Zhang, Y.H.P., What is vital (and not vital) to advance economically-competitive biofuels production, Process Biochemistry, 46(11):2091-2110, 2011. Research Area: Biomass Deconstruction and Conversion 10.1016/j.procbio.2011.08.005
09/01/2009 Zhang Cellulase Assays

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Biofuels: Methods and Protocols Y.H. Percival Zhang, Jiong Hong, and Xinhao Ye, Cellulase Assays, Biofuels: Methods and Protocols, Methods in Molecular Biology, Jonathan R. Mielenz (ed.), vol. 581; 2009 Chapter 14 Research Area: Biomass Deconstruction and Conversion 10.1007/978-1-60761-214-8_14
10/10/2010 Zhang Ethanol Production From Paper Sludge by Simultaneous Saccharification and Co-Fermentation Using Recombinant Xylose-Fermenting Microorganisms

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Biotechnology and Bioengineering Zhang, Jiayi, Lynd, L. R., Ethanol Production from Paper Sludge by Simultaneous Saccharification and Co-Fermentation Using Recombinant Xylose-Fermenting Microorganisms, Biotechnology and Bioengineering, Vol. 107, No. 2., pp 235-244, October 2010. Research Area: Biomass Deconstruction and Conversion 10.1002/bit.22811
06/01/2010 Zhang Glycoside hydrolase family 9 processive endoglucanase from Clostridium phytofermentans: Heterologous expression, purification, and synergy with family 48 cellobiohydrolase

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Bioresource Technology Glycoside hydrolase family 9 processive endoglucanase from Clostridium phytofermentans: heterologous expression, purfication, and synergy with family 48 cellobiohydrolase, Bioresource Technology, Zhang, X.Z., Sathisuksanoh, N., Zhang, Y.H.P., Volume 101, Issue 14 pp 5534-5538, 2010 Research Area: Biomass Deconstruction and Conversion 10.1016/j.biortech.2010.01.152
07/11/2011 Zhang Hydrogen Production from Carbohydrates: A mini-review

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ACS Symposium Series Zhang, Y.H.P., Hydrogen Production from Carbohydrates: a mini-review, Sustainable Production of Fuels, Chemicals, and Fibers from Forest Biomass, ACS Symposium Series, V 1067, 8, pp 203-216. Research Area: Biomass Deconstruction and Conversion ISBN13: 9780841226432eISBN: 9780841226449
03/01/2010 Zhao A NAC transcription factor orchestrates multiple features of cell wall development in Medicago truncatula

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Plant Journal Zhao Q, Gallego‐Giraldo L, Wang H, Zeng Y, Ding SY, Chen F, Dixon RA. (2010) An NAC transcription factor orchestrates multiple features of cell wall development in Medicago truncatula. Plant J. 63(1):100‐14. Research Area: Biomass Formation and Modification 10.1111/j.1365-313X.2010.04223.x
07/01/2010 Zhao Syringyl lignin biosynthesis is directly regulated by a secondary cell wall master switch

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PNAS Zhao, Q. A., Wang, H. Z., Yin, Y. B., Xu, Y., Chen, F., Dixon, R. A., Syringyl lignin biosynthesis is directly regulated by a secondary cell wall master switch, PNAS, Volume 107, Issue 32, pp 14496-14501, 2010. Research Area: Biomass Formation and Modification 10.1073
01/01/2009 Zhao Two poplar methyl salicylate esterases display comparable biochemical properties but divergent expression patterns

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Phytochemistry Zhao, N., Guan, J., Forouhar, F., Tschaplinski, T.J., Cheng, C‐M., Tong L., and Chen, F. (2009) Two poplar methyl salicylate esterases display comparable biochemical properties but divergent expression patterns. Phytochemistry 70: 37‐44. Research Area: Biomass Formation and Modification 10.1016/j.phytochem.2008.11.014
06/28/2013 Zhao Loss of function of cinnamyl alcohol dehydrogenase 1 leads to unconventional lignin and a temperature-sensitive growth defect in Medicago truncatula

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PNAS Zhao, Q., Tobimatsu, Y., Zhou, R., Pattathil, S., Gallego-Giraldo, L., Fu, Chuxiang, Jackson, L.A., Hahn, M.G., Kim, H., Chen, F., Ralph, J., Dixon, R.A., Loss of function of cinnamyl alcohol dehydrogenase 1 leads to unconventional lignin and a temperature-sensitive growth defect in Medicago truncatula, PNAS, 2013 Research Area: Biomass Formation and Modification 10.1073/pnas.1312234110
01/01/2014 Zhou The Trans-acting short interfering RNA3 pathway and NO APICAL MERISTEM anttagonistically regulate leaf margin development and lateral organ separation, as revealed by analysis of an argonaute7/lobed leaflet1 mutant in medicago truncatula

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The Plant Cell Zhou, C., Han, L., Fu, C., Wen, J., Cheng, X., Nakashima, J., Ma., J., Tang, Y., Tadege, M., Mysore, K.S., Xia, G., Wang, Z.Y., The Trans-acting short interfering RNA3 pathway and NO APICAL MERISTEM anttagonistically regulate leaf margin development and lateral organ separation, as revealed by analysis of an argonaute7/lobed leaflet1 mutant in medicago truncatula, The Plant Cell, 25, 2014. Research Area: Biomass Formation and Modification 10.1105/tpc.113.117788
02/22/2013 Zhou An atypical glycolysis in Clostridium thermocellum

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Applied and Environmental Microbiology Zhou, J., Olson, D.G., Argyros, D.A., Deng, Y., van Gulik, W.M., van Dijken, J.P., Lynd, L.R., An atypical glycolysis in Clostridium thermocellum, Applied and Environmental Microbiology, 79(9):3000-8, 2013. Research Area: Biomass Deconstruction and Conversion 10.1128/​AEM.04037-12
03/05/2012 Zhou Qserver: A Biclustering Server for Prediction and Assessment of Co-Expressed Gene Clusters

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PLoS One Zhou F, Ma Q, Li G, Xu Y (2012). "Qserver: A Biclustering Server for Prediction and Assessment of Co-Expressed Gene Clusters." PLoS ONE 7(3): e32660. Research Area: Characterization and Modeling 10.1371/journal.pone.0032660
08/14/2012 Zhou Identification and characterization of petiolule-like pulvinus mutants with abolished nyctinastic leaf movement in the model legume Medicago truncatula

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New Phytologist Zhou, C., Han, L., Fu, C., Chai, M., Zheng, W., Li, G., Tang, Y., Wang, Z., Identification and characterization of petiolule-like pulvinus mutants with abolished nyctinastic leaf movement in the model legume Medicago truncatula, New Phytologist, 2012 Research Area: Biomass Formation and Modification 10.1111/j.1469-8137.2012.04268.x
01/09/2009 Zhou RepPop: a database for repetitive elements in Populus trichocarpa

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BMC Genomics Zhou, F., Xu, Ying, RepPop: a database for repetitive elements in Populus trichocarpa, BMC Genomics, 10:14, 2009 Research Area: Biomass Formation and Modification 10.1186/1471-2164-10-14),
12/01/2009 Zhou Large scale analyses of glycosylation in cellulases

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Genomics, Proteomics and Bioinformatics Zhou, Fengfeng, Olman, Victor, Xu, Ying, Large scale analyses of glycosylation in cellulases, Genomics, Proteomics and Bioinformatics, Volume 7, Issue 4, December 2009, Pages 194-199 Research Area: Characterization and Modeling 10.1016/S1672-0229(08)60049-2
06/16/2008 Zhou Barcodes for Genomes and Applications

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BMC Bioinformatics Zhou, Fengfeng, Victor Olman, Ying Xu , Barcodes for Genomes and Applications, BMC Bioinformatics, 9:546, 2008 Research Area: Characterization and Modeling 10.1186/1471-2105-9-546
04/27/2009 Zhou Cellulose hydrolysis in evolving substrate morphologies I: a general modeling formalism

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Biotechnology and Bioengineering Zhou, W., Schuttler, H.B., Hao, Z.Q., Xu, Y., Cellulose Hydrolysis in Evolving Substrate Morphologies I: A General Modeling Formalism, Biotechnology and Bioengineering, 104;(2), pp 261-274, 2009. Research Area: Characterization and Modeling 10.1016/S1672-0229(08)60049-2
04/27/2009 Zhou Cellulose hydrolysis in evolving substrate morphologies II: numerical results and analysis

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Biotechnology and Bioengineering Zhou, W., Hao, Z., Xu, Y., Shuttler, B., Cellulose hydrolysis in evolving substrate morphologies II: numerical results and analysis, Biotechnology and Bioengineering, 2009 Oct 1;104(2):275-89 Research Area: Characterization and Modeling
06/01/2010 Zhou Cellulose hydrolysis in evolving substrate morphologies III: time scale analysis

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Biotechnology and Bioengineering Zhou, W., Xu, Y., Schuttler, H.B., Cellulose hydrolysis in evolving substrate morphologies III:time scale analysis, Biotechnology and Bioengineering, Volume 107, Issue 2, pp 224-234 Research Area: Characterization and Modeling 10.1002/bit.22814
08/05/2010 Zhou Identification of Novel Proteins Involved in Plant Cell-Wall Synthesis Based on Protein−Protein Interaction Data

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Journal of Proteome Research Zhou, C., Yin, Y.B., Dam, P., Xu, Y., Identification of Novel Proteins Involved in Plant Cell-Wall Synthesis Based on Protein-Protein Interaction Data, Journal of Proteome Research, Volume 9, Issue 10, pp 5025-5037, 2010. Research Area: Characterization and Modeling 10.1021/pr100249c
03/04/2010 Zhou GASdb: a large-scale and comparative exploration database of glycosyl hydrolysis systems

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BMC Microbiology Zhou, F., Chen, H., Xu, Y, GASdb: a large-scale and comparative exploration database of glycosyl hydrolysis system, 2010 March; 10:69 Research Area: Characterization and Modeling 10.1186/1471-2180-10-69
06/01/2011 Zhou Developmental Analysis of a Medicago truncatula smooth leaf margin1 Mutant Reveals Context-Dependent Effects on Compound Leaf development

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The Plant Cell Zhou, Chuanen, Han, Lu, Hou, Chunyan, Metelli, Allessandra, Qi, Liying, Tadege, Million, Mysore, Kirankumar S., Wang, Zeng-Yu, Developmental Analysis of a Medicago truncatula smooth leaf margin1 Mutant Reveals Context-Dependent Effects on Compound Leaf development, The Plant Cell, 23(6): 2106-2124, 2011. Research Area: Biomass Formation and Modification 10.1105/tpc.111.085464
Zhou New Insights into clostridia through comparative analyses of their 40 genomes Bioenergy Research Zhou, C., Ma, Q., Mao, X., Yin, Y., Xu, Y., New Insights into Clostridia through Comparative 1 Analyses of Their 40 Genomes, Bioenergy Research, 2014 Research Area: Characterization and Modeling
01/01/2009 Zhu Direct quantitative determination of adsorbed cellulase on lignocellulosic biomass with its application to study cellulase desorption for potential recycling

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Analyst Zhiguang Zhu, Noppadon Sathitsuksanoha and Y.-H. Percival Zhang, Direct quantitative determination of adsorbed cellulase on lignocellulosic biomass with its application to study cellulase desorption for potential recycling, Analyst, 2009 1347:2267-2272 Research Area: Biomass Deconstruction and Conversion 10.1039/b906065k
04/22/2011 Zhu Maltodextrin-Powered Enzymatic Fuel Cell though a Non-Natural Enzymatic Pathway

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Journal of Power Sources Zhu, Zhiguang, Wang, Yiran, Minteer Shelley D., Zhang, Y.H. Percival, Maltodextrin-Powered Enzymatic Fuel Cell though a Non-Natural Enzymatic Pathway, Journal of Power Sources, 196(18): 7505-7509, 2011. Research Area: Biomass Deconstruction and Conversion 10.1016/j.jpowsour.2011.04.038
07/01/2009 Zhu Comparative study of corn stover pretreated by dilute acid and cellulose solvent‐based lignocellulose fractionation: Enzymatic hydrolysis, supramolecular structure, and substrate accessibility

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Biotechnology and Bioengineering Zhu, Z. G., Sathitsuksanoh, N., Vinzant, T., Schell, D. J., McMillan, J. D., Zhang, Y. H. P., Comparative Study of Corn Stover Pretreated by Dilute Acid and Cellulose Solvent-Based Lignocellulose Fractionation: Enzymatic Hydrolysis, Supramolecular Structure, and Substrate Accessibility, Biotechnology and Bioengineering, (2009), Volume 103(4), 715-724 Research Area: Biomass Deconstruction and Conversion 10.1039/b906065k
04/11/2012 Zhu Deep oxidation of glucose in enzymatic fuel cells through a synthetic enzymatic pathway containing a cascade of two thermostable dehydrogenases

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Biosensors and Bioelectronics Zhu, Z., Sun, F., Zhang, X., Zhang, Y.-H.P., Deep oxidation of glucose in enzymatic fuel cells through a synthetic enzymatic pathway containing a cascade of two thermostable dehydrogenases, Biosensors and Bioelectronics, in press, 2012. Research Area: Biomass Deconstruction and Conversion 10.1016/j.bios.2012.04.001
06/01/2010 Zhu Virus-Induced Gene Silencing Offers a Functional Genomics Platform for Studying Plant Cell Wall Formation Molecular Plant Zhu X, Pattathil S, Mazumder K, Brehm A, Hahn MG, Dinesh-Kumar SP, Joshi CP., Virus-Induced Gene Silencing Offers a Functional Genomics Plantform for Studying Plant Cell Wall Formation, Molecular Plant, Volume 3, Issue 5, pp 818-833, 2010. Research Area: Characterization and Modeling 10.1093/mp/ssq023
04/15/2013 Zhu Isolation and diversity analysis of resistance gene homologues from switchgrass

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G3: Genes, Genomes, Genetics Zhu, Q., Bennetzen, J.L., Smith, S.M., Isolation and diversity analysis of resistance gene homologues from switchgrass, G3: Genes, Genomes, Genetics, 3(6):1031-42, 2013. Research Area: Biomass Formation and Modification 10.1534/g3.112.005447
01/01/2009 Zhulin (Jouline) It Is Computation Time for Bacteriology!

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Journal of Bacteriology Zhulin, Igor B., It Is Computation Time for Bacteriology!, Journal of Bacteriology, January 2009, p. 20-22; Volume 191, No. 1 Research Area: Characterization and Modeling 10.1128/JB.01491-08
10/04/2010 Ziebell Increase in 4-coumaryl alcohol units during lignification in alfalfa (Medicago sativa) alters the extractability and molecular weight of lignin

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Journal of Biological Chemistry Ziebell, A., Gracom, K., Katahira, R., Chen, F., Pu, Y. Q., Ragauskas, A., Dixon, R. A., Davis, M., Increase in 4-coumaryl alcohol units during lignification in alfalfa (Medicago sativa) alters the extractability and molecular weight of lignin, The Journal of Biological Chemistry, 285(50), 38961-38968, 2010. Research Area: Characterization and Modeling 10.1074/jbs.M110.137315
01/01/2014 Zurawski The Extremely Thermophilic Genus Caldicellulosiruptor: Physiological and Genomic Characteristics for Complex Carbohydrate Conversion to Molecular Hydrogen

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Microbial BioEnergy: Hydrogen Production Zurawski, J.W., Blumer-Schuette, S.E., Conway, J.M., Kelly, R.M., The Extremely Thermophilic Genus Caldicellulosiruptor: Physiological and Genomic Characteristics for Complex Carbohydrate Conversion to Molecular Hydrogen, Microbial BioEnergy: Hydrogen Production, chapter 8, pp 177-195, 2014. Research Area: Biomass Deconstruction and Conversion ISBN 978-94-017-8553-2