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Publications: 733
Citations: 13204

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Publication Date Citation Number of Citations Research Areas
09/01/2015 Lin, P.P., Mi, L., Morioka, A.H., Yoshino, K.M., Konishi, S., Xu, S.C., Papanek, B.A., Riley, L.A., Guss, A.M., Liao, J.C., Consolidated bioprocessing of cellulose to isobutanol using Clostridium thermocellum, Metabolic Engineering, 31, (44-52), 2015
DOI: 10.1016/j.ymben.2015.07.001
PDF
  Biomass Deconstruction and Conversion
08/27/2015 Sun, Q., Pu, Y., Meng, X., Wells, T., Ragauskas, A.J., Structural transformation of isolated poplar and switchgrass, ACS Sustainable Chemistry and Engineering, 2015
DOI: 10.1021/acssuschemeng.5b00426
PDF
  Characterization and Modeling
08/24/2015 Slater, S.C., Simmons, B.A., Rogers, T.S., Phillips, M.E., Nordahl, K., Davison, B.H., The DOE Bioenergy Research Centers: history, operations and scientific output, 2015
DOI: 10.1007/s12155-015-9660-8
PDF
  Biomass Formation and Modification
Biomass Deconstruction and Conversion
Characterization and Modeling
08/11/2015 Yao, J., Guo, H., Chairprasongsuk, M., Zhao, N., Chen, F., Yang, Y., Guo, H., Substrate-assisted catalysis in the reaction catalyzed by salicylic acid binding protein 2 (SABP2), a potential mechanism of substrate discrimination for some promiscuous enzymes, Biochemistry, 2015
DOI: 10.1021/acs.biochem.5b00638
PDF
  Biomass Formation and Modification
08/01/2015 Rooney, et. al., Draft genome sequence of the cellulolytic and xylanolytic thermophile Clostridum clariflavum Strain 4-2a, Genome Announcements, 3, 4, 2015.
DOI: 10.1128/genomeA.00797-15
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  Biomass Deconstruction and Conversion
08/01/2015 Wilson, D.B., Processive Cellulases, "Direct Microbial Conversion of Biomass to Advanced Biofuels", 5 (91-110), 2015.
DOI: 10.1016/B978-0-444-59592-8.00005-1
  Biomass Deconstruction and Conversion
08/01/2015 Kruer-Zerhusen, N., Wilson, D.B., "Bacterial AA10 Lytic Polysaccharide Monooxygenases Enhance the Hydrolytic Degradation of Recalcitrant Substrates", Direct Microbial Conversion of Biomass to Advanced Biofuels, 7 (111-127), 2015.
DOI: 10.1016/B978-0-444-59592-8.00007-5
  Biomass Deconstruction and Conversion
08/01/2015 Hobdey, S.E., Donohoe, B.S., Brunecky, R., Himmel, M., Bomble, Y.J., "New Insights into Microbial Strategies for Biomass Conversion", Direct Microbial Conversion of Biomass to Advanced Biofuels, 7 (111-127), 2015.
DOI: 10.1016/B978-0-444-59592-8.00007-5
  Biomass Deconstruction and Conversion
08/01/2015 Morais, S., Himmel, M.E., Bayer, E.A., "New Paradigms for Engineering Plant Cell Wall Degrading Enzymes", Direct Microbial Conversion of Biomass to Advanced Biofuels, 8 (129-149), 2015.
DOI: 10.1016/B978-0-444-59592-8.00008-7
  Biomass Deconstruction and Conversion
08/01/2015 Takasumi, J.L., Liao, J.C., "Outlook for the Production of Butanol from Cellulolytic Strains of Clostridia", Direct Microbial Conversion of Biomass to Advanced Biofuels, 14 (291-306), 2015.
DOI: 10.1016/B978-0-444-59592-8.00014-2
  Biomass Deconstruction and Conversion
08/01/2015 Yarbrough, J.M., Mittal, A., Bomble, Y.J., Olstad, J., Wolfrum, E.J., Hobdey, S.E., Himmel, M.E., Vinzant, T.B., "Influence of Particle Size on Direct Microbial Conversion of Hot Water Pretreated Poplar by Clostridium thermocellum", Direct Microbial Conversion of Biomass to Advanced Biofuels, 15 (307-319), 2015.
DOI: 10.1016/B978-0-444-59592-8.00015-4
  Biomass Deconstruction and Conversion
08/01/2015 Brown, S.D., Sander, K.B., Wu, C-W., Guss, A.M., "Clostridium thermocellum: Engineered for the Production of Bioethanol", Direct Microbial Conversion of Biomass to Advanced Biofuels, 16 (321-333), 2015.
DOI: 10.1016/B978-0-444-59592-8.00016-6
  Biomass Deconstruction and Conversion
08/01/2015 Pu, Y., Hu, F., Huang, F., Ragauskas, A.J., "Lignin structural alterations in thermochemical pretreatments with limited delignification", Bioenergy Research, 2015
DOI: 10.1007/s12155-015-9655-5
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  Characterization and Modeling
08/01/2015 Chung, D., Verbeke, T.J., Cross, K.L., Westpheling, J., Elkins, J.G., Expression of a heat-stable NADPH-dependent alcohol dehydrogenase in Caldicellulosiruptor bescii results in furan aldehyde detoxification
DOI: 10.1186/s13068-015-0287-y
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  Biomass Deconstruction and Conversion
08/01/2015 Chung, D., Young, J., Cha, M., Brunecky, R., Bomble, Y.J., Himmel, M.E., Westpheling, J., "Expression of the Acidothermus cellulolyticus E1 endoglucanase in Caldicellulosiruptor bescii enhances its ability to deconstruct crystalline cellulose", Biotechnology for Biofuels, 8:113, 2015.
DOI: 10.1186/s13068-015-0296-x
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  Biomass Deconstruction and Conversion
07/27/2015 Scott, I.M., Rubinstein, G.M., Lipscomb, G.L., Basen, M., Schut, G.J., Rhaesa, A.M., Lancaster, W.A., Poole II, F.L., Kelly, R.M., Adams, M.W.W., "A new class of tungsten-containing oxidoreductase in the genus of the plant biomass-degrading, thermophilic bacteria Caldicellulosiruptor", 2015
DOI: 10.1128/AEM.01634-15
  Biomass Deconstruction and Conversion
07/25/2015 Yee, K.L., Rodriguez Jr., Miguel, Hamilton, C.Y., Hamilton-Brehm, S.D., Thompson, O.A., Elkins, J.G., Davison, B.H., Mielenz, J.R., Fermentation of dilute acid pretreated Populus by Clostridium thermocellum, Caldicellulosiruptor bescii, and Caldicellulosiruptor obsidiansis, Bioenergy Research, 2015
DOI: 10.1007/s12155-015-9659-1
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  Characterization and Modeling
07/24/2015 Zurawski, J.V., Conway, J.M., Lee, L.L., Simpson, H., Izquierdo, J.A., Blumer-Schuette, S., Nookaew, I., Adams, M.W.W., Kelly, R.M., Comparative analysis of extremely thermophilic Caldicellulosiruptor species reveals common and differentiating cellular strategies for plant biomass utilization, Applied and Environmental Microbiology, 2015
DOI: 10.1128/AEM.01622-15
  Biomass Deconstruction and Conversion
07/20/2015 Wuddineh, W.A., Mazarei, M., Turner, G.B., Sykes, R.W., Decker, S.R., Davis, M.F., Stewart, Jr., C.N., Identification and molecular characterization of the switchgrass AP2/ERF transcription factor superfamily, and overexpression of PvERF001 for improvement of biomass characteristics for biofuel, Frontiers in Bioengineering and Biotechnology, 13:636-647, 2015.
DOI: 10.3389/fbioe.2015.00101
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  Biomass Formation and Modification
Characterization and Modeling
07/20/2015 Alahuhta, M., Taylor II, L.E., Brunecky, R., Sammond, D.W., Michener, W., Adams, M.W.W., Himmel, M.E., Bomble, Y.J., Lunin, V., The catalytic mechanism and unique low pH optimum of Caldicellulosiruptor bescii family 3 pectate lyase, Acta Crystallography, D71 (1946-1954), 2015.
DOI: 10.1107/S1399004715013760
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  Biomass Deconstruction and Conversion
07/15/2015 Yu, M., Ji, L., Neumann, D.A., Chung, D-H., Groom, J., Westpheling, J., He, C., Schmitz, R.J., Base-resolution detection of N4-methylcytosine in genomic DNA using 4mC-Tet-assisted-bisulfite-sequencing, 2015
DOI: 10.1093/nar/gkv738
PDF
  Biomass Deconstruction and Conversion
07/15/2015 Rydzak, T., Lynd, L.R., Guss, A.M., Elimination of formate production Clostridium thermocellum, Journal of Industrial Biotechnology, 2015
DOI: 10.1007/s10295-015-1644-3
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3 Biomass Deconstruction and Conversion
07/09/2015 McLean, R., Hobbs, J.K., Suits, M.D., Tuomivaara, S.T., Jones, D., Boraston, A.B., Abbott, D.W., Functional analyses of resurrected and contemporary enzymes illuminate an evolutionary path for the emergence of exolysis in polysaccharide lyase family two, The Journal of Biological Chemistry, 2015
DOI: 10.1074/jbs.M115.664847
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  Biomass Formation and Modification
07/01/2015 Gallego-Giraldo, L., Shadle, G., Shen, H., Barros-Rios, J., Corrales, S. F., Wang, H., Dixon, R.A., Combining enhanced biomass density with reduced lignin level for improved forage quality, 2015
DOI: 10.1111/pbi.12439
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  Biomass Formation and Modification
07/01/2015 Tetard, L., Passian, A., Farahi, R.H., Thundat, T., Davison, B.H., Opto-nanomechanical spectroscopic material characterization, Nature Nanotechnology, 2015
DOI: 10.1038/NNANO.2015.168
PDF
  Characterization and Modeling
07/01/2015 Bekiaris, G., Lindedam, J., Peltre, C., Decker, S.R., Turner, G.B., Magid, J., Bruun, S., Rapid estimation of sugar release from winter wheat straw during bioethanol production using FTIR-photoacoustic spectroscopy, Biotechnology for Biofuels, 8:85, 2015.
DOI: 10.1186/s13068-015-0267-2
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  Characterization and Modeling
06/29/2015 Lo, J., Zheng T., Olson, D.G., Ruppertsberger, N., Truipathi, S.A., Guss, A.M., Lynd, L.R., Deletion of nfnAB in Thermoanaerobacterium saccharolyticum and its effect on metabolism, Journal of Bacteriology, 2015
DOI: 10.1128/JB.00347-15
  Biomass Deconstruction and Conversion
06/26/2015 Currie, D.H., Raman, B., Gowen, C.M., Tschaplinski, T.., Land, M.L., Brown, Steven D., Covalla, S.L., Klingeman, D.M., Yang, Z.K., Engle, N.L., Johnson, C.M., Rodriguez, M., Shaw, A.J., Kenealy, W.R., Lynd, L.R., Fong, S.S., Mielenz, J.R., Davison, B.H., Hogsett, D.A., Herring, C.D., Genome-scale resources for Thermoanaerobacterium saccharolyticum, BMC Systems Biology, 9:30, 2015.
DOI: 10.1186/s12918-015-0159-x
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  Biomass Deconstruction and Conversion
06/26/2015 Zheng, T., Olson, D.G., Tian, L., Bomble, Y.J., Himmel, M.E., Lo, J., Hon, S., Shaw, A.J., van Dijken, J.P., Lynd, L.R., Cofactor specificity of the bifunctional alcohol and aldehyde dehydrogenase (AdhE) in wild-type and mutants of Clostridium thermocellum and Thermoanaerobacterium saccharolyticum, Journal of Bacteriology, 2015
DOI: 10.1128/JB.00232-15
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  Biomass Deconstruction and Conversion
06/22/2015 Ray, P., Ishiga, T., Decker, S.R., Turner, G.B., Craven, K. D., A Novel Delivery Systemfor the Root Symbiotic Fungus, Sebacina vermifera, and Consequent Biomass Enhancement of Low Lignin COMT Switchgrass Lines, Bioenergy Research, 2015
DOI: 10.1007/s12155-015-9636-8
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  Biomass Formation and Modification
06/08/2015 Fulton, L.M., Lynd, L.R., Korner, A., Greene, N., Tonachel, L.R., The need for biofuels as part of a low carbon energy future, Biofuels, Bioproducts & Biorefining, 2015
DOI: 10.1002/bbb.1559
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  Biomass Deconstruction and Conversion
06/08/2015 Morrell-Falvey, J.L., Elkins, J.G., Wang, Z-W., Determination of the cellulase activity distribution in Clostridium thermocellum and Caldicellulosiruptor obsidiansis cultures using fluorescent substrate, Journal of Environmental Sciences, 2015
DOI: 10.1016/j.jes.2015.03.009
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  Biomass Deconstruction and Conversion
06/01/2015 Lee, L.L., et al, Complete genome sequences of Caldicellulosiruptor sp. Strain Rt8.B8, Caldicellulosiruptor sp. Strain Wai35.B1, and Thermoanaaerobacter cellulolyticus, Genome Announcements, 3:3, 2015.
DOI: 10.1128/genomeA.00440-15
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  Biomass Deconstruction and Conversion
05/21/2015 Mearls, E.B., Olson, D.G., Herring, C.D., Lynd, L.R., Development of a regulatable plasmid-based gene expression system for Clostridium thermocellum, Applied Genetics and Molecular Biotechnology, 2015
DOI: 10.1007/s00253-015-6610-5
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  Biomass Deconstruction and Conversion
05/20/2015 Mielenz, J.R., Rodriguez, M., Thompson, O.A., Yang, X., Yin, H., Development of Agave as a dedicated biomass source: production of biofuels from whole plants, Biotechnology for Biofuels, 2015
DOI: 10.1186/s13068-015-0261-8
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  Biomass Deconstruction and Conversion
05/14/2015 Davison, B.H., Brandt, C.C., Guss, A.M., Kaluri, U.C., Palumbo, A.V., Stouder, R.L., Webb, E.G., "The impact of biotechnological advances on the future of U.S. bioenergy", Biofuels, Bioproducts and Biorefining, 2015
DOI: 10.1002/bbb.1549
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  Characterization and Modeling
Biomass Formation and Modification
Biomass Deconstruction and Conversion
05/01/2015 O'Dell, K.B., Woo, H.L., Utturkar, S., Klingeman, D., Brown, S.D., Hazen, T.C., Genome sequence of halomonas sp. strain KO116 an ionic liquid-tolerant marine bacterium isolated from a lignin-enriched seawater microcosm, Genome Announcements, 3:3, 2015.
DOI: 10.1128/genomeA.00402-15
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  Characterization and Modeling
05/01/2015 Liu, W., Stewart, Jr., C.N., Plant synthetic biology, Trends in Plant Science, 20:309-317, 2015.
DOI: 10.1016/j.tplants.2015.02.004
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  Biomass Formation and Modification
04/23/2015 De Souza, A.P., Kamel, C.L.A., Torres, A.F., Pattathil, S., Hahn, M.G., Trindade, L.M., Buckeridge, M.S., How cell wall complexity influences saccharification efficiency in Miscanthus sinensis, Journal of Experimental Botany, 2015
DOI: 10.1093/jxb/erv183
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  Biomass Formation and Modification
Characterization and Modeling
04/15/2015 Sykes, R.W., Gjersing, E.L., Doeppke, C.L., Davis, M.F., High-throughput method for determining the sugar content in biomass with pyrolysis molecular beam mass spectrometry, BioEnergy Research, 2015
DOI: 10.1007/s12155-015-9610-5
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  Characterization and Modeling
04/14/2015 Utturkar, S.M., Klingeman, D.M., Bruno-Barcena, J.M., Chinn, M.S., Grunden, A.M., Kopke, M., Brown, S.D., Sequence data for clostridium autoethanogenum using three generations of sequencing technologies, Scientific Data, 2 (150014), 2015.
DOI: 10.1038/sdata.2015.14
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  Biomass Deconstruction and Conversion
04/07/2015 Olson, D.G., Maloney, M., Lanahan, A.A., Hon, S., Hauser, L.J., Lynd, L.R., Identifying promoters for gene expression in Clostridium thermocellum, Metabolic Engineering Communications, 2015
DOI: 10.1016/j.meteno.2015.03.002
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  Biomass Deconstruction and Conversion
Characterization and Modeling
03/27/2015 Weighill, D.A.; Jacobson, D.A., 3-way networks: application of hypergraphs for modelling increased complexity in comparative genomics, PLoS Computational Biology, 11(3), 2015.
DOI: 10.1371/journal.pcbi.1004079
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  Characterization and Modeling
03/23/2015 Chung, D., Young, J., Bomble, Y.J., Vander Wall, Todd A., Groom, J., Himmel, M.E., Westpheling, J., "Homologous expression of the Caldicellulosiruptor bescii CelA reveals that the extracellular protein is glycosylated", PLoS ONE, 2015
DOI: 10.1371/journal.pone.0119508
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  Biomass Deconstruction and Conversion
03/05/2015 Olson, D.G., Sparling, R., Lynd, L.R., Ethanol production by engineered thermophiles, Current Opinion in Biotechnology, 33, (130-141), 2015.
DOI: 10.1016/j.copbio.2015.02.006
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1 Biomass Deconstruction and Conversion
03/03/2015 Zhang, L., Lu, Z., Velarde, L., Fu, L., Pu, Y., Ding S-Y., Ragauskas, A.J., Wang, H-F., Yang, B., Vibrational spectral signatures of crystalline cellulose using high resolution broadband sum frequency generation vibrational spectroscopy (HR-BB-SFG-VS), Cellulose, 22:3, 1469-1484, .2015
DOI: 10.1007/s10570-015-0588-0
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  Characterization and Modeling
03/01/2015 Biswal, A.K., Hao, Z., Pattathil, S., Yang, X., Winkeler, K., Collins, C., Mohanty, S.S., Richardson, E.A., Gelineo-Albersheim, I., Hunt, K., Ryno, D., Sykes, R.W., Turner, G.B., Ziebell, A., Gjersing, E., Lukowitz, W., Davis, M.F., Decker, S.R., Hahn, M.G., Mohnen, D., Downregulation of GAUT12 in Populus deltoides by RNA silencing results in reduced recalcitrance, increased growth and reduced xylan and pectin in a woody biofuel feedstock, Biotechnology for Biofuels, 8, 2015
DOI: 10.1186/s13068-015-0204-4
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  Biomass Formation and Modification
Characterization and Modeling
03/01/2015 Blumer-Schuette, S.E., Alahuhta, M., Conway, J.M., Lee, L.L., Zurawski, J.V., Giannone, R.J., Hettich, R.L., Lunin, V.V., Himmel, M.E., Kelly, R.M., "Discrete and structurally unique proteins (tapirins) mediate attachment of extremely thermophilic Calcicellulosiruptor species to cellulose", Journal of Biological Chemistry, 2015
DOI: 10.1074/jbc.M115.641480
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  Biomass Deconstruction and Conversion
02/27/2015 Land, M., Hauser, L., Jun, S-R., Nookaew, I., Leuze, M.R., Ahn, T-H., Karpinets, T., Lund, O., Kora, G., Wassenaar, T., Poudel, S., Ussery, D.W., "Insights from 20 years of bacterial genome sequencing", Functional & Integrative Genomics, 2015
DOI: 10.1007/s10142-015-0433-4
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1 Characterization and Modeling
02/24/2015 Trumbo, J.L., Zhang, B., Stewart, Jr., C.N., "Manipulating microRNAs for improved biomass and biofuels from plant feedstocks", Plant Biotechnology Journal, 13 (337-354), 2015.
DOI: 10.1111/pbi.12319
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  Biomass Formation and Modification
02/18/2015 Wyman, C.E., Dale, B.E., Producing biofuels via the sugar platform, AICHE- CEP, 111 (45), 2015.   Characterization and Modeling
02/18/2015 Lo, J., Zheng, T., Hon, S., Olson, D.G., Lynd, L.R., The bifuncational alcohol and aldehyde dehydrogenase gene, adhE, is necessary for ethanol production in Clostridium thermocellum and Thermoanaerobacterium saccharolyticum, Journal of Bacteriology, 2015
DOI: 10.1128/JB.02450-14
1 Biomass Deconstruction and Conversion
02/11/2015 Nguyen, T.Y., Cai, C.M., Kumar, R., Wyman, C.E., "Co-solvent pretreatment reduces costly enzyme requirements for high sugar and ethanol yeilds from lignocellulosic biomass", ChemSusChem, 2015
DOI: 10.1002/cssc.201403045
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1 Characterization and Modeling
02/05/2015 Casler, M.D., Vermerris, W., Dixon, R.A., "Replication concepts for bioenergy research experiments", BioEnergy Research, 2015
DOI: 10.1007/s12155-015-9580-7
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  Biomass Formation and Modification
02/01/2015 Pattathil, S., Hahn, M.G., Dale, B.E., Chundawat, P.S., Insights into plant cell wall structure, architecture and integrity using glycome profiling of native and AFEXtm pretreated biomass, Journal of Experimental Botany, 2015
DOI: 10.1093/jxb/erv107
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  Characterization and Modeling
Biomass Formation and Modification
01/30/2015 Biswas, R., Zheng, T., Olson, D.G., Lynd, L.R., Guss, A.M., "Elimination of hydrogenase active site assembly blocks H2 production and increases ethanol yield in Clostridium thermocellum" Biotechnology for Biofuels, 2015
DOI: 10.1186/s13068-015-0204-4
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3 Biomass Deconstruction and Conversion
01/30/2015 Muchero, W., Guo, J., DiFazio, S.P., Chen, J-G., Ranjan, P., Slavov, G.T., Gunter, L.E., Jawdy, S., Bryan, A.C., Sykes, R., Ziebell, A., Klapste, J., Porth, I., Skyba, O., Unda, F., El-Kassaby, Y.A., Douglas, C.J., Mansfield, S.D., Martin, J., Schackwitz, W., Evans, L.M., Czarnecki, O., Tuskan, G.A., "High-resolution genetic mapping of allelic variants associated with cell wall chemistry in Populus", BMC Genomics, 16:24 2015.
DOI: 10.1186/s12864-015-1215-z
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  Biomass Formation and Modification
01/30/2015 Keller, M., Loder, A., Basen, M., Izquierdo, J., Kelly, R.M., Adams, M.W.W., "Production of lignofuels and electrofuels by extremely thermophilic microbes", Biofuels, 2015.
DOI: 10.1080/17597269.2014.996729
  Biomass Deconstruction and Conversion
01/20/2015 Serba, D.D., Uppalapati, S.R., Mukherjee, S., Krom, N., Tang, Y., Mysore, K.S., Saha, M.C., "Transcriptome profiling of rust resistance in switchgrass using RNA-Seq analysis", The Plant Genome, 2014
DOI: 10.3835/plantgenome2014.10.0075
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  Biomass Formation and Modification
01/07/2015 Baxter, H.L., Poovaiah, C.R., Yee, K., Mazarei, M., Rodriguez Jr., M., Thompson, O.A., Shen, H., Turner, G.B., Decker, S.R., Sykes, R.W., Chen, F., Davis, M.F., Mielenz, J.R., Davison, B.H., Dixon, R.A., Stewart Jr., C.N., "Field evaluation of transgenic switchgrass plants overexpressing PvMYB4 for reduced biomass recalcitrance, BioEnergy Research, 2014
DOI: 10.1007/s12155-014-9570-1
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  Biomass Formation and Modification
Characterization and Modeling
01/07/2015 Cuskin, et al, Human gut bacteroidetes can utilize yeast mannan through a selfish mechanism, Nature, 517 (165-169) 2015
DOI: 10.1038/nature13995
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5 Characterization and Modeling
12/29/2014 Yang, J., Worley, E., Udvardi, M., "A NAP-AA03 regulatory module promotes chlorophyll degradation via ABA biosynthesis in Arabidopsis leaves", The Plant Cell, 26:12, 4862-4874, 2014.
DOI: 10.1105/tpc.114.133769
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3 Biomass Formation and Modification
12/23/2014 Tan, L., Pu, Y., Pattathil, S., Avci, U., Qian, J., Arter, A., Chen, L., Hahn, M.G., Ragauskas, A.J., Kieliszewski, M.J., "Changes in cell wall properties coincide with overexpression of extension fusion proteins in suspension cultured tobacco cells", PloS ONE, 9(12): e115906, 2014.
DOI: 10.1371/journal.pone.0115906
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  Characterization and Modeling
12/16/2014 Yang, J., Worley, E., Torres-Jerez, I., Miller, R., Wang, M., Fu, C., Wang, Z-Y., Tang, Y., Udvardi, M., "PvNAC1 and PvNAC2 are associated with leaf senescence and nirtrogen use efficiency in switchgrass", Bioenergy Research, 8:2, (868-880), 2014.
DOI: 10.1007/s12155-014-9566-x
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  Biomass Formation and Modification
12/12/2014 Land, M.L., Hyatt, D., Jun, S-R., Kora, G.H., Hauser, L.J., Lukjancenko, O., Ussery, D.W., Quality scores for 32,000 genomes, Standards in Genomic Sciences, 9:20, 2014.
DOI: 10.1186/1944-3277-9-20
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  Characterization and Modeling
12/03/2014 Clarkson, S.M., Hamilton-Brehm, S.D., Giannone, R.J., Engle, N.L., Tschaplinski, T.J., Hettich, R.L., Elkins, J.G., "A comparative multidimensional LC-MS proteomic analysis reveals mechanisms for furan aldehyde detoxification in Thermoanaerobacter pseudethanolicus 39E", Biotechnology for Biofuels, 7:165, 2014.
DOI: 10.1186/s13068-014-0165-z
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1 Biomass Deconstruction and Conversion
12/02/2014 Brunner, A.M., Evans, L.M., Hsu, C-Y, Sheng, X., "Vernalization and the chilling requirement to exit bud dormancy: shared or separate regulation?", Frontiers in Plant Science, 5:732, 2014.
DOI: 10.3389/fpls.2014.00732
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  Biomass Formation and Modification
12/01/2014 Trajano, H.L., Pattathil, S., Tomkins, B.A., Tschaplinski, T.J., Hahn, M.G., Van Berkel, G.J., Wyman, C.E., "Xylan hydrolysis in Populus trichocarpa x P. deltoides and model substrates during hydrothermal pretreatment", Bioresource Technology, 2014
DOI: 10.1016/j.biortech.2014.11.090
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  Characterization and Modeling
11/25/2014 Bali, G., Meng, X., Deneff, J.I., Sun, Q., Ragauskas, A.J., "The effect of alkaline pretreatment methods on cellulose structure and accessibility", ChemSusChem Communications, 2014
DOI: 10.1002/cssc.201402752
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3 Characterization and Modeling
11/25/2014 Li, Z., Hwang, S., Ericson, J., Bowler, K., Bar-Peled, Maor, "Pen and Pal are nucleotide-sugar-dehydratases that convert UDP-GlcNAc to UDP-6-deoxy-D-GlcNAc-5,6-ene and then to UDP-4-keto-6-deoxy-L-AltNAc for CMP-pseudaminic acid synthesis in Bacillus thuringiensis", The Journal of Biological Chemistry, 290:2, (691-704), 2014.
DOI: 10.1074/jbc.M114.612747
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1 Biomass Formation and Modification
11/22/2014 Kumagai, A., Wu, L., Iwamoto, S., Lee, S-H., Endo, T., Rodriguez Jr., M., Mielenz, J.R., "Improvement of enzymatic saccharification of Populus and switchgrass by combined pretreatment with steam and wet disk milling", Renewable Energy, 76, (782-789), 2014.
DOI: 10.1016/j.renene.2014.11.070
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1 Characterization and Modeling
11/18/2014 Izquierdo, J.A., Pattathil, S., Guseva, A., Hahn, Michael G., Lynd, L.R., Comparative analysis of the ability of Clostridium clariflavum strains and Clostridium thermocellum to utilize hemicellulose and unpretreated plant material, Biotechnology for Biofuels, 7:136, 2014.
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1 Biomass Deconstruction and Conversion
11/11/2014 Kalluri, U.C., Yin, H., Davison, B.H., Systems and synthetic biology approaches to alter plant cell walls and reduce biomass recalcitrance, Plant Biotechnology Journal, 12:9, (1207-1216), 2014.
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2 Biomass Formation and Modification
Characterization and Modeling
11/11/2014 Basen, M., Schut, G.J., Nguyen D.M.N., Lipscomb, G.L., Benn, R.A., Prybol, C.J., Vaccaro, B.J., Poole, F.L., Kelly, R.M., Adams, M.W.W., Single gene insertion drives bioalcohol production by a thermophilic archaeon, PNAS, 111:49, 2014.
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2 Biomass Deconstruction and Conversion
11/10/2014 Archambault-Leger, V., Losordo, Z., Lynd, L.R., Energy, sugar dilution, and economic analysis of hot water flow-through pre-treatment for producing biofuel from sugarcane residues, Biofuels, Bioproducts and Biorefining, 2014
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  Biomass Deconstruction and Conversion
11/02/2014 Wuddineh, W.A., Mazarei, M., Poovaiah, C.R., Mann, D.G.J., Ziebell, A., Sykes, R.W., Davis, M.F., Udvardi, M.K., Stewart Jr., C.N., Identification and overexpress of gibberellin 2-oxidase (GA2ox) in switchgrass (Panicum virgatum L.) for improved plant architecture and reduced biomass recalcitrance, Plant Biotechnology Journal, 2014
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  Biomass Formation and Modification
Characterization and Modeling
11/01/2014 Carmona, C., Langan, P., Smith, Smith, J.C., Petridis, L., Why genetic modification of lignin leads to low-recalcitrance biomass, Physical Chemistry Chemical Physics, 17:1, 358-64, 2014.
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  Characterization and Modeling
10/30/2014 Zhou, C., Han, L., Li, G., Chai, M., Fu, C., Cheng, X., Wen, J., Tang, Y., Wang, Z-Y., STM/BP-Like KNOXI Is Uncoupled fromARP in the Regulation of Compound Leaf Development in Medicago truncatula, The Plant Cell, 26:4, 1464-1479, 2014.
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3 Biomass Formation and Modification
10/21/2014 Holwerda, E.K., Thorne, P.G., Olson, D.G., Amador-Noguez, D., Engle, N.L., Tschaplinski, T.J., van Dijken, J.P., Lynd, L.R., The exometabolome of Clostridium thermocellum reveals overflow metabolism at high cellulose loading, Biotechnology for Biofuels, 7:155 2014
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1 Biomass Deconstruction and Conversion
10/16/2014 Vishnivetskaya, T.A., Hamilton-Brehm, S.D., Podar, M., Mosher, J.J., Palumbo, A.V., Phelps, T.J., Keller, M., Elkins, J.G., Community analysis of plant biomass-degrading microorganisms from Obsidian Pool, Yellowstone National Park, Microbial Ecology, (1-13), 2014.
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  Biomass Deconstruction and Conversion
10/14/2014 Young, J., Chung, D., Bomble, Y.J., Himmel, M.E., Westpheling, J., "Deletion of CelA, the Most Abundant Cellulase in Caldicellulosiruptor bescii, Reveals its Crucial Role in the Deconstruction of Lignocellulosic Biomass", Biotechnology for Biofuels, 7:1, 2014.
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2 Biomass Deconstruction and Conversion
10/14/2014 Chai, J., Kora, G., Ahn, T-H., Hyatt, D., Pan, C., Functional phylogenomics analysis of bacteria and archaea using consistent genome annotation with UniFam, BMC Evolutionary Biology, 14:207, 2014.
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3 Characterization and Modeling
10/14/2014 Sun, Q., Foston, M., Meng, X., Pingali, V., O'Neill, Li, H., Wyman, C., Langan, P., Ragauskas, A., Kumar, R., The Effect of Lignin Content on Changes that Occur in Poplar Cellulose Ultrastructure during Dilute Acid Pretreatment, Biotechnology for Biofuels, 7:150, 2014.
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1 Characterization and Modeling
10/11/2014 Singh, S., Cheng, G., Sathitsuksanoh, N., Wu, D., Varanasi, P., George, A., Balan, V., Gao, X., Kumar, R., Dale, B., Wyman, C., Comparision of different biomass pretreatment techniques and their impact on chemistry, structure, and recalcitrance, Frontiers in Energy Research, 2014
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  Characterization and Modeling
10/07/2014 Payyavula, R.S., Tschaplinski, T.J., Jawdy, S.S., Sykes, R.W., Tuskan, G.A., Kalluri, U.C., Metabolic profiling reveals altered sugar and secondary metabolism in response to UGPase overexpression in Populus, BMC Plant Biology, 14:265 2014
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  Biomass Formation and Modification
10/01/2014 Chung, D., Pattathil, S., Biswal, A.K., Hahn, M.G., Mohnen, D., Westpheling, J., Deletion of a Gene Cluster Encoding Pectin Degrading Enzymes in Caldicellulosiruptor bescii Reveals an Important Role for Pectin in Plant Biomass Recalcitrance, Biotechnology for Biofuels, 7:147 2014
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Biomass Deconstruction and Conversion
09/18/2014 Qin, M., Chen, X., Chao, L., XiZeng, M., Yuan, Z.H., Fei, J.L., ChunGuo, W.U., Ying, X.U., "Understanding the commonalities and differences in genomic organizations across closely related bacteria from an energy perspective", Science China Life Science, 57:11, 1121-30, 2014.
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1 Characterization and Modeling
09/16/2014 Groom, J., Chung, D., Young, J., Westpheling, J., Heterologous complementation of a pyrF deletion in Caldicellulosiruptor hydrothermalis generates a new host for the analysis of biomass deconstruction, Biotechnology for Biofuels, 7:132, 2014.
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1 Biomass Deconstruction and Conversion
09/14/2014 Urbanowicz, B.R., Pena, M.J., Moniz, H.A., Moremen, K.W., York, W.S., Two Arabidopsis Proteins Synthesize Acetylated Xylan in Vitro, The Plant Journal, 80:2 (197-206) 2014
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09/11/2014 Yang, S., Franden, M.A., Brown, S.D., Chou, Y.C., Pienkos, P.T., Zhang, M., Insights into acetate toxicity in Zymomonas mobilis 8b using different substrates, Biotechnology for Biofuels, 7:140, 2014.
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2 Characterization and Modeling
09/08/2014 Zaharov, V.V., Farahi, R.H., Snyder, P.J., Davison, B.H., Passian, A., Karhunen-Lo`eve treatment to remove noise and facilitate data analysis in sensing, spectroscopy and other applications, Analyst, 139:5927 2014
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1 Characterization and Modeling
09/02/2014 Mostofian, B., Cheng, X., Smith, J.C., Replica-exhange molecular dynamics simulations of cellulose solvated in water and in the ionic liquid 1-butyl-3-methylimidazolium choloride, The Journal of Physical Chemistry B, 118, 11037-11049, 2014.
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3 Characterization and Modeling
09/02/2014 Socha, A.M., Parthasarathi, J., Shi, R., Pattathil, S., Whyte, D., Bergerson, M., Venkatachalam, S., Hahn, M.G., Simmons, B.A., Singh, S., Efficient biomass pretreatment using ionic liquids derived from lignin and hemicellulose, 111:35 (3587-95) 2014.
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08/30/2014 Serba, D.D., Daverdin, G., Bouton, J.H., Devos, K.M., Brummer, C.E., Saha, M.C., Quantitative trait loci (QTL) underlying biomass yield and plant height in switchgrass, Bioenergy Research, 2014
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2 Biomass Formation and Modification
08/28/2014 Hao, Z., Avci, U., Tan, L., Zhu, X., Glushka, J., Pattathil, S., Eberhard, S., Scholes, T., Rothstein, Lukowitz, W., Orlando, R., Hahn, M.G., Mohnen, D., Loss of Arabidopsis GAUT12/IRX8 causes anther indehiscence and leads to reduced G lignin associated with altered matrix polysaccharide deposition, Frontiers in Plant Science, 5:357, 2014.
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3 Biomass Formation and Modification
08/24/2014 Evans, L.M., Slavov, G.T., Rodgers-Melnick, E., Martin, J., Ranjan, P., Muchero, W., Brunner, A.M., Schackwitz, W., Gunter, L., Chen, J.G., Tuskan, G.A., DiFazio, S.P., Population genomics of the model tree Populus trichocarpa identifies signatures of selection and adaptive trait associations, Nature Genetics, 46 (1089-1096) 2014
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  Biomass Formation and Modification
08/21/2014 Poovaiah, C.R., Mazarei, M., Decker, S.R., Turner, G.B., Sykes, R.W., Davis, M.F., Stewart, Jr. C.N., Transgenic switchgrass (Panicum virgatum L.) biomass is increased by overexpression of switchgrass sucrose synthase (PvSUS1), Biotechnology Journal, 10:4, 552-563, 2015.
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1 Biomass Formation and Modification
Characterization and Modeling
08/16/2014 Linville, J.L., Rodriguez Jr., M., Brown, S.D., Mielenz, J.R., Cox, C.D., Transcriptomic analysis of Clostridium thermocellum Populus hydrolysate-tolerant mutant strain shows increased cellular efficiency in response to Populus hydrolysate compared to the wild type strain, BMC Microbiology, 14:215, 2014.
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  Characterization and Modeling
08/14/2014 Chauhan, A., Smartt, A., Wang, J., Utturkar, S., Frank, A., Meng, B., Liu, J., Williams, D., Xu, T., Eldridge, M., Arreaza, A., Rogers, A., Gonzalez, H., Layton, A., Baxter, H., Mazarei, M., DeBruyn, J., Stewart Jr, C.N., Brown, S., Hauser, L., Sayler, G., Integrated metagenomics and metatranscriptomics analyses of root associated soil from transgenic switchgrass, Genome Announcements, 4, 2014.
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  Biomass Formation and Modification
Characterization and Modeling
08/05/2014 Zhao, Q., Zeng, Y., Yin, Y., Pu, Y., Jackson, L.A., Engle, N.L., Martin, M.Z., Tschaplinski, T.J., Ding, S-Y., Ragauskas, A.J. and Dixon, R.A., Pinoresinol reductase 1 impacts lignin distribution during secondary cell wall biosynthesis in Arabidopsis. Phytochemistry, 112 (170-178), 2014.
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  Biomass Formation and Modification
Characterization and Modeling
08/01/2014 Kyrpides, et al., Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains, PLOS One, 12:8 2014.
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Biomass Deconstruction and Conversion
Characterization and Modeling
08/01/2014 Pyne, M.E., Utturkar, S., Brown, S.D., Moo-Young, M., Chung, D.A., Cho, C.P., Improved draft genome sequence of Clostridium pasteurianum strain ATCC 6013 (DSM 525) using a hybrid next-generation sequencing approach, Genome Announcements, 2:4, 2014.
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  Characterization and Modeling
08/01/2014 Archambault-Leger, V., Shao, X., Lynd, L.R., Simulated performance of reactor configurations for hot-water pretreatment of sugarcane bagasse, ChemSusChem, 7:9, 2721-7, 2014.
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1 Biomass Deconstruction and Conversion
07/30/2014 Daverdin, G., Bahri, B.A., Wu, X., Serba, D.S., Tobias, C., Saha, M.C., Devos, K.M., Comparative relationships and chromosome evolution in switchgrass (Panicum virgatum) and its genomic model, foxtail millet (setaria italica), Bioenergy Research, 2014
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  Biomass Formation and Modification
07/28/2014 Akinosho, H., Yee, K., Close, D., Ragauskas, A.J., The emergence of clostridium thermocellum as a high utility candidate for consolidated bioprocessing applications, Frontiers in Chemistry, 2:66, 2014.
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  Characterization and Modeling
07/26/2014 Nageswara-Rao, M., Hanson, M., Agarwal, S., Stewart Jr. C.N., Kwit, C., Genetic diversity analysis of switchgrass (Panicum virgatum L.) populations using microsatellites and chloroplast sequences, Agroforest Systems, 88 (823-834) 2014
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  Biomass Formation and Modification
07/22/2014 Poovaiah, C.R., Nageswara-Rao, M., Soneji, J.R., Baxter, H.L., Stewart Jr. C.N., "Altered lignin biosynthesis using biotechnology to improve lignocellulosic biofuel feedstocks", Plant Biotechnology Journal, 12:9, 1163-73, 2014.
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07/22/2014 Xiao, L., Wei, H., Himmel, M.E., Jameel, H., Kelley, S.S., NIR and Py-mbms coupled with multivariate data analysis as a high-throughput biomass characterization technique: a review, Frontiers in Plant Science, 5:388, 2014.
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07/07/2014 Bahulikar, R.A., Torres-Jerez, I., Worley, E., Craven, K., Udvardi, M.K., Diversity of nitrogen-fixing bacteria associated with switchgrass in the native tall-grass prairie of northern Oklahoma, Applied and Environmental Microbiology, 80:18, (5636-43), 2014.
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  Biomass Formation and Modification
07/01/2014 Lupoi, J.S., Singh, S., Davis, M., Lee, D.J., Shepherd, M., Simmons, B.A., Henry, R. J., High-throughput prediction of eucalypt lignin syringyl/guaiacyl content using multivariate analysis: a comparison between mid-infrared, near-infrared, and Raman spectroscopies for model development, Biotechnology for Biofuels, 7:93, 2014.
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1 Characterization and Modeling
07/01/2014 Woo, H.L., Utturkar, S., Klingeman, D., Simmons, B.A., DeAngelis, K.M., Brown, S.D., Hazen, T.C., Draft genome sequence of the lignin-degrading Burkholderia sp. Strain LIG30, isolated from wet tropical forest soil, 2, 2014
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  Characterization and Modeling
07/01/2014 Li, Y., Xu, T., Tschaplinski, T.J., Engle, N.L., Yang, Y., Graham, D.E., He, Z., Zhou, J., Improvement of cellulose catabolism in Clostridium cellulolyticum by sporulation abolishment and carbon alleviation, Biotechnology for Biofuels, 7:25, 2014.
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2 Characterization and Modeling
06/19/2014 Myburg, et al., The genome of Eucalyptus grandis, Nature, 510, 356-364, 2014.
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06/06/2014 Currie, D.H., Guss, A.M., Herring, C.D., Giannone, R.J., Johnson, C.M., Lankford, P.K., Brown, S.D., Hettich, R.L., Lynd, L.R., Profile of secreted hydrolases, associated proteins, and SipA in thermoanaerobacterium saccharolyticum during the degradation of hemicellulose, Applied and Environmental Microbiology, 80:16, 5001-5011, 2014.
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  Biomass Deconstruction and Conversion
06/05/2014 Mearls, E.B., Lynd, L.R., The identification of four histidine kinases that influence sporulation in Clostridium thermocellum, Anaerobe, 1:11 (109-19) 2014
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1 Biomass Deconstruction and Conversion
06/03/2014 Zhou, C., Mao, F., Yin, Y., Huang, J., Gogarten, J.P., Xu, Y., AST: An automated sequence-sampling method for improving the taxonomic diversity of gene phylogenetic trees, 9:6, 2014.
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  Characterization and Modeling
06/03/2014 Zhou, C., Ma, Q., Mao, X., Yin, Y., Xu, Y., New Insights into Clostridia through Comparative 1 Analyses of Their 40 Genomes, Bioenergy Research, 7:4 2014
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2 Characterization and Modeling
06/02/2014 Chung, D., Cha, M., Guss, A.M., Westpheling, J., Direct conversion of plant biomass to ethanol by engineered Caldicellulosiruptor bescii, PNAS, 111:24, 8931-8936, 2014.
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05/22/2014 Yang, S., Pan, C., Hurst, G.B., Dice, L., Davison, B.H., Brown, S.D., Elucidation of zymomonas mobilis physiology and stress responses by quantitative proteomics and transcriptomics, Frontiers, 5:246 2014
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2 Characterization and Modeling
05/22/2014 Yee, K.L., Rodriguez Jr., M., Thompson, O.A., Fu, C., Wang, Z.Y., Davison, B.H., Mielenz, J.R., "Consolidated bioprocessing of transgenic switchgrass by an engineered and evolved Clostridium thermocellum strain", Biotechnology for Biofuels, 7:75, 2014.
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2 Characterization and Modeling
05/15/2014 Ragauskas, A.J., Beckham, G.T., Biddy, M.J., Chandra, R., Chen, F., Davis, M.F., Davison, B.H., Dixon, R.A., Gilna, P., Keller, M., Langan, P., Naskar, A.K., Saddler, J.N., Tschaplinski, T.J., Tuskan, G.A., Wyman, C.E., Lignin Valorization: improving lignin processing in the biorefinery, Science, 344, 2014.
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05/14/2014 Sun, Q., Foston, M., Sawada, D., Pingali, S.V., O'Neill, H.M., Li, H., Wyman, C.E., Langan, P., Pu, Y., Ragauskas, A.J., Comparison of changes in cellulose ultrastructure during different pretreatments of poplar, Cellulose, 21 (2419-2431) 2014
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3 Characterization and Modeling
05/13/2014 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, 7:71, 2014.
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05/01/2014 Zhao, Q., Dixon, R.A., Altering the cell wall and its impact on plant disease: from forage to bioenergy, Annual Review of Phytopathology, 52:69-91, 2014.
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05/01/2014 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., Lumin, V.V., Himmel, M.E., Bomble, Y.J., Response to Comment on "Revealing Nature's Cellulase Diversity: The Digestion Mechanism of Caldicellulosiruptor bescii CelA", Science, 344, 2014.
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04/30/2014 Lin, P.P., Rabe, K.S., Takasumi, J.L., Kadisch, M., Arnold, F.H., Liao, J.C., Isobutanol production at elevated temperatures in thermophilic Geobacillus thermoglucosidasius, Metabolic Engineering, 24:1-8, 2014.
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04/21/2014 Baxter, H.L., Mazarei, M., Labbe, N., Kline, L.M., Cheng, Q., Windham, M.T., Mann, D.G.J., Fu, C., Ziebell, A., Sykes, R.W., Rodriguez Jr, M., Davis, M.F., Mielenz, J.R., Dixon, R.A., Wang, Z.W., Stewart Jr, C.N., Two-year field analysis of reduced recalcitrance transgenic switchgrass, Plant Biotechnology Journal, 12:914-924, 2014.
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Characterization and Modeling
04/21/2014 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, 42:W1-W12 2014
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04/14/2014 Tolbert, A., Akinosho, H., Khunsupat, R., Naskas, A.K., Ragauskas, A.J., Characterization and analysis of the molecular weight of lignin for biorefining studies, Biofuels, Bioproducts and Biorefining, 8:6, 2014.
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  Characterization and Modeling
04/13/2014 Myung, S., Rollin, J., You, C., Sun, F., Chandrayan, S., Adams, M.W.W., Zhang, Y.-H P., In vitro metabolic engineering of hydrogen production at theoretical yield from sucrose , Metabolic Engineering, 24:70-77, 2014.
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04/13/2014 Uppugundia, N., da Costa Sousa, L., Chundawat, S., Yu, X., Simmons, B., Singh, S., Gao, X., Kumar, R., Wyman, C.E., Dale, B.E., Balan V., A comparative study of ethanol production using dilute acid, ionic liquid and AFEXTM pretreated corn stover, Biotechnology for Biofuels, 7:72, 2014.
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04/04/2014 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
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Biomass Deconstruction and Conversion
04/04/2014 Biswas, R., Persad, A., Bisaria, V.S., Production of Cellulolytic Enzymes, Bioprocessing of Renewable Resources to Commodity Bioproducts, Chapter 5, pp 105-132, 2014.
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04/03/2014 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, 7:48 2014
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04/01/2014 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, 162, (89-95), 2014.
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3 Characterization and Modeling
04/01/2014 Kostylev, M., Alahuhta, M., Chen, M., Brunecky, R., Himmel, M.E., Lunin, V.V., Brady, J., Wilson, D.B., Cel48A From Thermobifida fusca: Structure and Site Directed Mutagenesis of Key Residues, Biotechnology and Bioengineering, 114:4 (664-673) 2013.
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03/26/2014 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, 4:33 (17282-17292) 2014
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1 Characterization and Modeling
03/21/2014 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.
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03/21/2014 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, 66 (261-267) 2014.
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  Characterization and Modeling
03/18/2014 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, 202:4 (1223-1236) 2014
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1 Biomass Formation and Modification
03/14/2014 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.
ISBN: 978-1-4665-9636-8 eBook ISBN: 978-1-4665-9637-5
  Biomass Formation and Modification
03/07/2014 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.
DOI: 10.1080/07352689.2014.870417
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3 Biomass Formation and Modification
03/03/2014 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, 49:3 (212-214) 2014
DOI: 10.3109/10409238.2014.889651
6 Biomass Formation and Modification
03/01/2014 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.
DOI: 10.1007/s10295-013-1394-z
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  Characterization and Modeling
03/01/2014 Robinson, W., Farming for Fuels, Dimensions, 16:2 (46-48) 2014
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  Characterization and Modeling
03/01/2014 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
DOI: 10.1093/nar/gkv177
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  Characterization and Modeling
03/01/2014 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, 84:4-4 (565-576) 2013
DOI: 10.1007/s11103-013-0152-y
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4 Biomass Formation and Modification
Characterization and Modeling
02/12/2014 Kumar, R., Wyman, C.E., Strong cellulase inhibition by mannan polysaccharides in cellulose conversion to sugars, Biotechnology and bioengineering, 111:7 (1341-1353) 2014.
DOI: 10.1002/bit.25218
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4 Characterization and Modeling
02/12/2014 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, 27:7 (664-667) 2014
DOI: 10.1094/MPMI-12-13-0368-R
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1 Characterization and Modeling
02/07/2014 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, e86386, 2014.
DOI: 10.1371/journal.pone.0086389
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6 Biomass Deconstruction and Conversion
02/01/2014 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
DOI: 10.1128/genomeA.00054-14
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  Characterization and Modeling
02/01/2014 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.
DOI: 10.1016/j.copbio.2014.01.014
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22 Characterization and Modeling
02/01/2014 Lara-Chavez, A., Lowman, S., Kim, S., Tang, Y., Zhang, J., Udvardi, M., Nowak, J., Flinn, B., Mei, C., "Global gene expression profiling of two switchgrass cultivars following inoculation with Burkholderia phytofirmans strain PsJN", Journal of Experimental Botany, 2015
DOI: 10.1093/jxb/erv096
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  Biomass Formation and Modification
01/30/2014 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, 7:3 (899-908) 2014
DOI: 10.1007/s12155-014-9410-3
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2 Characterization and Modeling
01/29/2014 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, 118:9 (2306-2315) 2014.
DOI: 10.1021/jp408767j
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  Biomass Deconstruction and Conversion
01/20/2014 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.
DOI: 10.3389/fenrg.2013.00014
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  Characterization and Modeling
Biomass Formation and Modification
01/14/2014 Kostylev, M., Wilson D., A Distinct Model of Synergism between a Processive Endocellulase (TfCel9A) and an Exocellulase (TfCel48A) from Thermobifida fusca, Applied and Environmental Microbiology, 80:1, (339-344), 2014.
DOI: 10.1128/AEM.02706-13
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1 Biomass Deconstruction and Conversion
01/12/2014 Archambault-Leger, V., Lynd, L.R., Fluid mechanics relevant to flow through pretreatment of cellulosic biomass, Bioresource Technology, 157; (278-283) 2014.
DOI: 10.1016/j.biortech.2014.01.035
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3 Biomass Deconstruction and Conversion
01/12/2014 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.
DOI: 10.1016/j.biortech.2013.11.024
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6 Biomass Deconstruction and Conversion
01/07/2014 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.
DOI: 10.1186/1754-6834-7-11
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10 Characterization and Modeling
01/01/2014 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.
ISBN: 978-1-4822-1058-3 eBook ISBN: 978-1-4822-1059-0
  Biomass Deconstruction and Conversion
01/01/2014 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, 25:12 (4845-4862) 2014.
DOI: 10.1105/tpc.113.117788
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5 Biomass Formation and Modification
01/01/2014 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.
ISBN 978-94-017-8553-2
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  Biomass Deconstruction and Conversion
01/01/2014 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, pp 183-192, 2014.
DOI: 10.1007/978-1-62703-764-8_13
1 Biomass Deconstruction and Conversion
12/30/2013 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 (164-170) 2014.
DOI: 10.1021/jp411998t
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4 Characterization and Modeling
12/20/2013 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.
DOI: 10.1126/science.1244273
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12/17/2013 Gao, X., Kumar, R., Wyman, C.E., Fast hemicellulose quantification via a simple one-step acid hydrolysis, Biotechnology and Bioengineering, 111:6 (1088-10963) 2013
DOI: 10.1002/bit.25174
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1 Characterization and Modeling
12/16/2013 Hu, F., Ragauskas, A., Suppression of pseudo-lignin formation under dilute acid pretreatment conditions, RCS Advances, 4:9, (4317-4323), 2014.
DOI: 10.1039/C3RA42841A
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4 Characterization and Modeling
12/12/2013 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, 155 (50-56) 2013.
DOI: 10.1016/j.biortech.2013.12.051
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2 Biomass Deconstruction and Conversion
12/12/2013 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, 1:6, 2013.
DOI: 10.1128/genomeA.01039-13
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  Characterization and Modeling
12/12/2013 Ding, S.Y., Zhao, S., Zeng, Y., Size, shape, and arrangement of native cellulose fibrils in maize cell walls, Cellulose, 21:2 (863-871) 2013
DOI: 10.1007/s10570-013-0147-5
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3 Characterization and Modeling
12/02/2013 Wilson, C.M., Rodriguez Jr., M., Johnson, C.M., Martin, S.L., Chu, T.M., Wolfinger, R.D., Hauser, L.J., Land, M.L., Klingeman, D.M., Syed, M.H., Ragauskas, A.J., Tschaplinski, T.J., Mielenz, J.R., Brown, S.D., Global transcriptome analysis of Clostridium thermocellum ATCC 27405 during growth on dilute acid pretreated Populus and switchgrass, Biotechnology for Biofuels, 6:179, 2013.
DOI: 10.1186/1754-6834-6-179
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4 Characterization and Modeling
12/01/2013 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.
DOI: 10.1007/978-94-007-7076-8_25
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  Biomass Formation and Modification
11/30/2013 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.
DOI: 10.1107/S1744309113030005
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1 Biomass Deconstruction and Conversion
11/30/2013 Shen, H., Mazarei, M., Hisano, H., Escamilla-Trevino, L., Fu, C., Pu, Y., Rudis, M.R., Tang, Y., Xiao, X., Jackson, L., Li, G., Hernandez, T., Chen, F., Ragauskas, A.J., Stewart Jr., C.N., Wang, Z-Y., Dixon, R.A., A genomics approach to deciphering lignin biosynthesis in switchgrass, 25:11 (4342-61) 2013.
DOI: 10.1105/tpc.113.118828
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Characterization and Modeling
11/29/2013 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, 6:175 2013.
DOI: 10.1186/1754-6834-6-175
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2 Biomass Deconstruction and Conversion
11/28/2013 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, 12:3 (354-366) 2013.
DOI: 10.1111/pbi.12142
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11/26/2013 Liu, W., Yuan, J.S., Stewart J., C.N., Advanced genetic tools for plant biotechnology, Nature Reviews, 14:11 (781-793) 2013.
DOI: 10.1038/nrg3583
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11/20/2013 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.
0975-2900 & E-ISSN: 0975-9204,
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  Characterization and Modeling
11/18/2013 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.
DOI: 10.1039/9781849734738-00014
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  Biomass Deconstruction and Conversion
11/18/2013 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.
DOI: 10.1039/9781849734738-00026
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  Characterization and Modeling
11/15/2013 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, 13:2 (692-701) 2013.
DOI: 10.1021/pr400788e
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  Biomass Deconstruction and Conversion
11/09/2013 Bhandiwad, A., Shaw, A.J., Guss, A., Guseva, A., Bahl, H., Lynd, L.R., Metabolic engineering of Thermoanaerobacterium saccharolyticum for n-butanol production, Metabolic Engineering, 21, (71-25), 2014.
DOI: 10.1016/j.ymben.2013.10.012
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7 Biomass Deconstruction and Conversion
11/07/2013 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.
DOI: 10.1093/nar/gkt1048
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9 Characterization and Modeling
11/01/2013 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, 33:2 (313-322) 2014.
DOI: 10.1007/s00299-013-1531-1
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2 Biomass Formation and Modification
11/01/2013 Baxter, H.L., Stewart Jr., C.N., Effects of altered lignin biosynthesis on phenylpropanoid metabolism and plant stress, Biofuels, 4:6, (635-667), 2013.
DOI: 10.4155/bfs.13.56
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  Biomass Formation and Modification
10/21/2013 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.
DOI: 10.1371/journal.pone.0078829
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1 Characterization and Modeling
10/12/2013 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, 111:3, 2013.
DOI: 10.1002/bit.25108
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17 Characterization and Modeling
10/01/2013 Ratnaparkhe, S., Venkatachalam, S., Hahn, M.G., Pattathil, S., Analyses using Cell Wall Glycan-directed Monoclonal Antibodies Reveal Xylan-degradation by Two Microbial Glycosyl Hydrolases in Cell Walls from Poplar and Switchgrass Biomass, Journal of Bioremediation & Biodegradation, S4:004, 2013.
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  Characterization and Modeling
Biomass Formation and Modification
10/01/2013 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, 1443-8, 2013.
DOI: 10.1007/s10295-013-1345-8
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Biomass Formation and Modification
10/01/2013 Zhao, N., Yao, J., Chaiprasongsuk, M., Li, G., Guan, J., Tschaplinski, T.J., Guo, H., Chen, F., Molecular and biochemical characterization of the jasmonic acid methyltransferase gene from black cottonwood (Populus trichocarpa), Phytochemistry, 94 (74-81), 2014.
DOI: 10.1016/j.phytochem.2013.06.014
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1 Biomass Formation and Modification
Biomass Deconstruction and Conversion
09/27/2013 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.
DOI: 10.1371/journal.pone.0073523
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4 Biomass Deconstruction and Conversion
09/12/2013 Wilson, C.M., Yang, S., Rodriguez Jr., M., Ma. Q., Johnson, C.M., Dice, L., Xu, Y., Brown, S.D., Clostridium thermocellum transcriptomic profiles after exposure to furfural or heat stress, Biotechnology for Biofuels, 6:131, 2013
DOI: 10.1186/1754-6834-6-131
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7 Characterization and Modeling
09/10/2013 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.
DOI: 10.1186/1471-2164-14-608
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3 Biomass Formation and Modification
09/04/2013 GhattyVenkataKrishna, P.K., Mostofian, B., Dynamics of water in the amphiphilic pore of amyloid b fibrils, Chemical Physics Letters, 582, (1-5), 2013.
DOI: 10.1016/j.cplett.2013.07.026
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1 Characterization and Modeling
09/01/2013 Voit, E.O., Characterizability of metabolic pathway systems from time series data, Mathematical Biosciences, 246:2 (315-325) 2013.
DOI: 10.1016/j.mbs.2013.01.008
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3 Characterization and Modeling
09/01/2013 Voit, E.O., Biochemical Systems Theory: A Review, ISRN Biomathematics, 53, (897658) 2013
DOI: 10.1155/2013/897658
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  Characterization and Modeling
08/30/2013 Xi, Q., Ding,S.Y., Brunecky, R., Bomble, Y.J., Himmel, M.E., Baker, J.O., Improving activity of minicellulosomes by integration of intra- and intermolecular synergies, Biotechnology for Biofuels, 6:126, 2013.
DOI: 10.1186/1754-6834-6-126
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4 Biomass Deconstruction and Conversion
08/20/2013 Linville, J.L., Rodiguez Jr., M., Mielenz, J. R., Cox, C.D., Kinetic modeling of batch fermentation for Populus hydrolysate tolerant mutant and wild type strains of Clostridium thermocellum, Bioresource Technology, 147, pp 605-613, 2013.
DOI: 10.1016/j.biortech.2013.08.086
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3 Characterization and Modeling
08/08/2013 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.
DOI: 10.1128/genomeA.00605-13
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  Biomass Deconstruction and Conversion
08/01/2013 Mostofian, B., Smith, J.C., Cheng, X., Simulation of a cellulose fiber in ionic liquid suggests a synergistic approach to dissolution, 21(2):938-997, 2014.
DOI: 10.1007/s10570-013-0018-0
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1 Characterization and Modeling
08/01/2013 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, 21:2:SI, (937-949), Cellulose, 2013.
DOI: 10.1007/s10570-013-0011-7
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  Characterization and Modeling
08/01/2013 Trajano, H.L., Engle, N.L., Foston, M., Ragauskas, A.J., Tschaplinski, T.J., Wyman, C.E., The fate of lignin during hydrothermal pretreatment, Biotechnology for Biofuels, 6:110; 2013.
DOI: 10.1186/1754-6834-6-110
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17 Characterization and Modeling
08/01/2013 Blumer-Schuette, S.E., Sander, K.E., Bayer, E.A., Zurawski, J.V., Conway, J.M., Adams, M.W.W., Kelly, R.M., Thermophilic lignocellulose deconstruction, FEMS Microbial Review, 38:3 (393-448) 2014
DOI: 10.1111/1574-6976.12044
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8 Biomass Deconstruction and Conversion
07/31/2013 Tobimatsu, Y., Chen, F., Nakashima, J., Escamilla-Trevino, L.L., Jackson, L., Dixon, R.A., Ralph, J., Coexistence but Independent Biosynthesis of Catechyl and Guaiacyl/Syringyl Lignin Polymers in Seed Coats, Plant Cell, 25:7:2587-600, 2013.
DOI: 10.1105/tpc.113.113142
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10 Biomass Formation and Modification
07/16/2013 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, 8(7), 2013.
DOI: 10.1371/journal.pone.0068886
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11 Characterization and Modeling
07/12/2013 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.
DOI: 10.1002/9781118642047.ch8
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  Biomass Deconstruction and Conversion
07/10/2013 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.
DOI: 10.1093/bioinformatics/btt397
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6 Characterization and Modeling
07/09/2013 Kostylev, M., Wilson, D., Two-parameter kinetic model based on a time-dependent activity coefficient accurately describes enzymatic cellulose digestion, Biochemistry, 52:33, (5656–5664), 2013.
DOI: 10.1021/bi400358v
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8 Biomass Deconstruction and Conversion
07/08/2013 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.
DOI: 10.1016/j.febslet.2013.06.050
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4 Characterization and Modeling
07/08/2013 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.
DOI: 10.1016/j.biortech.2013.06.091
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8 Characterization and Modeling
07/01/2013 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.
DOI: 10.1021/pr400192r
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3 Biomass Formation and Modification
06/28/2013 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, 110, 2013.
DOI: 10.1073/pnas.1312234110
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06/15/2013 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.
DOI: 10.1016/j.carbpol.2013.06.007
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1 Biomass Deconstruction and Conversion
06/01/2013 Gilna, P., Cellulosic biofuels, Science Omege Review Europe, Issue 2, 2013.
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  Biomass Formation and Modification
Biomass Deconstruction and Conversion
Characterization and Modeling
06/01/2013 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.
DOI: 10.1016/j.copbio.2013.09.008
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06/01/2013 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.
DOI: 10.1128/genomeA.00323-13
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  Biomass Deconstruction and Conversion
06/01/2013 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.
DOI: 10.1186/1754-6834-6-82
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06/01/2013 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.
DOI: 10.1186/1754-6834-6-85
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Biomass Deconstruction and Conversion
05/08/2013 Atmodjo, M.A., Hao, Z., Mohnen, D., Evolving views of pectin biosynthesis, Annual Review of Plant Biology, 64:, 747-779, 2013.
DOI: 10.1146/annurev-arplant-042811-105534
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05/01/2013 Ragauskas, A.J., When to accept no … to yesterday's solutions, Biofuels, Bioproducts and Biorefining, 7(3), 2013.
DOI: 10.1002/bbb.1414
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  Characterization and Modeling
05/01/2013 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.
DOI: 10.1186/1754-6834-6-77
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4 Biomass Formation and Modification
05/01/2013 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, 6, 2186-2195, 2013
DOI: 10.1039/C3EE40932E
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Biomass Deconstruction and Conversion
Characterization and Modeling
05/01/2013 Wyman, C.E., Introduction, Aqueous Pretreatment of Plant Biomass for Biological and Chemical Conversion to Fuels and Chemicals, (ed Wyman, C.E.), chapter 1, pp 1-20, 2013.
DOI: 10.1002/9780470975831
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  Characterization and Modeling
05/01/2013 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.
DOI: 10.1002/9780470975831.ch2
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  Biomass Deconstruction and Conversion
05/01/2013 Trajano, H.L., Wyman, C.E., Fundamentals of Biomass Pretreatment at Low pH, Aqueous Pretreatment of Plant Biomass for Biological and Chemical Conversion to Fuels and Chemicals, (ed Wyman, C.E.), chapter 6, pp 103-123, 2013.
DOI: 10.1002/9780470975831.ch6
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  Characterization and Modeling
05/01/2013 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.
DOI: 10.1002/9780470975831.ch10
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  Characterization and Modeling
05/01/2013 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.
DOI: 10.1002/9780470975831.ch14
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  Characterization and Modeling
05/01/2013 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.
DOI: 10.1002/9780470975831.ch18
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  Characterization and Modeling
05/01/2013 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.
DOI: 10.1002/9780470975831.ch19
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  Characterization and Modeling
05/01/2013 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.
DOI: 10.1002/9780470975831.ch22
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  Characterization and Modeling
05/01/2013 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, 110:11, (2894-2901), 2013.
DOI: 10.1002/bit.24951
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1 Characterization and Modeling
04/24/2013 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.
DOI: 10.1002/biot.201200233
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2 Characterization and Modeling
04/17/2013 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.
DOI: 10.1093/nar/gkt261
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5 Characterization and Modeling
04/15/2013 van der Veen, D., Lo, J., Brown, S.D., Johnson, C.M., Tschaplinski, T.J., Martin,k M., Engle, N.L., van den Berg, R.A., Argyros, A.D., Caiazza, N.C., Guss, A.M., Lynd, L.R., Characterization of Clostridium thermocellum strains with disrupted fermentation end product pathways, 40(7), 725-734, 2013.
DOI: 10.1007/s10295-013-1275-5
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04/15/2013 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.
DOI: 10.1534/g3.112.005447
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1 Biomass Formation and Modification
04/15/2013 Wang, Z.W., Lee, S.H., Elkins, J.G., Li, Y., Hamilton-Brehm, S., Morrell-Falvey, J.L., Continuous live cell imaging of cellulose attachment by microbes under anaerobic and thermophilic conditions using confocal microscopy, Journal of Environmental Sciences, 25(5), 849-856, 2013.
DOI: 10.1016/S1001-0742(12)60104-1
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2 Biomass Deconstruction and Conversion
04/11/2013 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.
DOI: 10.1002/bit.24914
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3 Biomass Deconstruction and Conversion
04/11/2013 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.
DOI: 10.1002/bit.24915
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04/11/2013 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.
DOI: 10.1128/genomeA.00162-13
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  Characterization and Modeling
Biomass Deconstruction and Conversion
04/09/2013 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.
DOI: 10.1111/tpj.12204
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04/08/2013 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.
DOI: 10.1039/C3EE00019B
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04/04/2013 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.
DOI: 10.1016/j.ultramic.2013.03.016
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  Characterization and Modeling
04/03/2013 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.
DOI: 10.1371/journal.pone.0062881
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04/01/2013 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, 6:71, 2013.
DOI: 10.1186/1754-6834-6-71
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Characterization and Modeling
Characterization and Modeling
04/01/2013 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.
DOI: 10.1073/pnas.1302420110
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03/24/2013 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.
DOI: 10.1007/s12155-013-9315-6
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Biomass Formation and Modification
03/19/2013 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.
DOI: 10.1002/anie.201300766
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03/19/2013 Li, H., Qing, Q., Kumar, R., Wyman, C.E., Chromatographic determination of 1, 4-beta-xylooligosaccharides of different chain lengths to follow xylan deconstruction in biomass conversion , Journal of Industrial Microbiology Biotechnology, 40:551-559, 2013.
DOI: 10.1007/s10295-013-1254-x
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03/19/2013 Trajano, H.L., DeMartini, J.D., Studer, M.H., Wyman, C.E., Comparison of the effectiveness of a fluidized sand bath and a steam chamber for reactor heating, Industrial & Engineering Chemistry Research, 52 (13), pp 4932–4938, 2013.
DOI: 10.1021/ie301869a
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1 Characterization and Modeling
03/10/2013 Chung, D., Farkas, J., Westpheling, Detection of a novel active transposable element in Caldicellulosiruptor hydrothermalis and a new search for elements in this genus, Journal of Industrial Microbiology and Biotechnology, 40:517-521, 2013.
DOI: 10.1007/s10295-013-1244-z
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4 Biomass Deconstruction and Conversion
03/01/2013 Bhandiwad, A., Guseva, A., Lynd, L. R., Metabolic engineering of thermoanaerobacterium thermosaccharolyticum for increased n-butanol production, 3, 46-51, 2013.
DOI: 10.4236/aim.2013.31007
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03/01/2013 Wyman, C.E., Wyman, C.J., Chemical and Biological Deconstruction of Aqueous Phase, editors; Behrens, M., and Datye, .K., Catalysis for the Conversion of Biomass and Its Derivates, chapter 6, p. 165-182, 2013.
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  Characterization and Modeling
03/01/2013 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.
DOI: 10.1107/S0907444912050512
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1 Biomass Deconstruction and Conversion
02/22/2013 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.
DOI: 10.1128/AEM.04037-12
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8 Biomass Deconstruction and Conversion
02/15/2013 Mao, F., Olman, V., Wang, Y., Xu, Y., Barcode Server: A visualization-based genome analysis system, PLoS ONE, 8(2): e56726, 2013.
DOI: 10.1371/journal.pone.0056726
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  Characterization and Modeling
02/04/2013 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.
DOI: 10.1039/C3RA40578H
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02/01/2013 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.
DOI: 10.1186/1754-6834-6-32
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02/01/2013 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, 104:4, (904-912), 2013.
DOI: 10.1016/j.bpj.2012.12.052
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02/01/2013 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.
DOI: 10.1104/pp.112.208694
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02/01/2013 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.
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  Biomass Deconstruction and Conversion
01/29/2013 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.
DOI: 10.1371/journal.pone.0014021
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Characterization and Modeling
01/28/2013 Pu, Y., Hu, F., Huang, F., Davison, B.H., Ragauskas, A.J., Assessing the molecular structure basis for biomass recalcitrance during dilute acid and hydrothermal pretreatments , Biotechnology for Biofuels, 6:15, 2013.
DOI: 10.1186/1754-6834-6-15
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01/25/2013 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.
DOI: 10.1016/j.gpb.2013.01.004
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2 Characterization and Modeling
01/17/2013 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.
DOI: 10.1007/s12155-012-9292-1
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01/08/2013 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.
DOI: 10.1039/C3EE23801F
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Biomass Formation and Modification
01/05/2013 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.
DOI: 10.1111/tpj.12104
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Characterization and Modeling
01/04/2013 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.
DOI: 10.1007/s00792-013-0512-1
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01/01/2013 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.
DOI: 10.1105/tpc.112.107334
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Biomass Formation and Modification
01/01/2013 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.
DOI: 10.1007/978-1-62703-278-0_2
2 Biomass Formation and Modification
12/20/2012 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.
DOI: 10.1111/nph.12014
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12/10/2012 Shao, X., Lynd, L., Kinetic modeling of xylan hydrolysis in co- and countercurrent liquid hot water flow-through pretreatments, Bioresource Technology, 130:117-124, 2012.
DOI: 10.1016/j.biortech.2012.11.109
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7 Biomass Deconstruction and Conversion
12/07/2012 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.
DOI: 10.1371/journal.pone.0051252
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4 Characterization and Modeling
12/05/2012 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.
DOI: 10.1016/j.biortech.2012.12.028
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12/01/2012 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.
DOI: 10.1371/journal.pone.0047399
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Biomass Deconstruction and Conversion
12/01/2012 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.
DOI: 10.1128/JB.01908-12
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12/01/2012 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.
DOI: 10.1128/JB.02014-12
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12/01/2012 Deng, Y., Olson, D.G., Zhou, J., Herring, C.D., Shaw, A., Lynd, L.R., Redirecting carbon Flux through exogenous pyruvate kinase to achieve high ethanol yields in Clostridium thermocellum, Metabolic Engineering, 15:151-8, 2012.
DOI: 10.1016/j.ymben.2012.11.006
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11/30/2012 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.
DOI: 10.1002/jctb.3959
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11/23/2012 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.
DOI: 10.1126/science.1227491
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Characterization and Modeling
11/12/2012 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.
DOI: 10.1186/1754-6834-5-81
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8 Characterization and Modeling
Biomass Deconstruction and Conversion
11/08/2012 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.
DOI: 10.1371/journal.pcbi.1002769
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7 Characterization and Modeling
Biomass Formation and Modification
11/06/2012 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.
DOI: 10.1007/s12155-012-9268-1
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11/04/2012 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.
DOI: 10.1111/tpj.12073
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Biomass Formation and Modification
11/01/2012 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.
DOI: 10.1002/bit.24751
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3 Characterization and Modeling
10/29/2012 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.
DOI: 10.3389/fpls.2012.00236
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10 Biomass Formation and Modification
10/25/2012 Wullschleger, S.D., Weston, D.J., DiFazio, S.P., Tuskan, G.A., Revisiting the sequencing of the first tree genome: Populus trichocarpa, Tree Physiology, 33(4):357-64, 2012.
DOI: 10.1093/treephys/tps081
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11 Biomass Formation and Modification
10/18/2012 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), 2013.
DOI: 10.1002/bit.24741
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2 Characterization and Modeling
10/16/2012 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.
DOI: 10.1074/mcp.M112.022996
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5 Biomass Formation and Modification
Characterization and Modeling
10/14/2012 Uppalapati, S.R., Serba, D.D., Ishiga, Y., Szabo, L.J., Mittal, S., Bhandari, H.S., Bouton, J.H., Mysore, K.S., Saha, M.C., Characterization of the Rust Fungus, Puccinia emaculata, and Evaluation of Genetic Variability for Rust Resistance in Switchgrass Populations, Bioenergy Research, 6 (2) 458-468, 2012.
DOI: 10.1007/s12155-012-9263-6
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4 Biomass Formation and Modification
Biomass Formation and Modification
10/10/2012 Waller, B.H., Olson, D.G., Currie, D.H., Guss, A.M., Lynd, L.R., Exchange of type II dockerin-containing subunits of the Clostridium thermocellum cellulosome as revealed by SNAP-tags , FEMS Microbiology Letters, 338(1):46-53, 2012.
DOI: 10.1111/1574-6968.12029
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6 Biomass Deconstruction and Conversion
10/10/2012 Sukharnikov, L, Alahuhta, M., Brunecky, R., Upadhyay, A., Himmel, M., Lunin, V.V., Zhulin, I, Sequence , Structure, and Evolution of Cellulases in the Glycoside Hydrolase Family 48, The Journal of Biological Chenistry, 287(49):41068-77, 2012.
DOI: 10.1074/jbc.M112.405720
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7 Characterization and Modeling
Biomass Deconstruction and Conversion
10/01/2012 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.
DOI: 10.1002/bit.24744
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37 Characterization and Modeling
09/28/2012 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
DOI: 10.1128/AEM.02130-12
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4 Biomass Deconstruction and Conversion
09/28/2012 Tschaplinski, et. al, Down-regulation of the caffeic acid O-methyltransferase gene in switchgrass reveals a novel monolignol analog, Biotechnology for Biofuels, 5:71, 2012.
DOI: 10.1186/1754-6834-5-71
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10 Characterization and Modeling
Biomass Formation and Modification
Characterization and Modeling
09/28/2012 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.
DOI: 10.1002/anie.201205243
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12 Characterization and Modeling
Biomass Formation and Modification
09/25/2012 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.
DOI: 10.1021/sc300032j
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6 Characterization and Modeling
09/19/2012 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.
DOI: 10.1007/s10295-012-1202-1
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13 Biomass Deconstruction and Conversion
09/14/2012 NMR a critical tool to study the production of carbon fiber from lignin, Carbon, 52 p 65-73, 2012.
DOI: 10.1016/j.carbon.2012.09.006
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9 Characterization and Modeling
09/07/2012 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, 73(2): 201-211, 2012.
DOI: 10.1111/tpj.12012
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9 Biomass Formation and Modification
09/01/2012 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.
DOI: 10.1039/C2RA22045H
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22 Characterization and Modeling
08/22/2012 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.
DOI: 10.1371/journal.pone.0043844
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16 Biomass Deconstruction and Conversion
08/16/2012 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.
DOI: 10.1186/1471-2180-12-180
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6 Biomass Deconstruction and Conversion
08/16/2012 Foston, M., Ragauskas, A.J., Biomass Characterization: Recent Progress in Understanding Biomass Recalcitrance, Industrial Biotechnology, 8(4); 191-208, 2012.
DOI: 10.1089/ind.2012.0015
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  Characterization and Modeling
08/16/2012 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.
DOI: 10.1007/s10722-012-9903-x
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3 Biomass Formation and Modification
08/14/2012 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, 196:1, (92-100), 2012.
DOI: 10.1111/j.1469-8137.2012.04268.x
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6 Biomass Formation and Modification
08/14/2012 Urbanowicz, B.R., Pena, J.J., Ratnaparkhe, S., Avci, U., Backe, J., Steet, H.F., Foston, M., Li, Hongjia, O'Neill, M.A., Ragauskas, A.J., Darvill, A.G., Wyman, C., Gilbert, H.J., York, W.S., 4-O-methylation of glucuronic acid in Arabidopsis glucuronoxylan is catalyzed by a domain of unknown function family 579 protein, PNAS, 109:35, 14253-14258, 2012.
DOI: 10.1073/pnas.1208097109
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34 Biomass Formation and Modification
Characterization and Modeling
08/09/2012 Wang, S., Yin, Y., Ma, Q., Tang, Xiaojia, Hao, D., Xu, Y., Genome-scale identification of cell-wall related genes in Arabidopsis based on co-expression network analysis, BMC Plant Biology, 12:138, 2012.
DOI: 10.1186/1471-2229-12-138
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13 Characterization and Modeling
08/09/2012 Chou, I.C., Voit, E.O., Estimation of dynamic flux profiles from metabolic time series data, BMC Systems Biology, 6:84, 2012.
DOI: 10.1186/1752-0509-6-84
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8 Characterization and Modeling
08/01/2012 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.
DOI: 10.1111/j.1469-8137.2012.04258.x
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41 Biomass Formation and Modification
08/01/2012 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.
DOI: 10.1007/978-1-61779-956-3_1
1 Biomass Deconstruction and Conversion
08/01/2012 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.
DOI: 10.1007/978-1-61779-956-3_3
3 Biomass Deconstruction and Conversion
Characterization and Modeling
08/01/2012 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.
DOI: 10.1007/978-1-61779-956-3_5
5 Biomass Deconstruction and Conversion
Characterization and Modeling
08/01/2012 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.
DOI: 10.1007/978-1-61779-956-3_6
22 Biomass Deconstruction and Conversion
08/01/2012 Wilson, D.B., Kostylev, M., Cellulase Processivity, Methods in Molecular Biology Biomass Conversion: Methods and Protocols, 908;93-99, 2012.
DOI: 10.1007/978-1-61779-956-3_9
6 Biomass Deconstruction and Conversion
08/01/2012 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.
DOI: 10.1007/978-1-61779-956-3_13
1 Biomass Deconstruction and Conversion
Characterization and Modeling
08/01/2012 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.
DOI: 10.1007/978-1-61779-956-3_14
  Biomass Deconstruction and Conversion
08/01/2012 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.
DOI: 10.1007/978-1-61779-956-3_15
  Biomass Deconstruction and Conversion
08/01/2012 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.
DOI: 10.1007/978-1-61779-956-3_17
2 Characterization and Modeling
Biomass Deconstruction and Conversion
08/01/2012 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.
DOI: 10.1007/978-1-61779-956-3_18
3 Biomass Deconstruction and Conversion
08/01/2012 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.
DOI: 10.1007/978-1-61779-956-3_19
1 Biomass Formation and Modification
08/01/2012 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.
DOI: 10.1007/978-1-61779-956-3_20
  Biomass Deconstruction and Conversion
08/01/2012 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.
DOI: 10.1007/978-1-61779-956-3_21
2 Biomass Deconstruction and Conversion
08/01/2012 Kulkarni, A.R., Pattathil, S., Hahn, M.G., York, W.S., O'Neill, M.A., Comparison of Arabinoxylan Structure in Bioenergy and Model Grasses, Industrial Biotechnology, 8:4, (222-229), 2012.
DOI: 10.1089/ind.2012.0014
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  Biomass Formation and Modification
08/01/2012 Tetard, L., Passian, A., Jung, S., Ragauskas, A.J., Davison, B.H., Development of New Methods in Scanning Probe Microscopy for Lignocellulosic Biomass Characterization, Industrial Biotechnology, 8:4, 2012.
DOI: 10.1089/ind.2012.0017
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  Characterization and Modeling
Characterization and Modeling
07/31/2012 Davison, Brian H., The Increasing Importance and Capabilities of Biomass Characterization, Industrial Biotechnology, 8:4, 2012.
DOI: 10.1089/ind.2012.1527
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  Characterization and Modeling
07/31/2012 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.
DOI: 10.1089/ind.2012.0013
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  Biomass Formation and Modification
07/25/2012 Frock, A.D., Kelly, R.M., Extreme thermophiles: moving beyond single-enzyme biocatalysis, Current Opinion in Chemical Engineering, 1;4, pp 363-372, 2012.
DOI: 10.1016/j.coche.2012.07.003
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6 Biomass Deconstruction and Conversion
07/23/2012 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.
DOI: 10.1186/1471-2164-13-336
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22 Biomass Deconstruction and Conversion
Characterization and Modeling
07/23/2012 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.
DOI: 10.1002/anie.201202441
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35 Biomass Deconstruction and Conversion
07/19/2012 Archambault-Leger, V., Show, X., Lynd, L.R., Integrated analysis of hydrothermal flow through pretreatment, Biotechnology for Biofuels, 5:49, 2012.
DOI: 10.1186/1754-6834-5-49
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7 Biomass Deconstruction and Conversion
07/12/2012 Hyatt, D., LoCascio, P.F., Hauser, L.J., Uberbacher, E.C., Gene and Translation Initiation Site Prediction in Metagenomic Sequences, Bioinformatics, 28:17, (2223-2230), 2012.
DOI: 10.1093/bioinformatics/bts429
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17 Characterization and Modeling
07/01/2012 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.
DOI: 10.1002/bbb.1353
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48 Characterization and Modeling
06/26/2012 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.
DOI: 10.1093/nar/gks605
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10 Characterization and Modeling
06/15/2012 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.
DOI: 10.1186/1754-6834-5-43
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8 Biomass Deconstruction and Conversion
06/06/2012 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.
DOI: 10.1186/1754-6834-5-38
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18 Characterization and Modeling
05/30/2012 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.
DOI: 10.4137/GRSB.S9357
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4 Characterization and Modeling
05/29/2012 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,137:17 (3904-3909), 2012.
DOI: 10.1039/c2an35344j
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8 Characterization and Modeling
05/29/2012 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.
DOI: 10.1093/nar/gks479
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71 Characterization and Modeling
05/25/2012 Karpinets, T.V., Park, B.H., Uberbacher, Analyzing large biological datasets with association networks, Nucleic Acids Research, 40L:17, 2012.
DOI: 10.1093/nar/gks403
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10 Characterization and Modeling
05/25/2012 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.
DOI: 10.1128/JB.00266-12
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10 Biomass Deconstruction and Conversion
Biomass Deconstruction and Conversion
Characterization and Modeling
05/25/2012 Hu, F., Ragauskas, A., Pretreatment and Lignocellulosic Chemistry, BioEnergy Research, 5:4, (1043-1066), 2012.
DOI: 10.1007/s12155-012-9208-0
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51 Characterization and Modeling
05/25/2012 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.
DOI: 10.1128/JB.00473-12
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7 Biomass Deconstruction and Conversion
Characterization and Modeling
05/22/2012 You, C., Zhang, Y.H.P, Easy preparation of a large-size random gene mutagenesis library in Escherichia coli, Analytical Biochemistry, 428(1):7-12, 2012.
DOI: 10.1016/j.ab.2012.05.022
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4 Biomass Deconstruction and Conversion
05/17/2012 Olson, D.G., Lynd, L.R., Transformation of Clostridium thermocellum by electroporation, Methods in Enzymology, 510, p 317-330, 2012.
DOI: 10.1016/B978-0-12-415931-0.00017-3
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12 Biomass Deconstruction and Conversion
05/17/2012 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.
DOI: 10.1016/B978-0-12-415931-0.00007-0
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3 Biomass Formation and Modification
05/15/2012 Bennetzen, J.L., et. al., Reference genome sequence of the model plant Setaria, Nature Biotechnology, 30,555–561, 2012.
DOI: 10.1038/nbt.2196
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Biomass Formation and Modification
05/14/2012 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.
DOI: 10.1021/ie300487z
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1 Biomass Deconstruction and Conversion
05/11/2012 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, Frontiers in Plant Science, 3:92, 2012.
DOI: 10.3389/fpls.2012.00092
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5 Biomass Formation and Modification
05/11/2012 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.
DOI: 10.1186/1754-1611-6-5
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5 Biomass Deconstruction and Conversion
05/09/2012 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
DOI: 10.1007/s12155-012-9204-4
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4 Biomass Formation and Modification
05/06/2012 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.
DOI: 10.1186/1754-6834-5-30
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10 Biomass Deconstruction and Conversion
05/01/2012 van der Lelie, D., Taghavi, S., McCorkle, S.M., Li, L.L., Malfatti, S.A., Monteleone, D., Donohoe, B.S., Ding, S.Y., Adney, W.S., Himmel, M.E., Tringe, S.G., The metagenome of an anaerobic microbial community decomposing poplar wood chips, PLoS One, 7:5, e36740, 2012.
DOI: 10.1371/journal.pone.0036740
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17 Biomass Deconstruction and Conversion
Characterization and Modeling
04/27/2012 Basen, M., Sun, J., Adams, M.W.W., Engineering a Hyperthermophilic Archaeon for Temperature-Dependent Product Formation, mBio, 3(2), 2012.
DOI: 10.1128/mBio.00053-12
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  Biomass Deconstruction and Conversion
04/24/2012 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.
DOI: 10.1073/pnas.1117686109
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18 Biomass Formation and Modification
Biomass Formation and Modification
04/21/2012 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.
DOI: 10.1016/j.biortech.2012.04.088
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16 Biomass Deconstruction and Conversion
04/11/2012 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.
DOI: 10.1016/j.bios.2012.04.001
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14 Biomass Deconstruction and Conversion
04/10/2012 Wei, H., Tucker, M., Baker, J., Harris, M., Luo, Y., Xu, Q., Himmel, M., Ding, S-Y., Tracking dynamics of plant biomass composting by changes in substrate structure, microbial community, and enzyme activity, Biotechnology for Biofuels, 5:20, 2012.
DOI: 10.1186/1754-6834-5-20
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8 Biomass Deconstruction and Conversion
Characterization and Modeling
04/04/2012 Sangha, A.K., Parks, J.M., Standaert, R.F., Ziebell, A., Davis, M.F., Smith, J.C., Radical Coupling Reactions in Lignin Synthesis: A Density Functional Theory Study, The Journal of Physical Chemistry B, 116(16):4760-4768, 2012.
DOI: 10.1021/jp2122449
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18 Characterization and Modeling
Characterization and Modeling
04/03/2012 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.
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04/01/2012 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, 78:13, (4669-4676), 2012.
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Biomass Deconstruction and Conversion
04/01/2012 Hu, F., Jung, S., Ragauskas, A., Pseudo-lignin formation and its impact on enzymatic hydrolysis, Bioresource Technology, 117, 7-12, 2012.
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04/01/2012 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, 8(6):1815-1823, 2012.
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9 Biomass Deconstruction and Conversion
04/01/2012 Sathitsuksanoh, N., Zhu, Z., Zhang, Y.H.P., Cellulose solvent-based pretreatment for corn stover and avicel: concentrated phosphoric acid versus ionic liquid [BMIM]C1, Cellulose, 19(4):1161-1172, 2012.
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03/29/2012 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.
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03/28/2012 Hoover, E. E., J. J. Field, et al. Eliminating the scattering ambiguity in multifocal, multimodal, multiphoton imaging systems." Journal of Biophotonics, 5-6, (425-436), 2012.
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03/28/2012 Sun, G.L., Stewart, C.N., Xiao, P., Zhang, B.H., MicroRNA Expression Analysis in the Cellulosic Biofuel Crop Switchgrass (Panicum virgatum) under Abiotic Stress, PLoS ONE 7:3, e32017, 2012.
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03/28/2012 Tuskan, G., DiFazio, S., Faivre-Rampant, R., Gaudet, M., Harfouche, A., Jorge, V., Labbe, J.L., Ranjan, P., Sabatti, M., Slavov, G., Street, N., Tschplinski, T.J., Yin, T.M., The obscure events contributing to the evolution of an incipient sex chromosome in Populus: a retrospective working hypothesis, Tree Genetics and Genomes, 8(3):559-571, 2012.
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Characterization and Modeling
03/12/2012 Izquierdo, J. A., L. Goodwin, et al. (2012). Complete Genome Sequence of Clostridium clariflavum DSM 19732. Standards In Genomic Sciences, 6:1, (104-115), 2012.
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Characterization and Modeling
03/08/2012 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, 32:5, (626-638), 2012.
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03/05/2012 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.
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2 Characterization and Modeling
03/03/2012 Percival Zhang, Y.-H., J.-H. Xu, et al., A new high-energy density hydrogen carrier—carbohydrate—might be better than methanol, International Journal of Energy Research, 37(7):769-779, 2013.
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03/01/2012 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.
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Characterization and Modeling
02/28/2012 Wang, Z.-Y. and E. C. Brummer (2012). "Is genetic engineering ever going to take off in forage, turf and bioenergy crop breeding?" Annals of Botany, 110(6):1317-1325, 2012.
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Biomass Formation and Modification
02/15/2012 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, 63, 2012.
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02/14/2012 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, 39:6, (943-947), 2012.
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02/09/2012 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-The Journal of Biological Databases and Curation, Article ID bas013, 2012.
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Characterization and Modeling
02/08/2012 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, 8:2, 302-307, 2012.
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02/08/2012 Lee, S., T. Warnick, et al., "Biological conversion assay using Clostridium phytofermentans to estimate plant feedstock quality." Biotechnology for Biofuels 5:1, 2012.
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02/07/2012 Wang, L.Q., Wang, Y.Q., Ragauskas, A.J., Determination of cellulase colocalization on cellulose fiber with quantitative FRET measured by acceptor photobleaching and spectrally unmixing fluorescence microscopy, Analyst, 137(6):1319-1324, 2012.
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02/01/2012 Foston, M., R. Katahira, et al. "Solid-State Selective C-13 Excitation and Spin Diffusion NMR To Resolve Spatial Dimensions in Plant Cell Walls ." Journal of Agricultural and Food Chemistry 60:6 (1419–1427), 2012.
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8 Characterization and Modeling
01/17/2012 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.
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01/12/2012 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, (443-452), 2012.
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01/11/2012 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., 28:5, 750-751, 2012.
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Biomass Deconstruction and Conversion
01/06/2012 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.
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Biomass Formation and Modification
01/04/2012 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.
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Characterization and Modeling
01/03/2012 Zhang, H., Y. Yin, et al. (2012). "Genomic Arrangement of Regulons in Bacterial Genomes." PLoS ONE 7(1):6, 2012.
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01/01/2012 Kwit, C., Stewart, C. N. , Gene flow matters in switchgrass (Panicum virgatum L.), a potential widespread biofuel feedstock, Ecological Applications, 22:1, (3-7), 2012.
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01/01/2012 Yang, S., Keller, M., Brown, S.D., Microbial Stress Tolerance for Biofuels, Microbiology Monographs, 2012, Volume 22/2012, 161-175.
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01/01/2012 Kostylev, M. and D. Wilson, "Synergistic interactions in cellulose hydrolysis." Biofuels, 3:1, (61-70), 2011.
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01/01/2012 Vishnivetskaya T.A., Raman B., Phelps T.J., Podar M., Elkins J.G. Cellulolytic Microorganisms from Thermal Environments. 2012. In book "Extremophiles: Microbiology and Biotechnology” (ed. Anitori R.), Caister Academic Press, Norfolk, UK, Chapter 7, p. 131-158.
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Biomass Deconstruction and Conversion
01/01/2012 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, 2012.
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12/30/2011 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.
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12/29/2011 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.
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12/22/2011 Wisniewski-Dye´ F, Borziak K, Khalsa-Moyers G, Alexandre G, Sukharnikov LO, et al. (2011) "Azospirillum Genomes Reveal Transition of Bacteria from Aquatic to Terrestrial Environments." PLoS Genet 7(12): e1002430.
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Characterization and Modeling
12/20/2011 Yang, T., Y. Bar-Peled, et al. (2012). "In-microbe formation of nucleotide sugars in engineered Escherichia coli." Analytical Biochemistry 421(2): 691-698.
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12/14/2011 Olson, D.G., McBride, J.E., Joe, Shaw, Olson, D. G., J. E. McBride, Lynd, L.L., Recent progress in consolidated bioprocessing, Current Opinion in Biotechnology, 23(3):396-405, 2012.
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12/08/2011 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.
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12/01/2011 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.
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12/01/2011 You, C., Zhang, X.Z., Sathitsuksanon, N., Lynd, L.R., Zhang, Y.H.P "Enhanced microbial cellulose utilization of recalcitrant cellulose by an ex vivo cellulosome-microbe complex", Applied and Environmental Microbiology, 78:5, 1437-1444, 2012.
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12/01/2011 You, C., Zhang, Y.-H. P., Simple Cloning and DNA Assembly in Escherichia coli by Prolonged Overlap Extension PCR, DNA Cloning and Assembly MethodsMethods in Molecular Biology, 1116 (183-192) 2014
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11/24/2011 Wilson, D. , "Processive and nonprocessive cellulases for biofuel production—lessons from bacterial genomes and structural analysis." Applied Microbiology and Biotechnology 93:2, 497-502, 2012.
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11/21/2011 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.
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11/19/2011 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.
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11/18/2011 Yin, Y., Huang, J., Gu, X., Bar-Peled, M., Xu, Y. (2011) "Evolution of Plant Nucleotide-Sugar Interconversion Enzymes." Plos one, 6(11), 2011
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Biomass Formation and Modification
Biomass Deconstruction and Conversion
11/15/2011 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
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11/02/2011 Kulkarni, A., M. J. Peña, et al. , "The ability of land plants to synthesize glucuronoxylans predates the evolution of tracheophytes." Glycobiology 22:3, (439-451), 2012.
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Characterization and Modeling
11/01/2011 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
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11/01/2011 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.
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Biomass Formation and Modification
11/01/2011 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.
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11/01/2011 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.
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Biomass Formation and Modification
10/21/2011 Tetard, L., Passian, A., Farahi, R.H., Davison, B.H., Lereu, A.L., Thundat, T. "Optical and plasmonic spectroscopy with cantilever shaped materials." Journal of Physics D: Applied Physics 44:445102, 2011.
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Characterization and Modeling
10/20/2011 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
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Biomass Formation and Modification
10/14/2011 Escamilla-Trevino, L., "Potential of Plants from the Genus Agave as Bioenergy Crops." Bioenergy Research, 5:1, (1-9), 2012.
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10/11/2011 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.
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Characterization and Modeling
10/11/2011 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.
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10/05/2011 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.
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10/01/2011 Wang, Z.W., Lee, S.H., Elkins, J.G., Morrell-Falvey, J.L., Spatial and temporal dynamics of cellulose degradation and biofilm formation by Caldicellulosiruptor obsidiansis and Clostridium thermocellum, AMB Express, 1:30, 2011.
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10/01/2011 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
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09/30/2011 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
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09/29/2011 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
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09/28/2011 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.
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09/27/2011 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.
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09/12/2011 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.
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Biomass Formation and Modification
09/11/2011 Gallego-Giraldo, L., Escamilla-Trevino, L., Jackson, L.A., Dixon, R.A. "Salicylic acid mediates the reduced growth of lignin down-regulated plant." PNAS, 108:31, (20814-20819), 2011.
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09/06/2011 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, 4:10, 4332-4339, 2011.
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09/05/2011 Stewart Jr., C. N., Liu, G.S., Bioenergy plants in the United States and China, Plant Science, 181:6, pp 621-622, 2011.
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09/05/2011 Tetard, L., Passian, A., Farahi, R.H., Davison, B.H., Jung, S., Ragauskas, A.J., Lereu, A.L., Thundat, T. "Nanometrology of delignified Populus using mode synthesizing atomic force microscopy." Nanotechnology 22:465702, 2011.
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Characterization and Modeling
09/01/2011 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.
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09/01/2011 Yuan, J.S., Wang, X., Stewart Jr., C.N., Biomass feedstock: diversity as a solution, Biofuels, 2:5, 491-493, 2011.
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09/01/2011 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.
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  Characterization and Modeling
09/01/2011 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.
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Characterization and Modeling
09/01/2011 Tetard, L., Passian, A., Farahi, R. H., Davison, B.H., Thundat, T., Optomechanical spectroscopy with broadband interferometric and quantum cascade laser sources, Optics Letters, Vol. 36, No. 17, September 1, 2011.
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08/30/2011 Wang, Q.Q., He, Z., Zhu, Z., Zhang, Y-H.P., Ni, Y., Luo, X.L., Zhu, J.Y., Evaluations of Cellulose Accessibilities of Lignocelluloses by Solute Exclusion and Protein Adsorption Techniques, Biotechnology and Bioengineering, 109(2):381-389, 2012
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08/27/2011 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
DOI: 10.1007/s00253-011-3492-z
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24 Biomass Deconstruction and Conversion
08/25/2011 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.
DOI: 10.1016/j.polymdegradstab.2011.08.015
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23 Biomass Deconstruction and Conversion
Characterization and Modeling
08/18/2011 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.
DOI: 10.1007/s11295-011-0431-1
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3 Biomass Formation and Modification
08/16/2011 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.
DOI: 10.1073/pnas.1102444108
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Characterization and Modeling
Characterization and Modeling
08/12/2011 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.
DOI: 10.2135/cropsci2011.02.0104
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21 Biomass Formation and Modification
08/12/2011 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
DOI: 10.1128/AEM.05225-11
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08/12/2011 Joyce, B.L., Stewart Jr., C.N., Designing the perfect plant feedstock for biofuel production: Using the whole buffalo to diversify fuels and products, Biotechnology Advance, 30:5, (1011-1022), 2012.
DOI: 10.1016/j.biotechadv.2011.08.006
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7 Biomass Formation and Modification
08/11/2011 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, 51:6, (2698-2705), 2011.
DOI: 10.2135/cropsci2011.01.0057
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08/05/2011 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.
DOI: 10.1016/B978-0-08-088504-9.00167-7
  Biomass Deconstruction and Conversion
Characterization and Modeling
08/04/2011 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.
DOI: 10.1186/1754-6834-4-23
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10 Biomass Deconstruction and Conversion
08/01/2011 Voit, E.O.: What if the fit is unfit? Criteria for biological systems estimation beyond residual errors. In: M. Dehmer, F. Emmert-Streib and A. Salvador (Eds.): Applied Statistics for Biological Networks. J. Wiley and Sons, New York, pp. 183-200, 2011.
DOI: 10.1002/9783527638079.ch9
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  Characterization and Modeling
08/01/2011 Zhang, Y.H.P., What is vital (and not vital) to advance economically-competitive biofuels production, Process Biochemistry, 46(11):2091-2110, 2011.
DOI: 10.1016/j.procbio.2011.08.005
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39 Biomass Deconstruction and Conversion
08/01/2011 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.
DOI: 10.1117/12.875285
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1 Biomass Deconstruction and Conversion
Characterization and Modeling
07/25/2011 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.
DOI: 10.1111/j.1469-8137.2011.03830.x
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Biomass Formation and Modification
07/23/2011 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.
DOI: 10.1007/s10709-011-9597-6
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32 Biomass Formation and Modification
07/22/2011 Mao, X., Zhang, Y., Xu, Y., SEAS: A system for SEED-Based Pathway Enrichment Analysis, Plos One, 6 (7), e22556, 2011.
DOI: 10.1371/journal.pone.0022556
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3 Characterization and Modeling
07/22/2011 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.
DOI: 10.1128/AEM.05057-11
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10 Biomass Deconstruction and Conversion
Biomass Deconstruction and Conversion
07/16/2011 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.
DOI: 10.1007/s00253-011-3458-1
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17 Biomass Deconstruction and Conversion
07/15/2011 Kostylev, M., Wilson, D.B., Determination of the catalytic base in family 48 glycosyl hydrolases, Applied Environmental Microbiology, 77:17, (6274-6276), 2011.
DOI: 10.1128/AEM.05532-11
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4 Biomass Deconstruction and Conversion
07/14/2011 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.
DOI: 10.1128/JB.05209-11
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20 Biomass Deconstruction and Conversion
Characterization and Modeling
07/12/2011 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, 4:19, 2011.
DOI: 10.1186/1754-6834-4-19
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10 Characterization and Modeling
07/11/2011 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.
ISBN13: 9780841226432eISBN: 9780841226449
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  Biomass Deconstruction and Conversion
07/11/2011 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.
DOI: 10.1186/1472-6750-11-74
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19 Biomass Formation and Modification
07/05/2011 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.
ISBN: 978-953-307-478-8
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  Biomass Formation and Modification
07/04/2011 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.
DOI: 10.1039/c1jm12078f
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23 Biomass Deconstruction and Conversion
07/01/2011 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.
DOI: 10.1021/cs200218f
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07/01/2011 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, 2011.
DOI: 10.1371/journal.pone.0022113
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9 Biomass Deconstruction and Conversion
07/01/2011 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.
DOI: 10.1002/biot.201100157
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13 Biomass Deconstruction and Conversion
07/01/2011 Yang, B., Z. Dai, et al. "Enzymatic hydrolysis of cellulosic biomass." Biofuels 2:4, (421-450), 2011.
DOI: 10.4155/bfs.11.116
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  Characterization and Modeling
06/17/2011 Mohnen, D., Tierney, Mary L., Plants Get Hyp to O-Glycosylation, Science, 332:1393-1394, 2011.
DOI: 10.1126/science.1208641
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4 Biomass Formation and Modification
06/14/2011 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.
DOI: 10.1186/1471-2180-11-134
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29 Biomass Deconstruction and Conversion
Characterization and Modeling
06/07/2011 Zhang, Y.-H.P. (2011). Substrate channeling and enzyme complexes for biotechnological applications. Biotechnology Advances 29:715-725.
DOI: 10.1016/j.biotechadv.2011.05.020
56 Biomass Deconstruction and Conversion
06/01/2011 Bomble, Y.J., Beckham, G.T., Matthews, J.F., Nimlos, M.R., Himmel, M.E., Crowley, M.F., Modeling the Self-assembly of the Celluosome Enzyme Complex, The Journal of Biological Chemistry, volume 286(7), pp. 5614-5623, 2011.
DOI: 10.1074/jbc.M110.186031
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06/01/2011 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.
DOI: 10.1016/j.biortech.2011.05.021
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06/01/2011 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.
DOI: 10.1105/tpc.111.085464
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21 Biomass Formation and Modification
05/22/2011 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.
DOI: 10.1007/s10295-011-0976-x
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10 Biomass Deconstruction and Conversion
05/20/2011 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.
DOI: 10.1074/jbc.M110.217315
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05/16/2011 Lee, Y., Chen, F., Gallego-Giraldo, L., Dixon, Richard A., Voit, E.O.,Integrative analysis of transgenic alfalfa (Medicago sativa L.) suggests new metabolic control mechanisms for monolignol biosynthesis, PLoS Computational Biology, 7:5, 2011.
DOI: 10.1371/journal.pcbi.1002047
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Biomass Formation and Modification
05/06/2011 Tetard, L., Passian, A., Eslami, S., Jalili, N., Farahi, R.H., Thundat, T., Virtual Resonance and Frequency Difference Generation by van der Waals Interaction, Physical Review Letters, 106(18): 180801, 2011.
DOI: 10.1103/PhysRevLett.106.180801
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11 Characterization and Modeling
05/03/2011 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.
DOI: 10.1016/j.ymben.2011.04.003
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05/03/2011 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
DOI: 10.1007/s00253-011-3346-8
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12 Biomass Deconstruction and Conversion
05/01/2011 Pu, Y., Cao, S., Ragauskas, A.J., Application of quantitative (31)P NMR in biomass lignin and biofuel precursors characterization, Energy and Environmental Science, 4, pp 3154-3166, Jun 2011.
DOI: 10.1039/c1ee01201k
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39 Characterization and Modeling
05/01/2011 Srivastava, A.C., Palanichelvam, K., Ma, J.Y., Steele, J., Blancaflor, E.B., Tang, Y.H., Collection and Analysis of Expressed Sequence Tags Derived from Laser Capture Microdissected Switchgrass (Panicum virgatum L. Alamo) Vascular Tissues, BioEnergy Research, 3(3):278-294, 2010.
DOI: 10.1007/s12155-010-9080-8
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8 Biomass Formation and Modification
05/01/2011 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.
DOI: 10.1016/j.plantsci.2011.01.021
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7 Biomass Formation and Modification
Characterization and Modeling
05/01/2011 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.
DOI: 10.1016/j.tibtech.2011.04.008
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14 Characterization and Modeling
Biomass Deconstruction and Conversion
05/01/2011 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.
DOI: 10.1007/978-3-540-85546-0_4
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05/01/2011 Wilson, David B., Microbial diversity of cellulose hydrolysis, Current Opinion in Microbiology, 14(3): 259-263, 2011.
DOI: 10.1016/j.mib.2011.04.004
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05/01/2011 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.
DOI: 10.1016/j.plantsci.2010.12.010
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05/01/2011 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.
DOI: 10.1201/b10819-2
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  Biomass Formation and Modification
04/22/2011 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.
DOI: 10.1016/j.jpowsour.2011.04.038
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04/15/2011 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.
DOI: 10.1128/AEM.02811-10
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04/11/2011 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.
DOI: 10.1016/j.fuel.2011.04.021
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04/01/2011 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.
DOI: 10.1128/AEM.02454-10
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Biomass Deconstruction and Conversion
04/01/2011 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.
DOI: 10.1021/bk-2010-1052.ch003
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  Characterization and Modeling
Biomass Deconstruction and Conversion
03/21/2011 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.
DOI: 10.1002/btpr.606
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03/18/2011 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.
DOI: 10.1186/1471-2105-12-79
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7 Biomass Formation and Modification
03/11/2011 VanFossen, Amy L., Ozdemir, Inci, Zelin, Samantha L., Kelly, Robert M., Glycoside Hydrolase Inventory Drives Plant Polysaccharide Deconstruction by the Extremely Thermophilic Bacterium Caldicellulosiruptor saccharolyticus, Biotechnology and Bioengineering, 108(7): 1559-1569, 2011.
DOI: 10.1002/bit.23093
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03/02/2011 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, 21:4, (634-641), 2011.
DOI: 10.1101/gr.109280.110
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Biomass Deconstruction and Conversion
03/01/2011 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.
DOI: 10.1073/pnas.1100310108
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Biomass Formation and Modification
Characterization and Modeling
03/01/2011 Wang, Yiran, Huang, Weidong, Sathitsuksanoh, Noppadon, Zhu, Zhiguang, Zhang, Y.H. Percival, Biohydrogenation from Biomass mediated by in vitro synthetic enzymatic pathways, Chemistry and Biology, Volume 18:3, (372-380), 2011.
DOI: 10.1016/j.chembiol.2010.12.019
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03/01/2011 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.
DOI: 10.1073/pnas.1009252108
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03/01/2011 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.
DOI: 10.1146/annurev-arplant-042110-103918
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03/01/2011 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.
DOI: 10.1201/b10819-6
  Biomass Formation and Modification
03/01/2011 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.
DOI: 10.1104/pp.110.168278
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02/17/2011 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 comparative genomics, Plant Science, 181(6):675-687, 2011.
DOI: 10.1016/J.plantsci.2011.01.020
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  Biomass Formation and Modification
02/16/2011 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.
DOI: 10.1074/jbc.M110.215962
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Biomass Formation and Modification
02/11/2011 Sizova, M. V., Izquierdo, J. A., Panikow, N. S., Lynd, L. R., Cellulose- and Xylan-Degrading Thermophilic Anaerobic Bacteria from Biocompost , Applied and Environmental Microbiology, 77(7): 2282-2291, 2011.
DOI: 10.1128/AEM.01219-10
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02/04/2011 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.
DOI: 10.1146/annurev-chembioeng-061010-114205
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02/02/2011 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.
DOI: 10.1007/s10529-011-0526-7
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02/01/2011 Lee, Y., Chen, Po-Wei, Voit, Eberhard O., 2011, Analysis of Operating Principles with S-system Models, Mathematical Biosciences, 231:1, (49-60), 2011.
DOI: 10.1016/j.mbs.2011.03.001
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7 Characterization and Modeling
02/01/2011 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.
DOI: 10.1074/jbc.M110.216556
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01/31/2011 Zhang, Y-H Percival, Mielenz, Jonathan R., Renewable Hydrogen Carrier -- Carbohydrate: Constructing the Carbon-Neutral Carbohydrate Economy, energies, 4, 254-275, 2011.
DOI: 10.3390/en4020254
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12 Biomass Deconstruction and Conversion
01/20/2011 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, 39:8 (3240-3254), 2011.
DOI: 10.1093/nar/gkq1281
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38 Biomass Deconstruction and Conversion
Characterization and Modeling
01/13/2011 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.
DOI: 10.1104/pp.110.168278
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17 Biomass Formation and Modification
01/07/2011 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, (153-164), 2011.
DOI: 10.1007/s12155-010-9109-z
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Biomass Formation and Modification
01/04/2011 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.
DOI: 10.1111/j.1751-7915.2010.00230.x
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01/01/2011 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.
DOI: 10.1111/j.1365-313X.2011.04520.x
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01/01/2011 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.
ISSN 1744-3091
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Characterization and Modeling
01/01/2011 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 Trnasformation Technologies, Journal, 10(2):226-236, 2012.
ISBN: 978-0-8138-2195-5
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14 Biomass Formation and Modification
01/01/2011 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.
DOI: 10.1186/1471-2105-12-S1-S1
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3 Characterization and Modeling
01/01/2011 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.
DOI: 10.1128/JB.01515-10
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21 Biomass Deconstruction and Conversion
Characterization and Modeling
12/29/2010 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.
DOI: 10.1002/bit.23050
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10 Biomass Deconstruction and Conversion
12/22/2010 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.
DOI: 10.1002/9781444391015.ch6
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  Biomass Formation and Modification
Characterization and Modeling
12/21/2010 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.
DOI: 10.1038/msb.2010.98
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12/17/2010 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.
DOI: 10.1021/jp1086812
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4 Biomass Formation and Modification
12/04/2010 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.
DOI: 10.1021/jp109798p
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12/01/2010 Sannigrahi, P., Kim, Dong Ho., Seokwon, Jung, Ragauskas, Arthur, Pseudo-lignin and pretreatment chemistry, Energy and Environmental Science, 4:4:1306-1310, 2011.
DOI: 10.1039/c0ee00378f
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12/01/2010 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.
DOI: 10.1093/glycob/cwq106
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12/01/2010 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, 4:3, (784-792), 2011.
DOI: 10.1039/C0EE00069H
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12/01/2010 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.
DOI: 10.1016/j.copbio.2010.11.005
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55 Biomass Deconstruction and Conversion
Characterization and Modeling
11/30/2010 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, 24:22, (3230-3236), 2010.
DOI: 10.1002/rcm.4757
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6 Characterization and Modeling
11/22/2010 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.
DOI: 10.1371/journal.pone.0014021
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11/12/2010 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.
DOI: 10.1002/bit.22964
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11/01/2010 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, (19-27), 2010.
DOI: 10.1007/s13225-010-0085-6
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10/25/2010 Tyler, Ludmila, Bragg, Jennifer N., Wu, Hiajie, Yang, Xiaohan, Guskan, Gerald A., Vogel, John P., Annotation and comparative analysis of the glycoside hydrolase genes in Brachypodium distachyon, BMC Genomics, 2010, 11:600.
DOI: 10.1186/1471-2164-11-600
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14 Biomass Formation and Modification
10/22/2010 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
DOI: 10.1128/AEM.01400-10
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10/12/2010 Saharay, M., Guo, H., Smith, J.C., Catalytic Mechanism of Cellulose Degradation by a Cellobiohydrolase, CelS, Plos One, 5(10), e12947, 2010.
DOI: 10.1371/journal.pone.0012947
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8 Characterization and Modeling
10/10/2010 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.
DOI: 10.1002/bit.22811
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24 Biomass Deconstruction and Conversion
10/04/2010 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.
DOI: 10.1074/jbc.M110.137315
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Characterization and Modeling
10/01/2010 Wang, Z.W., Hamilton-Brehm, S.D., Lochner, A., Elkins, J.G., Morrell-Falvey, J.L., Mathematical modeling of hydrolysate diffusion and utilization in cellulolytic biofilms of the extreme thermophile Caldicellulosiruptor obsidiansis, Bioresource Technology, 102:3155-62, 2010.
DOI: 10.1016/j.biortech.2010.10.104
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Biomass Deconstruction and Conversion
10/01/2010 Wang, H. Z., Avci, U., Nakashima, J., Hahn, M. G., Chen, F., Dixon, R. A., Mutation of WRKY transcription factors initiates pith secondary wall formation and increases stem biomass in dicotyledonous plants, PNAS, Volume 107, Issue 51, pp 22338-22343, 2010.
DOI: 10.1073/pnas.1016436107
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10/01/2010 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.
DOI: 10.1002/cssc.201000120
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4 Characterization and Modeling
10/01/2010 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.
DOI: 10.1016/j.bpj.2010.08.014
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2 Biomass Formation and Modification
10/01/2010 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.
DOI: 10.1128/JB.00950-10
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Characterization and Modeling
10/01/2010 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.
DOI: 10.1016/j.biortech.2010.08.123
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9 Characterization and Modeling
10/01/2010 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.
DOI: 10.1016/j.carres.2010.06.017
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09/30/2010 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.
DOI: 10.1021/ef100882t
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09/30/2010 In Kole, C., and A. Albert (eds). Vol. 3: Advanced Genomics. Science Publishers, Enfield, New Hampshire (accepted)
ISBN: 978-1-57808-683-2
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  Biomass Formation and Modification
09/29/2010 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.
DOI: 10.1093/nar/gkq948
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11 Characterization and Modeling
09/16/2010 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, 157, (260-269), 2011.
DOI: 10.1099/mic.0.040758-0
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9 Biomass Formation and Modification
09/01/2010 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.
DOI: 10.1002/bit.22937
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25 Characterization and Modeling
09/01/2010 Lee, Y., Voit, E.O., Mathematical modeling of monolignol biosysthesis in Populus xylem, Mathematical Bioscience, 228:1, (78-89), 2010.
DOI: 10.1016/j.mbs.2010.08.009
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6 Characterization and Modeling
08/31/2010 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.
DOI: 10.1007/s11240-010-9826-1
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Characterization and Modeling
08/30/2010 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
DOI: 10.1002/bit.22919
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08/23/2010 Chou, W.C., Yin, Y., Xu, Y., GolgiP: prediction of Golgi resident proteins in plants, Bioinformatics, 26:19, 2464-2465
DOI: 10.1093/bioinformatics/btq446
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2 Characterization and Modeling
08/16/2010 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.
DOI: 10.1073/pnas.1003584107
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08/05/2010 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.
DOI: 10.1021/pr100249c
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3 Characterization and Modeling
Biomass Formation and Modification
08/03/2010 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.
DOI: 10.1093/protein/gzq049
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1 Characterization and Modeling
08/02/2010 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.
DOI: 10.1002/elsc.201000011
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08/01/2010 Tripathi, S.A., Olson, D.G., Argyros, D.A., Miller, B.B., Barrett, T.F., Murphy, D.M., McCool, JD., Warner, A.K., Rajgarhia, V.B., Lynd, L.R., Hogsett, D.A., Caiazza, N.C., Development of pyrF-based genetic system for targeted gene deletion in Clostridium thermocellum and creation of a pta mutant, Applied and Environmental Microbiology, Volume 76, Issue 19, pp 6591-6599, 2010.
DOI: 10.1128/AEM.01484-10
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08/01/2010 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.
DOI: 10.1007/978-3-642-13440-1_11
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08/01/2010 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
DOI: 10.1007/978-3-642-13440-1_10
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  Biomass Formation and Modification
08/01/2010 Wang, L.Q., Wang, Y.Q., Ragauskas, A.J., A novel FRET approach for in situ investigation of cellulase–cellulose interaction, Analytical and Bioanalytical Chemistry, Volume 398, Issue 3, pp 1257-1262, 2010.
DOI: 10.1007/s00216-010-4057-1
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6 Characterization and Modeling
Biomass Deconstruction and Conversion
07/22/2010 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 COMT (caffeic acid O-methyl transferase) mutant Atomt1 , Organic and Biomolecular Chemistry, 8:17, (3928-3946), 2010.
DOI: 10.1039/c004817h
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07/19/2010 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
DOI: 10.1021/bk-2010-1052.ch004
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  Biomass Deconstruction and Conversion
07/02/2010 Vuong, T.V., Wilson, D.B., Glycoside Hydrolases: Catalytic Base/Nucleophile Diversity , Biotechnology and Bioengineering, Volume 107, Issue 2, pages 195-205, 2010.
DOI: 10.1002/bit.22838
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Biomass Deconstruction and Conversion
07/01/2010 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.
DOI: 10.1016/j.biombioe.2010.07.023
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07/01/2010 Voelker, SL; Lachenbruch, B; Meinzer, FC; Jourdes, M; Ki, CY; Patten, AM; Davin, LB; Lewis, NG; Tuskan, GA; Gunter, L; Decker, SR; Selig, MJ; Sykes, R; Himmel, ME; Kitin, P; Shevchenko, O; Strauss, S.H., Antisense Down‐Regulation of 4CL Expression Alters Lignification, Tree Growth, and Saccharification Potential of Field‐Grown Populas, Plant Physiology, 154 (2): 874‐ 886, 2010.
DOI: 10.1104/pp.110.159269
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Characterization and Modeling
07/01/2010 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.
DOI: 10.1007/s00216-010-3955-6
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07/01/2010 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.
DOI: 10.1007/s00216-010-3929-8
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2 Biomass Deconstruction and Conversion
07/01/2010 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.
DOI: 10.1016/j.carres.2010.07.034
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20 Biomass Formation and Modification
07/01/2010 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.
DOI: 10.1016/j.ijhydene.2010.07.132
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07/01/2010 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.
DOI: 10.1016/j.jmb.2010.07.028
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Characterization and Modeling
07/01/2010 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.
DOI: 10.1107/S1744309110022529
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4 Biomass Deconstruction and Conversion
Characterization and Modeling
07/01/2010 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, 3:9, (1182-1190), 2010.
DOI: 10.1039/b926617h
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07/01/2010 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.
DOI: 10.1073/pnas.1009170107
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06/30/2010 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, 154:1, (121-133), 2010.
DOI: 10.1104/pp.110.155242
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21 Characterization and Modeling
06/29/2010 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.
DOI: 10.1002/ange.201000900
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Characterization and Modeling
06/17/2010 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.
DOI: 10.1042/BJ20100315
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06/11/2010 Kalluri U.C and Keller M, “Bioenergy Research: A new paradigm in multidisciplinary research”, Journal of the Royal Society Interface. 7:51, (1391‐1401), 2010.
DOI: 10.1098/rsif.2009.0564
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Biomass Deconstruction and Conversion
06/07/2010 Gu X, Glushka J, Lee SG, Bar-Peled M., Biosynthesis of a new UDP-sugar, UDP-2-acetamido-2-deoxyxylose, in the human pathogen Bacillus cereus subspecies cytotoxis NVH 391-98, Journal of Biological Chemistry, 285:32, (24825-33), 2010.
DOI: 10.1074/jbc.M110.125872
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11 Biomass Formation and Modification
06/01/2010 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.
DOI: 10.1016/j.copbio.2010.05.005
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36 Biomass Deconstruction and Conversion
06/01/2010 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
DOI: 10.1002/bit.22814
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11 Characterization and Modeling
06/01/2010 Zhang, X.Z., Sathisuksanoh, N., Zhang, Y.H.P., Glycoside hydrolase family 9 processive endoglucanase from Clostridium phytofermentans: heterologous expression, purfication, and synergy with family 48 cellobiohydrolase, Bioresource Technology, Volume 101, Issue 14 pp 5534-5538, 2010
DOI: 10.1016/j.biortech.2010.01.152
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21 Biomass Deconstruction and Conversion
06/01/2010 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, 76:11, (3545-3553), 2010.
DOI: 10.1128/AEM.02689-09
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31 Biomass Deconstruction and Conversion
06/01/2010 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.
DOI: 10.1016/j.copbio.2010.05.008
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40 Biomass Deconstruction and Conversion
06/01/2010 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.
DOI: 10.1128/AEM.00958-10
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38 Biomass Deconstruction and Conversion
06/01/2010 Yang T, Bar-Peled M., "Identification of a novel UDP-sugar pyrophosphorylase with a broad substrate specificity in Trypanosoma cruzi". Biochem J.;429:3, 533-43, 2010.
DOI: 10.1042/BJ20100238
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19 Biomass Formation and Modification
06/01/2010 Wuichet, K., Zhulin, I.B., Origins and Diversification of a Complex Signal Transduction System in Prokaryotes, Science Signaling, Vol. 3, Issue 128, p. 50, 2010.
DOI: 10.1126/scisignal.2000724
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06/01/2010 Voit, E.O., Chou I.C., Parameter Estimation in Canonical Biological Systems Models, International Journal of Systems and Synthetic Biology, Volume 1, Issue 1, pp 1-19, 2010
PDF
  Characterization and Modeling
06/01/2010 Tetard, L., Passian, A., Rarahi, R.H., Kalluri, U.C., Davison, B.H., Thundat, T., Atomic force microscopy of silica nanoparticles and carbon nanohorns in macrophages and red blood cells, Ultramicroscopy, 110(6):586-591, 2010.
DOI: 10.1016/j.ultramic.2010.02.035
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11 Characterization and Modeling
Biomass Formation and Modification
06/01/2010 Zhu X, Pattathil S, Mazumder K, Brehm A, Hahn MG, Dinesh-Kumar SP, Joshi CP., Virus-Induced Gene Silencing Offers a Functional Genomics Platform for Studying Plant Cell Wall Formation, Molecular Plant, Volume 3, Issue 5, pp 818-833, 2010.
DOI: 10.1093/mp/ssq023
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18 Characterization and Modeling
05/29/2010 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.
DOI: 10.1007/s00267-010-9503-5
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9 Biomass Formation and Modification
05/14/2010 Hubbell, Christopher A., Ragauskas, Arthur J., Effect of acid-chlorite delignification on cellulose degree of polymerization, Bioresource Technology, 101, 7410-7415, 2010.
DOI: 10.1016/j.biortech.2010.04.029
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58 Characterization and Modeling
05/05/2010 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.
DOI: 10.1038/hdy.2010.73
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13 Biomass Formation and Modification
05/01/2010 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.
DOI: 10.1128/AEM.00402-10
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26 Biomass Deconstruction and Conversion
05/01/2010 Hu, Z., R. Sykes, M.F. Davis, E.C. Brummer, and A.J. Ragauskas, Chemical profiles of switchgrass. Bioresource Technology, 101:9, (3253-3257), 2010.
DOI: 10.1016/j.biortech.2009.12.033
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29 Characterization and Modeling
Biomass Formation and Modification
05/01/2010 A High - Throughput Transient Gene Expression System for Switchgrass (Panicum virgatum L.) Seedlings, Biotechnology for Biofuels, 7;3:9, 2010
DOI: 10.1186/1754-6834-3-9
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24 Biomass Formation and Modification
04/11/2010 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.
DOI: 10.1007/s00299-010-0850-8
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9 Biomass Formation and Modification
Biomass Formation and Modification
04/07/2010 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.
DOI: 10.1186/1471-2180-10-135
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23 Biomass Deconstruction and Conversion
04/01/2010 Albersheim, P., Darvill, A., Roberts, K., Sederoff, R., Staehelin, A., Plant Cell Walls,, Plant Cell Walls, 2010.
ISBN: 978-0-8153-1996-2
  Biomass Formation and Modification
04/01/2010 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.
DOI: 10.1073/pnas.0914506107
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Characterization and Modeling
04/01/2010 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, 76:8, (2582-2588), 2010.
DOI: 10.1128/AEM.02735-09
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17 Biomass Deconstruction and Conversion
04/01/2010 Selig, Michael J., Tucker, Melvin P., Sykes, R., Reichel, D., Brunecky, R., Himmel, M.E., Davis, M.F., Decker, S.R., Lignocellulose recalcitrance screening by integrated high- throughput hydrothermal pretreatment and enzymatic, Industrial Biotechnology , 6(2), 2010.
DOI: 10.1089/ind.2010.0009
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5 Biomass Deconstruction and Conversion
Characterization and Modeling
04/01/2010 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.
DOI: 10.1016/j.procbio.2010.03.017
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31 Biomass Deconstruction and Conversion
03/22/2010 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.
DOI: 10.1073/pnas.0911237107
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14 Biomass Formation and Modification
03/19/2010 Gu X, Glushka J, Yin Y, Xu Y, Denny T, Smith J, Jiang Y, Bar-Peled M., 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, Journal of Biological Chemistry, 285:12, (9030-9040), 2010.
DOI: 10.1074/jbc.M109.066803
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Characterization and Modeling
03/12/2010 Petridis, L., Smith, J.C., A Molecular Mechanics Force Field for Lignin, Journal of Computational Chemistry, 30(3), pp 457-67, 2009.
DOI: 10.1002/jcc.21075
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19 Characterization and Modeling
03/04/2010 Zhou, F., Chen, H., Xu, Y, GASdb: a large-scale and comparative exploration database of glycosyl hydrolysis system, 2010 March; 10:69
DOI: 10.1186/1471-2180-10-69
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4 Characterization and Modeling
03/01/2010 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.
DOI: 10.1104/pp.110.154229
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Characterization and Modeling
03/01/2010 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.
DOI: 10.1111/j.1365-313X.2010.04223.x
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03/01/2010 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.
ISBN 155581512X
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03/01/2010 Chen, Y., Sarkanen, S., Macromolecular replication during lignin biosynthesis, Phytochemistry, Volume 71, Issue 4, March 2010, Pages 453-462
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03/01/2010 Himmel, Michael E., Xu, Qi, Luo, Yonghua, Ding, Shi-You, Lamed, Raphael, Bayer, Edward A., Microbial enzyme systems for biomass conversion: emerging paradigms, Biofuels, Vol. 1, No. 2, Pages 323-341, 2010.
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03/01/2010 Mielenz, J.R., Hogsett, D.A., Improving microbial robutsness using systems biology, Manual of Industrial Microbiology and Biotechnology, 3rd Edition, p. 605-620, 2010.
ISBN 978-1-55581-512-7
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03/01/2010 Sannigrahi, P., Ragauskas, A.J., Tuskan, G.A., Poplar as a feedstock for biofuels: A review of compositional characteristics, Biofuels Bioproducts and Biorefining-Biofpr, 4(2):209-226, 2010.
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03/01/2010 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
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14 Biomass Deconstruction and Conversion
03/01/2010 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, 86(2):525-533, 2010.
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22 Biomass Deconstruction and Conversion
02/25/2010 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, 2010.
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23 Characterization and Modeling
Biomass Formation and Modification
Biomass Deconstruction and Conversion
02/11/2010 Vogel, John P., Tuskan, G. A., Kalluri, U. C., Yang, Xiaohan, et al., Genome sequencing and analysis of the model grass Brachypodium distachyon, Nature, 463(7282):763-768, 2010.
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02/02/2010 Xie, Zhihong, Ulrich, Luke E., Zhulin, Igor B., Alexandre, Gladys, PAS domain containing chemoreceptor couples dynamic changes in metabolism with chemotaxis, PNAS, Volume 107, Issue 5, pp 2235-2240, 2010.
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22 Biomass Formation and Modification
Characterization and Modeling
02/01/2010 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.
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01/11/2010 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, (1347-1357), 2011.
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29 Characterization and Modeling
Characterization and Modeling
01/01/2010 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.
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01/01/2010 Samuel, R., Pu, Y., Foston, M., Ragauskas, A.J., Solid-state NMR characterization of switchgrass cellulose after dilute acid pretreatment, Biofuels, 1:1, 85-90, 2010.
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01/01/2010 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.
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01/01/2010 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.
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7 Characterization and Modeling
01/01/2010 Wuichet, Kristin, Cantwell, Brian J., Zhulin, Igor B., Evolution and phyletic distribution of two-component signal transduction systems, Current Opinion in Microbiology, Volume 13, Issue 2, pp 219-225, 2010.
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01/01/2010 Stewart, 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.
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01/01/2010 Xu, Y., Computational Challenges in Deciphering Genomic Structures of Bacteria, Journal of Computer Science and Technology, 25;1, pp 53-70, 2010.
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01/01/2010 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, 1:1, (163-176), 2010.
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12/21/2009 Kim, S., Rahman, T., Senesac, L.R., Davison, B.H., Thundat, T., Piezoresistive cantilever array sensor for consolidated bioprocess monitoring, Scanning, 31:5, (204-210), 2009.
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7 Characterization and Modeling
12/20/2009 Tetard, L., Passian, A., Thundat, T., New modes for subsurface atomic force microscopy through nanomechanical coupling, Nature Nanotechnology, 20 December 2009
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39 Characterization and Modeling
12/18/2009 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.
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35 Biomass Deconstruction and Conversion
12/15/2009 Vanfossen Amy L, Verhaart Marcel R A, Kengen Serve M W, Kelly Robert M., Carbohydrate utilization patterns for the extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus reveal broad growth substrate preferences, Applied and Environmental Microbiology 75(24):7718-24, 2009.
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12/11/2009 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
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11 Biomass Deconstruction and Conversion
12/01/2009 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
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23 Characterization and Modeling
Biomass Formation and Modification
12/01/2009 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.
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12/01/2009 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
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11 Characterization and Modeling
12/01/2009 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, 2(4):246-256, 2009.
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24 Biomass Formation and Modification
Characterization and Modeling
12/01/2009 Jeremy C. Smith, Mark Nimlos, Mike Himmel, Mike Crowley, John Brady, Supercomputers Tackle BIOFUEL Production Problems, SciDAC, 2009.
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12/01/2009 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, 2:4 / December, 2009.
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5 Characterization and Modeling
12/01/2009 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
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12/01/2009 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
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12/01/2009 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.
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3 Characterization and Modeling
12/01/2009 Dixon, Richard, DOE BioEnergy Center Special Issue, The BioEnergy Sciences Center (BESC), Bioenergy Research, Volume 2, Number 4 / December, 2009
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2 Biomass Formation and Modification
12/01/2009 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.
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12/01/2009 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.
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12/01/2009 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.
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19 Characterization and Modeling
11/15/2009 Tran, T.,; Zhou, F; Marshburn, S; Stead, M; Kushner, S; Xu, Ying; De novo computational prediction of non-coding RNA genes in prokaryotic genomes, Bioinformatics, Volume 25, Number 22 Pp. 2897-2905, 2009.
DOI: 10.1093/bioinformatics/btp537
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22 Characterization and Modeling
11/01/2009 Voit E O, Goel G, Chou I-C, Fonseca L L, Estimation of Metabolic Pathway Systems from Different Data Sources, November 2009 -- Volume 3, Issue 6, p.513–522
DOI: 10.1049/iet-syb.2008.0180
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6 Characterization and Modeling
11/01/2009 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.
DOI: 10.1007/s12155-009-9060-z
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11 Biomass Formation and Modification
11/01/2009 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.
DOI: 10.1002/bit.22630
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11/01/2009 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.
DOI: 10.1002/pmic.200800854
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18 Biomass Formation and Modification
Biomass Deconstruction and Conversion
Characterization and Modeling
10/22/2009 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.
DOI: 10.1039/b819206e
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16 Biomass Deconstruction and Conversion
10/20/2009 Shen H, Fu C, Xiao X, Ray T, Tang Y, Wang Z. and Chen F., Developmental Control of Lignification in Stems of Lowland Switchgrass Variety Alamo and the Effects on Saccharification Efficiency. Bioenerg. Res. 2:233–245, 2009.
DOI: 10.1007/s12155-009-9058-6
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10/16/2009 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
DOI: 10.1007/s12155-009-9047-9
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10/14/2009 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.
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27 Biomass Formation and Modification
10/09/2009 Ulrich, Luke E., Zhulin, Igor B., The MiST2 database: a comprehensive genomics resource on microbial signal transduction, Nucleic Acids Research, Volume 38, pp D401-D407
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93 Characterization and Modeling
10/09/2009 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.
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66 Biomass Formation and Modification
Characterization and Modeling
10/01/2009 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.
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47 Characterization and Modeling
10/01/2009 Podar, Mircea, Keller, Martin, Hugenholtz, Philip, 2009, Single Cell Whole Genome Amplification of Uncultivated Organisms, Microbial Monogr, Series; Volume 10/2009.
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10/01/2009 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.
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38 Biomass Deconstruction and Conversion
Characterization and Modeling
09/28/2009 Caffall KH, Mohnen D., The structure, function, and biosynthesis of plant cell wall pectic polysaccharides., Carbohydrate Research 2009;344(14):1879-1900.
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277 Biomass Formation and Modification
09/25/2009 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.
DOI: 10.1016/j.biortech.2009.09.081
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51 Biomass Deconstruction and Conversion
09/18/2009 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.
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22 Characterization and Modeling
09/11/2009 Caffall, Kerry H., Pattathil, Sivakumar, Phillips, Sarah E., Hahn, Michael G., Mohnen, Debra, Arabidopsis thaliana T-DNA Mutants Implicate GAUT Genes in the Biosynthesis of Pectin and Xylan in Cell Walls and Seed Testa, Molecular Plant, Volume 2, Number 5, pp 1000 - 1014
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44 Biomass Formation and Modification
Characterization and Modeling
09/05/2009 Zong-Ming Cheng and Gerald A. Tuskan. 2009 Populus community mega-genomics: coming of age. Critical Reviews in Plant Sciences. 28(5):282-284.
DOI: 10.1080/07352680903240933
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3 Biomass Formation and Modification
09/01/2009 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
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5 Characterization and Modeling
09/01/2009 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.
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1 Biomass Deconstruction and Conversion
09/01/2009 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
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13 Biomass Deconstruction and Conversion
09/01/2009 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.
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29 Biomass Formation and Modification
Characterization and Modeling
09/01/2009 Yingzhen Konga, Gongke Zhoua, Utku Avcia, Xiaogang Gua, Chelsea Jonesa, Yanbin Yin, Ying Xu, and M. G. Hahn, Two Poplar Glycosyltransferase Genes, PdGATL1.1 and PdGATL1.2, Are Functional Orthologs to PARVUS/AtGATL1 in Arabidopsis, Molecular Plant, 2:5, (1040–1050), 2009.
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21 Biomass Formation and Modification
Characterization and Modeling
08/24/2009 Samuel,R., Pu, Y., Babu, R., Ragauskas, A.J.Structural Characterizations and comparison of switchgrass ball-milled lignin before and after dilute acid pretreatment A. Applied Biochemistry and Biotechnology, 162 (1), 62-74, 2010.
DOI: 10.1007/s12010-009-8749-y
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70 Characterization and Modeling
Biomass Deconstruction and Conversion
08/07/2009 Yang T, Bar-Peled L, Gebhart L, Lee SG, Bar-Peled M., 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), 2009.
DOI: 10.1074/jbc.M109.014761
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19 Biomass Formation and Modification
07/31/2009 Yin, Y.B., Huang, J.L., Xu, Y., The cellulose synthase superfamily in fully sequenced plants and algae, BMC Plant Biology, 9;99, 2009.
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50 Characterization and Modeling
07/27/2009 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, 106:2, 2009.
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21 Characterization and Modeling
07/01/2009 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
DOI: 10.1039/b906065k
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89 Biomass Deconstruction and Conversion
Characterization and Modeling
06/28/2009 Wang, Y. R., Zhang, Y. H. P., Cell-free protein synthesis energized by slowly-metabolized maltodextrin, BMC Biotechnology, 2009, 9:58.
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35 Biomass Deconstruction and Conversion
06/19/2009 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.
DOI: 10.1007/s10570-009-9306-0
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20 Characterization and Modeling
Biomass Deconstruction and Conversion
06/15/2009 Gu X, Wages CJ, Davis KE, Guyett PJ, Bar-Peled M., Enzymatic characterization and comparison of various poaceae UDP-GlcA 4-epimerase isoforms, Journal of Biochemistry, 146:4, (527-34) 2009.
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6 Biomass Formation and Modification
06/04/2009 Wang, Y., Zhang, Y.H.P., Overexpression and simple purification of the Thermotoga maritima 6-phosphogluconate dehydrogenase in Escherichia coli and its application for NADPH regeneration, Microbial Cell Factories, 2009, 8:30.
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30 Biomass Deconstruction and Conversion
06/01/2009 Ye, X., B-g Kang, L. D. Osburn, and Z.-M. Cheng. 2009 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. PCTOC: J. of Plant Biotechnology 97:271–283(2009).
DOI: 10.1007/s11240-009-9526-x
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10 Biomass Formation and Modification
Biomass Formation and Modification
06/01/2009 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.
DOI: 10.1007/s11627-009-9213-y
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4 Characterization and Modeling
06/01/2009 Ghimire, S. R, Charlton, N., and Craven, K. D., "The mycorrhizal fungus, Sebacina vermifera, enhances seed germination and biomass production in switchgrass (Panicum virgatum L)", Bioenergy Research, 2:1-2, (51-58), 2009.
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17 Biomass Formation and Modification
06/01/2009 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
DOI: 10.1016/j.mbs.2009.03.002
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06/01/2009 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 Cellulolytic Bacterium "Anaerocellum thermophilum" DSM 6725, Journal of Bacteriology, 191:11, (3760-3761), 2009.
DOI: 10.1128/JB.00256-09
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39 Biomass Deconstruction and Conversion
Characterization and Modeling
06/01/2009 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.
DOI: 10.1111/j.1365-313X.2009.03828.x
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16 Biomass Formation and Modification
05/28/2009 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, 48(13):6441-6447, 2009.
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41 Biomass Deconstruction and Conversion
05/01/2009 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
DOI: 10.1002/pro.105
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8 Biomass Deconstruction and Conversion
Characterization and Modeling
05/01/2009 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 DSM 6725, Applied and Environmental Microbiology, 75(14):4762-4769, 2009
DOI: 10.1128/AEM.00236-09
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79 Biomass Deconstruction and Conversion
Characterization and Modeling
04/27/2009 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.
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28 Characterization and Modeling
04/27/2009 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
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16 Characterization and Modeling
04/22/2009 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)
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93 Biomass Deconstruction and Conversion
Characterization and Modeling
04/01/2009 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.
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27 Biomass Deconstruction and Conversion
03/27/2009 Guyett P, Glushka J, Gu X, Bar-Peled M., Real-time NMR monitoring of intermediates and labile products of the bifunctional enzyme UDP-apiose/UDP-xylose synthase, Carbohydrate Research, 344:9, (1072-8), 2009.
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20 Biomass Formation and Modification
03/13/2009 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, (1072-1078), 2009.
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65 Biomass Formation and Modification
03/09/2009 Keller, Martin, Hettich, Robert, Environmental Proteomics: a Paradigm Shift in Characterizing Microbial Activities at the Molecular Level, Microbiology and Molecular Biology Reviews, 73:1, (62-), 2009.
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63 Biomass Deconstruction and Conversion
02/26/2009 Karpinets, T., Pelletier, D, Pan, C., Uberbacher, E.C., Melnichenko, G.V., Hettich, R.L., Samatove, N.F., Phenotype fingerprinting suggests the involvement of single-genotype consortia in degradation of aromatic compounds by Rhodopseudomonas palustris, PLoS ONE, 4:2, 2009.
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4 Characterization and Modeling
Biomass Deconstruction and Conversion
02/01/2009 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.
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56 Biomass Deconstruction and Conversion
01/20/2009 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.
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47 Biomass Deconstruction and Conversion
Characterization and Modeling
01/09/2009 Zhou, F., Xu, Ying, RepPop: a database for repetitive elements in Populus trichocarpa, BMC Genomics, 10:14, 2009
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11 Biomass Formation and Modification
01/01/2009 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.
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10 Biomass Formation and Modification
01/01/2009 Keller, M., Schadt, C.W., Palumbo, A.V., Environment to Organisms and Genomes and Backed. Karsten Zengler, (2009), ASM Press.   Biomass Deconstruction and Conversion
01/01/2009 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
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63 Biomass Deconstruction and Conversion
01/01/2009 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, 11:11, (1762 - 1766), 2009.
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26 Characterization and Modeling
01/01/2009 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
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28 Biomass Formation and Modification
Characterization and Modeling
01/01/2009 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.
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01/01/2009 Zhulin, Igor B., It Is Computation Time for Bacteriology!, Journal of Bacteriology, January 2009, p. 20-22; Volume 191, No. 1
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4 Characterization and Modeling
01/01/2009 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)
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25 Biomass Formation and Modification
01/01/2009 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.
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01/01/2009 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.
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1 Biomass Deconstruction and Conversion
01/01/2009 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, 267-274, December 2009.
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24 Biomass Formation and Modification
01/01/2009 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
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50 Biomass Deconstruction and Conversion
01/01/2009 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.
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41 Biomass Formation and Modification
01/01/2009 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.
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13 Biomass Formation and Modification
Characterization and Modeling
12/01/2008 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.
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5 Characterization and Modeling
12/01/2008 Sykes, R., Kodrzycki, B., Tuskan, G., Foutz, K., Davis, M., Within tree variability of lignin composition in Populus, Wood Science and Technology, 42:8, 649-661, 2008.
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34 Biomass Formation and Modification
Characterization and Modeling
11/01/2008 Possible impacts of the US EPA Notice of Proposed Rulemaking on the biofuels industry, Industrial Biotechnology, Volume 4, No:4; pages 322-333, 2008.
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  Characterization and Modeling
10/06/2008 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.
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132 Characterization and Modeling
Biomass Deconstruction and Conversion
08/01/2008 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
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57 Biomass Deconstruction and Conversion
Characterization and Modeling
08/01/2008 Goel, Gautam, I-Chun Chou and Eberhard O. Voit , System estimation from metabolic time-series data sys, Bioinformatics, 24:21, (2505-2511), 2008.
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33 Characterization and Modeling
08/01/2008 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
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160 Biomass Deconstruction and Conversion
07/01/2008 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.
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48 Biomass Deconstruction and Conversion
06/20/2008 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, 1194:2, (150-154), 2008.
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48 Biomass Deconstruction and Conversion
06/16/2008 Zhou, Fengfeng, Victor Olman, Ying Xu , Barcodes for Genomes and Applications, BMC Bioinformatics, 9:546, 2008
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35 Characterization and Modeling
06/12/2008 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.
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20 Characterization and Modeling
06/01/2008 York WS, O'Neill MA. 2008. Biochemical control of xylan biosynthesis - which end is up? Current Opinion in Plant Biology 11(3):258-265.
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06/01/2008 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
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53 Characterization and Modeling
Biomass Deconstruction and Conversion
06/01/2008 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.
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06/01/2008 Mohnen, D., Pectin structure and biosysthesis, Current Opinion in Plant Biology, Vol. 11(3), 266- 277, 2008.
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374 Biomass Formation and Modification
04/01/2008 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.
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03/01/2008 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
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14 Biomass Formation and Modification
02/01/2008 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.
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504 Biomass Deconstruction and Conversion
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01/07/2008 Keller, Martin, Ramos, Juan L., 2008, Microbial goods from single cells and metagenomes, Current Opinion in Microbiology, 11:3, (195-197), 2008.
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3 Biomass Deconstruction and Conversion
01/01/2008 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.
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  Biomass Formation and Modification
01/01/2008 Ding, S.Y., Himmel, M., Xie, X.S., Identify Molecular Structural Features of Biomass Recalcitrance Using Nondestructive Microscopy and Spectroscopy, Abstracts of papers of the american chemical society, 237, 2009.
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  Characterization and Modeling
Biomass Deconstruction and Conversion
Dassa, B., Utturkar, S., Hurt, R.A., Klingeman, D.M., Keller, M., Xu, J., Reddy, H.K., Borovok, I., Rozman, I., Grinberg, R.L., Zhivin, O., Bayer, E.A., Brown, S.D., "Near-complete genome sequence of the cellulolytic bacterium", Genome Announcements, 2015   Biomass Deconstruction and Conversion
Wyman, C.E., Ragauskas, A.J., Lignin Bioproducts to Enable Biofuels, Biofuels, Bioproducts and Biorefining, 2015   Characterization and Modeling

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