As new publications are available from The Center of Bioenergy Innovation (CBI) researchers, information about the publications will be available on this site.


Publication ID Date Published Publication Title Authors
60 2018-11-06 Sustainable Energy and Fuels Overexpression of a serine hydroxymethyltransferase increases biomass production and reduces recalcitrance in the bioenergy crop Populus Zhang, J., Li, M., Bryan, A.C., Yoo, C.G., Rottmann, W., Winkeler, K.A., Collins, C.M., Singan, V., Lindquist, E.A., Jawdy, S.S., Gunter, L.E., Engle, N.L., Yang, X., Barry, K., Tschaplinski, T.J., Schmutz, J., Pu, Y., Ragauskas, A.J., Tuskan, G.A., Muche
59 2018-10-23 Frontiers in Energy Research High throughput screening technologies in biomass characterization Decker, S.R., Harman-Ware, A.E., Happs, R.M., Wolfrum, E.J., Tuskan, G.A., Kainer, D., Oguntimein, G., Rodriguez, M., Weighill, D., Jones, P.C., and Jacobson, D.
58 2018-11-06 Frontiers in Plant Science A new calmodulin-binding protein expresses in the context of secondary cell wall biosynthesis and impacts biomass properties in Populus Badmi, R., Payyavula, R.S., Bali, G., Guo, H-B., Jawdy, S.S., Gunter, L., Yang, X., Winkeler, K., Collins, C., Rottmann, W.H., Yee, K., Rodriguez Jr., M., Sykes, R., Decker, S.R., Davis, M.F., Ragauskas, A.J., Tuskan, G., and Kalluri, U.C.
57 2018-10-23 Frontiers in Plant Science Recent advances in the transcriptional regulation of secondary cell wall biosynthesis in the woody plants Zhang, J., Xie, M., Tuskan, G.A., Muchero, W., and Chen, J-G.
56 2018-10-15 PNAS Association mapping, transcriptomics, and transient expression identify candidate genes mediating plant-pathogen interactions in a species of forest tree Muchero, W., Sondreli, K.L., Chen, J-G., Urbanowicz, B.R., Zhang, J., Singal, V., Yang, Y., Brueggeman, R.S., Franco-Coronado, J., Abraham, N., Yang, J-Y., Moremen, K.W., Weisberg, A.J., Chang, J.H., Lindquist, E., Barry, K., Ranjan, P., Jawdy, S., Schmut
55 2018-09-18 Plant Physiology Identification of key enzymes for pectin synthesis in seed mucilage Voiniciuc, C., Engle, K.A., Gunl, M., Dieluwit, S., Heinich-Wilhelm Schmidt, M., Yang, J-Y, Moremen, K.W., Mohnen, D., and Usadel, B.
54 2018-07-20 Metabolic Engineering Multiobjective strain design: a framework for modular cell engineering Garcia, S., and Trinh, C.T.
53 2018-10-09 Microbiology Resource Announcements Complete genome sequence of salinispaera sp. Strain LB1, a moderately halo-acidophilic bacterium isolated from lake brown, western Australia O'Dell, K.B., Hatmaker, E.A., Guss, A.M., Mormile, M.R.
52 2018-10-02 Oikos Environmental resource deficit may drive the evolution of intraspecific trait variation in invasive plant populations Liu, S., Streich, J., Borevita, J.O., Rice, K.J., Li, T., Li, B.
51 2018-10-02 Sustainable Energy and Fuels Cellulose solvents-based pretreatment for enhanced second-generation biofuels production: A review Satari, B., Karimi, K., Kumar, R.
50 2018-10-02 Microbiology Resource Announcements Draft genome assemblies of five robust yarrowia lipolytica strains exhibiting high lipid production, pentose sugar utilization, and sugar alcohol secretion from undetoxified lignocellulosic biomass hydrolysates Walker, C., Ryu, S., Na, Hyunsoo, Zane, M., LaButti, K., Lipzen, A., Haridas, S., Barry, K., Grigoriev, IV., Quarterman, J., Slininger, P., Dien, B., Trinh, C.T.
49 2018-10-02 Current Opinion in Biotechnology Development and commercialization of reduced lignin alfalfa Barros, J., Temple, S., Dixon, R.A.
48 2018-09-28 Biotechnology for Biofuels Deletion of a single glycosyltransferase in Caldicelulosiruptor bescii eliminates protein glycosylation and growth on crystalline cellulose Russell, J., Kim, S-K., Duma, J., Nothaft, H., Himmel, M.E., Bomble, Y.J., Szymanski, C.M., Westpheling, J.
47 2018-09-28 Frontiers in Plant Science Regulation of lignin biosynthesis and its role in growth-defense tradeoffs Xie, M., Zhang, J., Tschaplinski, T.J., Tuskan, G.A., Chen, J-G., Muchero, W.
46 2018-09-25 GCB Bioenergy Breeding progress and preparedness for mass-scale deployment of perenial lignocellulosic biomass crops switchgrass, miscanthus, willow, and poplar Clifton-Brown, J., et al.
45 2018-09-19 Bioresource Technology From lignin to valuable products-strategies, challenges, and prospects Wang, H., Pu, Y., Ragauskas, A.J., Yang, B.
44 2018-09-19 Metabolic Engineering Characterization of the Clostridium thermocellum AdhE, NfnAB, ferredoxin and Pfor proteins for their ability to support high titer ethanol production in Thermoanaerobacterium saccharolyticum Cui, J., Olson, D.G., Lynd, L.R.
43 2018-09-11 Biotechnology for Biofuels Rheological properties of corn stover slurries during fermentation by Clostridium thermocellum Ghosh, S., Holwerda, E.K., Worthen, R.S., Lynd, L.R., Epps, B.P.
42 2018-09-11 Metabolic Engineering Engineering a spermidine biosynthetic pathway in Clostridium thermocellum results in increased resistance to furans and increased ethanol production Kim, S-K., Westpheling, J.
41 2018-09-11 Biotechnology for Biofuels Expressing the thermoanaerobacterium saccharolticum pforA in engineereed Clostridium thermocellum improves ethanol production Hon, S., Holwerda, E.K., Worthen, R.S., Maloney, M.I., Tian, L., Cui, J., Lin, P.L., Lynd, L.R., Olson, D.G.
40 2018-08-27 Chemistry Select Communication Topochemical understanding of lignin distribution during hydrothermal flowthrough pretreatment Jung, S., Trajano, H.L., Yoo, C.G., Foston, M.B., Hu, F., Tolbert, A.K., Wyman, C.E., Ragauskas, A.J
39 2018-08-27 Plant Biotechnology Journal Gene regulatory networks of lignin biosynthesis in switchgrass (Panicum virgatum) Rao, X., Chen, X., Shen, H., Ma, Q., Tang, Y., Pena, M., York, W., Frazier, T.P., Lenaghan S., Xiao, X., Chen, F., Dixon, R.A.
38 2018-09-10 Energy & Fuels Methods and Challenges in the determination of molecular weight metrics of bio-oils Harman-Ware, A.E., Ferrell III, J.R.
37 2018-09-10 Journal of Industrial Microbiology and Biotechnology Transcriptomic and proteomic changes from medium supplementation and strain evolution in high-yielding Clostridium thermocellum strains Papanek, B., O'Dell, K.B., Manga, P., Giannone, R.J., Klingeman, D.M. Hettich, R.L., Brown, S.D., Guss, A.M.
36 2018-08-21 ACS Sustainable Chemistry and Engineering Characterization and catalytic transfer hydrogenolysis of deep eutectic solvent extracted sorghum lignin to phenolic compounds Das, L., Li, M., Stevens, J., Li, W., Pu, Y., Ragauskas, A.J., Shi, J.
35 2018-08-21 PLOS ONE Defining the genetic components of callus formation: A GWAS approach Tuskan, G.A., Mewalal, R., Gunter, L.E., Palla, K.J., Carter, K., Jacobson, D.A., Jones, P.C., Garcia, B.J., Weighill, D.A., Hyatt, P.D., Yang, Y., Zhang, J., Reis, N., Chen, J-G., Muchero, W.
34 2018-08-21 ACS Sustainable Chemistry & Engineering Reductive Catalytic Fractionation of C-Lignin Stone, M.L., Anderson, E.M., Meek, K.M., Reed, M., Katahira, R., Chen, F., Dixon, R.A., Beckham, G.T., Roman-Leshkov, Y.
33 2018-08-13 BMC Genomics Diel rewiring and positive selection of ancient plant proteins enabled evolution of CAM photosynthesis in Agave Yin, H., Guo, H-B., Weston, D.J., Borland, A.M., Ranjan, P., Abraham, P.E., Jawdy, S.S., Wachira, J., Tuskan, G.A., Tschaplinski, T.J., Wullschleger, S.D., Guo, H., Hettich, R.L., Gross, S.M., Wang, Z., Visel, A., Yang, X.
32 2018-07-30 Metabolic Engineering Communications Harnessing a P450 fatty acid decorboxylase from Macrococcus caseolyticus for microbial biosynthesis of odd chain terminal alkenes Lee, J-W., Niraula, N.P., Trinh, C.T.
31 2018-07-30 Current Protocols Environmental isolation and whole-genome sequencing of Campylobacter Kelley, B.R., Ellis, J., Hyatt, D., Jacobson, D., Johnson, J.
30 2018-07-17 AIChE Journal Novel multi-domain, multi-functional glycoside hydrolases from highly lignocellulolytic Caldicellulosiruptor species Conway, J.M., Crosby, J.R., Hren, A.P., Southerland, R.T., Lee, L.L., Lunin, V.V., Alahuhta, P., Himmel, M.E., Bomble, Y.J., Adams, M.W.W., Kelly, R.M.
29 2018-07-16 New Phytologist Genome-wide association studies and expression-based quantitative trait loci analyses reveal roles of HCT2 in caffeoylquinic acid biosynthesis and its regulation by defense-responsive transcription factors in Populus Zhang, J., Yang, Y., Zheng, K., Xie, M., Feng, K., Jawdy, S.S., Gunter, L.E., Ranjan, P., Singan, V.R., Engle, N., Lindquist, E., Barry, K., Schmutz, J., Zhao, N., Tschaplinski, T.J., LeBoldus, J., Tuskan, G.A., Chen, J-G., Muchero, W.
28 2018-07-16 Green Chemistry Cellulose-hemicellulose interactions at elevated temperatures increase cellulose recalcitrance to biological conversion Kumar, R., Bhagia, S., Smith, M.D., Petridis, L., Ong, R.G., Cai, C.M., Mittal, A., Himmel, M.H., Balan V., Dale, B.E., Ragauskas, A.J., Smith, J.C., Wyman, C.E.
27 2018-07-12 ACS Sustainable Chemistry & Engineering Chemical transformations of poplar lignin during c0-solvent enhanced lignocellulosic fractionation process Meng, X., Parikh, A., Seemala, B., Kumar, R., Cai, C.M., Ragauskas, A.J.
26 2018-02-15 PLOS ONE Quantitative proteome profile of water deficit stress responses in eastern cottonwood (Populus deltoides) leaves Abraham, P.E., Garcia, B.J., Gunter, L.E., Jawdy, S.S., Engle, N., Yang, Y., Jacobson, D.A., Hettich, R.L., Tuskan, G.A., Tschaplinski, T.J.
25 2018-01-14 Biotechnology for Biofuels Working towards recalcitrance mechanisms: increased xylan and homogalacturonan production by overexpression of GAlactUronosylTransferase12 (GAUT12) causes increased recalcitrance and decreased growth in Populus Biswal, A.K., Atmodjo, M.A., Pattathil, S., Amos, R.A., Yang, X., Winkeler, K., Collins, C., Mohanty, S.S., Ryno, D., Tan, L., Gelineo-Albersheim, I., Hunt, K., Sykes, R.W., Turner, G.B., Ziebell, A., Davis, M.F., Decker, S.R., Hahn, M.G., Mohnen, D.
24 2018-02-20 New Phytologist Identification of an algal xylan synthase indicates that there is functional orthology between algal and plant cell wall biosynthesis Jensen, J.K., Busse-Wicher, M., Pulsen, C.P., Fangel, J.U., Smith, P.J., Yang, J-Y., Pena, M.J., Dinesen, M.H., Martens, H.J., Melkonian, M., Wong, G.K-S., Moremen, K.W., Wilkerson, C.G., Scheller, H.V., Dupree, P., Ulvskov, P., Urbanowicz, B.R., Harholt, J.
23 2018-04-17 Energy and Environmental Science Thermochemical wastewater valorization via enhanced microbial toxicity tolerance Jayakody, L.N., Johnson, C.W., Whitham, J.M., Giannone, R.J., Black, B.A., Cleveland, N.S., Klingeman, D.M., Michener, W.E., Olstad, J.L., Vardon, D.R., Brown, R.C., Brown, S.D., Hettich, R.L., Guss, A.M., Beckham, G.T.
22 2018-04-18 Metabolic Engineering Communications Identification of parallel and divergent optimization solutions for homologous metabolic enzymes Standaert, R.F., Giannone, R.J., Michener, J.K.
21 2018-05-11 Biotechnology and Bioengineering Building a genome engineering toolbox in nonmodel prokaryotic microbes Freed, E., Fenster, J., Smolinski, S.L., Walker, J., Henard, C.A., Gill, R., Eckert, C.A.
20 2015-06-05 The Plant Cell A 5-enolpyruvylshikimate 3-phosphate synthase functions as a transcriptional repressor in Populus Xie, M., Muchero, W., Bryan, A.C., Yee, K., Guo, H-B., Zhang, J., Tschaplinski, T.J., Singan, V.R., Lindquist, E., Payyavula, R.S., Barros-Rios, J., Dixon, R., Engle, N., Sykes, R.W., Davis, M., Jawdy, S.S., Gunter, L.E., Thompson, O., DiFazio, S.P., Evans, M., Winkeler, K., Collins, C., Schmutz, J., Guo, H., Kalluri, U., Rodriguez, M., Feng, K., Chen, J-G., Tuskan, G.A.
19 2018-06-19 Biotechnology Journal CRISPR-enabled tools for engineering microbial genomes and phenotypes Tarasava, K., Oh, E.J., Eckert, C.A., Gill, R.T.
18 2018-07-02 New Phytologist Elicitors and defense gene induction in plants with altered lignin compositions Gallego-Giraldo, L., Pose, S., Pattathil, S., Peralta, A.G., Hahn, M.G., Ayre, B.G., Sunuwar, J., Herandez, J., Patel, M., Shah, J., Rao, X., Knox, J.P., Dixon, R.A.
17 2018-07-02 Genes, Genomes and Genetics A variable polyglutamine repeat affects subcellular localization and regulatory activity of a Populus ANGUSTIFOLIA protein Bryan, A.C., Zhang, J, Guo, J., Ranjan, P., Singan, V., Barry, K., Schmutz, J., Weighill, D., Jacobson, D., Jawdy, S., Tuskan, G.A., Chen, J-C., Muchero, W.
16 2018-07-02 Genes, Genomes and Genetics Accuracy of genomic prediction for foliar terpene traits in eucalyptus polybractea Kainer, D., Stone, E.A., Padovan, A., Foley, W.J., Kulheim, C.
15 2018-06-14 Journal of Industrial Microbiology and Biotechnology Deletion of the Clostridium thermocellum recA gene reveals that it is required for thermophilic plasmid replication but not plasmid integration at homologous DNA sequences Groom, J., Chung, C., Kim, S-K., Guss, A., and Westpheling, J.
13 2018-04-12 PLOS One The redox-sensing protein Rex modulates ethanol production in Thermoanaerobacterium saccharolyticum Zheng, T., Lanahan, A.A., Lynd, L.R., Olson, D.G.
12 2018-04-06 Frontiers in Energy Research Pleiotropic and Epistatic Network-Based Discovery: Integrated Networks for Target Gene Discove Weighill, D., Sykes, R., Zhao, N., Martin, M., DiFazio, S., Tschaplinski, T., Tuskan, G.A, Jacobson, D., Macaya Sanz, D., Sreedasyam, A., Schmutz, J., Muchero, W., Ranjan, P., Shah, M., Jones, P.
11 2018-03-19 Frontiers in Plant Science Current Models for Transcriptional Regulation of Secondary Cell Wall Biosynthesis in Grasses Rao, X., Dixon, R.A.
10 2018-01-31 ChemBioChem Analyzing Xyloglucan Endotransglycosylases by Incorporating Synthetic Oligosaccharides into Plant Cell Walls Ruprecht, C., Dallabermardina, P., Smith, P.J, Urbanowicz, B.R., Pfrengle, F.
9 2018-04-11 ACS Sustainable Chemistry & Engineering Fast Fractionation of Technical Lignins by Organic Cosolvents Yun-Yan Wang, Mi Li, Charles E. Wyman, Charles M. Cai, Arthur J. Ragauskas
8 2018-04-10 Green Chemistry Recent advances in understanding the pseudo-lignin formation in a lignocellulosic biorefinery Somnath D. Shinde, Xianzhi Meng, Rajeev Kumarbcd, Arthur J. Ragauskas
7 2018-04-04 Biochemical Society Transactions Exploring the combinatorial space of complete pathways to chemicals Lin Wang, Chiam Yu Ng, Satyakam Dash, Costas D. Maranas
6 2018-03-01 Journal of Sustainable Bioenergy Systems Phenotyping Winter Dormancy in Switchgrass to Extend the Growing Season and Improve Biomass Yield Rasyidah Mohamad Razar, Ali Missaoui
5 2018-03-23 Biotechnology for Biofuels The diversity and specificity of the extracellular proteome in the cellulolytic bacterium Caldicellulosiruptor bescii is driven by the nature of the cellulosic growth substrate Poudel, S., Giannone, R.J., Basen, M., Nookaew, I., Poole II, F.L., Kelly, R.M., Adams, M.W.W., Hettich, R.L.
4 2018-02-15 ACS Sustainable Chemistry & Engineering Significance of lignin S/G ratio in biomass recalcitrance of Populus trichocarpa variants for bioethanol production Yoo, C.G., Dumitrache, A., Muchero, W., Natzke, J., Akinosho, H., Li, M., Sykes, R.W., Brown, S.D., Davison, B.H., Tuskan, G.A., Pu, Y., Ragauskas, A.J.
3 2018-02-12 Nature Biotechnology Sugar release and growth of biofuel crops are improved by downregulation of pectin biosynthesis Biswal, A.K., Atmodjo, M.A., Li, M., Baxter, H.L., Yoo, C.G., Pu, Y.J., Lee, Y-C., Mazarei, M., Black, I.M., Zhang, J-Y., Ramanna, H., Bray, A.L., King, Z.R., LaFayette, P.R., Pattathil, S., Donohoe, B.S., Mohanty, S.S., Ryno, D., Yee, K., Thompson, O.A.,
2 2018-02-06 Biotechnology for Biofuels High activity CAZyme cassette for improving biomass degradation in thermophiles Roman Brunecky, Daehwan Chung, Nicholas S. Sarai, Neal Hengge, Jordan F. Russell, Jenna Young, Ashutosh Mittal, Patthar Pason, Todd Vander Wall, William Michener, Todd Shollenberger, Janet Westpheling, Michael E. Himmel and Yannick J. Bomble
1 2018-01-12 Nature Comunications Pathway design using de novo steps through uncharted biochemical spaces Akhil Kumar , Lin Wang, Chiam Yu Ng, Costas D. Maranas