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


Date Published Publication Title Authors
2019-09-17 Frontiers in Plant Science Finding new cell wall regulatory genes in Populus trichocarpa using multiple lines of evidence Furches, A., Kainer, D., Weighill, D., Large, A., Jones, P., Walker, A.M., Romero, J., Gazolla, J.G.F.M., Joubert, W., Shah, M., Streich, J., Ranjan, P., Schmutz, J., Sreedasyam, A., Macaya-Sanz, D., Zhao, N., Martin, M.Z., Rao, X., Dixon, R.A., DiFazio,
2019-09-11 The Plant Journal Enzymatic basis for C-lignin monomer biosynthesis in the seed coat of Cleome hassleriana Zhuo, C., Rao, X., Azad, R., Pandey, R., Xiao, X., Harkelroad, A., Wang, X., Chen, F., and Dixon, R.A.
2019-09-11 Plant Physiology Ectopic defense gene expression is associated with growth defects in medicago thrncatula lignin pathway mutants Ha, C.M., Fine, D., Bhatia, A., Rao, X., Martin, M.Z., Engle, N.L., Wherritt, D.J., Tschaplinski, T.J.; Sumner, L.W., and Dixon, R.A.
2019-09-10 PNAS Enabling microbial syringol conversion through structure-guided protein engineering Machovina, M.M., Mallinson, S.J.B., Knott, B.,C., Meyers, A.W., Garcia-Borras, M., Bu, L., Gado, J.E., Oliver, A., Schmidt, G.P., Hinchen, D.J., Crowley, M.F., Johnson, C.W., Neidle, E.L., Payne, C.M., Houk, K. N., Beckham, G.T., McGeehan , J.E., and DuB
2019-09-10 Journal of Experimental Biology CRISPR/Cas9-mediated targeted mutagenesis for functional genomics research of crassulacean acid metabolism plants Liu, D., Chen, M., Mendoza, B., Cheng, H., Hu, R., Li, L., Trinh, C.T., Tuskan, G.A.
2019-09-10 Journal of Experimental Biology Comparative genomics can provide new insights into the evolutionary mechanisms and genefunction in CAM plants Yang, X., Liu, D., Tschaplinski, T.J., and Tuskan, G.A.
2019-09-05 PLOS Computational Biology From escherichia coli mutant 13C labeling data to a core kinetic model: A kinetic model parameterization pipeline Foster, C. J., Gopalakrishnan, S., Antoniewicz, M. A., Maranas, C.D.
2019-09-05 Processes Predicting the longitudinally and radially varying gut microbiota composition using multi-scale microbial metabolic modeling Chan, S.H.J., Friedman, E.S., Wu, G.D., and Maranas, C.D.
2019-09-05 Frontiers in Genetics Data integration in Poplar: 'Omics layers and integration strategies Weighill, D., Tschaplinski, T.J., Tuskan, G.A., and Jacobson, D.A.
2019-09-04 Plant Biotechnology Journal Overexpression of a Prefoldin β subunit gene reduces biomass recalcitrance in the bioenergy crop Populus Zhang, J., Li, M., Ding, J., Pu, Y ., Bryan, A., Rottmann, W., Winkeler, K., Collins, C., Singan, V., Lindquist, E., Jawdy, S., Gunter, L., Engle, N., Yang, X., Barry, K., Tschaplinski, T., Schmutz, J., Tuskan, G.A., Muchero, W., and Chen, J-G.
2019-09-04 Processes Comparison of multi-objective evolutionary algorithms to solve the modular cell design problem for novel biocatalysis Garcia, S., and Trinh, C.T.
2019-09-04 Biotechnology for Biofuels Performance of three delignifying pretreatments on hardwoods: hydrolysis yields Bhalla, A., Cai, C.M., Xu, F., Singh, S., Bansal, N., Phongpreecha, T., Dutta, T., Foster, C.E., Kumar, R., Simmons, B., Singh, S., Wyman, C.E., Hegg, E.L., and Hodge, D.B.
2019-08-23 Acta Biochimica et Biophysica Sinica Co-expression networks for plant biology: why and how Rao, X., and Dixon, R.A.
2019-08-09 Nature Protocols Determination of hydroxyl groups in biorefinery resources via quantitative 31P NMR spectroscopy Meng, X., Crestini, C., Ben, H., Hao, N., Pu, Y., Ragauskas, A.J., and Argyropoulos, D.S.
2019-08-08 Microbiology Research Announcements Complete genome sequence of Caloramator sp. Strain E03, a novel ethanologenic, thermophilic, obligately anaerobic bacterium Hatmaker, E.A., Klingeman, D.M., Martin, R.K., Guss, A.M., and Elkins, J.G.
2019-08-08 Microbiology Research Announcements Complete genome sequence of Caloramator sp. Strain E03, a novel ethanologenic, thermophilic, obligately anaerobic bacterium Hatmaker, E.A., Klingeman, D.M., Martin, R.K., Guss, A.M., and Elkins, J.G.
2019-07-31 Journal of the American Chemical Society A multifunctional cosolvent pair reveals molecular principles of biomass deconstruction Patri, A.S., Mostofian, B., Pu, Y., Ciaffone, N., Soliman, M., Smith, M.D., Kumar, R., Cheng, X., Wyman, C.E., Tetard, L., Ragauskas, A.J., Smith, J.C., Petridis, L., and Cai, C.M.
2019-07-30 Journal of Industrial Microbiology and Biotechnology Rational development of transformation in Clostridium thermocellum ATCC 27405 via complete methylome analysis and evasion of native restriction-modification systems Riley, L.A., Ji, L., Schmitz, R.J., Westpheling, J., and Guss, A.M.
2019-07-24 Nature Communications Differences in S/G ratio in natural poplar variants do not predict catalytic depolymerization monomer yields Anderson, E.M., Stone, M.L., Katahira, R., Reed, M., Muchero, W., Ramirez, K.J., Beckham, G.T., and Roman-Leshkov, Y.
2019-07-24 Frontiers in Plant Science Plant host-associated mechanisms for microbial selection Jones, P., Garcia, B.J., Furches, A., Tuskan, G.A., and Jacobson, D.
2019-07-24 Biotechnology for Biofuels Metabolic engineering of Clostridium thermocellum for n-butanol production from cellulose Tian, L., Conway, P.M., Cervenka, N.D., Cui, J., Maloney, M., Olson, D.G., and Lynd, L.R.
2019-07-18 Trends in Biotechnology Accelerating climate resilient plant breeding by applying next-generation artificial intelligence Harfouche, A.L., Jacobson, D.A., Kainer, D., Romero, J.C., Harfouche, A.H., Mugnozza, G.S., Moshelion, M., Tuskan, G.A., Keurentjes, J.J.B., and Altman, A.
2019-07-16 Metabolic Engineering Thermodynamic analysis of the pathway for ethanol production from cellobiose in Clostridium thermocellum Dash, S., Olson, D.G., Chan, S.H.J., Amador-Noguez, D., Lynd, L.R., and Maranas, C.D.
2019-07-16 Nature Methods EcoFABs: advancing microbiome science through standardized fabricated ecosystems Zengler, K., Hofmockel, K., Baliga, N.S., Behie, S.W., Bernstein, H.C., Brown, J.B., Dinneny, J.R.; Floge, S.A.; Forry, S.P., Hess, M., Jackson, S.A.; Jansson, C., Lindemann, S.R., Pett-Ridge, J., Maranas, C., Venturelli, O.S., Wallenstein, M.D., Shank, E
2019-07-16 Frontiers in Plant Science Critical review of plant cell wall matrix polysaccharide glycosyltransferase activities verified by heterologous protein expression Amos, R.A., and Mohnen, D.
2019-07-15 Nature Plants Mediation of plant-mycorrhizal interaction by a lectin receptor-like kinase Labbe, J., Muchero, W., Czarnecki, O., Wang, J., Wang, X., Bryan, A.C., Zheng, K., Yang, Y., Xie, M., Zhang, J., Wang, D., Meidl, P., Wang, H., Morrell-Falvey, J.L., Cope, K.R., Maia, L.G.S., Ane, J-M., Mewalal, R., Jawdy, S.S., Gunter, L.E., Schackwitz,
2019-07-15 Biotechnology for Biofuels CELF significantly reduces milling requirements and improves soaking effectiveness for maximum sugar recovery of Alamo switchgrass over dilute sulfuric acid pretreatment Patri, A.S., McAlister, L., Cai, C.M., Kumar, R., and Wyman, C.E.
2019-06-18 Green Chemistry Cellulolytic enzyme-aided hemicellulose extraction and its characteristics from switchgrass Ding, J., Yoo, C.G., Pu, Y., Meng, X., Bhagia, S., Yu, C., and Ragauskas, A.J.
2019-06-14 Biotechnology for Biofuels Genetic variation of biomass recalcitrance in a natural Salix viminalis (L.) population Ohlsson, J.A., Hallingback, H.R., Jebrane, M., Harman-Ware, A.E., Shollenberger, T., Decker, S.R., Sandgren, M., Ronnberg-Wastljung, A.C.
2019-06-13 Biotechnology Advances Modular design: Implementing proven engineering principles in biotechnology Garcia, S., and Trinh, C.T.
2019-06-13 Biotechnology for Biofuels Biomass augmentation through thermochemical pretreatments greatly enhances digestion of switchgrass by Clostridium thermocellum Kothari, N., Holwerda, E.K., Cai, C.M., Kumar, R., and Wyman, C.E.
2019-06-11 Phytobiomes Journal More than serendipity: the potential to manage soil carbon and emissions while promoting low-input agriculture with serendipitoid mycorrhizae Craven, K., and Ray, P.
2019-06-10 Joule Innovative chemicals and materials from bacterial aromatic catabolic pathways Johnson, C. W., Salvachua, D., Rorrer, N.A., Black, B.A., Vardon, D.R., St. John, P.C., Cleveland, N.S., Dominick, G., Elmore, J.R., Grundl, N., Khanna, P., Martinez, C.R., Michener, W.E., Peterson, D.J., Ramirez, K.J., Singh, P., Vander Wall, T.A., Wilso
2019-06-10 Bioresource Technology Investigating the correlation of biomass recalcitrance with pyrolysis oil using poplar as the feedstock Lu, K., Hao, N., Meng, X., Luo, Z., Tuskan, G.A., and Ragauskas, A.J.
2019-06-03 PNAS Integration of renewable deep eutectic solvents with engineered biomass to achieve a closed-loop biorefinery Kim, K.H., Eudes, A., Jeong, K., Yoo, C.G., Kim, C.S., and Ragauskas, A.J.
2019-05-14 New Phytologist High marker density GWAS provides novel insights into the genomic architecture of terpene oil yield in Eucalyptus Kainer, D., Padovan, A., Degenhardt, J., Krause, S., Mondal, P., Foley, W.J., and Kulheim, C.
2019-05-14 Green Chemistry Cellulose hydrolysis by Clostridium thermocellum is agnostic to substrate structural properties in contrast to fungal cellulases Kothari, N., Bhagia, S., Zaher, M., Pu, Y., Mittal, A., Yoo, C.G., Himmel, M.E., Ragauskas, A.J., Kumar, R., and Wyman, C.E.
2019-05-14 Biotechnology for Biofuels Combining loss of function of folypolyglutamate synthetase1 and cafeoyl-coa 3-0-methyltransferase1 for lignin reduction and improved saccharification efficiency in Arabidopsis thaliana Xie, H., Engle, N.L., Venketachalam, S., Yoo, C.G., Barros, J., Lecoultre, M., Howard, N., Li, G., Sun, L., Srivastava, A.C., Pattathil, S., Pu, Y., Hahn, M.G., Ragauskas, A.J., Nelson, R.S., Dixon, R.A., Tschaplinski, T.J., Blancaflor, E.B., and Tang, Y.
2019-05-13 Nature Communications 4-Coumarate 3-hydroxylase in the lignin biosynthesis pathway is a cytosolic ascorbate peroxidase Barros, J., Escamilla-Trevino, L., Song, L., Rao, X., Serrani-Yance, J.C., Palacios, M.D., Engle, N., Choudhury, F.K., Tschaplinski, T.J., Venables, B.J., Mittler, R., and Dixon, R.A.
2019-05-10 Frontiers in Genetics Multi-phenotype association decomposition: unraveling complex gene-phenotype relationships Weighill, D., Jones, P., Bleker, C., Ranjan, P., Shah, M., Zao, N., Martin, M., DiFazio, S., Macaya-Sanz, D., Schmutz, J., Sreedasyam, A., Tschaplinski, T., Tuskan, G., and Jacobson, D.
2019-05-01 Frontiers in Genetics Wavelet-based Genomic Signal Processing for Centromere Identification and Hypothesis Generation Weighill, D., Macaya-Sanz, D., DiFazio, S.P., Joubert, W., Shah, M., Schmutz, J., Sreedasyam, A., Tuskan, G., and Jacobson, D.
2019-04-25 Processes Modular engineering of biomass degradation pathways Chaves, J.E., Presley, G.N., and Michener, J.K.,
2019-04-23 BioTechnology for Biofuels Impacts of cellulase deactivation at the moving air-lizuid interface on cellulose conversions ata low enzyme loadings Bhagia, S., Wyman, C.E., and Kumar, R.
2019-04-17 Environmental Microbiology Reports Scavenging organic nitrogen and remodeling lipid metabolism are key survival strategies adopted by the endophytic fugi, Serendipita vermifera and Serendipita bescii to alleviate nitrogen and phosphorous starvation in vitro Ray, P., Abraham, P.E., Guo, Y., Giannone, R.J., Engle, N.L., Yang, Z.K., Jacobson, D.J., Hettich, R.L., Tschaplinski, T.J., and Craven, K.D.,
2019-04-08 FASEB Journal A new model for the biochemistry of pectin synthesis: GAUTs synthesize diverse HG glycans in structurally and functionally distinct plant cell wall polymers Mohnen, D., Amos, R.A., Biswal, A.K., Engle, K.A., Ryno, Mohanty, S.S., and Atmodjo, Melani A.
2019-04-05 Frontiers in Plant Science Engineering tree seasonal cycles of growth through chromatin modification Conde, D., Perales, M., Sreedasyam, A., Tuskan, G.A., Lloret, A., Badenes, M.L., Gonzalez-Melendi, P., Rios, G., and Allona, I.,
2019-03-27 Current Opinion in Biotechnology Population-level approaches reveal novel aspects of lignin biosynthesis, content, composition and structure Tuskan, G.A., Muchero, W., Tschaplinski, T.J., and Ragauskas, A.J.
2019-03-19 Scientific Reports Pareto optimality explanation of the glycolytic alternatives in nature Ng. C.Y., Wang, L., Chowdhury, A., and Maranas, C.D.
2019-03-13 New Phytologist Multi-trait genome-wide association analysis ofPopulus trichocarpa identifies key polymorphisms controlling morphological ad physiological traits Chhetri, H.B., Macaya-Sanz, D., Kainer, D., Biswal, A.K., Evans, L.M., Chen, J-G., Collins, C., Hunt, K., Mohanty, S.S., Rosenstiel, T., Ryno, D., Winkeler, K., Yang, X., Jacoson, D., Mohnen, D., Muchero, W., Strauss, S.H., Tschaplinski, T.J., Tuskan, G.A
2019-03-07 Green Chemistry A critical review on the analysis of lignin carbohydrate bonds Giummarella, N., Pu, Y., Ragauskas, A.J., and Lawoko, M.
2019-03-05 Frontiers in Plant Science Comparative genomics analysis provides new insight into molecular basis of stomatal movement in Kalanchoe fedtschenkoi Moseley, R.C., Tuskan, G.A., and Yang, X.
2019-03-05 Journal of Industrial Microbiology and Biotechnology Heterologous co-expression of two β-glucanases and a cellobiose phosphorylase resulted in a significant increase in the cellulolytic activity of the Caldicellulosiruptor bescii exoproteome Kim, S.K., Chung, D., Himmel, M.E., Bomble, Y.J., and Westpheling, J
2019-03-05 Biotechnology for Biofuels Creation of a functional hyperthermostable designer cellulosome Kahn, A., Morais, S., Galanopoulou, A.P., Chung, D., Sarai, N.S., Hengge, N., Hatzinikolaou, D.G., Himmel, M.E., Bomble, Y.J., and Bayer, E.A.
2019-02-11 Scientific Reports A mutation in the AdhE alcohol dehydrogenase of Clostridium thermocellum increases tolerance to several primary alcohols, including isobutanol, n-butanol and ethanol Tian, L., Cervenka, N.D., Low, A.M., Olson, D.G., and Lynd, L.R.,
2019-02-05 Tree Genetics and Genomes Genome-wide association studies of bark texture in Populus trichocarpa Bdeir, R., Muchero, W., Yordanov, Y., Tuskan, G.A., Busov, V., and Gailing, O.
2019-02-01 Nature Plants The unexpected malleability of lignin Tuskan, G.A., Groover, A.T., Schmuta, J., DiFazio, S.P., Myburg, A., Grattapaglia, D., Smart, L., Yin, Y., Aury, J-M., Kremer, A., Leroy, T., Provost, G.L., Plomion, C., Carlson, J.E., Randall, J., Westbrook, J., Grimwod, J., Muchero, W., Jacobson, D., an
2019-02-01 Annals of Botany The nature of the progression of drought stress drives differential metabolomic responses in Populus deltoides Tschaplinski, T.J., Abraham, P.E., Jawdy, S.S., Gunter, L.E., Martin, M.Z., Engle, N.L., Yang, X., and Tuskan, G.A.
2019-02-01 ACS Sustainable Chemistry and Engineering Glycosylation is vital for industrial performance of hyperactive cellulases Chung, D., Sarai, N.S., Knott, B.C., Hengge, N., Russell, J.F., Yarbrough, J.M., Brunecky, R., Young, J., Supekar, N., Vander Wall, T., Sammond, D.W., Crowley, M.F., Szymanski, C.M., Wells, L., Azadi, P., Westpheling, J., Himmel, M.E., and Bomble, Y.J.
2019-01-25 Advances in Botanical Research Molecular Physiology and Biotechnology of Trees Cell wall pectins in tree growth and woody biomass utilization Harding, S.A., and Tsai, C.J.
2019-01-18 Biotechnology for Biofuels Multiple levers for overcoming the recalcitrance of lignocellulosic biomass Holwerda, E.K., Worthen, R.S., Kothari, N., Lasky, R.C., Davison, B.H., Fu, C., Wang, Z.Y., Dixon, R.A., Biswal, A.J., Mohnen, D., Nelson, R.S., Baxter, H.L., Mazarei, M., Stewart, C. N., Muchero, W., Tuskan, G.A., Cai, C.M., Gjersing, E.E., Davis, M.F.,
2019-01-17 Communication Biology Downregulation of pectin biosynthesis gene GAUT4 leads to reduced ferulate and lignin-carbohydrate cross-linking in switchgrass Li, M., Yoo, C.G., Pu, Y., Biswal, A.K., Tolbert, A.K., Mohnen, D., and Ragauskas, A.J.
2019-01-17 Microbiology Resource Annoucements Complete genome sequences of two megasphaera elsdenii strains, NCIMB 702410 and ATCC 25940 Hatmaker, E.A., Klingeman, D.M., O'Dell, K.B., Riley, L.A., Papanek, B., and Guss, A.M.
2018-12-18 ACS Sustainable Chemistry and Engineering Automated transformation of lignin topologies into atomic structures with LigninBuilder Vermaas, J.V., Dellon, L., Broadbelt, L.J., Beckham, G.T., and Crowley, M.F.
2018-12-18 Phytobiomes Journal Phytobiome and transcriptional adaptation of Populus deltoides to acute progressive drought and cyclic drought Garcia, B.J., Labbe, J., Jones, P., Abraham, P., Hodge, I., Climer, S., Jawdy, S., Gunter, L., Tuskan, G., Yang, X., Tschaplinski, T., and Jacobson, D.J.
2018-12-10 Bioresource Technology Understanding the influences of different pretreatments on recalcitrance of Populus natural variants Yao, L., Yang, H., Yoo, C.G., Pu, Y., Meng, X., Muchero, W., Tuskan, G.A., Tschaplinski, T.J., and Ragauskas, A.J.
2018-12-10 Bioinformatics Acelerating flux balance calculations in genome-scale metabolic models by localizing the application of loopless constraints Chan, S.H.J., Wang, L., Dash, S., and Maranas, C.D.,
2018-12-10 SC18 Attacking the opioid epidemic: determining the epistatic and pleiotropic genetic architectures for chronic pain and opioid addiction Joubert, W., Weighill, D., Kainer, D., Climer, S., Justice, A., Fagnan, K., and Jacobson, D.
2018-12-10 Green Chemistry Systematic parameterization of lignin for the CHARMM force field Vermaas, J.V., Petridis, L., Ralph, J., Crowley, M.F., and Beckham, G.T.
2018-12-10 Current Protocols in Microbiology Isolation and whole-genome sequencing of environmental campylobacter Kelley, B.R., Ellis, J.C., Hyatt, D., Jacobson, D., and Johnson J.
2018-12-04 Plant Physiology Lignin biosynthesis and control of lignin composition Chen, F.
2018-11-27 Frontiers in Plant Science Hardwood tree genomics: Unlocking woody plant biology Tuskan, G.A., Groover, A.T., Schmuta, J., DiFazio, S.P., Myburg, A., Grattapaglia, D., Smart, L., Yin, Y., Aury, J-M., Kremer, A., Leroy, T., Provost, G.L., Plomion, C., Carlson, J.E., Randall, J., Westbrook, J., Grimwod, J., Muchero, W., Jacobson, D., an
2018-11-27 Frontiers in Plant Science Genome editing in trees: from multiple repair pathways to long-term stability Bewg, W.P., Ci, D., and Tsai, C-J.
2018-11-19 Frontiers in Plant Science Conservation and diversification of circadian rhythmicity between a model crassulacean acid metabolism plant kalanchoe fedtschenkoi and a model C3 photosynthesis plant arabidopsis thaliana Moseley, R.C., Mewalal, R., Motta, F., Haase, S., Tuskan, G.A., and Yang, X.
2018-11-08 Frontiers in Energy Research Editorial: Advancements in biomass recalcitrance: The use of lignin for the production of fuels and chemicals Ragauskas, A.J., and Yoo, C.G.
2018-11-08 Biotechnology for Biofuels Fractionation and characterization of lignin streams from unique high-lignin content endocarp feedstocks Li, W., Amos, K., Pu, Y., Debolt, S., Ragauskas, A.J., and Shi, J.
2018-11-07 Bioresource Technology Characterization of fractional cuts of co-solvent enhanced lignocellulosic fractionation lignin isolated by sequential precipitation Meng, X., Parikh, A., Seemala, B., Kumar, R., Pu, Y., Wyman, C.E., Cai, C.M., and Ragauskas, A.J.
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
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.
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.
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.
2018-10-16 Journal of Biological Chemistry A two-phase model for the non-processive biosynthesis of homogalacturonan polysaccharides by the GAUT1:GAUT7 complex Amos, R.A., Pattathil, S., Yang, J-Y., Atmodjo, M.A., Urbanowicz, B.R., Moremen, K.W., and Mohnen, D.
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
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.
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.
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.
2018-10-02 Current Opinion in Biotechnology Development and commercialization of reduced lignin alfalfa Barros, J., Temple, S., Dixon, R.A.
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.
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.
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.
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.
2018-09-19 Bioresource Technology From lignin to valuable products-strategies, challenges, and prospects Wang, H., Pu, Y., Ragauskas, A.J., Yang, B.
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.
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.
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.
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.
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.
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.
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.
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.
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
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.
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.
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.
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.
2018-07-30 Current Protocols Environmental isolation and whole-genome sequencing of Campylobacter Kelley, B.R., Ellis, J., Hyatt, D., Jacobson, D., Johnson, J.
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.
2018-07-20 Metabolic Engineering Multiobjective strain design: a framework for modular cell engineering Garcia, S., and Trinh, C.T.
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.
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.
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.
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.
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.
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.
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.
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.
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.
2018-06-05 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.
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.
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.
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.
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.
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
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
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.
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
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.
2018-03-19 Frontiers in Plant Science Current Models for Transcriptional Regulation of Secondary Cell Wall Biosynthesis in Grasses Rao, X., Dixon, R.A.
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
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.
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.
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.
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.,
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
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.
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.
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