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
2020-11-12 The Journal of Physical Chemistry B The catalytic mechanism of aryl-ether bond cleavage in lignin by LigF and LigG Teixeira Prates, E., Crowley, M.F., Skaf, M.S., and Beckham, G.T.
2020-10-25 Bioresources Physicochemical changes of cellulose and their influences on Populus trichocarpa digestibility after different pretreatments Yao, L., Yoo, C-G., Pu, Y., Meng, X., Muchero, W., Tuskan, G.A., Tschaplinski, T.J., Ragauskas, A.J., and Yang, H.
2020-10-01 ACS Sustainable Chemistry & Engineering Mechanistic Insight into Lignin Slow Pyrolysis by Linking Pyrolysis Chemistry and Carbon Material Properties Wenqi Li, Namal Wanninayake, Xin Gao, Mi Li, Yunqiao Pu, Doo-Young Kim, Arthur J. Ragauskas, and Jian Shi
2020-09-28 Appl Environ Microbiol Deletion of a Peptidylprolyl Isomerase Results in the Inability of Caldicellulosiruptor besciito Grow on Crystalline Cellulose without Affecting Protein Glycosylation Jordan F. Russell, Matthew L. Russo, Xuewen Wang, Neal Hengge, Daehwan Chung, Lance Wells, Yannick J. Bomble, Janet Westpheling
2020-09-28 Ecology and Evolution Host plant genetic control of associated fungal and insect species in a Populus hybrid cross Sandra J. Simon, Timothy J. Tschaplinski, Jared M. LeBoldus, Ken Keefover‐Ring, Muhammad Azeem, Jin‐Gui Chen, David Macaya‐Sanz, William L. MacDonald, Wellington Muchero, Stephen P. DiFazio
2020-09-27 Applied and Environmental Microbiology Metabolic fluxes of nitrogen and pyrophosphate in chemostat cultures of Clostridium thermocellum and Thermoanaerobacterium saccharolyticum Evert K. Holwerda, Jilai Zhou, Shuen Hon, David M. Stevenson, Daniel AmadorNoguez, Lee R. Lynd, Johannes P. van Dijken
2020-09-27 Environmental Biology Serendipita bescii promotes winter wheat growth and modulates host root transcriptome under phosphorus and nitrogen starvation Prasun Ray, Yingqing Guo, Myoung‐Hwan Chi, Nick Krom, Malay C. Saha, Kelly D. Craven
2020-09-27 Frontiers in Plant Science Pectin Synthesis and Pollen Tube Growth in Arabidopsis Involves Three GAUT1 Golgi-Anchoring Proteins: GAUT5, GAUT6, and GAUT7 Christian Have Lund, Anne Stenbæk, Melani A. Atmodjo, Randi Engelberth Rasmussen, Isabel E. Moller, Simon Matthé Erstad, Ajaya Kumar Biswal, Debra Mohnen, Jozef Mravec, Yumiko Sakuragi
2020-09-27 Plant Direct Defoliation-induced compensatory transpiration is compromised in SUT4-RNAi Populus Scott A. Harding, Christopher J. Frost, Chung‐Jui Tsai
2020-09-22 Computational and Structural Biotechnology Journal Computational biophysical characterization of the SARS-CoV-2 spike protein binding with the ACE2 receptor and implications for infectivity Ratul Chowdhury, Veda Sheersh Boorla, and Costas D. Maranas
2020-09-22 Cell Press - Structure IPRO+/−: Computational Protein Design Tool Allowing for Insertions and Deletions+C236 Ratul Chowdhury, Matthew J. Grisewood, Veda Sheersh Boorla, Qiang Yan, Brian F. Pfleger, Costas D. Maranas
2020-09-22 biorxiv De novo design of high-affinity antibody variable regions (Fv) against the SARS-CoV-2 spike protein Veda Sheersh Boorla, Ratul Chowdhury, Costas D. Maranas
2020-09-22 Nature Microbiology Bacterial colonization reprograms the neonatal gut metabolome Kyle Bittinger, Chunyu Zhao, Yun Li, Eileen Ford, Elliot S. Friedman, Josephine Ni, Chiraag V. Kulkarni, Jingwei Cai, Yuan Tian, Qing Liu, Andrew D. Patterson, Debolina Sarkar, Siu H. J. Chan, Costas Maranas, Anumita Saha-Shah, Peder Lund, Benjamin A. Gar
2020-09-21 GCB Bioenergy Genome-wide QTL detection for biofuel traits in switchgrass (Panicum virgatum L.) Shahjahan Ali, Desalegn D. Serba, Dennis Walker, Jerry Jenkins, Jeremy Schmutz, Suresh Bhamidimarri, Malay C. Saha
2020-09-16 BioDesign Research Reconfiguring Plant Metabolism for Biodegradable Plastic Production Haiwei Lu, Guoliang Yuan, Steven H. Strauss, Timothy J. Tschaplinski, Gerald A. Tuskan, Jin-Gui Chen, Xiaohan Yang
2020-09-10 Frontiers Bioengineering and Biotechnology Development of an updated genome-scale metabolic model of Clostridium thermocellum and its application for integration of multi-omics datasets and modular cell design Sergio Garcia, R. Adam Thompson, Richard J. Giannone, Satyakam Dash, Costas D. Maranas, Cong T. Trinh
2020-08-31 PNAS Robust paths to net greenhouse gas mitigation and negative emissions via advanced biofuels John L. Field, Tom L. Richard, Erica A. H. Smithwick, Hao Cai, Mark S. Laser, David S. LeBauer, Stephen P. Longh, Keith Paustiana, Zhangcai Qine, John J. Sheehann, Pete Smith, Michael Q. Wang, Lee R. Lynd
2020-08-31 Frontiers in Plant Science Genome-Wide Association Study of Wood Anatomical and Morphological Traits in Populus trichocarpa Hari B. Chhetri, Anna Furches, David Macaya-Sanz, Alejandro R. Walker, David Kainer, Piet Jones, Anne E. Harman-Ware, Timothy J. Tschaplinski, Daniel Jacobson, Gerald A. Tuskan, Stephen P. DiFazio
2020-08-31 ChemSusChem Emerging Strategies for Modifying Lignin Chemistry to Enhance Biological Lignin Valorization Zhi-Min Zhao, Zhi-Hua Liu, Yunqiao Pu, Xianzhi Meng, Jifei Xu, Joshua S. Yuan, Arthur J. Ragauskas
2020-08-28 Current Opinion in Chemical Engineering Metabolic flux analysis reaching genome wide coverage: lessons learned and future perspectives Hendry, J.I., Dinh, H.V., Foster, C., Gopalakrishnan, S., Wang, L., Maranas, C.D.
2020-08-26 BMC Plant Biology QTL mapping of winter dormancy and associated traits in two switchgrass pseudo-F1 populations: lowland x lowland and lowland x upland Rasyidah Mohamad, Razar, Ali Missaoui
2020-08-26 GCB Bioenergy 21st‐century biogeochemical modeling: Challenges for Century‐based models and where do we go from here? Danielle Berardi, Edward Brzostek, Elena Blanc-Betes, Brian Davison, Evan H. DeLucia, Melannie D. Hartman, Jeffrey Kent, William J. Parton, Debasish Saha, Tara W. Hudiburg
2020-08-06 Metabolic Pathway Engineering  Methods for Metabolic Engineering of Thermoanaerobacterium saccharolyticum Hon, S., Tian, L., Zheng, T., Cui, J., Lynd, L.R., Olson, D.G.
2020-08-04 mSystems Plant Hosts Modify Belowground Microbial Community Response to Extreme Drought "Veach A.M., Chen H., Yang Z.K., Labbe A.D., Engle N.L., Tschaplinski T.J., Schadt C.W., Cregger M.A."
2020-07-30 ACS Sustainable Chemistry & Engineering ACS Sustainable Chemistry & Engineering Virtual Special Issue on Recent Advances in Biomass Characterization and Modeling Ragauskas, A.J., Meng, X.
2020-07-30 ACS Sustainable Chemistry & Engineering Enzymatic Synthesis of Artificial Polysaccharides for Materials Applications Smith, P.J., Ortiz-Soto, M.E., Roth, C., Barnes, W.J., Seibel, J., Urbanowicz, B.R., Pfrengle, F.
2020-07-28 New Phytologist Arabidopsis C‐terminal Binding Protein ANGUSTIFOLIA modulates transcriptional co‐regulation of MYB46 and WRKY33 Xie, M., Zhang, J., Yao, T., Bryan, A.C., Pu, Y., Labbé, J., Pelletier, D.A., Engle, N., Morrell‐Falvey, J.L., Schmutz, J., Ragauskas, A.J., Tschaplinski, T.J., Chen, F., Tuskan, G.A., Muchero, W. and Chen, J.‐G.
2020-07-28 PNAS Deconstruction of biomass enabled by local demixing of cosolvents at cellulose and lignin surfaces Pingali, S.V., Smith, M.D., Liu, S.H., Rawal, T.B., Pu, Y., Shah, R., Evans B.R., Urban, V.S., Davison, B.H., Cai, C.M., Ragauskas, A.J., O’Neill, H.M, Smith, J.C., Petridis, L.
2020-07-28 Genes Sequencing and Analysis of the Sex Determination Region of Populus trichocarpa Zhou, R., Macaya-Sanz, D., Schmutz, J., Jenkins, J.W., Tuskan, G.A., DiFazio, S.P.
2020-07-09 Frontiers in Bioengineering and Biotechnology Synthetic Biology and Metabolic Engineering Employing Escherichia coli for C2–C6 Bioalcohol Production Liang L., Liu R., Freed, E.F., Eckert, C.A.
2020-07-07 Microbiology Resource Announcements Methylome and Complete Genome Sequence of Parageobacillus toebii DSM 14590T, a Thermophilic Bacterium Hatmaker, E.A., O’Dell, K.B., Riley, L.A., Payne, I.C., Guss, A.M.
2020-07-07 Frontiers in Energy Research Effects of CELF pretreatment severity on lignin structure and the lignin-polyurethane composites properties Wang, Y.Y., Sengupta, P., Scheidemantle, B., Pu, Y., Wyman, C.E., Cai, C.M., Ragauskas, A.J.
2020-06-24 BioDesign Research Plant Biosystems Design for a Carbon-Neutral Bioeconomy Kalluri, U.C., Yang, X., Wullschleger, S.D.
2020-06-23 Frontiers in Plant Science Silencing folylpolyglutamate synthetase1 (FPGS1) in switchgrass (Panicum virgatum L.) improves lignocellulosic biofuel production Mazarei, M., Baxter, H.L., Srivastava, A., Li, G., Xie, H., Dumitrache, A., Rodriguez, M., Jr., Natzke, J.M., Zhang, J-Y., Turner, G.B., Sykes, R.W., Davis, M.F., Udvardi, M.K., Wang, Z-Y., Davison, B.H., Blancaflor, E.B., Tang, Y., Stewart, C.N., Jr.
2020-06-22 BioEnergy Research Natural Variation in Lignin and Pectin Biosynthesis-Related Genes in Switchgrass (Panicum virgatum L.) and Association of SNP Variants with Dry Matter Traits Bahri, B.A., Daverdin, G., Xu, X. et al.
2020-06-22 AIChE Journal Challenges of cultivated meat production and applications of genome‐scale metabolic modeling Suthers, P.F., Maranas, C.D.
2020-06-22 Plant Physiology Compensatory guaiacyl lignin biosynthesis at the expense of syringyl lignin in 4CL1-knockout poplar Tsai C.J., Xu, P., Xue L.J., Hu, H., Nyamdari, B., Naran, R., Zhou, X., Goeminne, G., Gao, R., Gjersing, E., Dahlen, J., Pattathil, S., Hahn, M.G., Davis, M.F., Ralph, J., Boerjan, W., Harding, S.A.
2020-06-22 Green Chemistry A biomass pretreatment using cellulose-derived solvent Cyrene Meng, X., Pu, Y., Li, M., Ragauskas, A.J.
2020-06-17 Under review - Biotechnology for Biofuels Accurate Determination of Genotypic Variance of Cell Wall Characteristics of a Populus trichocarpa Pedigree Using High-Throughput Pyrolysis-Molecular Beam Mass Spectrometry Harman-Ware, A.E., Macaya-Sans, D., Abeyratne, C.R., Doeppke, C., Haiby, K., Tuskan, G.A., Stanton, B., DiFazio, S.P., Davis, M.F.
2020-06-16 Angewandte Chemie A Glycan Array-Based Assay for the Identification and Characterization of Plant Glycosyltransferases Ruprecht, C., Bartetzko, M.P., Senf, D., Lakhina, A., Smith, P.J., Soto, M.J., Oh, H., Yang, J.‐Y., Chapla, D., Varon Silva, D., Clausen, M.H., Hahn, M.G., Moremen, K.W., Urbanowicz, B.R., Pfrengle, F.
2020-06-16 Molecules Water-Dependent Blending of Pectin Films: The Mechanics of Conjoined Biopolymers Zheng, Y., Pierce, A., Wagner, W.L., et al.
2020-06-16 Methods in Cell Biology Heterologous expression of plant glycosyltransferases for biochemistry and structural biology Prabhakar, P.K., Wang, H.T., Smith, P.J., Yang, J.Y., Barnes, W.J., Peña, M.J., Moremen, K.W., Urbanowicz, B. R.
2020-06-16 ACS Omega Nanocellulose-Based Sustainable Dyeing of Cotton Textiles with Minimized Water Pollution Liyanapathiranage, A., Peña, M.J., Sharma, S., Minko, S.
2020-06-16 ACS Synthetic Biology  Harnessing natural modularity of metabolism with goal attainment optimization to design a modular chassis cell for production of diverse chemicals Garcia, S., Trinh, C.T.
2020-06-15 Biotechnology and Bioengineering Endogenous carbohydrate esterases of Clostridium thermocellum are identified and disrupted for enhanced isobutyl acetate production from cellulose Seo, H, Nicely, PN, Trinh, CT.
2020-06-15 BMC Genomics P finder: genomic and metagenomic annotation of RNase P RNA gene (rnpB) Ellis, J.C.
2020-05-21 Front. Energy Res. Developing a Cell-Free Extract Reaction (CFER) system in Clostridium thermocellum to identify metabolic limitations to ethanol production Cui, J., Stevenson, D., Korosh, T., Amador-Noguez, D., Olson, D.G., Lynd, L.R.
2020-05-15 Polymers Lignin as a UV Light Blocker—A Review Sadeghifar, H., Ragauskas, A.
2020-05-14 Frontiers in Plant Science Transcriptional and post-transcriptional regulation of lignin biosynthesis pathway genes in Populus Zhang, J., Tuskan, G.A., Tschaplinski, T., Muchero, W.,  Chen, J.
2020-05-14 Natural Product Reports Engineering biosynthetic enzymes for industrial natural product synthesis Galanie, S., Entwistle, D., Lalonde, J.
2020-05-05 Trends in Plant Science Transgenic Poplar Designed for Biofuels Bryant, N.D., Pu, Y., Tschaplinski, T.J., Tuskan, G.A., Muchero, M., Kalluri, U.C., Yoo, C.G., Ragauskas, A.J.
2020-04-27 Nature Communications Development of a thermophilic coculture for corn fiber conversion to ethanol Beri, D., York, W.S., Lynd, L.R. et al.
2020-04-07 PNAS Outer membrane vesicles catabolize lignin-derived aromatic compounds in Pseudomonas putida KT2440 Salvachúa, D., Werner, A.Z., Pardoa, I., Michalskac, M., Black, B.A., Donohoe, B.S., Haugen, S.J., Katahira, R., Notonier, S., Ramirez, K.J, Amore, A., Purvine, S.O., Zink, E.M., Abraham, P.E., Giannone, R.J., Poudel, S., Laible, P.D., Hettich, R.L., Bec
2020-04-07 ACS Sustainable Chemistry and Engineering "Enhancing enzyme-mediated hydrolysis of mechanical pulps by deacetylation and delignification" Wu, J., Chandra, R.P., Kim, K.H., Kim, S.K., Pu, Y., Ragauskas, A.J., Saddler, J.N.
2020-04-01 Plant Cell Reports Lipofection-mediated genome editing using DNA-free delivery of the Cas9/gRNA ribonucleoprotein into plant cells Liu, W., Rudis, M.R., Cheplick, M.H., Millwood, R.J., Yang, J-P,, Ondzighi-Assoume, C.A., Montgomery, G.A., Burris, K.P., Mazarei, M., Chesnut, J.D., Stewart, C.N. Jr.
2020-04-01 Euphytica  Development and field assessment of transgenic hybrid switchgrass for improved biofuel traits Alexander, L., Hatcher, C., Mazarei, M. et al.
2020-04-01 APS Publications Nitrogen Fertilization Reduces Nitrogen Fixation Activity of Diverse Diazotrophs in Switchgrass Roots Bahulikar, R.A., Chaluvadi, S.R., Torres-Jerez, I., Mosali, J., Bennetzen, J.L., Udvardi, M.
2020-03-31 Plant Cell (in revision accepted at Plant Cell) 4/2/2020 Structure of the Xylan O-Acetyltransferase AtXOAT1 Reveals Molecular Insight into Polysaccharide Acetylation in Plants Lunin, V., Wang, H. T., Bharadwaj, V. S., Alahuhta, P., Peña, M. J., Yang, J. Y., Archer-Hartmann, S. A., Azadi, P. A., Himmel, M. E., Moremen, K. W., York, W. S. Bomble, Y. J., Urbanowicz, B. R.
2020-03-31 Biotechnology for Biofuels Gene targets for engineering osmotolerance in Caldicellulosiruptor bescii Sander, K.B., Chung, D., Klingeman, D.M. et al.
2020-03-31 Genes "A High-Performance Computing Implementation of Iterative Random Forest for the Creation of Predictive Expression Networks" Cliff, A., Romero, J., Kainer, D., Walker, A., Furches, A., Jacobson, D.
2020-03-31 SLAS Analytical Techniques for Determining the Role of Domain of Unknown Function 579 Proteins in the Synthesis of O-Methylated Plant Polysaccharides Smith, P. J., O’Neill, M. A., Backe, J., York, W. S., Peña, M. J., & Urbanowicz, B. R.
2020-03-31 Genome Biology A willow sex chromosome reveals convergent evolution of complex palindromic repeats Zhou, R., Macaya-Sanz, D., Carlson, C.H. et al.
2020-03-31 Microbial Pathogenesis Novel derivatives of plant monomeric phenolics: act as inhibitors of bacterial cell-to-cell communication Srivastava N., Tiwari S., Bhandari K., Biswal A.K., Rawat, A.K.S.
2020-03-31 The Plant Journal SNPeffect: Identifying Functional Roles of SNPs using Metabolic Networks Sarker, D., Maranas, C.
2020-03-31 Genome Biology The somatic genetic and epigenetic mutation rate in a wild long-lived perennial Populus trichocarpa Hofmeister, B.T., Denkena, J., Colomé-Tatché, M., Shahryary, Y., Hazarika, R., Grimwood, J., Mamidi, S., Jenkins, J., Grabowski, P.P., Sreedasyam, A., Shu, S., Barry, K., Lail, K., Adam, C., Lipzen, A., Sorek, R., Kudrna, D., Talag, J., Wing, R., Hall, D.
2020-03-31 The FEBS Journal Glycosylation of hyperthermostable designer cellulosome components yields enhanced stability and cellulose hydrolysis Kahn, A., Moraïs, S., Chung, D., Sarai, N.S., Hengge, N.N., Kahn, A., Himmel, M.E., Bayer, E.A., Bomble, Y.J.
2020-03-31 Biotechnology for Biofuels Metabolic and evolutionary responses of Clostridium thermocellum to genetic interventions aimed at improving ethanol production Holwerda, E.K., Olson, D.G., Ruppertsberger, N.M. et al.
2020-03-31 Bioresource Technology "The critical role of lignin in lignocellulosic biomass conversion and recent pretreatment strategies: A comprehensive review" Yoo, C.G., Meng, X., Pu, Y., Ragauskas, A.J.
2020-03-31 mSystems "In Vivo Thermodynamic Analysis of Glycolysis in Clostridium thermocellum and Thermoanaerobacterium saccharolyticum Using 13C and 2H Tracers" Jacobson TB, Korosh TK, Stevenson DM, Foster C, Maranas C, Olson DG, Lynd LR, Amador-Noguez D.
2020-03-31 Plant Physiology Targeting root ion uptake kinetics to increase plant productivity and nutrient use efficiency Griffiths, M., York, L.M.
2020-03-25 Chemistry Select 2D HSQC Chemical Shifts of Impurities from Biomass Pretreatment Bryant, N., Yoo, C., Pu, Y., Ragauskas, A.J.
2020-03-14 GigaScience Light-responsive expression atlas reveals the effects of light quality and intensity in Kalanchoë fedtschenkoi, a plant with crassulacean acid metabolism Zhang, J. Hu, R., Sreedasyam, A., Garcia, T., Lipzen, A., Wang, M., Yerramsetty, P., Liu, D., Ng, V., Schmutz, J., Cushman, J., Borland, A., Pasha, A., Provart, N., Chen, J.G., Muchero, W., Tuskan, G.A., Yang, X.
2020-03-02 Metabolic Enineering Communications Conversion of phosphoenolpyruvate to pyruvate in Thermoanaerobacterium saccharolyticum Cui, J., Olson, D., Lynd, L.
2020-03-02 Journal of Biological Chemistry The pentose phosphate pathway of cellulolytic clostridia relies on 6-phosphofructokinase instead of transaldolase Koendjbiharie J.G., Hon S., Pabst M., Hooftman R., Stevenson D.M., Jingxuan Cui, Amador-Noguez D., Lynd L.R., Olson D.G., and van Kranenburg R.
2020-03-02 Journal of Experimental Botany CRISPR/Cas9-mediated Targeted Mutagenesis for Functional Genomics Research of Crassulacean Acid Metabolism Plants Liu, D., Chen, Mei, C., Mendoza, B., Cheng, H., Hu, R., Li, L., Trinh, C.T., Tuskan, G.A., Yang, X.
2020-03-02 ChemSusChem Heterogeneous Catalyst Design Principles for the Conversion of Lignin into High Value Commodity Fuels and Chemicals Gale, M., Cai, C.M., Abdul-Aziz, K.
2020-03-02 Current Opinion in Biotechnology Can exascale computing and explainable artificial intelligence applied to plant biology deliver on the United Nations sustainable development goals? Streich, J., Romero, J., Gazolla, J.G.F.M., Kainer, D., Cliff, A., Prates, E.T., Brown, J.B., Khoury, S., Tuskan, G.A., Garvin, M., Jacobson, D., and Harfouche, A.L.
2020-03-02 Plant Direct Identification of functional single nucleotide polymorphism of Populus trichocarpa PtrEPSP‐TF and determination of its transcriptional effect Xie, M., Zhang, J., Singan, V.R., McGranahan, M.J., LaFayette, P.R., Jawdy, S.S., Engle, N., Doeppke, C., Tschaplinski, T.J., Davis, M.F., Lindquist E., Barry, K., Schmuta, J., Parrott, W.A., Chen, F., Tuskan, G.A., Chen, J.G., Muchero, W.
2020-02-28 Chemical Catalysts for Biomass Upgrading Conversion of Terpenes to Chemicals and Related Products Harman‐Ware, A.E.
2020-02-28 In Press Analysis of Segregation Ratio Distortion and Linkage Mapping in Two Switchgrass F1 Populations: Lowland-lowland and Lowland-upland Using Genotyping by Sequencing Data Razar, R., Devos, K., Missaoui, A.
2020-02-27 BMC Chemical Engineering Engineering microbial chemical factories using metabolic models Sarkar, D., Maranas, C.D.
2020-02-27 Metabolic Engineering Communications K-FIT: An accelerated kinetic parameterization algorithm using steady-state fluxomic data Gopalakrishnan, S.; Dash, S.; Maranas, C.D.
2020-02-27 Biofuels Bioproducts and Biorefining (BIOFUEL BIOPROD BIOR) Lignin‐derived electrochemical energy materials and systems Wu, X., Jiang, J., Wang, C., Liu, J., Pu, Y., Ragauskas, A.J, Li, S., Yang, B.
2020-02-06 Frontiers in Plant Science Epigenetic footprints of CRISPR/Cas9-mediated genome editing in plants Lee, J.H., Mazarei, M., Pfotenhauer, A.C., Dorrough, A.B., Poindexter, M.R., Hewezi, T. Lenaghan, S.C., Graham, D.W., and Stewart Jr., C.N.
2020-02-06 International Journal of Molecular Science Occurrence of Thermophilic microorganisms in different full scale biogas plants Kushkevych, I., Cejnar, J., Vitezova, M., Vitez, T., Dordevic, D., and Bomble Y.J.
2020-01-29 Current Opinion in Biotechnology Towards renewable flavors, fragrances, and beyond Lee, J-W., Trinh, C.T.
2020-01-28 PNAS Arabidopsis dehiscence aone polygalacturonase 1 (ADPG1) releases latent defense signals in stems with reduced lignin content Gallego-Giraldo, L., Liu, C., Pose-Albacete, S., Pattathil, S., Peralta, A.G., Young, J., Westpheling, J., Hahn, M.G., Rao, X., Knox, J.P., De Meester, B., Boerjan, W., and Dixon, R.A.
2020-01-21 Nature Sustainability Socio-environmental and land-use impacts of double-cropped maize ethanol in Brazil Moreira, M.M.R., Seabra, J.E.A., Lynd, L.R., Arantes, S.M., Cunha, M.P., and Guilhoto, J.J.M.
2020-01-20 Plants Current progress in nitrogen fixing plants and microbiome research Mahmud, K., Makaju, S., Ibrahim, and Missaoui, A.
2020-01-17 BioDesign Research Biodesign Research to Advance the Principles and Applications of Biosystems Design Yang, X., Qi, L.S., Jaramillo, A., and Cheng Z.M.
2020-01-16 Global Change Biology Assessment of yield gaps on global grazed-only permanent pasture using climate binning Monteiro, L.A., Allee, A.M., Campbell, E.E., Lynd, L.R., Soares, J.R., Jaiswal, D., de Castro Oliveira, J., dos Santos Vianna, M., Morishige, A.E., Figueiredo, G.K.D.A., Lamparelli, R.A.C., Mueller, N.D., Gerber, J., Cortez, L.A.B., and Sheehan, J.J.
2020-01-03 Metabolic Engineering Communications Development of both type I-B and type II CRISPR/Cas genome editing systems in the cellulolytic bacterium Clostridium thermocellum Walker, J.E., Lanahan, A.A., Zheng, T., Toruno, C., Lynd, L.R., Cameron, J.C., Olson, D.G., and Eckert, C.A.
2020-01-03 BioEnergy Research Biomass recalcitrance in willow under two biological conversion paradigms: enzymatic hydrolysis and anaerobic digestion Ohlsson, J.A., Harman-Ware, A.E., Sandgren, M., and Schnurer, A.
2020-01-02 Green Chemistry Synthetic fungal multifunctional cellulases for enhanced biomass conversion Brunecky, R., Subramanian, V., Yarbrough, J.M., Donohoe, B.S., Vinzant, T.B., Vanderwall, T.A., Knott, B.C., Chaudhari, Y.B., Bomble, Y.J., Himmel, M.E., and Decker, S.R.
2019-11-25 PNAS Technoeconomic and life-cycle analysis of single-step catalytic conversion of wet ethanol into fungible fuel blendstocks Hannon, J.R., Lynd, L.R., Andrade, O., Benavides, P.T., Beckham, G.T., Biddy, M.J., Brown, N., Chagas, M.F., Davison, B.H., Foust, T., Junqueira, T.L., Laser, M.S., Li, Z., Richard, T., Tao, L., Tuskan, G.A., Wang, M.
2019-11-18 BMC Plant Biology PdWND3A, a wood-associated NAC domain-containing protein, affects lignin biostynthesis and composition in Populus Yang, Y., Yoo, C-G., Rottmann, W., Winkeler, K.A., Collins, C.M., Gunter, L.E., Jawdy, S.S., Yang, X., Pu, Y., Raguskas, A.J., Tuskan, G.A., and Chen, J-G.
2019-11-12 Open Biology Lignin biosynthesis: old roads revisted and new roads explored Dixon, R.A., and Barros, J.
2019-11-01 PNAS Passive membrane transport of lignin-related compounds Vermaas, J.V., Dixon, R.A., Chen, F., Mansfield, S.D., Boerjan, W., Ralph, J., Crowley, M.F., and Beckham, G.T.
2019-10-22 Global Change Biology Analysis of yield gaps on global grazed-only permanent pasture using climate binning Monteiro, L.A., Allee, A.M., Campbell, E.E., Lynd, L.R., Soares, J.R., Jaiswal, D., de C. Oliverira, J., dos Santos Viannna, M., Morishige, A.E., K.D.A. Figueiredo, G., Lamparelli, R.A.C., Mueller, N.D., Gerber, J., A. B. Cortez, L., and Sheehan, J.J.
2019-10-19 Bioresource Technology Structural changes of lignins in natural Populus variants during different pretreatments Yang, H., Yoo, C.G., Meng, X., Pu, Y., Muchero, W., Tuskan, G.A., Tschaplinski, T.J., Ragauskas, A.J., and Yao, L.
2019-10-03 Critical Reviews in Plant Sciences Plant fucosyltransferases and the emerging biological importance of fucosylated plant structures Soto, M.J., Urbanowicz, B.R., and Hahn, M.G.
2019-10-01 Biotechnology for Biofuels Single mutation at a highly conserved region of chloramphenicol acetyltransferase enables isobutyl acetate production directly from cellulose by Clostridium thermocellum at elevated temperatures Seo, H., Lee, J., Garcia, S., and Trinh, C.T.
2019-09-30 Comprehensive Biotechnology Fundamentals and industrial applicability of multifunctional CAZyme systems Sarai, N.S., Himmel, M.E., Bomble, Y.J., Kahn, A., and Bayer, E.A.
2019-09-30 Understanding Lignocellulose: Synergistic Computational and Analytic Methods Exploring molecular mechanisms of cosolvent enhanced biomass deconstruction: an overview of recent progress Mostofian, B., Petridis, L., and Cai, C.M.
2019-09-30 Peer J Effects of field-grown transgenic switchgrass carbon inputs on soil organic carbon cycling Xu, S., Ottinger, S.L., Schaeffer, S.M., DeBruyn, J.M., Mazarei, M., Stewart, Jr., C.N., and Jagadamma, S.
2019-09-30 Understanding lignocellulose: Synergistic Computational and Analytical Methods Measurement of physicochemical properties of lignin Yoo, C.G., Ragauskas, A.J., and Pu, Y.
2019-09-25 Biotechnology for Biofuels Microbial biosynthesis of lactate esters Lee, J-W., and Trinh, C.T.,
2019-09-24 Proteins Target highlights in CSP13: Experimental target struc tures through the eYES of their authors Lepore, R., Kryshtafavych, A., Alahuhta, M., Veraszto, H.A., Bomble, Y.J., Bufton, J.C., Bullock, A.N., Caba, C., Cao, H., Davies, O.R., Desfosses, A., Dunne, M., Fidelis, K., Goulding, C.W., Gurasaran, M., Gutsche, I., Harding, C.J., Hartmann, M.D., HaYE
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 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.
2019-09-10 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
2019-09-05 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.
2019-09-05 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.
2019-09-04 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.
2019-09-04 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.
2019-08-23 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 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.
2019-07-24 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.
2019-07-18 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 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.
2019-07-16 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.
2019-07-15 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 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.
2019-05-14 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.
2019-05-13 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 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.
2019-03-05 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.
2019-02-11 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 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.
2019-02-01 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.
2019-01-25 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 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.
2018-12-18 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.
2018-12-10 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.
2018-12-10 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.
2018-12-04 Plant Physiology Lignin biosynthesis and control of lignin composition Chen, F.
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.
2018-11-27 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
2018-11-19 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 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.
2018-10-23 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.
2018-10-16 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 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.
2018-10-02 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.
2018-09-28 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 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.
2018-09-19 Bioresource Technology From lignin to valuable products-strategies, challenges, and prospects Wang, H., Pu, Y., Ragauskas, A.J., Yang, B.
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 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.
2018-09-11 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.
2018-09-10 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 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
2018-08-27 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.
2018-08-21 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.
2018-08-21 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.
2018-08-13 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 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.
2018-07-02 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.
2018-06-19 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

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