Publications

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    Birkel, G. W., Ghosh, A., Kumar, V. S., Weaver, D., Ando, D., Backman, T. W. H., . . . Martin, H. G. (2017). “The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism”. BMC Bioinformatics, 18(1), 205. doi, 10.1186/s12859-017-1615-y http://www.ncbi.nlm.nih.gov/pubmed/28381205.

    Breunig, H. M., Jin, L., Robinson, A., & Scown, C. D. (2017). “Bioenergy Potential from Food Waste in California”. Environ Sci Technol. doi, 10.1021/acs.est.6b04591 https://www.ncbi.nlm.nih.gov/pubmed/2807252

    Brown, M. E., Mukhopadhyay, A., & Keasling, J. D. (2017). “Engineering Bacteria to Catabolize the Carbonaceous Component of Sarin: Teaching E. coli to Eat Isopropanol”. ACS Synth Biol, 5(12), 1485-1496. doi, 10.1021/acssynbio.6b00115 https://www.ncbi.nlm.nih.gov/pubmed/27403844.

    C Gach, Philip, Iwai, Kosuke, Kim, Peter, Hillson, Nathan, & Singh, Anup. (2017). Droplet Microfluidics for Synthetic Biology.

    Chubukov, Victor, Desmarais, John James, Wang, George, Chan, Leanne Jade G., Baidoo, Edward E. K., Petzold, Christopher J., . . . Mukhopadhyay, Aindrila. (2017). “Engineering glucose metabolism of Escherichia coli under nitrogen starvation”. [Article]. Npj Systems Biology And Applications, 3, 16035. doi, 10.1038/npjsba.2016.35

    http://www.nature.com/articles/npjsba201635 – supplementary-information d’Espaux, L., Ghosh, A., Runguphan, W., Wehrs, M., Xu, F., Konzock, O., . . . Keasling, J. D. (2017). “Engineering high-level production of fatty alcohols by Saccharomyces cerevisiae from lignocellulosic feedstocks”. Metab Eng, 42, 115-125. doi, 10.1016/j.ymben.2017.06.004 https://www.ncbi.nlm.nih.gov/pubmed/28606738.

    Daly, P., van Munster, J. M., Blythe, M. J., Ibbett, R., Kokolski, M., Gaddipati, S., . . . Archer, D. B. (2017). “Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments”. [journal article]. Biotechnol Biofuels, 10(1), 35. doi, 10.1186/s13068-017-0700-9 https://www.ncbi.nlm.nih.gov/pubmed/28184248

    de Raad, M., de Rond, T., Rubel, O., Keasling, J. D., Northen, T. R., & Bowen, B. P. (2017). “OpenMSI Arrayed Analysis Toolkit: Analyzing Spatially Defined Samples Using Mass Spectrometry Imaging”. Anal Chem. doi, 10.1021/acs.analchem.6b05004 http://www.ncbi.nlm.nih.gov/pubmed/28467051.

    Degreif, D., de Rond, T., Bertl, A., Keasling, J. D., & Budin, I. (2017). “Lipid engineering reveals regulatory roles for membrane fluidity in yeast flocculation and oxygen-limited growth”. Metab Eng, 41, 46-56. doi, 10.1016/j.ymben.2017.03.002 http://www.ncbi.nlm.nih.gov/pubmed/28323063.

    Eudes, A., Dutta, T., Deng, K., Jacquet, N., Sinha, A., Benites, V. T., . . . Loque, D. (2017). “SbCOMT (Bmr12) is involved in the biosynthesis of tricin-lignin in sorghum”. PLoS One, 12(6), e0178160. doi, 10.1371/journal.pone.0178160 https://www.ncbi.nlm.nih.gov/pubmed/28594846.

    Eudes, Aymerick, Mouille, Maxence, Robinson, David S., Benites, Veronica T., Wang, George, Roux, Lucien, . . . Loqué, Dominique. (2017). “Exploiting members of the BAHD acyltransferase family to synthesize multiple hydroxycinnamate and benzoate conjugates in yeast”. [journal article]. Microbial Cell Factories, 15(1), 198. doi, 10.1186/s12934-016-0593-5 http://dx.doi.org/10.1186/s12934-016-0593-5

    Fang, L., Ishikawa, T., Rennie, E. A., Murawska, G. M., Lao, J., Yan, J., . . . Mortimer, J. C. (2017). “Loss of Inositol Phosphorylceramide Sphingolipid Mannosylation Induces Plant Immune Responses and Reduces Cellulose Content in Arabidopsis”. Plant Cell. doi, 10.1105/tpc.16.00186 https://www.ncbi.nlm.nih.gov/pubmed/27895225.

    Fernandez-Bayo, Jesus D., Toniato, Juliano, Simmons, Blake A., & Simmons, Christopher W. (2017). “Structure and activity of thermophilic methanogenic microbial communities exposed to quaternary ammonium sanitizer”. Journal of Environmental Sciences. doi, 10.1016/j.jes.2016.10.005 http://www.sciencedirect.com/science/article/pii/S1001074216308348

    Fukushima, T., Gupta, S., Rad, B., Cornejo, J. A., Petzold, C. J., Chan, L. J. G., . . . Ajo-Franklin, C. M. (2017). “The Molecular Basis for Binding of an Electron Transfer Protein to a Metal Oxide Surface”. J Am Chem Soc. doi, 10.1021/jacs.7b06560 https://www.ncbi.nlm.nih.gov/pubmed/28806874.

    Haushalter, R. W., Phelan, R. M., Hoh, K. M., Su, C., Wang, G., Baidoo, E. E., & Keasling, J. D. (2017). “Production of Odd-Carbon Dicarboxylic Acids in Escherichia coli Using an Engineered Biotin-Fatty Acid Biosynthetic Pathway”. J Am Chem Soc, 139(13), 4615-4618. doi, 10.1021/jacs.6b11895 http://www.ncbi.nlm.nih.gov/pubmed/28291347.

    He, H., Yan, J., Yu, X., Liang, Y., Fang, L., Scheller, H. V., & Zhang, A. (2017). “The NADPH-oxidase AtRbohI plays a positive role in drought-stress response in Arabidopsis thaliana”. Biochem Biophys Res Commun. doi, 10.1016/j.bbrc.2017.05.131 http://www.ncbi.nlm.nih.gov/pubmed/28559135.

    He, L., Xiu, Y., Jones, J. A., Baidoo, E. E., Keasling, J. D., Tang, Y. J., & Koffas, M. A. (2017). “Deciphering flux adjustments of engineered E. coli cells during fermentation with changing growth conditions”. Metab Eng, 39, 247-256. doi, 10.1016/j.ymben.2016.12.008 https://www.ncbi.nlm.nih.gov/pubmed/28017690

    Heinemann, J., Deng, K., Shih, S. C., Gao, J., Adams, P. D., Singh, A. K., & Northen, T. R. (2017). “On-chip integration of droplet microfluidics and nanostructure-initiator mass spectrometry for enzyme screening”. Lab Chip. doi, 10.1039/c6lc01182a http://pubs.rsc.org/en/content/articlepdf/2017/lc/c6lc01182a.

    Hollinshead, W. D., Rodriguez, S., Martin, H. G., Wang, G., Baidoo, E. E., Sale, K. L., . . . Tang, Y. J. (2017). “Examining Escherichia coli glycolytic pathways, catabolite repression, and metabolite channeling using Deltapfk mutants”. Biotechnol Biofuels, 9, 212. doi, 10.1186/s13068-016-0630-y https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5057261/pdf/13068_2016_Article_630.pdf.

    Kang, A., Meadows, C. W., Canu, N., Keasling, J. D., & Lee, T. S. (2017). “High-throughput enzyme screening platform for the IPP-bypass mevalonate pathway for isopentenol production”. Metab Eng, 41, 125-134. doi, 10.1016/j.ymben.2017.03.010 http://www.ncbi.nlm.nih.gov/pubmed/28389395.

    Kim, K. H., Brown, R. C., Daugaard, T., Tivol, W. F., Auer, M., Simmons, B., & Singh, S. (2017a). “Strategy for extending the stability of bio-oil derived phenolic oligomer via mild hydrotreatment with ionic liquid stabilized nanoparticles”. ChemSusChem. doi, 10.1002/cssc.201601515 https://www.ncbi.nlm.nih.gov/pubmed/27992678

    Kim, K. H., Brown, R. C., Daugaard, T., Tivol, W. F., Auer, M., Simmons, B., & Singh, S. (2017b). “Strategy for Extending the Stability of Bio-oil-Derived Phenolic Oligomers by Mild Hydrotreatment with Ionic-Liquid-Stabilized Nanoparticles”. ChemSusChem, n/a-n/a. doi, 10.1002/cssc.201601515 https://www.ncbi.nlm.nih.gov/pubmed/27992678

    Kim, K. H., Dutta, T., Ralph, J., Mansfield, S. D., Simmons, B. A., & Singh, S. (2017). “Impact of lignin polymer backbone esters on ionic liquid pretreatment of poplar”. [journal article]. Biotechnol Biofuels, 10(1), 101. doi, 10.1186/s13068-017-0784-2 http://www.ncbi.nlm.nih.gov/pubmed/28439294.

    Kim, Kwang Ho, Dutta, Tanmoy, Walter, Eric D., Isern, Nancy G., Cort, John R., Simmons, Blake A., & Singh, Seema. (2017). “Chemoselective Methylation of Phenolic Hydroxyl Group Prevents Quinone Methide Formation and Repolymerization During Lignin Depolymerization”. ACS Sustainable Chemistry & Engineering. doi, 10.1021/acssuschemeng.6b03102 http://dx.doi.org/10.1021/acssuschemeng.6b03102

    Kim, Kwang Ho, Simmons, Blake A., & Singh, Seema. (2017). “Catalytic transfer hydrogenolysis of ionic liquid processed biorefinery lignin to phenolic compounds”. [10.1039/C6GC02473D]. Green Chemistry. doi, 10.1039/C6GC02473D http://dx.doi.org/10.1039/C6GC02473D

    Kirby, J., Dietzel, K. L., Wichmann, G., Chan, R., Antipov, E., Moss, N., . . . Zhao, L. (2017). “Engineering a functional 1-deoxy-D-xylulose 5-phosphate (DXP) pathway in Saccharomyces cerevisiae”. Metab Eng. doi, 10.1016/j.ymben.2016.10.017 https://www.ncbi.nlm.nih.gov/pubmed/27989805

    Kohler, A. C., Mills, M. J. L., Adams, P. D., Simmons, B. A., & Sale, K. L. (2017). “Structure of aryl O-demethylase offers molecular insight into a catalytic tyrosine-dependent mechanism”. Proc Natl Acad Sci U S A, 114(16), E3205-E3214. doi, 10.1073/pnas.1619263114 http://www.ncbi.nlm.nih.gov/pubmed/28373573.

    Lao, Jeemeng, Smith-Moritz, Andreia M., Mortimer, Jennifer C., & Heazlewood, Joshua L. (2017). Enrichment of the Plant Cytosolic Fraction. In Nicolas L. Taylor & A. Harvey Millar (Eds.), Isolation of Plant Organelles and Structures: Methods and Protocols (pp. 213-232). New York, NY: Springer New York.

    Li, G., Jain, R., Chern, M., Pham, N. T., Martin, J. A., Wei, T., . . . Ronald, P. C. (2017). “The Sequences of 1504 Mutants in the Model Rice Variety Kitaake Facilitate Rapid Functional Genomic Studies”. Plant Cell, 29(6), 1218-1231. doi, 10.1105/tpc.17.00154 https://www.ncbi.nlm.nih.gov/pubmed/28576844.

    Li, W., Zhu, Z., Chern, M., Yin, J., Yang, C., Ran, L., . . . Chen, X. (2017). “A Natural Allele of a Transcription Factor in Rice Confers Broad-Spectrum Blast Resistance”. Cell, 170(1), 114-126 e115. doi, 10.1016/j.cell.2017.06.008 https://www.ncbi.nlm.nih.gov/pubmed/28666113.

    Liang, Yan, Richardson, Sarah, Yan, Jingwei, Benites, Veronica T., Cheng-Yue, Clarabelle, Tran, Thu, . . . Loqué, Dominique. (2017). “Endoribonuclease-Based Two-Component Repressor Systems for Tight Gene Expression Control in Plants”. ACS Synthetic Biology. doi, 10.1021/acssynbio.6b00295 http://dx.doi.org/10.1021/acssynbio.6b00295

    McAndrew, Ryan P., Sathitsuksanoh, Noppadon, Mbughuni, Michael M., Heins, Richard A., Pereira, Jose H., George, Anthe, . . . Adams, Paul D. (2017). “Structure and mechanism of NOV1, a resveratrol-cleaving dioxygenase”. Proceedings of the National Academy of Sciences, 201608917. doi, 10.1073/pnas.1608917113 http://www.pnas.org/content/early/2016/11/29/1608917113.abstract

    Meadows, Corey W., Kang, Aram, & Lee, Taek Soon. (2017). “Metabolic engineering for advanced biofuels production and recent advances towards commercialization”. Biotechnology Journal, 1600433-n/a. doi, 10.1002/biot.201600433 http://dx.doi.org/10.1002/biot.201600433.

    Mendez-Perez, Daniel, Alonso-Gutierrez, Jorge, Hu, Qijun, Molinas, Margaux, Baidoo, Edward E. K., Wang, George, . . . Lee, Taek Soon. (2017). “Production of jet fuel precursor monoterpenoids from engineered Escherichia coli”. Biotechnology and Bioengineering, n/a-n/a. doi, 10.1002/bit.26296 http://dx.doi.org/10.1002/bit.26296

    Mills, M. J. L., Sale, K. L., Simmons, B. A., & Popelier, P. L. A. (2017). “Rhorix: An interface between quantum chemical topology and the 3D graphics program blender”. J Comput Chem, n/a-n/a. doi, 10.1002/jcc.25054 https://www.ncbi.nlm.nih.gov/pubmed/28857244.

    Morrell, W., Birkel, G., Forrer, M., Lopez, T., Backman, T., Dussault, M., . . . Garcia Martin, H. (2017). “The Experiment Data Depot: a web-based software tool for biological experimental data storage, sharing, and visualization”. ACS Synth Biol. doi, 10.1021/acssynbio.7b00204 https://www.ncbi.nlm.nih.gov/pubmed/28826210.

    Mortimer, J. C. (2017). “Structural Analysis of Cell Wall Polysaccharides Using PACE”. Methods Mol Biol, 1544, 223-231. doi, 10.1007/978-1-4939-6722-3_16 https://www.ncbi.nlm.nih.gov/pubmed/28050839.

    Neupane, Binod, & Rubin, Jonathan. (2017). “Implications of U.S. biofuels policy for sustainable transportation energy in Maine and the Northeast”. Renewable and Sustainable Energy Reviews. doi, 10.1016/j.rser.2016.11.253 http://ac.els-cdn.com/S1364032116310334/1-s2.0-S1364032116310334-main.pdf?_tid=68595bb6-df6e-11e6-81f5-00000aab0f6c&acdnat=1484957777_5f1a34cd5c8b52137c940ad53e2da221.

    Oberortner, Ernst, Cheng, Jan-Fang, Hillson, Nathan J., & Deutsch, Samuel. (2017). “Streamlining the Design-to-Build transition with Build-Optimization Software Tools (BOOST)”. ACS Synthetic Biology. doi, 10.1021/acssynbio.6b00200 http://dx.doi.org/10.1021/acssynbio.6b00200

    Papa, Gabriella, Feldman, Taya, Sale, Kenneth L., Adani, Fabrizio, Singh, Seema, & Simmons, Blake A. (2017). “Parametric study for the optimization of ionic liquid pretreatment of corn stover”. Bioresource Technology. doi, 10.1016/j.biortech.2017.05.167 http://www.sciencedirect.com/science/article/pii/S0960852417308350.

    Papa, Gabriella, Kirby, James, Murthy Konda, N. V. S. N., Tran, Kim, Singh, Seema, Keasling, Jay D., . . . Simmons, Blake A. (2017). “Development of an integrated approach for α-pinene recovery and sugar production from loblolly pine using ionic liquids”. [10.1039/C6GC02637K]. Green Chem. doi, 10.1039/c6gc02637k http://dx.doi.org/10.1039/C6GC02637K

    Parisutham, V., Chandran, S. P., Mukhopadhyay, A., Lee, S. K., & Keasling, J. D. (2017). “Intracellular cellobiose metabolism and its applications in lignocellulose-based biorefineries”. Bioresour Technol. doi, 10.1016/j.biortech.2017.05.001 http://www.ncbi.nlm.nih.gov/pubmed/28535986.

    Park, C. J., Wei, T., Sharma, R., & Ronald, P. C. (2017). “Overexpression of Rice Auxilin-Like Protein, XB21, Induces Necrotic Lesions, up-Regulates Endocytosis-Related Genes, and Confers Enhanced Resistance to Xanthomonas oryzae pv. oryzae”. [journal article]. Rice (N Y), 10(1), 27. doi, 10.1186/s12284-017-0166-1 https://www.ncbi.nlm.nih.gov/pubmed/28577284.

    Perez-Pimienta, J. A., Sathitsuksanoh, N., Thompson, V. S., Tran, K., Ponce-Noyola, T., Stavila, V., . . . Simmons, B. A. (2017). “Ternary ionic liquid-water pretreatment systems of an agave bagasse and municipal solid waste blend”. [journal article]. Biotechnol Biofuels, 10(1), 72. doi, 10.1186/s13068-017-0758-4 https://www.ncbi.nlm.nih.gov/pubmed/28344647

    Perez-Pimienta, J. A., Vargas-Tah, A., Lopez-Ortega, K. M., Medina-Lopez, Y. N., Mendoza-Perez, J. A., Avila, S., . . . Martinez, A. (2017). “Sequential enzymatic saccharification and fermentation of ionic liquid and organosolv pretreated agave bagasse for ethanol production”. Bioresour Technol, 225, 191-198. doi, 10.1016/j.biortech.2016.11.064 https://www.ncbi.nlm.nih.gov/pubmed/27889478

    Pruitt, R. N., Joe, A., Zhang, W., Feng, W., Stewart, V., Schwessinger, B., . . . Ronald, P. C. (2017). “A microbially derived tyrosine-sulfated peptide mimics a plant peptide hormone”. New Phytol, 215(2), 725-736. doi, 10.1111/nph.14609 https://www.ncbi.nlm.nih.gov/pubmed/28556915.

    Rautengarten, C., Birdseye, D., Pattathil, S., McFarlane, H. E., Saez-Aguayo, S., Orellana, A., . . . Ebert, B. (2017). “The elaborate route for UDP-arabinose delivery into the Golgi of plants”. Proc Natl Acad Sci U S A, 114(16), 4261-4266. doi, 10.1073/pnas.1701894114 http://www.ncbi.nlm.nih.gov/pubmed/28373556

    Reider Apel, A., d’Espaux, L., Wehrs, M., Sachs, D., Li, R. A., Tong, G. J., . . . Mukhopadhyay, A. (2017). “A Cas9-based toolkit to program gene expression in Saccharomyces cerevisiae”. Nucleic Acids Res. doi, 10.1093/nar/gkw1023 https://www.ncbi.nlm.nih.gov/pubmed/27899650

    Scheller, H. V. (2017). “Plant cell wall: Never too much acetate”. [News and Views]. Nat Plants, 3, 17024. doi, 10.1038/nplants.2017.24 https://www.ncbi.nlm.nih.gov/pubmed/28260793.

    Shymansky, C. M., Wang, G., Baidoo, E. E. K., Gin, J., Apel, A. R., Mukhopadhyay, A., . . . Keasling, J. D. (2017). “Flux-Enabled Exploration of the Role of Sip1 in Galactose Yeast Metabolism”. [Original Research]. Front Bioeng Biotechnol, 5(31), 31. doi, 10.3389/fbioe.2017.00031 https://www.ncbi.nlm.nih.gov/pubmed/28596955.

    Sun, J., Shi, J., Murthy Konda, Nvsn, Campos, D., Liu, D., Nemser, S., . . . Singh, S. (2017). “Efficient dehydration and recovery of ionic liquid after lignocellulosic processing using pervaporation”. [journal article]. Biotechnol Biofuels, 10(1), 154. doi, 10.1186/s13068-017-0842-9 https://www.ncbi.nlm.nih.gov/pubmed/28638441.

    Sun, Jian, Dutta, Tanmoy, Parthasarathi, Ramakrishnan, Kim, Kwang Ho, Tolic, Nikola, Chu, Rosalie K., . . . Singh, Seema. (2017). “Rapid room temperature solubilization and depolymerization of polymeric lignin at high loadings”. [10.1039/C6GC02258H]. Green Chem., 18(22), 6012-6020. doi, 10.1039/c6gc02258h http://dx.doi.org/10.1039/C6GC02258H

    Sun, Jian, Konda, Suryanarayana, Ramakrishnan, Parthasarathi, Dutta, Tanmoy, Valiev, Marat, Xu, Feng, . . . Singh, Seema. (2017). “One-pot integrated biofuel production using low-cost biocompatible protic ionic liquids”. [10.1039/C7GC01179B]. Green Chem. doi, 10.1039/c7gc01179b http://dx.doi.org/10.1039/C7GC01179B.

    Tian, Tian, & Lee, Taek Soon. (2017). Advanced Biodiesel and Biojet Fuels from Lignocellulosic Biomass. In Sang Yup Lee (Ed.), Consequences of Microbial Interactions with Hydrocarbons, Oils, and Lipids: Production of Fuels and Chemicals (pp. 1-25). Cham: Springer International Publishing.

    To, Trang, Procter, Kerryn, Simmons, Blake, Subashchandrabose, Suresh, & Atkin, Rob. (2017). “Low cost ionic liquid-water mixtures for effective extraction of carbohydrate and lipid from algae”. [10.1039/C7FD00158D]. Faraday Discuss. doi, 10.1039/c7fd00158d http://dx.doi.org/10.1039/C7FD00158D.

    To, Trang Q., Shah, Kalpit, Tremain, Priscilla, Simmons, Blake A., Moghtaderi, Behdad, & Atkin, Rob. (2017). “Treatment of lignite and thermal coal with low cost amino acid based ionic liquid-water mixtures”. Fuel, 202, 296-306. doi, http://doi.org/10.1016/j.fuel.2017.04.051

    Tsai, A. Y., Chan, K., Ho, C. Y., Canam, T., Capron, R., Master, E. R., & Brautigam, K. (2017). “Transgenic expression of fungal accessory hemicellulases in Arabidopsis thaliana triggers transcriptional patterns related to biotic stress and defense response”. PLoS One, 12(3), e0173094. doi, 10.1371/journal.pone.0173094 https://www.ncbi.nlm.nih.gov/pubmed/28253318

    Verhertbruggen, Yves, Walker, Jesse L., Guillon, Fabienne, & Scheller, Henrik V. (2017). “A Comparative Study of Sample Preparation for Staining and Immunodetection of Plant Cell Walls by Light Microscopy”. [Original Research]. Frontiers in Plant Science, 8(1505). doi, 10.3389/fpls.2017.01505 http://journal.frontiersin.org/article/10.3389/fpls.2017.01505.

    Walker, J. A., Pattathil, S., Bergeman, L. F., Beebe, E. T., Deng, K., Mirzai, M., . . . Fox, B. G. (2017). “Determination of glycoside hydrolase specificities during hydrolysis of plant cell walls using glycome profiling”. [Article]. Biotechnol Biofuels, 10, 31. doi, 10.1186/s13068-017-0703-6 https://www.ncbi.nlm.nih.gov/pubmed/28184246

    Wan, N., DeLorenzo, D. M., He, L., You, L., Immethun, C. M., Wang, G., . . . Tang, Y. J. (2017). “Cyanobacterial carbon metabolism: Fluxome plasticity and oxygen dependence”. Biotechnol Bioeng, n/a-n/a. doi, 10.1002/bit.26287 http://www.ncbi.nlm.nih.gov/pubmed/28295163.

    Wei, T., Chen, T. C., Ho, Y. T., & Ronald, P. C. (2017). “Mutation of the rice XA21 predicted nuclear localization sequence does not affect resistance to Xanthomonas oryzae pv. oryzae”. PeerJ, 4, e2507. doi, 10.7717/peerj.2507 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5068440/pdf/peerj-04-2507.pdf.

    Welner, D. H., Shin, D., Tomaleri, G. P., DeGiovanni, A. M., Tsai, A. Y., Tran, H. M., . . . Adams, P. D. (2017). “Plant cell wall glycosyltransferases: High-throughput recombinant expression screening and general requirements for these challenging enzymes”. PLoS One, 12(6), e0177591. doi, 10.1371/journal.pone.0177591 https://www.ncbi.nlm.nih.gov/pubmed/28598995.

    Welner, D. H., Tsai, A. Y., DeGiovanni, A. M., Scheller, H. V., & Adams, P. D. (2017). “X-ray diffraction analysis and in vitro characterization of the UAM2 protein from Oryza sativa”. Acta Crystallogr F Struct Biol Commun, 73(Pt 4), 241-245. doi, 10.1107/S2053230X17004587 http://www.ncbi.nlm.nih.gov/pubmed/28368284.

    Wong, J., Rios-Solis, L., & Keasling, J. D. (2017). Microbial Production of Isoprenoids. In Sang Yup Lee (Ed.), Consequences of Microbial Interactions with Hydrocarbons, Oils, and Lipids: Production of Fuels and Chemicals (pp. 1-24). Cham: Springer International Publishing.

    Woo, H. L., DeAngelis, K. M., Teshima, H., Davenport, K., Daligault, H., Erkkila, T., . . . Hazen, T. C. (2017). “High-Quality Draft Genome Sequences of Four Lignocellulose-Degrading Bacteria Isolated from Puerto Rican Forest Soil: Gordonia sp., Paenibacillus sp., Variovorax sp., and Vogesella sp”. Genome Announc, 5(18). doi, 10.1128/genomeA.00300-17 http://www.ncbi.nlm.nih.gov/pubmed/28473393.

    Wu, W., Dutta, T., Varman, A. M., Eudes, A., Manalansan, B., Loque, D., & Singh, S. (2017). “Lignin Valorization: Two Hybrid Biochemical Routes for the Conversion of Polymeric Lignin into Value-added Chemicals”. Sci Rep, 7(1), 8420. doi, 10.1038/s41598-017-07895-1 https://www.ncbi.nlm.nih.gov/pubmed/28827602.

    Wu, Y. W., Higgins, B., Yu, C., Reddy, A. P., Ceballos, S., Joh, L. D., . . . VanderGheynst, J. S. (2017). “Ionic Liquids Impact the Bioenergy Feedstock-Degrading Microbiome and Transcription of Enzymes Relevant to Polysaccharide Hydrolysis”. mSystems, 1(6). doi, 10.1128/mSystems.00120-16 http://msystems.asm.org/content/msys/1/6/e00120-16.full.pdf.

    Yu, C., Simmons, B. A., Singer, S. W., Thelen, M. P., & VanderGheynst, J. S. (2017). “Ionic liquid-tolerant microorganisms and microbial communities for lignocellulose conversion to bioproducts”. Appl Microbiol Biotechnol, 100(24), 10237-10249. doi, 10.1007/s00253-016-7955-0 https://www.ncbi.nlm.nih.gov/pubmed/27838839

    0.1007%2Fs00253-016-7955-0*~hmac=9b2a00117a75d25d82281e10f4e44c2dae8e9ba6f8e5287f30aa3641d9001744.

    Yu, Chaowei, Harrold, Duff R., Claypool, Joshua T., Simmons, Blake A., Singer, Steven W., Simmons, Christopher W., & VanderGheynst, Jean S. (2017). “Nitrogen amendment of green waste impacts microbial community, enzyme secretion and potential for lignocellulose decomposition”. Process Biochemistry. doi, 10.1016/j.procbio.2016.11.002 http://www.sciencedirect.com/science/article/pii/S1359511316308133

    Yuan, X., Duan, Y., He, L., Singh, S., Simmons, B., & Cheng, G. (2017). “Characterization of white poplar and eucalyptus after ionic liquid pretreatment as a function of biomass loading using X-ray diffraction and small angle neutron scattering”. Bioresour Technol, 232, 113-118. doi, 10.1016/j.biortech.2017.02.014 https://www.ncbi.nlm.nih.gov/pubmed/28214697

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    Rautengarten, C., Ebert, B., Moreno, I., Temple, H., Herter, T., Link, B., Doñas-Cofré, D., Moreno, A., Saéz-Aguayo, S., Blanco, F., Mortimer, J. C., Schultink, A., Reiter, W.-D., Dupree, P., Pauly, M., Heazlewood, J. L., Scheller, H. V., & Orellana, A. (2014). “The Golgi localized bifunctional UDP-rhamnose/UDP-galactose transporter family of Arabidopsis”. Proceedings of the National Academy of Sciences. doi, 10.1073/pnas.1406073111 http://www.pnas.org/content/111/31/11563.full.pdf

    Reddy, A. P., Liles, M. R., Simmons, C. W., D’haeseleer, P., Khudyakov, J., Burd, H., Hadi, M., Simmons, B. A., Singer, S. W., Thelen, M. P., & VanderGheynst, J. S. (2013). “Discovery of Microorganisms and Enzymes Involved in High-Solids Decomposition of Rice Straw Using Metagenomic Analyses”. [Research Support, Non-U.S. Gov’t Research Support, U.S. Gov’t, Non-P.H.S.]. PLoS One, 8(10), e77985. doi, 10.1371/journal.pone.0077985 http://www.ncbi.nlm.nih.gov/pubmed/24205054

    Ren, Y., Hansen, S. F., Ebert, B., Lau, J., & Scheller, H. V. (2014). “Site-Directed Mutagenesis of IRX9, IRX9L and IRX14 Proteins Involved in Xylan Biosynthesis: Glycosyltransferase Activity Is Not Required for IRX9 Function in Arabidopsis”. PLoS One, 9(8), e105014. doi, 10.1371/journal.pone.0105014 http://www.ncbi.nlm.nih.gov/pubmed/25118690

    Rennie, E. A., Ebert, B., Miles, G. P., Cahoon, R. E., Christiansen, K. M., Stonebloom, S., Khatab, H., Twell, D., Petzold, C. J., Adams, P. D., Dupree, P., Heazlewood, J. L., Cahoon, E. B., & Scheller, H. V. (2014). “Identification of a Sphingolipid alpha-Glucuronosyltransferase That Is Essential for Pollen Function in Arabidopsis”. [Journal article]. Plant Cell, 26(8), 3314-3325. doi, 10.1105/tpc.114.129171 http://www.ncbi.nlm.nih.gov/pubmed/25122154

    Rennie, E. A., & Scheller, H. V. (2014). “Xylan biosynthesis”. [Research Support, U.S. Gov’t, Non-P.H.S. Review]. Curr Opin Biotechnol, 26, 100-107. doi, 10.1016/j.copbio.2013.11.013 http://www.ncbi.nlm.nih.gov/pubmed/24679265

    Rhee, M., Liu, P., Meagher, R. J., Light, Y. K., & Singh, A. K. (2014). “Versatile on-demand droplet generation for controlled encapsulation”. Biomicrofluidics, 8(3). doi, Artn 034112 Doi 10.1063/1.4874715 <Go to ISI>://000339004500012 http://scitation.aip.org/docserver/fulltext/aip/journal/bmf/8/3/1.4874715.pdf?expires=1415048961&id=id&accname=2091706&checksum=1DEDD0E528251D33C8C603AA56F8CF63

    Rodriguez, S., Kirby, J., Denby, C. M., & Keasling, J. D. (2014). “Production and quantification of sesquiterpenes in Saccharomyces cerevisiae, including extraction, detection and quantification of terpene products and key related metabolites”. [Research Support, U.S. Gov’t, Non-P.H.S.]. Nat Protoc, 9(8), 1980-1996. doi, 10.1038/nprot.2014.132 http://www.ncbi.nlm.nih.gov/pubmed/25058645 http://www.nature.com/nprot/journal/v9/n8/pdf/nprot.2014.132.pdf

    Ronald, P. C. (2014). “Lab to farm: applying research on plant genetics and genomics to crop improvement”. [Research Support, N.I.H., Extramural Research Support, U.S. Gov’t, Non-P.H.S.]. PLoS Biol, 12(6), e1001878. doi, 10.1371/journal.pbio.1001878 http://www.ncbi.nlm.nih.gov/pubmed/24915201 http://www.plosbiology.org/article/fetchObject.action?uri=info%3Adoi%2F10.1371%2Fjournal.pbio.1001878&representation=PDF

    Rotavera, B., Zador, J., Welz, O., Sheps, L., Scheer, A. M., Savee, J. D., Akbar Ali, M., Lee, T. S., Simmons, B. A., Osborn, D. L., Violi, A., & Taatjes, C. A. (2014). “Photoionization Mass Spectrometric Measurements of Initial Reaction Pathways in Low-Temperature Oxidation of 2,5-Dimethylhexane”. [Journal article]. J Phys Chem A, 19, 19. doi, 10.1021/jp507811d http://www.ncbi.nlm.nih.gov/pubmed/25234586 http://pubs.acs.org/doi/pdfplus/10.1021/jp507811d

    Ruegg, T. L., Kim, E. M., Simmons, B. A., Keasling, J. D., Singer, S. W., Soon Lee, T., & Thelen, M. P. (2014). “An auto-inducible mechanism for ionic liquid resistance in microbial biofuel production”. [Research Support, Non-U.S. Gov’t Research Support, U.S. Gov’t, Non-P.H.S.]. Nat Commun, 5, 3490. doi, 10.1038/ncomms4490 http://www.ncbi.nlm.nih.gov/pubmed/24667370

    Runguphan, W., & Keasling, J. D. (2014). “Metabolic engineering of Saccharomyces cerevisiae for production of fatty acid-derived biofuels and chemicals”. [Research Support, U.S. Gov’t, Non-P.H.S.]. Metab Eng, 21, 103-113. doi, 10.1016/j.ymben.2013.07.003 http://www.ncbi.nlm.nih.gov/pubmed/23899824

    Sarria, S., Wong, B., Martin, H. G., Keasling, J. D., & Peralta-Yahya, P. (2014). “Microbial Synthesis of Pinene”. ACS Synth Biol, 3(7), 466-475. doi, 10.1021/sb4001382 http://www.ncbi.nlm.nih.gov/pubmed/24679043 http://pubs.acs.org/doi/pdfplus/10.1021/sb4001382

    Sathitsuksanoh, N., Holtman, K. M., Yelle, D. J., Morgan, T., Stavila, V., Pelton, J., Blanch, H., Simmons, B. A., & George, A. (2014). “Lignin fate and characterization during ionic liquid biomass pretreatment for renewable chemicals and fuels production”. Green Chemistry, 16(3), 1236-1247. doi, 10.1039/c3gc42295j <Go to ISI>://WOS:000332039200033 http://pubs.rsc.org/en/content/articlepdf/2014/gc/c3gc42295j

    Scullin, C., Stavila, V., Skarstad, A., Keasling, J. D., Simmons, B. A., & Singh, S. (2014). “Optimization of renewable pinene production from the conversion of macroalgae Saccharina latissima”. Bioresour Technol(0). doi, 10.1016/j.biortech.2014.09.105 http://www.ncbi.nlm.nih.gov/pubmed/25318906

    Shi, J., Balamurugan, K., Parthasarathi, R., Sathitsuksanoh, N., Zhang, S., Stavila, V., Subramanian, V., Simmons, B., & Singh, S. (2014). “Understanding the Role of Water during Ionic Liquid Pretreatment of Lignocellulose: Co-solvent or Anti-solvent?”. [10.1039/C4GC00373J]. Green Chemistry, 16(8), 3830. doi, 10.1039/c4gc00373j http://dx.doi.org/10.1039/C4GC00373J http://pubs.rsc.org/en/content/articlepdf/2014/gc/c4gc00373j

    Simmons, C. W., Claypool, J. T., Marshall, M. N., Jabusch, L. K., Reddy, A. P., Simmons, B. A., Singer, S. W., Stapleton, J. J., & VanderGheynst, J. S. (2014). “Characterization of bacterial communities in solarized soil amended with lignocellulosic organic matter”. Applied Soil Ecology, 73, 97-104. doi, DOI 10.1016/j.apsoil.2013.08.014 <Go to ISI>://000329415500013 http://ac.els-cdn.com/S0929139313002175/1-s2.0-S0929139313002175-main.pdf?_tid=0b99af80-22a0-11e4-90e5-00000aacb35f&acdnat=1407903331_443a43e5a632da3a1ad04859a48110f0

    Simmons, C. W., Reddy, A. P., Simmons, B. A., Singer, S. W., & VanderGheynst, J. S. (2014). “Effect of inoculum source on the enrichment of microbial communities on two lignocellulosic bioenergy crops under thermophilic and high-solids conditions”. [Research Support, U.S. Gov’t, Non-P.H.S.]. J Appl Microbiol, 117(4), 1025-1034. doi, 10.1111/jam.12609 http://www.ncbi.nlm.nih.gov/pubmed/25066414

    Simmons, C. W., Reddy, A. P., Vandergheynst, J. S., Simmons, B. A., & Singer, S. W. (2014). “Bacillus coagulans tolerance to 1-ethyl-3-methylimidazolium-based ionic liquids in aqueous and solid-state thermophilic culture”. [Research Support, Non-U.S. Gov’t Research Support, U.S. Gov’t, Non-P.H.S.]. Biotechnol Prog, 30(2), 311-316. doi, 10.1002/btpr.1859 http://www.ncbi.nlm.nih.gov/pubmed/24376258

    Socha, A. M., Parthasarathi, R., Shi, J., Pattathil, S., Whyte, D., Bergeron, M., George, A., Tran, K., Stavila, V., Venkatachalam, S., Hahn, M. G., Simmons, B. A., & Singh, S. (2014). “Efficient biomass pretreatment using ionic liquids derived from lignin and hemicellulose”. Proc Natl Acad Sci U S A, 111(35), E3587-3595. doi, 10.1073/pnas.1405685111 http://www.ncbi.nlm.nih.gov/pubmed/25136131 http://www.pnas.org/content/111/35/E3587.full.pdf

    Sun, N., Parthasarathi, R., Socha, A. M., Shi, J., Zhang, S., Stavila, V., Sale, K. L., Simmons, B. A., & Singh, S. (2014). “Understanding pretreatment efficacy of four cholinium and imidazolium ionic liquids by chemistry and computation”. Green Chemistry, 16(5), 2546-2557. Doi 10.1039/C3gc42401d <Go to ISI>://000335005200025

    Szmidt-Middleton, H. L., Ouellet, M., Adams, P. D., Keasling, J. D., & Mukhopadhyay, A. (2013). “Utilizing a highly responsive gene, yhjX, in E. coli based production of 1,4-butanediol”. chemical engineering science, 103, 68-73. doi, 10.1016/j.ces.2013.06.044 <Go to ISI>://000325945800010 http://ac.els-cdn.com/S0009250913004673/1-s2.0-S0009250913004673-main.pdf?_tid=15197748-22a0-11e4-8dd7-00000aab0f01&acdnat=1407903347_dd2da4193f590904e4048bf543df215c

    Tobimatsu, Y., Wagner, A., Donaldson, L., Mitra, P., Niculaes, C., Dima, O., Kim, J. I., Anderson, N., Loque, D., Boerjan, W., Chapple, C., & Ralph, J. (2013). “Visualization of plant cell wall lignification using fluorescence-tagged monolignols”. [Research Support, Non-U.S. Gov’t Research Support, U.S. Gov’t, Non-P.H.S.]. Plant J, 76(3), 357-366. doi, 10.1111/tpj.12299 http://www.ncbi.nlm.nih.gov/pubmed/23889038 http://onlinelibrary.wiley.com/store/10.1111/tpj.12299/asset/tpj12299.pdf?v=1&t=hys56zku&s=2706e2ba08ae57d6e513604d76b31d0b25546dfc

    Uppugundla, N., da Costa Sousa, L., Chundawat, S. P., Yu, X., Simmons, B., Singh, S., Gao, X., Kumar, R., Wyman, C. E., Dale, B. E., & Balan, V. (2014). “A comparative study of ethanol production using dilute acid, ionic liquid and AFEX pretreated corn stover”. Biotechnol Biofuels, 7(1), 72. doi, 10.1186/1754-6834-7-72 http://www.ncbi.nlm.nih.gov/pubmed/24917886 http://www.biotechnologyforbiofuels.com/content/pdf/1754-6834-7-72.pdf

    Weaver, L. J., Sousa, M. M., Wang, G., Baidoo, E., Petzold, C. J., & Keasling, J. D. (2014). “A kinetic-based approach to understanding heterologous mevalonate pathway function in E. coli.”. Biotechnol. Bioeng. doi, 10.1002/bit.25323 http://www.ncbi.nlm.nih.gov/pubmed/24981116 http://onlinelibrary.wiley.com/store/10.1002/bit.25323/asset/bit25323.pdf?v=1&t=hys576qx&s=1adbef0685840b034ffdd5d4bc48bc1a67e654ec

    Winger, A. M., Heazlewood, J. L., Chan, L. J., Petzold, C. J., Permaul, K., & Singh, S. (2014). “Secretome analysis of the thermophilic xylanase hyper-producer Thermomyces lanuginosus SSBP cultivated on corn cobs”. J Ind Microbiol Biotechnol. doi, 10.1007/s10295-014-1509-1 http://www.ncbi.nlm.nih.gov/pubmed/25223615

    Woo, H. L., Hazen, T. C., Simmons, B. A., & DeAngelis, K. M. (2014). “Enzyme activities of aerobic lignocellulolytic bacteria isolated from wet tropical forest soils”. [Research Support, U.S. Gov’t, Non-P.H.S.]. Syst Appl Microbiol, 37(1), 60-67. doi, 10.1016/j.syapm.2013.10.001 http://www.ncbi.nlm.nih.gov/pubmed/24238986 http://ac.els-cdn.com/S0723202013001598/1-s2.0-S0723202013001598-main.pdf?_tid=24f352e2-22a0-11e4-a700-00000aab0f6c&acdnat=1407903373_3d92bd1b7fe04cb83c13a176b26c1e76

    Woo, H. L., Utturkar, S., Klingeman, D., Simmons, B. A., DeAngelis, K. M., Brown, S. D., & Hazen, T. C. (2014). “Draft Genome Sequence of the Lignin-Degrading Burkholderia sp. Strain LIG30, Isolated from Wet Tropical Forest Soil”. [Journal]. Genome Announc, 2(3), doi: 10. doi, 10.1128/genomeA.00637-14 http://www.ncbi.nlm.nih.gov/pubmed/24948777

    Woo, H. M., Murray, G. W., Batth, T. S., Prasad, N., Adams, P. D., Keasling, J. D., Petzold, C. J., & Lee, T. S. (2013). “Application of targeted proteomics and biological parts assembly in E. coli to optimize the biosynthesis of an anti-malarial drug precursor, amorpha-4,11-diene”. chemical engineering science, 103, 21-28. doi, DOI 10.1016/j.ces.2013.04.033 <Go to ISI>://000325945800004 http://ac.els-cdn.com/S0009250913002923/1-s2.0-S0009250913002923-main.pdf?_tid=1ba85e94-22a0-11e4-bd13-00000aab0f26&acdnat=1407903358_c2ad9da79be920ef01ec889390ca8521

    Yuzawa, S., Eng, C. H., Katz, L., & Keasling, J. D. (2014). “Enzyme analysis of the polyketide synthase leads to the discovery of a novel analog of the antibiotic alpha-lipomycin”. [Research Support, U.S. Gov’t, Non-P.H.S.]. J Antibiot (Tokyo), 67(2), 199-201. doi, 10.1038/ja.2013.110 http://www.ncbi.nlm.nih.gov/pubmed/24169801 http://www.nature.com/ja/journal/v67/n2/pdf/ja2013110a.pdf


  • Alonso-Gutierrez, J., Chan, R., Batth, T. S., Adams, P. D., Keasling, J. D., Petzold, C. J. and Lee, T. S. (2013). “Metabolic engineering of Escherichia coli for limonene and perillyl alcohol production.” Metab Eng. 19C: 33-41.

    Bartley, L. E., Peck, M. L., Kim, S. R., Ebert, B., Maniseri, C., Chiniquy, D., Sykes, R., Gao, L., Rautengarten, C., Vega-Sanchez, M. E., Benke, P. I., Canlas, P. E., Cao, P., Brewer, S., Lin, F., Smith, W. L., Zhang, X., Keasling, J. D., Jentoft, R. E., Foster, S. B., Zhou, J., Ziebell, A., An, G., Scheller, H. V. and Ronald, P. C. (2013). “Overexpression of a BAHD Acyltransferase, OsAt10, alters rice cell wall hydroxycinnamic acid content and saccharification.Plant Physiol. 161: 1615-1633.

    Batth, T. S., Keasling, J. D. and Petzold, C. J. (2012). “Targeted proteomics for metabolic pathway optimization.” Methods Mol Biol. 944: 237-249.

    Bokinsky, G., Baidoo, E. E., Akella, S., Burd, H., Weaver, D., Alonso-Gutierrez, J., Garcia-Martin, H., Lee, T. S. and Keasling, J. D. (2013). “HipA-triggered growth arrest and ?-lactam tolerance in Escherichia coli is mediated by RelA-dependent ppGpp synthesis.J. Bacteriol. 195(14): 3173-3182.

    Cetinkol, O. P., Smith-Moritz, A. M., Cheng, G., Lao, J., George, A., Hong, K., Henry, R., Simmons, B. A., Heazlewood, J. L. and Holmes, B. M. (2012). “Structural and chemical characterization of hardwood from tree species with applications as bioenergy feedstocks.PLoS One 7(12): e52820.

    Chandrasekaran A, Deng K, Koh CY, Takasuka T, Bergeman LF, Fox BG, Adams PD, Singh AK. “A universal flow cytometry assay for screening carbohydrate-active enzymes using glycan microspheres.” Chem. Commun. 49(48): 5441-5443.

    Chang C, Sustarich J, Bharadwaj R, Chandrasekaran A, Adams PD, Singh AK. “Droplet-based microfluidic platform for heterogeneous enzymatic assays.” Lab Chip. 13(9): 1817-1822.

    Chen, X., Vega-Sánchez, M. E., Verhertbruggen, Y., Chiniquy, D., Canlas P, Fagerström, A., Prak, L., Christensen, U., Bartley, L., Oikawa, A., Chen, M., Zuo, S., Auer, M., Willats, W., Scheller, H., V, and Ronald, P. C. (2012). “Inactivation of OsIRX10 leads to decreased xylan content in rice culm cell walls and improved biomass saccharification. ” Molecular Plant. 6(2):570-573.

    Chiniquy, D., Varanasi, P., Oh, T., Harholt, J., Katnelson, J., Singh, S., Auer, M., Simmons, B. A., Adams, P. D., Scheller, H.V., Ronald, P.C. (2013). “Three novel rice genes closely related to the Arabidopsis IRX9, IRX9L, and IRX14 genes and their roles in xylan biosynthesis.Frontiers Plant Biotechnol. 4: 83.

    Chiniquy, D., Sharma, V., Schultink, A., Baidoo, E. E., Rautengarten, C., Cheng, K., Carroll, A., Ulvskov, P., Harholt, J., Keasling, J. D., Pauly, M., Scheller, H. V. and Ronald, P. C. (2012). “XAX1 from glycosyltransferase family 61 mediates xylosyltransfer to rice xylan.Proc Natl Acad Sci U S A. 109(42): 17117-17122.

    Chiu, T. Y., Christiansen, K., Moreno, I., Lao, J., Loque, D., Orellana, A., Heazlewood, J. L., Clark, G. and Roux, S. (2012). “AtAPY1 and AtAPY2 function as Golgi localized nucleoside diphosphatases in Arabidopsis thaliana.Plant and Cell Physiology. 53(11):1913-25.

    Chivian, D., Dehal, P. S., Keller, K. and Arkin, A. P. (2013). “MetaMicrobesOnline: phylogenomic analysis of microbial communities.Nucleic Acids Res 41(Database issue): D648-654.

    Chou, H. H. and Keasling, J. D. (2012). “Synthetic pathway for production of five-carbon alcohols from isopentenyl diphosphate.Appl Environ Microbiol. 78(22): 7849-7855.

    Cruz, A. G., Scullin, C., Mu, C., Cheng, G., Stavila, V., Varanasi, P., Xu, D., Mentel, J., Chuang, Y. D., Simmons, B. A. and Singh, S. (2013). “Impact of high biomass loading on ionic liquid pretreatment.Biotechnol Biofuels 6(1): 52.

    D’Haeseleer, P., Gladden, J. M., Allgaier, M., Chain, P., Tringe, S., Malfatti, S., Aldrich, J., Nicora, C., Robinson, E., Pasa-Tolic, L., Hugenholtz, P., Simmons, B. A. and Singer, S. W. (2013). “Proteogenomic Analysis of a thermophilic bacterial consortiu, adapted to deconstruct switchgrass.” PLoS One 8(7): e68465.

    DeAngelis, K., D’Haeseleer, P., Chivian, D., Simmons, B. A., Arkin, A. P., Mavromatis, K., Malfatti, S., Tringe, S. and Hazen, T. (2013). “Metagenomes of tropical soil-derived anaerobic switchgrass-adapted consortia with and without iron.Standards in Genomic Sciences. 7(3):382-398.

    DeAngelis, K. M., Sharma, D., Varney, R., Simmons, B., Isern, N. G., Markilllie, L. M., Nicora, C., Norbeck, A. D., Taylor, R. C., Aldrich, J. T. and Robinson, E. W. (2013). “Evidence supporting dissimilatory and assimilatory lignin degradation in Enterobacter lignolyticus SCF1.” Front Microbiol. 4: 280.

    De Michele, R., Ast, C., Loque, D., Ho, C. H., Andrade, S. L. A., Lanquar, V., Grossmann, G., Gehne, S., Kumke, M. U. and Frommer, W. B. (2013). “Fluorescent sensors reporting the activity of ammonium transceptors in live cells.” eLife 2: e00800.

    de Rond, T., Peralta-Yahya, P., Cheng, X., Northen, TR, and Keasling, JD (2013) “Versatile synthesis of probes for high throughput enzyme activity screening.” Anal.Bioanal. Chem. 405:4969-4973

    Dietrich, J. A., Shis, D. L., Alikhani, A. and Keasling, J. D. (2012). “Transcription Factor-Based Screens and Synthetic Selections for Microbial Small-Molecule Biosynthesis.ACS Synthetic Biology: 121114093111002.

    Eichorst, S. A., Varanasi, P., Stavila, V., Zemla, M., Auer, M., Singh, S., Simmons, B. A. and Singer, S. W. (2013). “Community dynamics of cellulose-adapted thermophilic bacterial consortia.” Environ Microbiol. 15(9):2573-87.

    Eudes, A., Juminaga, D., Baidoo, E. E., Collins, F. W., Keasling, J. D. and Loque, D. (2013). “Production of hydroxycinnamoyl anthranilates from glucose in Escherichia coli.” Microb Cell Fact. 12: 62.

    Gille S, Sharma V, Baidoo EEK, Keasling JD, Scheller HV, Pauly M (2013). “Arabinosylation of a cell wall arabinogalactanprotein impacts root growth as exemplified by the Arabidopsis glycosyltransferase mutant ray1.” Mol Plant. 6(4): 1369-1372.

    Goldberg, A., Linshiz, G., Koudritsky, M., Chemodanov, A., and Hillson, N.J. (2012). “Distributed marine biorefineries for developing economiesProceedings of the ASME 2012 International Mechanical Engineering Congress & Exposition IMECE2012-86051.

    Groff, D., George, A., Sun, N., Sathitsuksanh, N., Bokinsky, G., Simmons, B. A., Holmes, B. and Keasling, J. D. (2013). “Acid Enhanced Ionic Liquid Pretreatment of Biomass.Green Chemistry. 15: 1264-67.

    Keasling, J. D., Mendoza, A. and Baran, P. S. (2012). “Synthesis: A constructive debate.” Nature. 492(7428): 188-189.

    Klein-Marcuschamer D, Chisti Y, Benemann JR, Lewis D. “A matter of detail: Assessing the true potential of microalgal biofuels.” (2013) Biotechnology and Bioengineering. June 3, 2013. Epub ahead of print.

    Klein-Marcuschamer, D., Turner, C., Allen, M., Gray, P., Dietzgen, R. G., Gresshoff, P. M., Hankamer, B., Heimann, K., Scott, P. T., Stephens, E., Speight, R. and Nielsen, L. K. (2013). “Technoeconomic analysis of renewable aviation fuel from microalgae,Pongamia pinnata, and sugarcane.” Biofuels, Bioproducts and Biorefining. 7(4): 416-428.

    Kung, Y., Runguphan, W. and Keasling, J. D. (2013). “From fields to fuels: recent advances in the microbial production of biofuels.” ACS Synth Biol. 1(11): 498-513.

    Linshiz, G., Goldberg, A., Konry, T. and Hillson, N. J. (2012). “The fusion of biology, computer science, and engineering: towards efficient and successful synthetic biology.Perspect Biol Med 55(4): 503-520.

    Linshiz, G., Stawski, N., Poust, S., Bi, C., Keasling, J. D. and Hillson, N. J. (2012). “PaR-PaR Laboratory Automation Platform.ACS Synthetic Biology 2 (5), 216–222.

    Liwanag, A. J. M., Ebert, B., Verhertbruggen, Y., Rennie, E. A., Rautengarten, C., Oikawa, A., Andersen, M. C. F., Clausen, M. H. and Scheller, H. V. (2012). “Pectin Biosynthesis: GALS1 (AT2g33570) in arabidopsis thaliana is a beta-1,4-galactan beta-1,4-galactosyltransferase.Plant Cell. 24:5024-36.

    Lupoi, J., Singh, S., Simmons, B. A. and Henry, R. (2013). “Assessment of Lignocellulosic Biomass Using Analytical Spectroscopy: An Evolution to High Throughput Techniques.” Bioenergy Research [epub only]

    Manabe, Y., Verhertbruggen, Y., Gille, S., Harholt, J., Chong, S. L., Pawar, P. M. A., Mellerowicz, E., Tenkanen, M., Cheng, K., Pauly, M. and Scheller, H. (2013). “RWA Proteins Play Vital and Distinct Roles in Cell Wall O-Acetylation in Arabidopsis thaliana.” Plant Physiology. [epub only]

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