• 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

    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

    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

    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

    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

    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

    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

    de Rond, T., Stow, P., Eigl, I., Johnson, R. E., Chan, L. J. G., Goyal, G., . . . Keasling, J. D. (2017). “Oxidative cyclization of prodigiosin by an alkylglycerol monooxygenase-like enzyme”. [Brief Communication]. Nat Chem Biol, advance online publication. doi, 10.1038/nchembio.2471

    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

    Dutta, Tanmoy, Isern, Nancy G., Sun, Jian, Wang, Eileen, Hull, Sarah, Cort, John R., . . . Singh, Seema. (2017). “Survey of Lignin-Structure Changes and Depolymerization during Ionic Liquid Pretreatment”. ACS Sustainable Chemistry & Engineering. doi, 10.1021/acssuschemeng.7b02123

    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

    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

    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

    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

    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

    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

    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

    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

    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

    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

    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

    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

    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

    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

    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

    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

    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

    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

    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

    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

    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

    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

    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

    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

    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

    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

    Morrell, W. C., Birkel, G. W., Forrer, M., Lopez, T., Backman, T. W. H., 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

    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

    Neupane, Binod, Konda, N. V. S. N. Murthy, Singh, Seema, Simmons, Blake A., & Scown, Corinne D. (2017). “Life-Cycle Greenhouse Gas and Water Intensity of Cellulosic Biofuel Production Using Cholinium Lysinate Ionic Liquid Pretreatment”. ACS Sustainable Chemistry & Engineering. doi, 10.1021/acssuschemeng.7b02116

    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

    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

    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

    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

    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

    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

    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

    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

    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

    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

    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

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

    Shih, P. M., Ward, L. M., & Fischer, W. W. (2017). “Evolution of the 3-hydroxypropionate bicycle and recent transfer of anoxygenic photosynthesis into the Chloroflexi”. Proc Natl Acad Sci U S A, 114(40), 10749-10754. doi, 10.1073/pnas.1710798114

    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

    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

    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

    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

    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

    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,

    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

    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

    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

    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

    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

    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

    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

    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

    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

    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

    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

    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

    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

    Yuan, Xueming, He, Lilin, Singh, Seema, Simmons, Blake A., & Cheng, Gang. (2017). “Effect of Ionic Liquid Pretreatment on the Porosity of Pine: Insights from Small-Angle Neutron Scattering, Nitrogen Adsorption Analysis, and X-ray Diffraction”. Energy & Fuels. doi, 10.1021/acs.energyfuels.7b01567

    Yuan, Xueming, Singh, Seema, Simmons, Blake A., & Cheng, Gang. (2017). “Biomass Pretreatment Using Dilute Aqueous Ionic Liquid (IL) Solutions with Dynamically Varying IL Concentration and Its Impact on IL Recycling”. ACS Sustainable Chemistry & Engineering. doi, 10.1021/acssuschemeng.7b00480

    Yuzawa, S., Keasling, J. D., & Katz, L. (2017). “Bio-based production of fuels and industrial chemicals by repurposing antibiotic-producing type I modular polyketide synthases: opportunities and challenges”. J Antibiot (Tokyo). doi, 10.1038/ja.2016.136

    Zargar, A., Bailey, C. B., Haushalter, R. W., Eiben, C. B., Katz, L., & Keasling, J. D. (2017). “Leveraging microbial biosynthetic pathways for the generation of ‘drop-in’ biofuels”. Curr Opin Biotechnol, 45, 156-163. doi, 10.1016/j.copbio.2017.03.004

    Zeng, Jijiao, Mills, Matthew J. L., Simmons, Blake A., Kent, Michael S., & Sale, Kenneth L. (2017). “Understanding factors controlling depolymerization and polymerization in catalytic degradation of β-ether linked model lignin compounds by versatile peroxidase”. [10.1039/C6GC03379B]. Green Chem. doi, 10.1039/c6gc03379b

    Zeng, Wei, Ebert, Berit, Parsons, Harriet T., Rautengarten, Carsten, Bacic, Antony, & Heazlewood, Joshua L. (2017). Enrichment of Golgi Membranes from Triticum aestivum (Wheat) Seedlings. In Nicolas L. Taylor & A. Harvey Millar (Eds.), Isolation of Plant Organelles and Structures: Methods and Protocols (pp. 131-150). New York, NY: Springer New York.

    Zhang, J., Barajas, J. F., Burdu, M., Wang, G., Baidoo, E. E., & Keasling, J. D. (2017). “Application of an Acyl-CoA Ligase from Streptomyces aizunensis for Lactam Biosynthesis”. ACS Synth Biol. doi, 10.1021/acssynbio.6b00372

    Zhao, Wenwen, Xiao, Ling-Ping, Song, Guoyong, Sun, Run-Cang, He, Lilin, Singh, Seema, . . . Cheng, Gang. (2017). “From lignin subunits to aggregates: insights into lignin solubilization”. [10.1039/C7GC00944E]. Green Chem. doi, 10.1039/c7gc00944e



  • Beller, H. R., Zhou, P., Jewell, T. N. M., Goh, E.-B., & Keasling, J. D. (2016). “Enhanced fatty acid production in engineered chemolithoautotrophic bacteria using reduced sulfur compounds as energy sources”. Metabolic Engineering Communications, 3, 211-215. doi, 10.1016/j.meteno.2016.07.001

    Billings, A. F., Fortney, J. L., Hazen, T. C., Simmons, B., Davenport, K. W., Goodwin, L., Ivanova, N., Kyrpides, N. C., Mavromatis, K., Woyke, T., & DeAngelis, K. M. (2015). “Genome sequence and description of the anaerobic lignin-degrading bacterium Tolumonas lignolytica sp. nov”. [journal article]. Stand Genomic Sci, 10(1), 106. doi, 10.1186/s40793-015-0100-3

    Brunk, E., George, K. W., Alonso-Gutierrez, J., Thompson, M., Baidoo, E., Wang, G., Petzold, C. J., McCloskey, D., Monk, J., Yang, L., O’Brien, E. J., Batth, T. S., Martin, H. G., Feist, A., Adams, P. D., Keasling, J. D., Palsson, B. O., & Lee, T. S. (2016). “Characterizing Strain Variation in Engineered E. coli Using a Multi-Omics-Based Workflow”. Cell Syst, 2(5), 335-346. doi, 10.1016/j.cels.2016.04.004

    Chandran, A. K., Yoo, Y. H., Cao, P., Sharma, R., Sharma, M., Dardick, C., Ronald, P. C., & Jung, K. H. (2016). “Updated Rice Kinase Database RKD 2.0: enabling transcriptome and functional analysis of rice kinase genes”. Rice (N Y), 9(1), 40. doi, 10.1186/s12284-016-0106-5

    Chern, M., Xu, Q., Bart, R. S., Bai, W., Ruan, D., Sze-To, W. H., Canlas, P. E., Jain, R., Chen, X., & Ronald, P. C. (2016). “A Genetic Screen Identifies a Requirement for Cysteine-Rich-Receptor-Like Kinases in Rice NH1 (OsNPR1)-Mediated Immunity”. PLoS Genet, 12(5), e1006049. doi, 10.1371/journal.pgen.1006049

    Chubukov, V., Mukhopadhyay, A., Petzold, C. J., Keasling, J. D., & Martín, H. G. (2016). “Synthetic and systems biology for microbial production of commodity chemicals”. [Review Article]. npj Systems Biology and Applications, 2, 16009. doi, 10.1038/npjsba.2016.9

    Chuck, C., McManus, M., Allen, M. J., Singh, S. (2016). Biofuels for Aviation, 1st Edition Feedstocks, Technology and Implementation Biofuels for Aviation: Feedstocks, Technology and Implementation (pp. 17-34): Elsevier.

    Corno, L., Pilu, R., Tran , K., Tambone, F., Singh , S., Simmons , B. A., & Adani, F. (2016). “Sugars Production for Green Chemistry from 2nd Generation Crop (Arundo donax L.): A Full Field Approach”. ChemistrySelect, 1(11), 2617-2623. doi, 10.1002/slct.201600733

    Costa, T. H., Vega-Sanchez, M. E., Milagres, A. M., Scheller, H. V., & Ferraz, A. (2016). “Tissue-specific distribution of hemicelluloses in six different
    sugarcane hybrids as related to cell wall recalcitrance”. Biotechnol Biofuels, 9, 99. doi, 10.1186/s13068-016-0513-2

    d’Espaux, L., Mendez-Perez, D., Li, R., & Keasling, J. D. (2015). “Synthetic biology for microbial production of lipid-based biofuels”. Curr Opin Chem Biol, 29, 58-65. doi, 10.1016/j.cbpa.2015.09.009

    da Costa Sousa, L., Jin, M., Chundawat, S. P. S., Bokade, V., Tang, X., Azarpira, A., Lu, F., Avci, U., Humpula, J., Uppugundla, N., Gunawan, C., Pattathil, S., Cheh, A. M., Kothari, N., Kumar, R., Ralph, J., Hahn, M. G., Wyman, C. E., Singh, S., Simmons, B. A., Dale, B. E., & Balan, V. (2016). “Next-generation ammonia pretreatment enhances cellulosic biofuel production”. [10.1039/C5EE03051J]. Energy Environ. Sci., 9(4), 1215-1223. doi, 10.1039/c5ee03051j

    de Michele, R., McFarlane, H. E., Parsons, H. T., Meents, M. J., Lao, J., Gonzalez Fernandez-Nino, S. M., Petzold, C. J., Frommer, W. B., Samuels, A. L., & Heazlewood, J. L. (2016). “Free-Flow Electrophoresis of Plasma Membrane Vesicles Enriched by Two-Phase Partitioning Enhances the Quality of the Proteome from Arabidopsis Seedlings”. J Proteome Res, 15(3), 900-913. doi, 10.1021/acs.jproteome.5b00876

    Degreif, D., Bertl, A., Keasling, J. D., & Budin, I. (2015). “A novel flocculation pathway mediated by ER membrane fluidity”. [Meeting Abstract]. Yeast, 32, S117-S117. ://WOS:000361466200172.

    Deng, K., Takasuka, T. E., Bianchetti, C. M., Bergeman, L. F., Adams, P. D., Northen, T. R., & Fox, B. G. (2015). “Use of Nanostructure-Initiator Mass Spectrometry to Deduce Selectivity of Reaction in Glycoside Hydrolases”. [Methods]. Front Bioeng Biotechnol, 3, 165. doi, 10.3389/fbioe.2015.00165

    Dutta, T., Shi, J., Sun, J., Zhang, X., Cheng, G., Simmons, B. A., & Singh, S. (2015). CHAPTER 3. Ionic Liquid Pretreatment of Lignocellulosic Biomass for Biofuels and Chemicals Ionic Liquids in the Biorefinery Concept : Challenges and Perspectives (pp. 65-94).

    Eng, C. H., Yuzawa, S., Wang, G., Baidoo, E. E., Katz, L., & Keasling, J. D. (2016). “Alteration of Polyketide Stereochemistry from anti to syn by a Ketoreductase Domain Exchange in a Type I Modular Polyketide Synthase Subunit”. Biochemistry, 55(12), 1677-1680. doi, 10.1021/acs.biochem.6b00129

    Eudes, A., Pereira, J. H., Yogiswara, S., Wang, G., Teixeira Benites, V., Baidoo, E. E., Lee, T. S., Adams, P. D., Keasling, J. D., & Loque, D. (2016). “Exploiting the Substrate Promiscuity of Hydroxycinnamoyl-CoA:Shikimate Hydroxycinnamoyl Transferase to Reduce Lignin”. Plant Cell Physiol, 57(3), 568-579. doi, 10.1093/pcp/pcw016

    Eudes, A., Teixeira Benites, V., Wang, G., Baidoo, E. E., Lee, T. S., Keasling, J. D., & Loque, D. (2015). “Precursor-Directed Combinatorial Biosynthesis of Cinnamoyl, Dihydrocinnamoyl, and Benzoyl Anthranilates in Saccharomyces cerevisiae”. PLoS One, 10(10), e0138972. doi, 10.1371/journal.pone.0138972

    Eudes, A., Zhao, N., Sathitsuksanoh, N., Baidoo, E. E., Lao, J., Wang, G., Yogiswara, S., Lee, T. S., Singh, S., Mortimer, J. C., Keasling, J. D., Simmons, B. A., & Loque, D. (2016). “Expression of S-adenosylmethionine Hydrolase in Tissues Synthesizing Secondary Cell Walls Alters Specific Methylated Cell Wall Fractions and Improves Biomass Digestibility”. [Original Research]. Front Bioeng Biotechnol, 4, 58. doi, 10.3389/fbioe.2016.00058

    Frederix, M., Mingardon, F., Hu, M., Sun, N., Pray, T., Singh, S., Simmons, B. A., Keasling, J. D., & Mukhopadhyay, A. (2016). “Development of an E. coli strain for one-pot biofuel production from ionic liquid pretreated cellulose and switchgrass”. [10.1039/C6GC00642F]. Green Chemistry, 18(15), 4189-4197. doi, 10.1039/c6gc00642f ://WOS:000381328300007.

    Gach, P. C., Shih, S. C., Sustarich, J., Keasling, J. D., Hillson, N. J., Adams, P. D., & Singh, A. K. (2016). “A Droplet Microfluidic Platform for Automating Genetic Engineering”. ACS Synth Biol, 5(5), 426-433. doi, 10.1021/acssynbio.6b00011

    Gupta, S., Feng, J., Chan, L. J., Petzold, C. J., & Ralston, C. Y. (2016). “Synchrotron X-ray footprinting as a method to visualize water in proteins”. J Synchrotron Radiat, 23(Pt 5), 1056-1069. doi, 10.1107/S1600577516009024

    Hagen, A., Poust, S., Rond, T., Fortman, J. L., Katz, L., Petzold, C. J., & Keasling, J. D. (2016). “Engineering a Polyketide Synthase for In Vitro Production of Adipic Acid”. ACS Synth Biol, 5(1), 21-27. doi, 10.1021/acssynbio.5b00153

    Harkenrider, M., Sharma, R., De Vleesschauwer, D., Tsao, L., Zhang, X., Chern, M., Canlas, P., Zuo, S., & Ronald, P. C. (2016). “Overexpression of Rice Wall-Associated Kinase 25 (OsWAK25) Alters Resistance to Bacterial and Fungal Pathogens”. PLoS One, 11(1), e0147310. doi, 10.1371/journal.pone.0147310

    Healey, A. L., Lee, D. J., Furtado, A., Simmons, B. A., & Henry, R. J. (2015). “Efficient Eucalypt Cell Wall Deconstruction and Conversion for Sustainable Lignocellulosic Biofuels”. Front Bioeng Biotechnol, 3, 190. doi, 10.3389/fbioe.2015.00190

    Healey, A. L., Lupoi, J. S., Lee, D. J., Sykes, R. W., Guenther, J. M., Tran, K., Decker, S. R., Singh, S., Simmons, B. A., & Henry, R. J. (2016). “Effect of aging on lignin content, composition and enzymatic saccharification in Corymbia hybrids and parental taxa between years 9 and 12”. Biomass and Bioenergy, 93, 50-59. doi, 10.1016/j.biombioe.2016.06.016

    Helmich, K. E., Pereira, J. H., Gall, D. L., Heins, R. A., McAndrew, R. P., Bingman, C., Deng, K., Holland, K. C., Noguera, D. R., Simmons, B. A., Sale, K. L., Ralph, J., Donohue, T. J., Adams, P. D., & Phillips, G. N., Jr. (2016). “Structural Basis of Stereospecificity in the Bacterial Enzymatic Cleavage of beta-Aryl Ether Bonds in Lignin”. J Biol Chem, 291(10), 5234-5246. doi, 10.1074/jbc.M115.694307

    Hillson, N. J., Plahar, H. A., Beal, J., & Prithviraj, R. (2016). “Improving Synthetic Biology Communication: Recommended Practices for Visual Depiction and Digital Submission of Genetic Designs”. ACS Synth Biol, 5(6), 449-451. doi, 10.1021/acssynbio.6b00146

    Hiras, J., Wu, Y. W., Deng, K., Nicora, C. D., Aldrich, J. T., Frey, D., Kolinko, S., Robinson, E. W., Jacobs, J. M., Adams, P. D., Northen, T. R., Simmons, B. A., & Singer, S. W. (2016). “Comparative Community Proteomics Demonstrates the Unexpected Importance of Actinobacterial Glycoside Hydrolase Family 12 Protein for Crystalline Cellulose Hydrolysis”. MBio, 7(4). doi, 10.1128/mBio.01106-16

    Hoang, N. V., Furtado, A., Botha, F. C., Simmons, B. A., & Henry, R. J. (2015). “Potential for Genetic Improvement of Sugarcane as a Source of Biomass for Biofuels”. [Review]. Front Bioeng Biotechnol, 3, 182. doi, 10.3389/fbioe.2015.00182

    Hudson, C. M., Kirton, E., Hutchinson, M. I., Redfern, J. L., Simmons, B., Ackerman, E., Singh, S., Williams, K. P., Natvig, D. O., & Powell, A. J. (2015). “Lignin-modifying processes in the rhizosphere of arid land grasses”. Environ Microbiol, 17(12), 4965-4978. doi, 10.1111/1462-2920.13020

    Javidpour, P., Deutsch, S., Mutalik, V. K., Hillson, N. J., Petzold, C. J., Keasling, J. D., & Beller, H. R. (2016). “Investigation of Proposed Ladderane Biosynthetic Genes from Anammox Bacteria by Heterologous Expression in E. coli”. PLoS One, 11(3), e0151087. doi, 10.1371/journal.pone.0151087

    Joshua, C. J., Simmons, B. A., & Singer, S. W. (2016). “Ferricyanide-based analysis of aqueous lignin suspension revealed sequestration of water-soluble lignin moieties”. [10.1039/C6RA04443C]. Rsc Advances, 6(59), 54382-54393. doi, 10.1039/c6ra04443c ://WOS:000378521400096.

    Kang, A., George, K. W., Wang, G., Baidoo, E., Keasling, J. D., & Lee, T. S. (2016). “Isopentenyl diphosphate (IPP)-bypass mevalonate pathways for isopentenol production”. Metab Eng, 34, 25-35. doi, 10.1016/j.ymben.2015.12.002

    Kang, A., & Lee, T. S. (2015). “Converting Sugars to Biofuels: Ethanol and Beyond”. Bioengineering, 2(4), 184-203. doi, 10.3390/bioengineering2040184

    Kang, A., & Lee, T. S. (2016). Chapter 2 – Secondary Metabolism for Isoprenoid-based Biofuels A2 – Trinh, Carrie A. EckertCong T Biotechnology for Biofuel Production and Optimization (pp. 35-71). Amsterdam: Elsevier.

    Lechner, A., Brunk, E., & Keasling, J. D. (2016). “The Need for Integrated Approaches in Metabolic Engineering”. Cold Spring Harb Perspect Biol. doi, 10.1101/cshperspect.a023903

    Li, G., Chern, M., Jain, R., Martin, J. A., Schackwitz, W. S., Jiang, L., Vega-Sanchez, M. E., Lipzen, A. M., Barry, K. W., Schmutz, J., & Ronald, P. C. (2016). “Genome-Wide Sequencing of 41 Rice (Oryza sativa L.) Mutated Lines Reveals Diverse Mutations Induced by Fast-Neutron Irradiation”. Mol Plant, 9(7), 1078-1081. doi, 10.1016/j.molp.2016.03.009

    Lin, K. H., Liao, B. Y., Chang, H. W., Huang, S. W., Chang, T. Y., Yang, C. Y., Wang, Y. B., Lin, Y. T., Wu, Y. W., Tang, S. L., & Yu, H. T. (2015). “Metabolic characteristics of dominant microbes and key rare species from an acidic hot spring in Taiwan revealed by metagenomics”. BMC Genomics, 16(1), 1029. doi, 10.1186/s12864-015-2230-9

    Linshiz, G., Jensen, E., Stawski, N., Bi, C., Elsbree, N., Jiao, H., Kim, J., Mathies, R., Keasling, J. D., & Hillson, N. J. (2016). “End-to-end automated microfluidic platform for synthetic biology: from design to functional analysis”. [journal article]. J Biol Eng, 10(1), 3. doi, 10.1186/s13036-016-0024-5

    Liszka, M. J., Kang, A., Konda, N. V. S. N. M., Tran, K., Gladden, J. M., Singh, S., Keasling, J. D., Scown, C. D., Lee, T. S., Simmons, B. A., & Sale, K. L. (2016). “Switchable ionic liquids based on di-carboxylic acids for one-pot conversion of biomass to an advanced biofuel”. [10.1039/C6GC00657D]. Green Chemistry, 18(14), 4012-4021. doi, 10.1039/c6gc00657d ://WOS:000379438200014.

    Lupoi, J., Simmons, B., & Henry, R. (2016). “Editorial: Biomass Modification, Characterization, and Process Monitoring Analytics to Support Biofuel and Biomaterial Production”. Front Bioeng Biotechnol, 4, 25. doi, 10.3389/fbioe.2016.00025

    Ma, J. Y., Sun, W., Koteyeva, N. K., Voznesenskaya, E., Stutz, S. S., Gandin, A., Smith-Moritz, A. M., Heazlewood, J. L., & Cousins, A. B. (2016). “Influence of light and nitrogen on the photosynthetic efficiency in the C4 plant Miscanthus x giganteus”. Photosynth Res. doi, 10.1007/s11120-016-0281-7

    Nelson, W. C., Maezato, Y., Wu, Y. W., Romine, M. F., & Lindemann, S. R. (2016). “Identification and Resolution of Microdiversity through Metagenomic Sequencing of Parallel Consortia”. Appl Environ Microbiol, 82(1), 255-267. doi, 10.1128/AEM.02274-15

    Nielsen, J., & Keasling, J. D. (2016). “Engineering Cellular Metabolism”. Cell, 164(6), 1185-1197. doi, 10.1016/j.cell.2016.02.004

    Pace, S., Ceballos, S. J., Harrold, D., Stannard, W., Simmons, B. A., Singer, S. W., Thelen, M. P., & VanderGheynst, J. S. (2016). “Enrichment of microbial communities tolerant to the ionic liquids tetrabutylphosphonium chloride and tributylethylphosphonium diethylphosphate”. [journal article]. Appl Microbiol Biotechnol, 100(12), 5639-5652. doi, 10.1007/s00253-016-7525-5

    Parthasarathi, R., Sun, J., Dutta, T., Sun, N., Pattathil, S., Murthy Konda, N. V., Peralta, A. G., Simmons, B. A., & Singh, S. (2016). “Activation of lignocellulosic biomass for higher sugar yields using aqueous ionic liquid at low severity process conditions”. Biotechnol Biofuels, 9, 160. doi, 10.1186/s13068-016-0561-7

    Pereira, J. H., Heins, R. A., Gall, D. L., McAndrew, R. P., Deng, K., Holland, K. C., Donohue, T. J., Noguera, D. R., Simmons, B. A., Sale, K. L., Ralph, J., & Adams, P. D. (2016). “Structural and Biochemical Characterization of the Early and Late Enzymes in the Lignin beta-Aryl Ether Cleavage Pathway from Sphingobium sp. SYK-6”. J Biol Chem, 291(19), 10228-10238. doi, 10.1074/jbc.M115.700427

    Perez-Pimienta, J. A., Flores-Gomez, C. A., Ruiz, H. A., Sathitsuksanoh, N., Balan, V., da Costa Sousa, L., Dale, B. E., Singh, S., & Simmons, B. A. (2016). “Evaluation of agave bagasse recalcitrance using AFEX, autohydrolysis, and ionic liquid pretreatments”. Bioresour Technol, 211, 216-223. doi, 10.1016/j.biortech.2016.03.103

    Perez-Pimienta, J. A., Poggi-Varaldo, H. M., Ponce-Noyola, T., Ramos-Valdivia, A. C., Chavez-Carvayar, J. A., Stavila, V., & Simmons, B. A. (2016). “Fractional pretreatment of raw and calcium oxalate-extracted agave bagasse using ionic liquid and alkaline hydrogen peroxide”. Biomass and Bioenergy, 91, 48-55. doi, 10.1016/j.biombioe.2016.05.001

    Quinn, J. Y., Cox, R. S., 3rd, Adler, A., Beal, J., Bhatia, S., Cai, Y., Chen, J., Clancy, K., Galdzicki, M., Hillson, N. J., Le Novere, N., Maheshwari, A. J., McLaughlin, J. A., Myers, C. J., P, U., Pocock, M., Rodriguez, C., Soldatova, L., Stan, G. B., Swainston, N., Wipat, A., & Sauro, H. M. (2015). “SBOL Visual: A Graphical Language for Genetic Designs”. PLoS Biol, 13(12), e1002310. doi, 10.1371/journal.pbio.1002310

    Rautengarten, C., Ebert, B., Liu, L., Stonebloom, S., Smith-Moritz, A. M., Pauly, M., Orellana, A., Scheller, H. V., & Heazlewood, J. L. (2016). “The Arabidopsis Golgi-localized GDP-L-fucose transporter is required for plant development”. Nat Commun, 7, 12119. doi, 10.1038/ncomms12119

    Reider Apel, A., Ouellet, M., Szmidt-Middleton, H., Keasling, J. D., & Mukhopadhyay, A. (2016). “Evolved hexose transporter enhances xylose uptake and glucose/xylose co-utilization in Saccharomyces cerevisiae”. Sci Rep, 6, 19512. doi, 10.1038/srep19512

    Rodriguez, S., Denby, C. M., Van Vu, T., Baidoo, E. E., Wang, G., & Keasling, J. D. (2016). “ATP citrate lyase mediated cytosolic acetyl-CoA biosynthesis increases mevalonate production in Saccharomyces cerevisiae”. Microb Cell Fact, 15(1), 48. doi, 10.1186/s12934-016-0447-1

    Sawake, S., Tajima, N., Mortimer, J. C., Lao, J., Ishikawa, T., Yu, X., Yamanashi, Y., Yoshimi, Y., Kawai-Yamada, M., Dupree, P., Tsumuraya, Y., & Kotake, T. (2015). “KONJAC1 and 2 Are Key Factors for GDP-Mannose Generation and Affect l-Ascorbic Acid and Glucomannan Biosynthesis in Arabidopsis”. Plant Cell, 27(12), 3397-3409. doi, 10.1105/tpc.15.00379

    Schwessinger, B., Li, X., Ellinghaus, T. L., Chan, L. J., Wei, T., Joe, A., Thomas, N., Pruitt, R., Adams, P. D., Chern, M. S., Petzold, C. J., Liu, C. C., & Ronald, P. C. (2016). “A second-generation expression system for tyrosine-sulfated proteins and its application in crop protection”. Integr Biol (Camb), 8(4), 542-545. doi, 10.1039/c5ib00232j

    Shi, J., Pattathil, S., Parthasarathi, R., Anderson, N. A., Kim, J. I., Venketachalam, S., Hahn, M. G., Chapple, C., Simmons, B. A., & Singh, S. (2016). “Impact of engineered lignin composition on biomass recalcitrance and ionic liquid pretreatment efficiency”. [10.1039/C6GC01193D]. Green Chem. doi, 10.1039/c6gc01193d

    Shih, P. M., Hemp, J., Ward, L. M., Matzke, N. J., & Fischer, W. W. (2016). “Crown group Oxyphotobacteria postdate the rise of oxygen”. Geobiology. doi, 10.1111/gbi.12200

    Shih, P. M., Liang, Y., & Loque, D. (2016). “Biotechnology and synthetic biology approaches for metabolic engineering of bioenergy crops”. Plant J, 87(1), 103-117. doi, 10.1111/tpj.13176

    Shylesh, S., Gokhale, A. A., Scown, C. D., Kim, D., Ho, C. R., & Bell, A. T. (2016). “From Sugars to Wheels: The Conversion of Ethanol to 1,3-Butadiene over Metal-Promoted Magnesia-Silicate Catalysts”. ChemSusChem, 9(12), 1462-1472. doi, 10.1002/cssc.201600195

    Simmons, C. W., Higgins, B., Staley, S., Joh, L. D., Simmons, B. A., Singer, S. W., Stapleton, J. J., & VanderGheynst, J. S. (2016). “The role of organic matter amendment level on soil heating, organic acid accumulation, and development of bacterial communities in solarized soil”. Applied Soil Ecology, 106, 37-46. doi, 10.1016/j.apsoil.2016.04.018 ://WOS:000377359500006.

    Stavila, V., Parthasarathi, R., Davis, R. W., El Gabaly, F., Sale, K. L., Simmons, B. A., Singh, S., & Allendorf, M. D. (2016). “MOF-Based Catalysts for Selective Hydrogenolysis of Carbon–Oxygen Ether Bonds”. ACS Catalysis, 6(1), 55-59. doi, 10.1021/acscatal.5b02061

    Stonebloom, S., Ebert, B., Xiong, G., Pattathil, S., Birdseye, D., Lao, J., Pauly, M., Hahn, M. G., Heazlewood, J. L., & Scheller, H. V. (2016). “A DUF-246 family glycosyltransferase-like gene affects male fertility and the biosynthesis of pectic arabinogalactans”. BMC Plant Biol, 16(1), 90. doi, 10.1186/s12870-016-0780-x

    Sun, J., Konda, N. V. S. N. M., Shi, J., Parthasarathi, R., Dutta, T., Xu, F., Scown, C. D., Simmons, B. A., & Singh, S. (2016). “CO2enabled process integration for the production of cellulosic ethanol using bionic liquids”. [10.1039/C6EE00913A]. Energy Environ. Sci., 9(9), 2822-2834. doi, 10.1039/c6ee00913a

    Walker, J. A., Takasuka, T. E., Deng, K., Bianchetti, C. M., Udell, H. S., Prom, B. M., Kim, H., Adams, P. D., Northen, T. R., & Fox, B. G. (2015). “Multifunctional cellulase catalysis targeted by fusion to different carbohydrate-binding modules”. Biotechnol Biofuels, 8, 220. doi, 10.1186/s13068-015-0402-0

    Wei, T., Chern, M., Liu, F., & Ronald, P. C. (2016). “Suppression of bacterial infection in rice by treatment with a sulfated peptide”. Mol Plant Pathol, n/a-n/a. doi, 10.1111/mpp.12368

    Wu, W., Tran, W., Taatjes, C. A., Alonso-Gutierrez, J., Lee, T. S., & Gladden, J. M. (2016). “Rapid Discovery and Functional Characterization of Terpene Synthases from Four Endophytic Xylariaceae”. PLoS One, 11(2), e0146983. doi, 10.1371/journal.pone.0146983

    Wu, Y. W., Simmons, B. A., & Singer, S. W. (2016). “MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets”. Bioinformatics, 32(4), 605-607. doi, 10.1093/bioinformatics/btv638

    Xu, D., Shi, J., Rautengarten, C., Yang, L., Qian, X., Uzair, M., Zhu, L., Luo, Q., An, G., Wassmann, F., Schreiber, L., Heazlewood, J. L., Scheller, H. V., Hu, J., Zhang, D., & Liang, W. (2016). “Defective Pollen Wall 2 (DPW2) Encodes an Acyl Transferase Required for Rice Pollen Development”. Plant Physiol. doi, 10.1104/pp.16.00095

    Xu, F., Sun, J., Konda, N. V. S. N. M., Shi, J., Dutta, T., Scown, C. D., Simmons, B. A., & Singh, S. (2016). “Transforming biomass conversion with ionic liquids: process intensification and the development of a high-gravity, one-pot process for the production of cellulosic ethanol”. [10.1039/C5EE02940F]. Energy & Environmental Science, 9(3), 1042-1049. doi, 10.1039/c5ee02940f ://WOS:000372243600034.

    Yang, Y., Han, X., Liang, Y., Ghosh, A., Chen, J., & Tang, M. (2015). “The Combined Effects of Arbuscular Mycorrhizal Fungi (AMF) and Lead (Pb) Stress on Pb Accumulation, Plant Growth Parameters, Photosynthesis, and Antioxidant Enzymes in Robinia pseudoacacia L”. PLoS One, 10(12), e0145726. doi, 10.1371/journal.pone.0145726

    Yang, Y., Liang, Y., Han, X., Chiu, T. Y., Ghosh, A., Chen, H., & Tang, M. (2016). “The roles of arbuscular mycorrhizal fungi (AMF) in phytoremediation and tree-herb interactions in Pb contaminated soil”. [Article]. Sci Rep, 6, 20469. doi, 10.1038/srep20469

    Yu, C., Reddy, A. P., Simmons, C. W., Simmons, B. A., Singer, S. W., & VanderGheynst, J. S. (2015). “Preservation of microbial communities enriched on lignocellulose under thermophilic and high-solid conditions”. Biotechnol Biofuels, 8, 206. doi, 10.1186/s13068-015-0392-y

    Yuzawa, S., Keasling, J. D., & Katz, L. (2016). “Insights into polyketide biosynthesis gained from repurposing antibiotic-producing polyketide synthases to produce fuels and chemicals”. J Antibiot (Tokyo), 69(7), 494-499. doi, 10.1038/ja.2016.64

    Zargar, K., Saville, R., Phelan, R. M., Tringe, S. G., Petzold, C. J., Keasling, J. D., & Beller, H. R. (2016). “In vitro Characterization of Phenylacetate Decarboxylase, a Novel Enzyme Catalyzing Toluene Biosynthesis in an Anaerobic Microbial Community”. Sci Rep, 6, 31362. doi, 10.1038/srep31362

    Zhang, J., Kao, E., Wang, G., Baidoo, E. E. K., Chen, M., & Keasling, J. D. (2016). “Metabolic engineering of Escherichia coli for the biosynthesis of 2-pyrrolidone”. Metabolic Engineering Communications, 3, 1-7. doi, 10.1016/j.meteno.2015.11.001

    Zhang, W., Sathitsuksanoh, N., Simmons, B. A., Frazier, C. E., Barone, J. R., & Renneckar, S. (2016). “Revealing the thermal sensitivity of lignin during glycerol thermal processing through structural analysis”. [10.1039/C6RA00745G]. Rsc Advances, 6(36), 30234-30246. doi, 10.1039/c6ra00745g ://WOS:000373061600044.

    Zhu, Y., Yan, J., Liu, W., Liu, L., Sheng, Y., Sun, Y., Li, Y., Scheller, H. V., Jiang, M., Hou, X., Ni, L., & Zhang, A. (2016). “Phosphorylation of a NAC Transcription Factor by a Calcium/Calmodulin-Dependent Protein Kinase Regulates Abscisic Acid-Induced Antioxidant Defense in Maize”. Plant Physiol, 171(3), 1651-1664. doi, 10.1104/pp.16.00168

  • Alonso-Gutierrez, J., Kim, E. M., Batth, T. S., Cho, N., Hu, Q., Chan, L. J., Petzold, C. J., Hillson, N. J., Adams, P. D., Keasling, J. D., Garcia Martin, H., & Lee, T. S. (2015). “Principal component analysis of proteomics (PCAP) as a tool to direct metabolic engineering”. Metab Eng, 28, 123-133. doi, 10.1016/j.ymben.2014.11.011

    Baker, S. E., Schackwitz, W., Lipzen, A., Martin, J., Haridas, S., LaButti, K., Grigoriev, I. V., Simmons, B. A., & McCluskey, K. (2015). “Draft Genome Sequence of Neurospora crassa Strain FGSC 73”. Genome Announc, 3(2). doi, 10.1128/genomeA.00074-15

    Barajas, J. F., Phelan, R. M., Schaub, A. J., Kliewer, J. T., Kelly, P. J., Jackson, D. R., Luo, R., Keasling, J. D., & Tsai, S. C. (2015). “Comprehensive Structural and Biochemical Analysis of the Terminal Myxalamid Reductase Domain for the Engineered Production of Primary Alcohols”. Chem Biol, 22(8), 1018-1029. doi, 10.1016/j.chembiol.2015.06.022

    Beller, H. R., Lee, T. S., & Katz, L. (2015). “Natural products as biofuels and bio-based chemicals: fatty acids and isoprenoids”. Nat Prod Rep. doi, 10.1039/c5np00068h

    Cheng, G., Zhang, X., Simmons, B., & Singh, S. (2015). “Theory, practice and prospects of X- ray and neutron scattering for lignocellulosic biomass characterization: towards understanding biomass pretreatment”. [10.1039/C4EE03147D]. Energy & Environmental Science, 8(2), 436-455. doi, DOI 10.1039/c4ee03147d

    Chiu, T. Y., Lao, J., Manalansan, B., Loque, D., Roux, S. J., & Heazlewood, J. L. (2015). “Biochemical characterization of Arabidopsis APYRASE family reveals their roles in regulating endomembrane NDP/NMP homeostasis”. Biochem J. doi, 10.1042/bj20150235

    Chubukov, V., Mingardon, F., Schackwitz, W., Baidoo, E. E., Alonso-Gutierrez, J., Hu, Q., Lee, T. S., Keasling, J. D., & Mukhopadhyay, A. (2015). “Acute limonene toxicity in Escherichia coli is caused by limonene-hydroperoxide and alleviated by a point mutation in alkyl hydroperoxidase (AhpC)”. Appl Environ Microbiol, 81(14), 4690-4696. doi, 10.1128/AEM.01102-15

    Dolan, J. A., Sathitsuksanoh, N., Rodriguez, K., Simmons, B. A., Frazier, C. E., & Renneckar, S. (2015). “Biocomposite adhesion without added resin: understanding the chemistry of the direct conversion of wood into adhesives”. RSC Adv., 5(82), 67267-67276. doi, 10.1039/c5ra09676f

    Ebert, B., Rautengarten, C., Guo, X., Xiong, G., Stonebloom, S., Smith-Moritz, A. M., Herter, T., Chan, L. J., Adams, P. D., Petzold, C. J., Pauly, M., Willats, W. G., Heazlewood, J. L., & Scheller, H. V. (2015). “Identification and Characterization of a Golgi-Localized UDP-Xylose Transporter Family from Arabidopsis”. Plant Cell, 27(4), 1218-1227. doi, 10.1105/tpc.114.133827

    Eudes, A., Sathitsuksanoh, N., Baidoo, E. E., George, A., Liang, Y., Yang, F., Singh, S., Keasling, J. D., Simmons, B. A., & Loque, D. (2015). “Expression of a bacterial 3-dehydroshikimate dehydratase reduces lignin content and improves biomass saccharification efficiency”. Plant Biotechnol J. doi, 10.1111/pbi.12310

    Foo, J. L., Jensen, H. M., Dahl, R. H., George, K., Keasling, J. D., Lee, T. S., Leong, S., & Mukhopadhyay, A. (2014). “Improving microbial biogasoline production in Escherichia coli using tolerance engineering”. [Article]. MBio, 5(6), e01932. doi, 10.1128/mBio.01932-14

    Ford, K. L., Zeng, W., Heazlewood, J. L., & Bacic, A. (2015). “Characterization of protein N-glycosylation by tandem mass spectrometry using complementary fragmentation techniques”. Front Plant Sci, 6, 674. doi, 10.3389/fpls.2015.00674

    Furtado, A., Lupoi, J. S., Hoang, N. V., Healey, A., Singh, S., Simmons, B. A., & Henry, R. J. (2014). “Modifying plants for biofuel and biomaterial production”. Plant Biotechnol J, 12(9), 1246-1258. doi, 10.1111/pbi.12300

    Garcia Martin, H., Kumar, V. S., Weaver, D., Ghosh, A., Chubukov, V., Mukhopadhyay, A., Arkin, A., & Keasling, J. D. (2015). “A Method to Constrain Genome-Scale Models with 13C Labeling Data”. PLoS Comput Biol, 11(9), e1004363. doi, 10.1371/journal.pcbi.1004363

    Gardner, J. L., He, W., Li, C. L., Wong, J., Sale, K. L., Simmons, B. A., Singh, S., & Tanjore, D. (2015). “Calorimetric evaluation indicates that lignin conversion to advanced biofuels is vital to improving energy yields”. [10.1039/C5RA01503K]. Rsc Advances, 5(63), 51092-51101. doi, 10.1039/c5ra01503k

    George, A., Brandt, A., Tran, K., Zahari, S. M. S. N. S., Klein-Marcuschamer, D., Sun, N., Sathitsuksanoh, N., Shi, J., Stavila, V., Parthasarathi, R., Singh, S., Holmes, B. M., Welton, T., Simmons, B. A., & Hallett, J. P. (2014). “Design of low-cost ionic liquids for lignocellulosic biomass pretreatment”. [ ]. Green Chem., 17(3), 1728-1734. doi, 10.1039/c4gc01208a

    George, K. W., Alonso-Gutierrez, J., Keasling, J. D., & Lee, T. S. (2015). Isoprenoid Drugs, Biofuels, and Chemicals-Artemisinin, Farnesene, and Beyond Adv Biochem Eng Biotechnol (2015 Jan 11 ed.): Springer Berlin Heidelberg.

    George, K. W., Thompson, M. G., Kang, A., Baidoo, E., Wang, G., Chan, L. J., Adams, P. D., Petzold, C. J., Keasling, J. D., & Lee, T. (2015). “Metabolic engineering for the high-yield production of isoprenoid-based C5 alcohols in E. coli”. Sci Rep, 5, 11128. doi, 10.1038/srep11128

    Gondolf, V. M., Stoppel, R., Ebert, B., Rautengarten, C., Liwanag, A. J., Loque, D., & Scheller, H. V. (2014). “A gene stacking approach leads to engineered plants with highly increased galactan levels in Arabidopsis”. [Research Support, Non-U.S. Gov’t]. BMC Plant Biol, 14(1), 344. doi, 10.1186/s12870-014-0344-x

    González Fernández-Niño, S. M., Smith-Moritz, A. M., Chan, L. J. G., Adams, P. D., Heazlewood, J. L., & Petzold, C. J. (2015). “Standard flow liquid chromatography for shotgun proteomics in bioenergy research”. [Original Research]. Frontiers in Bioengineering and Biotechnology, 3. doi, 10.3389/fbioe.2015.00044

    Gonzalez, T. L., Liang, Y., Nguyen, B. N., Staskawicz, B. J., Loque, D., & Hammond, M. C. (2015). “Tight regulation of plant immune responses by combining promoter and suicide exon elements”. Nucleic Acids Res, 43(14), 7152-7161. doi, 10.1093/nar/gkv655

    Gupta, S., Guttman, M., Leverenz, R. L., Zhumadilova, K., Pawlowski, E. G., Petzold, C. J., Lee, K. K., Ralston, C. Y., & Kerfeld, C. A. (2015). “Local and global structural drivers for the photoactivation of the orange carotenoid protein”. Proc Natl Acad Sci U S A. doi, 10.1073/pnas.1512240112

    Haushalter, R. W., Groff, D., Deutsch, S., The, L., Chavkin, T. A., Brunner, S. F., Katz, L., & Keasling, J. D. (2015). “Development of an orthogonal fatty acid biosynthesis system in E. coli for oleochemical production”. Metab Eng, 30, 1-6. doi, 10.1016/j.ymben.2015.04.003

    Hiras, J., Wu, Y.-W., Eichorst, S. A., Simmons, B. A., & Singer, S. W. (2015). “Refining the phylum Chlorobi by resolving the phylogeny and metabolic potential of the representative of a deeply branching, uncultivated lineage”. [Original Article]. ISME J. doi, 10.1038/ismej.2015.158

    Johnson, R. E., de Rond, T., Lindsay, V. N., Keasling, J. D., & Sarpong, R. (2015). “Synthesis of Cycloprodigiosin Identifies the Natural Isolate as a Scalemic Mixture”. Org Lett, 17(14), 3474-3477. doi, 10.1021/acs.orglett.5b01527

    Jung, K. H., Cao, P., Sharma, R., Jain, R., & Ronald, P. C. (2015). “Phylogenomics databases for facilitating functional genomics in rice”. Rice (N Y), 8(1), 60. doi, 10.1186/s12284-015-0060-7

    Kent, M. S., Avina, I. C., Rader, N., Busse, M. L., George, A., Sathitsuksanoh, N., Baidoo, E., Timlin, J., Giron, N. H., Celina, M. C., Martin, L. E., Polsky, R., Chavez, V. H., Huber, D. L., Keasling, J. D., Singh, S., Simmons, B. A., & Sale, K. L. (2015). “Assay for lignin breakdown based on lignin films: insights into the Fenton reaction with insoluble lignin”. [10.1039/C5GC01083G]. Green Chem. doi, 10.1039/c5gc01083g

    Kirby, J., Nishimoto, M., Chow, R. W., Baidoo, E. E., Wang, G., Martin, J., Schackwitz, W., Chan, R., Fortman, J. L., & Keasling, J. D. (2015). “Enhancing Terpene yield from sugars via novel routes to 1-deoxy-d-xylulose 5-phosphate”. [Journal article]. Appl Environ Microbiol, 81(1), 130-138. doi, 10.1128/AEM.02920-14

    Klein-Marcuschamer, D., & Blanch, H. W. (2015). “Renewable fuels from biomass: Technical hurdles and economic assessment of biological routes”. Aiche Journal, 61(9), 2689-2701. doi, 10.1002/aic.14755 <Go to ISI>://WOS:000359311100003

    Konda, N. V. S. N. M., Singh, S., Simmons, B. A., & Klein-Marcuschamer, D. (2015). “An Investigation on the Economic Feasibility of Macroalgae as a Potential Feedstock for Biorefineries”. BioEnergy Research. doi, 10.1007/s12155-015-9594-1

    Lao, J., Sharma, M., Sharma, R., Fernandez-Nino, S. M., Schmutz, J., Ronald, P. C., Heazlewood, J. L., & Schwessinger, B. (2015). “Proteome profile of the endomembrane of developing coleoptiles from switchgrass (Panicum virgatum)”. Proteomics, 15(13), 2286-2290. doi, 10.1002/pmic.201400487

    Lee, T., Oh, T., Yang, S., Shin, J., Hwang, S., Kim, C. Y., Kim, H., Shim, H., Shim, J. E., Ronald, P. C., & Lee, I. (2015). “RiceNet v2: an improved network prioritization server for rice genes”. Nucleic Acids Res, 43(W1), W122-127. doi, 10.1093/nar/gkv253

    Leverenz, R. L., Sutter, M., Wilson, A., Gupta, S., Thurotte, A., Bourcier de Carbon, C., Petzold, C. J., Ralston, C., Perreau, F., Kirilovsky, D., & Kerfeld, C. A. (2015). “PHOTOSYNTHESIS. A 12 A carotenoid translocation in a photoswitch associated with cyanobacterial photoprotection”. Science, 348(6242), 1463-1466. doi, 10.1126/science.aaa7234

    Li, C., Tanjore, D., He, W., Wong, J., Gardner, J. L., Thompson, V. S., Yancey, N. A., Sale, K. L., Simmons, B. A., & Singh, S. (2015). “Scale-Up of Ionic Liquid-Based Fractionation of Single and Mixed Feedstocks”. BioEnergy Research, 1-10. doi, 10.1007/s12155-015-9587-0

    Loque, D., Scheller, H. V., & Pauly, M. (2015). “Engineering of plant cell walls for enhanced biofuel production”. Curr Opin Plant Biol, 25, 151-161. doi, 10.1016/j.pbi.2015.05.018

    Lund, C. H., Bromley, J. R., Stenbaek, A., Rasmussen, R. E., Scheller, H. V., & Sakuragi, Y. (2015). “A reversible Renilla luciferase protein complementation assay for rapid identification of protein-protein interactions reveals the existence of an interaction network involved in xyloglucan biosynthesis in the plant Golgi apparatus”. [Journal article]. J Exp Bot, 66(1), 85-97. doi, 10.1093/jxb/eru401

    Lupoi, J. S., Healey, A., Singh, S., Sykes, R., Davis, M., Lee, D. J., Shepherd, M., Simmons, B. A., & Henry, R. J. (2015). “High-Throughput Prediction of Acacia and Eucalypt Lignin Syringyl/Guaiacyl Content Using FT-Raman Spectroscopy and Partial Least Squares Modeling”. BioEnergy Research. doi, 10.1007/s12155-015-9578-1

    Lupoi, J. S., Singh, S., Parthasarathi, R., Simmons, B. A., & Henry, R. J. (2015). “Recent innovations in analytical methods for the qualitative and quantitative assessment of lignin”. Renewable & Sustainable Energy Reviews, 49, 871-906. doi, 10.1016/j.rser.2015.04.091

    Lupoi, J. S., Smith-Moritz, A., Singh, S., McQualter, R., Scheller, H. V., Simmons, B. A., & Henry, R. J. (2015). “Localization of polyhydroxybutyrate in sugarcane using Fourier-transform infrared microspectroscopy and multivariate imaging”. Biotechnol Biofuels, 8, 98. doi, 10.1186/s13068-015-0279-y

    McAndrew, R., Pruitt, R. N., Kamita, S. G., Pereira, J. H., Majumdar, D., Hammock, B. D., Adams, P. D., & Ronald, P. C. (2014). “Structure of the OsSERK2 leucine-rich repeat extracellular domain”. Acta Crystallogr D Biol Crystallogr, 70(Pt 11), 3080-3086. doi, 10.1107/S1399004714021178

    Mingardon, F., Clement, C., Hirano, K., Nhan, M., Luning, E. G., Chanal, A., & Mukhopadhyay, A. (2015). “Improving olefin tolerance and production in E. coli using native and evolved AcrB”. Biotechnol Bioeng, 112(5), 879-888. doi, 10.1002/bit.25511

    Mortimer, J. C., Faria-Blanc, N., Yu, X., Tryfona, T., Sorieul, M., Ng, Y. Z., Zhang, Z., Stott, K., Anders, N., & Dupree, P. (2015). “An unusual xylan in Arabidopsis primary cell walls is synthesised by GUX3, IRX9L, IRX10L and IRX14”. Plant J, 83(3), 413-426. doi, 10.1111/tpj.12898

    Mukhopadhyay, A. (2015). “Tolerance engineering in bacteria for the production of advanced biofuels and chemicals”. Trends Microbiol, 23(8), 498-508. doi, 10.1016/j.tim.2015.04.008

    Nafisi, M., Stranne, M., Fimognari, L., Atwell, S., Martens, H. J., Pedas, P. R., Hansen, S. F., Nawrath, C., Scheller, H. V., Kliebenstein, D. J., & Sakuragi, Y. (2015). “Acetylation of cell wall is required for structural integrity of the leaf surface and exerts a global impact on plant stress responses”. [Original Research]. Front Plant Sci, 6, 550. doi, 10.3389/fpls.2015.00550

    Papa, G., Rodriguez, S., George, A., Schievano, A., Orzi, V., Sale, K. L., Singh, S., Adani, F., & Simmons, B. A. (2015). “Comparison of different pretreatments for the production of bioethanol and biomethane from corn stover and switchgrass”. Bioresour Technol, 183C(0), 101-110. doi, 10.1016/j.biortech.2015.01.121

    Parsons, H. T., & Heazlewood, J. L. (2015). “Beyond the Western front: targeted proteomics and organelle abundance profiling”. Front Plant Sci, 6, 301. doi, 10.3389/fpls.2015.00301

    Parthasarathi, R., Balamurugan, K., Shi, J., Subramanian, V., Simmons, B. A., & Singh, S. (2015). “Theoretical Insights into the Role of Water in the Dissolution of Cellulose using IL/Water Mixed Solvent Systems”. J Phys Chem B. doi, 10.1021/acs.jpcb.5b02680

    Patron, N. J., Orzaez, D., Marillonnet, S., Warzecha, H., Matthewman, C., Youles, M., Raitskin, O., Leveau, A., Farre, G., Rogers, C., Smith, A., Hibberd, J., Webb, A. A., Locke, J., Schornack, S., Ajioka, J., Baulcombe, D. C., Zipfel, C., Kamoun, S., Jones, J. D., Kuhn, H., Robatzek, S., Van Esse, H. P., Sanders, D., Oldroyd, G., Martin, C., Field, R., O’Connor, S., Fox, S., Wulff, B., Miller, B., Breakspear, A., Radhakrishnan, G., Delaux, P. M., Loque, D., Granell, A., Tissier, A., Shih, P., Brutnell, T. P., Quick, W. P., Rischer, H., Fraser, P. D., Aharoni, A., Raines, C., South, P. F., Ane, J. M., Hamberger, B. R., Langdale, J., Stougaard, J., Bouwmeester, H., Udvardi, M., Murray, J. A., Ntoukakis, V., Schafer, P., Denby, K., Edwards, K. J., Osbourn, A., & Haseloff, J. (2015). “Standards for plant synthetic biology: a common syntax for exchange of DNA parts”. New Phytol. doi, 10.1111/nph.13532

    Perez-Pimienta, J. A., Lopez-Ortega, M. G., Chavez-Carvayar, J. A., Varanasi, P., Stavila, V., Cheng, G., Singh, S., & Simmons, B. A. (2015). “Characterization of agave bagasse as a function of ionic liquid pretreatment”. Biomass and Bioenergy, 75, 180-188. doi, 10.1016/j.biombioe.2015.02.026

    Poust, S., Hagen, A., Katz, L., & Keasling, J. D. (2014). “Narrowing the gap between the promise and reality of polyketide synthases as a synthetic biology platform”. Curr Opin Biotechnol, 30(0), 32-39. doi, 10.1016/j.copbio.2014.04.011

    Poust, S., Phelan, R. M., Deng, K., Katz, L., Petzold, C. J., & Keasling, J. D. (2015). “Divergent Mechanistic Routes for the Formation of gem-Dimethyl Groups in the Biosynthesis of Complex Polyketides”. [Article]. Angew Chem Int Ed Engl, 54(8), 2370-2373. doi, 10.1002/anie.201410124

    Poust, S., Piety, J., Bar-Even, A., Louw, C., Baker, D., Keasling, J. D., & Siegel, J. B. (2015). “Mechanistic Analysis of an Engineered Enzyme that Catalyzes the Formose Reaction”. Chembiochem. doi, 10.1002/cbic.201500228

    Rhee, M., Light, Y. K., Yilmaz, S., Adams, P. D., Saxena, D., Meagher, R. J., & Singh, A. K. (2014). “Pressure stabilizer for reproducible picoinjection in droplet microfluidic systems”. [Article]. Lab Chip, 14(23), 4533-4539. doi, 10.1039/c4lc00823e

    Sathitsuksanoh, N., Sawant, M., Truong, Q., Tan, J., Canlas, C. G., Sun, N., Zhang, W., Renneckar, S., Prasomsri, T., Shi, J., Çetinkol, Ö., Singh, S., Simmons, B. A., & George, A. (2015). “How Alkyl Chain Length of Alcohols Affects Lignin Fractionation and Ionic Liquid Recycle During Lignocellulose Pretreatment”. BioEnergy Research, 1-9. doi, 10.1007/s12155-015-9643-9

    Schicklberger, M., Shapiro, N., Loque, D., Woyke, T., & Chakraborty, R. (2015). “Draft Genome Sequence of Raoultella terrigena R1Gly, a Diazotrophic Endophyte”. Genome Announc, 3(3). doi, 10.1128/genomeA.00607-15

    Schwessinger, B., Bahar, O., Thomas, N., Holton, N., Nekrasov, V., Ruan, D., Canlas, P. E., Daudi, A., Petzold, C. J., Singan, V. R., Kuo, R., Chovatia, M., Daum, C., Heazlewood, J. L., Zipfel, C., & Ronald, P. C. (2015). “Transgenic Expression of the Dicotyledonous Pattern Recognition Receptor EFR in Rice Leads to Ligand-Dependent Activation of Defense Responses”. PLoS Pathog, 11(3), e1004809. doi, 10.1371/journal.ppat.1004809

    Scullin, C., Cruz, A. G., Chuang, Y. D., Simmons, B. A., Loque, D., & Singh, S. (2015). “Restricting lignin and enhancing sugar deposition in secondary cell walls enhances monomeric sugar release after low temperature ionic liquid pretreatment”. Biotechnol Biofuels, 8, 95. doi, 10.1186/s13068-015-0275-2

    Sharma, M. K., Sharma, R., Cao, P., Harkenrider, M., Jenkins, J., Grimwood, J., Zhang, J., Udvardi, M. K., Schmutz, J., & Ronald, P. C. (2015). “Targeted Switchgrass BAC Library Screening and Sequence Analysis Identifies Predicted Biomass and Stress Response-Related Genes”. BioEnergy Research, 1-14. doi, 10.1007/s12155-015-9667-1

    Shi, J., George, K. W., Sun, N., He, W., Li, C., Stavila, V., Keasling, J. D., Simmons, B. A., Lee, T. S., & Singh, S. (2015). “Impact of Pretreatment Technologies on Saccharification and Isopentenol Fermentation of Mixed Lignocellulosic Feedstocks”. BioEnergy Research, 1-10. doi, 10.1007/s12155-015-9588-z

    Shih, S. C., Gach, P. C., Sustarich, J., Simmons, B. A., Adams, P. D., Singh, S., & Singh, A. K. (2015). “A droplet-to-digital (D2D) microfluidic device for single cell assays”. [10.1039/C4LC00794H]. Lab Chip, 15(1), 225-236. doi, 10.1039/c4lc00794h

    Shih, S. C., Goyal, G., Kim, P. W., Koutsoubelis, N., Keasling, J. D., Adams, P. D., Hillson, N. J., & Singh, A. K. (2015). “A Versatile Microfluidic Device for Automating Synthetic Biology”. ACS Synth Biol. doi, 10.1021/acssynbio.5b00062

    Siegel, J. B., Smith, A. L., Poust, S., Wargacki, A. J., Bar-Even, A., Louw, C., Shen, B. W., Eiben, C. B., Tran, H. M., Noor, E., Gallaher, J. L., Bale, J., Yoshikuni, Y., Gelb, M. H., Keasling, J. D., Stoddard, B. L., Lidstrom, M. E., & Baker, D. (2015). “Computational protein design enables a novel one-carbon assimilation pathway”. Proc Natl Acad Sci U S A, 112(12), 3704-3709. doi, 10.1073/pnas.1500545112

    Simmons, C. W., Reddy, A. P., D’Haeseleer, P., Khudyakov, J., Billis, K., Pati, A., Simmons, B. A., Singer, S. W., Thelen, M. P., & VanderGheynst, J. S. (2014). “Metatranscriptomic analysis of lignocellulolytic microbial communities involved in high-solids decomposition of rice straw”. Biotechnol Biofuels, 7(1), 495. doi, 10.1186/s13068-014-0180-0

    Singh, S., Cheng, G., Sathitsuksanoh, N., Wu, D., Varanasi, P., George, A., Balan, V., Gao, X., Kumar, R., Dale, B. E., Wyman, C. E., & Simmons, B. A. (2015). “Comparison of Different Biomass Pretreatment Techniques and Their Impact on Chemistry and Structure”. [Original Research]. Frontiers in Energy Research, 2. doi, 10.3389/fenrg.2014.00062

    Sitepu, I. R., Shi, S., Simmons, B. A., Singer, S. W., Boundy-Mills, K., & Simmons, C. W. (2014). “Yeast tolerance to the ionic liquid 1-ethyl-3-methylimidazolium acetate”. FEMS Yeast Res, 14(8), 1286-1294. doi, 10.1111/1567-1364.12224

    Slater, S. C., Simmons, B. A., Rogers, T. S., Phillips, M. F., Nordahl, K., & Davison, B. H. (2015). “The DOE Bioenergy Research Centers: History, Operations, and Scientific Output”. BioEnergy Research, 1-16. doi, 10.1007/s12155-015-9660-8

    Smith-Moritz, A. M., Hao, Z., Fernández-Niño, S. G., Fangel, J. U., Verhertbruggen, Y., Holman, H.-Y. N., Willats, W. G. T., Ronald, P. C., Scheller, H. V., Heazlewood, J. L., & Vega-Sánchez, M. E. (2015). “Structural characterization of a mixed-linkage glucan deficient mutant reveals alteration in cellulose microfibril orientation in rice coleoptile mesophyll cell walls”. [Original Research]. Frontiers in Plant Science, 6. doi, 10.3389/fpls.2015.00628

    Sun, L., Singh, S., Joo, M., Vega-Sanchez, M., Ronald, P., Simmons, B. A., Adams, P., & Auer, M. (2015). “Non-invasive imaging of cellulose microfibril orientation within plant cell walls by polarized Raman microspectroscopy”. Biotechnol Bioeng. doi, 10.1002/bit.25690

    Sun, N., Xu, F., Sathitsuksanoh, N., Thompson, V. S., Cafferty, K., Li, C., Tanjore, D., Narani, A., Pray, T. R., Simmons, B. A., & Singh, S. (2015). “Blending municipal solid waste with corn stover for sugar production using ionic liquid process”. Bioresour Technol, 186(0), 200-206. doi, 10.1016/j.biortech.2015.02.087

    Tanger, P., Vega-Sánchez, M. E., Fleming, M., Tran, K., Singh, S., Abrahamson, J. B., Jahn, C. E., Santoro, N., Naredo, E. B., Baraoidan, M., Danku, J. M. C., Salt, D. E., McNally, K. L., Simmons, B. A., Ronald, P. C., Leung, H., Bush, D. R., McKay, J. K., & Leach, J. E. (2015). “Cell Wall Composition and Bioenergy Potential of Rice Straw Tissues Are Influenced by Environment, Tissue Type, and Genotype”. BioEnergy Research, 1-18. doi, 10.1007/s12155-014-9573-y

    Torr, K. M., Love, K. T., Simmons, B. A., & Hill, S. J. (2015). “Structural features affecting the enzymatic digestibility of pine wood pretreated with ionic liquids”. Biotechnol Bioeng. doi, 10.1002/bit.25831

    Vega-Sanchez, M. E., Loque, D., Lao, J., Catena, M., Verhertbruggen, Y., Herter, T., Yang, F., Harholt, J., Ebert, B., Baidoo, E. E., Keasling, J. D., Scheller, H. V., Heazlewood, J. L., & Ronald, P. C. (2015). “Engineering temporal accumulation of a low recalcitrance polysaccharide leads to increased C6 sugar content in plant cell walls”. Plant Biotechnol J. doi, 10.1111/pbi.12326

    Velasquez, S. M., Ricardi, M. M., Poulsen, C. P., Oikawa, A., Dilokpimol, A., Halim, A., Mangano, S., Denita Juarez, S. P., Marzol, E., Salgado Salter, J. D., Dorosz, J. G., Borassi, C., Moller, S. R., Buono, R., Ohsawa, Y., Matsuoka, K., Otegui, M. S., Scheller, H. V., Geshi, N., Petersen, B. L., Iusem, N. D., & Estevez, J. M. (2015). “Complex Regulation of Prolyl-4-Hydroxylases Impacts Root Hair Expansion”. Mol Plant, 8(0), 734-746. doi, 10.1016/j.molp.2014.11.017

    Voiniciuc, C., Schmidt, M. H., Berger, A., Yang, B., Ebert, B., Scheller, H. V., North, H. M., Usadel, B., & Guenl, M. (2015). “MUCI10 Produces Galactoglucomannan That Maintains Pectin and Cellulose Architecture in Arabidopsis Seed Mucilage”. Plant Physiol. doi, 10.1104/pp.15.00851

    Walley, J., Xiao, Y., Wang, J. Z., Baidoo, E. E., Keasling, J. D., Shen, Z., Briggs, S. P., & Dehesh, K. (2015). “Plastid-produced interorgannellar stress signal MEcPP potentiates induction of the unfolded protein response in endoplasmic reticulum”. Proc Natl Acad Sci U S A, 112(19), 6212-6217. doi, 10.1073/pnas.1504828112

    Wenz, C., Barbas, C., Lopez-Gonzalvez, A., Garcia, A., Benavente, F., Sanz-Nebot, V., Blanc, T., Freckleton, G., Britz-McKibbin, P., Shanmuganathan, M., de l’Escaille, F., Far, J., Haselberg, R., Huang, S., Huhn, C., Pattky, M., Michels, D., Mou, S., Yang, F., Neusuess, C., Tromsdorf, N., Baidoo, E. E., Keasling, J. D., & Park, S. S. (2015). “Interlaboratory study to evaluate the robustness of capillary electrophoresis with mass spectrometry for peptide mapping”. J Sep Sci. doi, 10.1002/jssc.201500551

    Woo, H. L., Ballor, N. R., Hazen, T. C., Fortney, J. L., Simmons, B., Davenport, K. W., Goodwin, L., Ivanova, N., Kyrpides, N. C., Mavromatis, K., Woyke, T., Jansson, J., Kimbrel, J., & DeAngelis, K. M. (2014). “Complete genome sequence of the lignin-degrading bacterium Klebsiella sp. strain BRL6-2”. Stand Genomic Sci, 9(1), 19. doi, 10.1186/1944-3277-9-19

    Wu, Y.-W., Joshua, C., Eichorst, S. A., Gladden, J. M., Simmons, B. A., & Singer, S. W. (2015). “Genomic Analysis of Xylose Metabolism in Members of the Deinoccocus-Thermus Phylum from Thermophilic Biomass-Deconstructing Bacterial Consortia”. BioEnergy Research, 1-8. doi, 10.1007/s12155-015-9600-7

    Yang, Y. R., Song, Y. Y., Scheller, H. V., Ghosh, A., Ban, Y. H., Chen, H., & Tang, M. (2015). “Community structure of arbuscular mycorrhizal fungi associated with Robinia pseudoacacia in uncontaminated and heavy metal contaminated soils”. [Article]. Soil Biology & Biochemistry, 86, 146-158. doi, 10.1016/j.soilbio.2015.03.018

    Zuo, S., Zhou, X., Chen, M., Zhang, S., Schwessinger, B., Ruan, D., Yuan, C., Wang, J., Chen, X., & Ronald, P. C. (2014). “OsSERK1 regulates rice development but not immunity to Xanthomonas oryzae pv. oryzae or Magnaporthe oryzae”. J Integr Plant Biol, 56(12), 1179-1192. doi, 10.1111/jipb.12290


  • Batth, T. S., Singh, P., Ramakrishnan, V. R., Sousa, M. M., Chan, L. J., Tran, H. M., Luning, E. G., Pan, E. H., Vuu, K. M., Keasling, J. D., Adams, P. D., & Petzold, C. J. (2014). “A targeted proteomics toolkit for high-throughput absolute quantification of Escherichia coli proteins”. Metab Eng, 26C(0), 48-56. doi, 10.1016/j.ymben.2014.08.004

    Bergmann, J. C., Costa, O. Y., Gladden, J. M., Singer, S., Heins, R., D’Haeseleer, P., Simmons, B. A., & Quirino, B. F. (2014). “Discovery of two novel beta-glucosidases from an Amazon soil metagenomic library”. [Research Support, Non-U.S. Gov’t Research Support, U.S. Gov’t, Non-P.H.S.]. FEMS Microbiol Lett, 351(2), 147-155. doi, 10.1111/1574-6968.12332

    Bi, C., Su, P., Muller, J., Yeh, Y. C., Chhabra, S. R., Beller, H. R., Singer, S. W., & Hillson, N. J. (2013). “Development of a broad-host synthetic biology toolbox for Ralstonia eutropha and its application to engineering hydrocarbon biofuel production”. [Research Support, U.S. Gov’t, Non-P.H.S.]. Microb Cell Fact, 12(1), 107. doi, 10.1186/1475-2859-12-107

    Carroll, A. W., Joshi, H. J., & Heazlewood, J. L. (2013). “Managing the green proteomes for the next decade of plant research”. Front Plant Sci, 4, 501. doi, 10.3389/fpls.2013.00501

    Chandrasekaran, A., & Singh, A. K. (2014). “One-pot, microscale cell-free enzyme expression and screening”. [Research Support, U.S. Gov’t, Non-P.H.S.]. Methods Mol Biol, 1118, 55-69. doi, 10.1007/978-1-62703-782-2_4

    Chen, X., Zuo, S., Schwessinger, B., Chern, M., Canlas, P. E., Ruan, D., Zhou, X., Wang, J., Daudi, A., Petzold, C. J., Heazlewood, J. L., & Ronald, P. C. (2014). “An XA21-associated kinase (OsSERK2) regulates immunity mediated by the XA21 and XA3 immune receptors”. [Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov’t]. Mol Plant, 7(5), 874-892. doi, 10.1093/mp/ssu003

    Chen, Z., Pereira, J. H., Liu, H., Tran, H. M., Hsu, N. S., Dibble, D., Singh, S., Adams, P. D., Sapra, R., Hadi, M. Z., Simmons, B. A., & Sale, K. L. (2013). “Improved activity of a thermophilic cellulase, Cel5A, from Thermotoga maritima on ionic liquid pretreated switchgrass”. [Research Support, U.S. Gov’t, Non-P.H.S.]. PLoS One, 8(11), e79725. doi, 10.1371/journal.pone.0079725

    Cheng, X., Hiras, J., Deng, K., Bowen, B., Simmons, B. A., Adams, P. D., Singer, S. W., & Northen, T. R. (2013). “High throughput nanostructure-initiator mass spectrometry screening of microbial growth conditions for maximal beta-glucosidase production”. Front Microbiol, 4, 365. doi, 10.3389/fmicb.2013.00365

    Chou, H. H., & Keasling, J. D. (2013). “Programming adaptive control to evolve increased metabolite production”. [Research Support, U.S. Gov’t, Non-P.H.S.]. Nat Commun, 4, 2595. doi, 10.1038/ncomms3595

    Cox, K., Renouf, M., Dargan, A., Turner, C., & Klein-Marcuschamer, D. (2014). “Environmental life cycle assessment (LCA) of aviation biofuel from microalgae,Pongamia pinnata, and sugarcane molasses”. Biofuels, Bioproducts and Biorefining, 8(4), 579-593. doi, 10.1002/bbb.1488

    Dahl, R. H., Zhang, F., Alonso-Gutierrez, J., Baidoo, E., Batth, T. S., Redding-Johanson, A. M., Petzold, C. J., Mukhopadhyay, A., Lee, T. S., Adams, P. D., & Keasling, J. D. (2013). “Engineering dynamic pathway regulation using stress-response promoters”. [Research Support, U.S. Gov’t, Non-P.H.S.]. Nat Biotechnol, 31(11), 1039-1046. doi, 10.1038/nbt.2689

    de Rond, T., Danielewicz, M., & Northen, T. (2014). “High throughput screening of enzyme activity with mass spectrometry imaging”. [Review]. Curr Opin Biotechnol, 31C, 1-9. doi, 10.1016/j.copbio.2014.07.008

    DeAngelis, K. M., Chivian, D., Fortney, J. L., Arkin, A. P., Simmons, B., Hazen, T. C., & Silver, W. L. (2013). “Changes in microbial dynamics during long-term decomposition in tropical forests”. Soil Biology & Biochemistry, 66, 60-68. doi, DOI 10.1016/j.soilbio.2013.06.010 <Go to ISI>://000325665400009

    Deng, K., Takasuka, T. E., Heins, R., Cheng, X., Bergeman, L. F., Shi, J., Aschenbrener, R., Deutsch, S., Singh, S., Sale, K. L., Simmons, B. A., Adams, P. D., Singh, A. K., Fox, B. G., & Northen, T. R. (2014). Rapid Kinetic Characterization of Glycosyl Hydrolases Based on Oxime Derivatization and Nanostructure-Initiator Mass Spectrometry (NIMS). Acs Chemical Biology, 1470-1479. Retrieved from doi:10.1021/cb5000289

    Dougherty, M. J., Tran, H. M., Stavila, V., Knierim, B., George, A., Auer, M., Adams, P. D., & Hadi, M. Z. (2014). “Cellulosic Biomass Pretreatment and Sugar Yields as a Function Of Biomass Particle Size”. PLOS ONE, 9(6), e100836. doi, DOI: 10.1371/journal.pone.0100836

    Eichorst, S. A., Joshua, C., Sathitsuksanoh, N., Singh, S., Simmons, B. A., & Singer, S. W. (2014). “Substrate-Specific Development of Thermophilic Bacterial Consortia Using Chemically Pretreated Switchgrass”. [Journal article]. Appl Environ Microbiol, 26, 02795-02714. doi, 10.1128/AEM.02795-14

    Estavillo, G. M., Verhertbruggen, Y., Pogson, B. J., Heazlewood, J. L., Scheller, H. V., & Ito, J. (2014). Isolation of the plant cytosolic fraction for proteomic analysis. In K. Jorrin-Novo, Weckwerth, Wienkoop (Ed.), Plant Proteomics: Methods and Protocols (Vol. 1072, pp. 453-467): Humana Press.

    Eudes, A., Liang, Y., Mitra, P., & Loque, D. (2014). “Lignin bioengineering”. [Research Support, U.S. Gov’t, Non-P.H.S. Review]. Curr Opin Biotechnol, 26, 189-198. doi, 10.1016/j.copbio.2014.01.002

    Frederix, M., Hütter, K., Leu, J., Batth, T. S., Turner, W. J., Rüegg, T. L., Blanch, H. W., Simmons, B. A., Adams, P. D., Keasling, J. D., Thelen, M. P., Dunlop, M. J., Petzold, C. J., & Mukhopadhyay, A. (2014). “Development of a Native Escherichia coli Induction System for Ionic Liquid Tolerance”. PLoS One, 9(7), e101115. doi, 10.1371/journal.pone.0101115

    Galdzicki, M., Clancy, K. P., Oberortner, E., Pocock, M., Quinn, J. Y., Rodriguez, C. A., Roehner, N., Wilson, M. L., Adam, L., Anderson, J. C., Bartley, B. A., Beal, J., Chandran, D., Chen, J., Densmore, D., Endy, D., Grunberg, R., Hallinan, J., Hillson, N. J., Johnson, J. D., Kuchinsky, A., Lux, M., Misirli, G., Peccoud, J., Plahar, H. A., Sirin, E., Stan, G.-B., Villalobos, A., Wipat, A., Gennari, J. H., Myers, C. J., & Sauro, H. M. (2014). “The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology”. [Computational Biology]. Nat Biotech, 32(6), 545-550. doi, 10.1038/nbt.2891

    Gao, X., Kumar, R., Singh, S., Simmons, B. A., Balan, V., Dale, B. E., & Wyman, C. E. (2014). “Comparison of enzymatic reactivity of corn stover solids prepared by dilute acid, AFEX, and ionic liquid pretreatments”. Biotechnol Biofuels, 7(71), 71. doi, 10.1186/1754-6834-7-71

    Garcia, D. E., & Keasling, J. D. (2014). “Kinetics of Phosphomevalonate Kinase from Saccharomyces cerevisiae”. [Research Support, U.S. Gov’t, Non-P.H.S.]. PLoS One, 9(1), e87112. doi, 10.1371/journal.pone.0087112 <Go to ISI>://WOS:000330507300143

    George, K. W., Chen, A., Jain, A., Batth, T. S., Baidoo, E. E., Wang, G., Adams, P. D., Petzold, C. J., Keasling, J. D., & Lee, T. S. (2014). “Correlation analysis of targeted proteins and metabolites to assess and engineer microbial isopentenol production”. [Research Support, U.S. Gov’t, Non-P.H.S.]. Biotechnol Bioeng, 111(8), 1648-1658. doi, 10.1002/bit.25226

    Geshi, N., Johansen, J. N., Dilokpimol, A., Rolland, A., Belcram, K., Verger, S., Kotake, T., Tsumuraya, Y., Kaneko, S., Tryfona, T., Dupree, P., Scheller, H. V., Hofte, H., & Mouille, G. (2013). “A galactosyltransferase acting on arabinogalactan protein glycans is essential for embryo development in Arabidopsis”. [Research Support, Non-U.S. Gov’t Research Support, U.S. Gov’t, Non-P.H.S.]. Plant J, 76(1), 128-137. doi, 10.1111/tpj.12281

    Ghosh, A., Nilmeier, J., Weaver, D., Adams, P. D., Keasling, J. D., Mukhopadhyay, A., Petzold, C. J., & Martin, H. G. (2014). “A Peptide-Based Method for 13C Metabolic Flux Analysis in Microbial Communities”. PLoS Comput Biol, 10(9), e1003827. doi, 10.1371/journal.pcbi.1003827

    Gladden, J. M., Park, J. I., Bergmann, J., Reyes-Ortiz, V., D’Haeseleer, P., Quirino, B. F., Sale, K. L., Simmons, B. A., & Singer, S. W. (2014). “Discovery and characterization of ionic liquid-tolerant thermophilic cellulases from a switchgrass-adapted microbial community”. Biotechnol Biofuels, 7(1), 15. doi, 10.1186/1754-6834-7-15

    Goh, E. B., Baidoo, E. E., Burd, H., Lee, T. S., Keasling, J. D., & Beller, H. R. (2014). “Substantial improvements in methyl ketone production in E. coli and insights on the pathway from in vitro studies”. [Journal article]. Metab Eng, 26C(14), 67-76. doi, 10.1016/j.ymben.2014.09.003

    Golberg, A., Linshiz, G., Kravets, I., Stawski, N., Hillson, N. J., Yarmush, M. L., Marks, R. S., & Konry, T. (2014). “Cloud-enabled microscopy and droplet microfluidic platform for specific detection of Escherichia coli in water”. [Research Support, Non-U.S. Gov’t Research Support, U.S. Gov’t, Non-P.H.S.]. PLoS One, 9(1), e86341. doi, 10.1371/journal.pone.0086341

    Golberg, A., Vitkin, E., Linshiz, G., Khan, S. A., Hillson, N. J., Yakhini, Z., & Yarmush, M. L. (2014). “Proposed design of distributed macroalgal biorefineries: thermodynamics, bioconversion technology, and sustainability implications for developing economies”. Biofuels Bioproducts & Biorefining-Biofpr, 8(1), 67-82. doi, Doi 10.1002/Bbb.1438 <Go to ISI>://000330801200008

    Hagen, A., Poust, S., de Rond, T., Yuzawa, S., Katz, L., Adams, P. D., Petzold, C. J., & Keasling, J. D. (2014). “In Vitro Analysis of Carboxyacyl Substrate Tolerance in the Loading and First Extension Modules of Borrelidin Polyketide Synthase”. Biochemistry, 53(38), 5975-5977. doi, 10.1021/bi500951c

    Haushalter, R. W., Kim, W., Chavkin, T. A., The, L., Garber, M. E., Nhan, M., Petzold, C. J., Katz, L., & Keasling, J. D. (2014). “Production of anteiso-branched fatty acids in Escherichia coli; next generation biofuels with improved cold-flow properties”. [Journal article]. Metab Eng, 20(14), 00116-00115. doi, 10.1016/j.ymben.2014.09.002

    Heins RA, Cheng X, Nath S, Deng K, Bowen BP, Chivian DC, Datta S, Friedland GD, D’Haeseleer P, Wu D, Tran-Gyamfi M, Scullin CS, Singh S, Shi W, Hamilton MG, Bendall ML, Sczyrba A, Thompson J, Feldman T, Guenther JM, Gladden JM, Cheng JF, Adams PD, Rubin EM, Simmons BA, Sale KL, Northen TR, & S., D. (2014). “Phylogenomically Guided Identification of Industrially Relevant GH1 ?-Glucosidases through DNA Synthesis and Nanostructure-Initiator Mass Spectrometry”. ACS. doi, 10.1021/cb500244v

    Hillson, N. J. (2014). j5 DNA assembly design automation. In S. Valla, Lale, Rahmi (Ed.), DNA Cloning and Assembly Methods (Vol. 1116, pp. 245-269): Humana Press.

    Ito, J., Herter, T., Baidoo, E. E., Lao, J., Vega-Sanchez, M. E., Michelle Smith-Moritz, A., Adams, P. D., Keasling, J. D., Usadel, B., Petzold, C. J., & Heazlewood, J. L. (2014). “Analysis of plant nucleotide sugars by hydrophilic interaction liquid chromatography and tandem mass spectrometry”. [Research Support, U.S. Gov’t, Non-P.H.S.]. Anal Biochem, 448, 14-22. doi, 10.1016/j.ab.2013.11.026

    Ito, J., Parsons, H. T., & Heazlewood, J. L. (2014). “The Arabidopsis cytosolic proteome: the metabolic heart of the cell”. [Review]. Front Plant Sci, 5(11), 21. doi, 10.3389/fpls.2014.00021

    Javidpour, P., Pereira, J. H., Goh, E. B., McAndrew, R. P., Ma, S. M., Friedland, G. D., Keasling, J. D., Chhabra, S. R., Adams, P. D., & Beller, H. R. (2014). “Biochemical and structural studies of NADH-dependent FabG used to increase the bacterial production of fatty acids under anaerobic conditions”. [Research Support, U.S. Gov’t, Non-P.H.S.]. Appl Environ Microbiol, 80(2), 497-505. doi, 10.1128/AEM.03194-13

    Joshua, C. J., Perez, L. D., & Keasling, J. D. (2013). “Functional characterization of the origin of replication of pRN1 from Sulfolobus islandicus REN1H1”. [Research Support, U.S. Gov’t, Non-P.H.S.]. PLoS One, 8(12), e84664. doi, 10.1371/journal.pone.0084664

    Kirby, J., Nishimoto, M., Chow, R. W., Pasumarthi, V. N., Chan, R., Chan, L. J., Petzold, C. J., & Keasling, J. D. (2014). “Use of non-ionic surfactants for improvement of terpene production in Saccharomyces cerevisiae”. [Journal article]. Appl Environ Microbiol, 22(21), 02155-02114. doi, 10.1128/AEM.02155-14

    Klein-Marcuschamer, D., & Blanch, H. W. (2013). “Survival of the Fittest: An Economic Perspective on the Production of Novel Biofuels”. AiChE Journal, 59(12), 4454-4460. doi, Doi 10.1002/Aic.14245 <Go to ISI>://000330039200001

    Konda, M., Shi, J., Singh, S., W, B. H., Simmons, B. A., & Klein-Marcuschamer, D. (2014). “Understanding cost drivers and economic potential of two variants of ionic liquid pretreatment for cellulosic biofuel production”. Biotechnology for Biofuels, 7, 86. doi, 10.1186/1754-6834-7-86

    Kung, Y., McAndrew, R. P., Xie, X., Liu, C. C., Pereira, J. H., Adams, P. D., & Keasling, J. D. (2014). “Constructing tailored isoprenoid products by structure-guided modification of geranylgeranyl reductase”. Structure, 22(7), 1028-1036. doi, 10.1016/j.str.2014.05.007

    Lafreniere, N. M., Shih, S. C., Abu-Rabie, P., Jebrail, M. J., Spooner, N., & Wheeler, A. R. (2014). “Multiplexed extraction and quantitative analysis of pharmaceuticals from DBS samples using digital microfluidics”. [Research Support, Non-U.S. Gov’t]. Bioanalysis, 6(3), 307-318. doi, 10.4155/bio.13.311

    Lao, J., Oikawa, A., Bromley, J. R., McInerney, P., Suttangkakul, A., Smith-Moritz, A. M., Plahar, H., Chiu, T.-Y., González Fernández-Niño, S. M., Ebert, B., Yang, F., Christiansen, K. M., Hansen, S. F., Stonebloom, S., Adams, P. D., Ronald, P. C., Hillson, N. J., Hadi, M. Z., Vega-Sánchez, M. E., Loqué, D., Scheller, H. V., & Heazlewood, J. L. (2014). “The plant glycosyltransferase clone collection for functional genomics”. The plant journal, 79(3), n/a-n/a. doi, 10.1111/tpj.12577

    Lee, S., Geller, J. T., Torok, T., Wu, C. H., Singer, M., Reid, F. C., Tarjan, D. R., Hazen, T. C., Arkin, A. P., & Hillson, N. J. (2014). “Characterization of wastewater treatment plant microbial communities and the effects of carbon sources on diversity in laboratory models”. PLoS One, 9(8), e105689. doi, 10.1371/journal.pone.0105689

    Li, C., Tanjore, D., He, W., Wong, J., Gardner, J. L., Sale, K. L., Simmons, B. A., & Singh, S. (2013). “Scale-up and evaluation of high solid ionic liquid pretreatment and enzymatic hydrolysis of switchgrass”. Biotechnol Biofuels, 6(1), 154. doi, 10.1186/1754-6834-6-154

    Linshiz, G., Stawski, N., Goyal, G., Bi, C., Poust, S., Sharma, M., Mutalik, V., Keasling, J. D., & Hillson, N. J. (2014). “PR-PR: Cross-Platform Laboratory Automation System”. ACS Synthetic Biology, 140114162902002. doi, 10.1021/sb4001728

    Lupoi, J. S., Singh, S., Davis, M., Lee, D. J., Shepherd, M., Simmons, B. A., & Henry, R. J. (2014). “High-throughput prediction of eucalypt lignin syringyl/guaiacyl content using multivariate analysis: a comparison between mid-infrared, near-infrared, and Raman spectroscopies for model development”. Biotechnology for Biofuels, 7, 93. doi, 10.1186/1754-6834-7-93

    Mac Dowell, N., Llovell, F., Sun, N., Hallett, J. P., George, A., Hunt, P. A., Welton, T., Simmons, B. A., & Vega, L. F. (2014). “New Experimental Density Data and Soft-SAFT Models of Alkylimidazolium ([CnC1im](+)) Chloride (Cl(-)), Methylsulfate ([MeSO4](-)), and Dimethylphosphate ([Me2PO4](-)) Based Ionic Liquids”. J Phys Chem B, 118(23), 6206-6221. doi, 10.1021/jp501619y

    Mack, J. H., Rapp, V. H., Broeckelmann, M., Lee, T. S., & Dibble, R. W. (2014). “Investigation of biofuels from microorganism metabolism for use as anti-knock additives”. Fuel, 117, 939-943. doi, DOI 10.1016/j.fuel.2013.10.024 <Go to ISI>://000327767400005

    Mann, G. W., Calley, P. C., Joshi, H. J., & Heazlewood, J. L. (2013). “MASCP gator: an overview of the Arabidopsis proteomic aggregation portal”. [Review]. Front Plant Sci, 4, 411. doi, 10.3389/fpls.2013.00411

    McInerney, P., Adams, P., & Hadi, M. Z. (2014). “Error Rate Comparison during Polymerase Chain Reaction by DNA Polymerase”. Mol Biol Int, 2014(10), 287430. doi, 10.1155/2014/287430

    Nielsen, J., Fussenegger, M., Keasling, J., Lee, S. Y., Liao, J. C., Prather, K., & Palsson, B. (2014). “Engineering synergy in biotechnology”. [Review]. Nature Chemical Biology, 10(5), 319-322. doi, 10.1038/nchembio.1519 <Go to ISI>://WOS:000334672700001

    Nowroozi, F. F., Baidoo, E. E., Ermakov, S., Redding-Johanson, A. M., Batth, T. S., Petzold, C. J., & Keasling, J. D. (2014). “Metabolic pathway optimization using ribosome binding site variants and combinatorial gene assembly”. [Research Support, U S Gov’t, Non-P H S]. Appl Microbiol Biotechnol, 98(4), 1567-1581. doi, DOI 10.1007/s00253-013-5361-4 <Go to ISI>://000332106000010

    Oleskowicz-Popiel, P., Klein-Marcuschamer, D., Simmons, B. A., & Blanch, H. W. (2014). “Lignocellulosic ethanol production without enzymes–technoeconomic analysis of ionic liquid pretreatment followed by acidolysis”. [Research Support, Non-U.S. Gov’t Research Support, U.S. Gov’t, Non-P.H.S.]. Bioresour Technol, 158, 294-299. doi, 10.1016/j.biortech.2014.02.016

    Paddon, C. J., & Keasling, J. D. (2014). “Semi-synthetic artemisinin: a model for the use of synthetic biology in pharmaceutical development”. [Research Support, Non-U.S. Gov’t Review]. Nature Reviews Microbiology, 12(5), 355-367. doi, 10.1038/nrmicro3240

    Parreiras, L. S., Breuer, R. J., Avanasi Narasimhan, R., Higbee, A. J., La Reau, A., Tremaine, M., Qin, L., Willis, L. B., Bice, B. D., Bonfert, B. L., Pinhancos, R. C., Balloon, A. J., Uppugundla, N., Liu, T., Li, C., Tanjore, D., Ong, I. M., Li, H., Pohlmann, E. L., Serate, J., Withers, S. T., Simmons, B. A., Hodge, D. B., Westphall, M. S., Coon, J. J., Dale, B. E., Balan, V., Keating, D. H., Zhang, Y., Landick, R., Gasch, A. P., & Sato, T. K. (2014). “Engineering and Two-Stage Evolution of a Lignocellulosic Hydrolysate-Tolerant Saccharomyces cerevisiae Strain for Anaerobic Fermentation of Xylose from AFEX Pretreated Corn Stover”. PLoS One, 9(9), e107499. doi, 10.1371/journal.pone.0107499

    Parsons, H. T., Gonzalez Fernandez-Nino, S. M., & Heazlewood, J. L. (2014). Separation of the plant golgi apparatus and endoplasmic reticulum by free-flow electrophoresis. In K. Jorrin-Novo, Weckwerth, Wienkoop (Ed.), Plant Proteomics: Methods and Protocols (Vol. 1072, pp. 527-539): Humana Press.

    Parsons, H. T., Weinberg, C. S., Macdonald, L. J., Adams, P. D., Petzold, C. J., Strabala, T. J., Wagner, A., & Heazlewood, J. L. (2013). “Golgi enrichment and proteomic analysis of developing Pinus radiata xylem by free-flow electrophoresis”. [Research Support, Non-U.S. Gov’t Research Support, U.S. Gov’t, Non-P.H.S.]. PLoS One, 8(12), e84669. doi, 10.1371/journal.pone.0084669

    Phelan, R. M., Sekurova, O. N., Keasling, J. D., & Zotchev, S. B. (2014). “Engineering Terpene Biosynthesis in Streptomyces for Production of the Advanced Biofuel Precursor Bisabolene”. ACS Synth Biol. doi, 10.1021/sb5002517

    Pradhan Mitra, P., & Loque, D. (2014). “Histochemical Staining of Arabidopsis thaliana Secondary Cell Wall Elements”. [Research Support, U.S. Gov’t, Non-P.H.S.]. J Vis Exp(87). doi, 10.3791/51381

    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

    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

    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

    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

    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

    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

    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

    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

    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

    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

    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

    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

    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

    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

    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

    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

    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

    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

    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

    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

    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

    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

    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

    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

    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

    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

    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

    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

  • 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]

    Mann GW, Joshi HJ, Petzold CJ, Heazlewood JL (2013) “Proteome coverage of the model plant Arabidopsis thaliana: implications for shotgun proteomic studies.Journal of Proteomics. 79: 195-99.

    McAndrew RP, Park JI, Heins RA, Reindl W, Friedland GD, D’haeseleer P, Northen T, Sale KL, Simmons BA, Adams PD. “From soil to structure: a novel dimeric ?-glucosidase belonging to glycoside hydrolase family 3 isolated from compost using metagenomic analysisJ. Biol. Chem. [epub ahead of print.]

    Mueller, J., MacEachran, D., Burd, H., Sathitsuksanoh, N., Bi, C., Yeh, Y. C., Lee, T. S., Hillson, N., Chhabra, S., Singer, S. W. and Beller, H. R. (2013). “Engineering of Ralstonia eutrophia H16 for Autotrophic and hetertrophic production of methyl ketones.” Appl Environ Microbiol 79(14): 4433-4439.

    Mutalik, V. K., Guimaraes, J. C., Cambray, G., Lam, C., Christoffersen, M. J., Mai, Q. A., Tran, A. B., Paull, M., Keasling, J. D., Arkin, A. P. and Endy, D. (2013). “Precise and reliable gene expression via standard transcription and translation initiation elements.” Nat Methods. 10(4): 354-360.

    Mutalik, V. K., Guimaraes, J. C., Cambray, G., Mai, Q. A., Christoffersen, M. J., Martin, L., Yu, A., Lam, C., Rodriguez, C., Bennett, G., Keasling, J. D., Endy, D. and Arkin, A. P. (2013). “Quantitative estimation of activity and quality for collections of functional genetic elements.” Nat Methods. 10(4): 347-353.

    Oikawa, A., Lund, C. H., Sakuragi, Y. and Scheller, H. V. (2013). “Golgi-localized enzyme complexes for plant cell wall biosynthesis.Trends Plant Sci 18(1): 49-58.

    Ozaydin, B., Burd, H., Lee, T. S. and Keasling, J. D. (2013). “Carotenoid-based phenotypic screen of the yeast deletion collection reveals new genes with roles in isoprenoid production.” Metab Eng. 15: 174-183.

    Paap, S. M., West, T. H., Manley, D. K., Steen, E. J., Beller, H. R., Keasling, J. D., Dibble, D. C., Chang, S. and Simmons, B. A. (2013). “Biochemical production of ethanol and fatty acid ethyl esters from switchgrass: A comparative analysis of environmental and economic performance.Biomass and Bioenergy. 49: 49-62.

    Parsons, H. T., Drakakaki, G. and Heazlewood, J. L. (2012). “Proteomic dissection of the Arabidopsis Golgi and trans-Golgi network.Front Plant Sci. 3: 298.

    Pereira, J. H., Goh, E. B., Keasling, J. D., Beller, H. R. and Adams, P. D. (2012). “Structure of FabH and factors affecting the distribution of branched fatty acids in Micrococcus luteus.Acta Crystallogr D Biol Crystallogr 68(Pt 10): 1320-1328.

    Perez-Pimienta, J. A., Lopez-Ortega, M. G., Varanasi, P., Stavila, V., Cheng, G., Singh, S. and Simmons, B. A. (2013). “Comparison of the impact of ionic liquid pretreatment on recalcitrance of agave bagasse and switchgrass.Bioresour Technol 127: 18-24.

    Petersen, P. D., Lau, J., Ebert, B., Yang, F., Verhertbruggen, Y., Kim, J. S., Varanasi, P., Suttangkakul, A., Auer, M., Loque, D. and Scheller, H. V. (2012). “Engineering of plants with improved properties as biofuels feedstocks by vessel-specific complementation of xylan biosynthesis mutants.Biotechnol Biofuels. 5:84.

    Reddy, A. P., Simmons, C. W., Claypool, J., Jabusch, L., Burd, H., Hadi, M. Z., Simmons, B. A., Singer, S. W. and VanderGheynst, J. S. (2012). “Thermophilic enrichment of microbial communities in the presence of the ionic liquid 1-ethyl-3-methylimidazolium acetate.J Appl Microbiol. 113(6): 1362-1370.

    Reyes-Ortiz, V., Heins, R., Cheng, G., Kim, E. Y., Vernon, B., Elandt, R., Adams, P., Sale, K., Hadi, M., Simmons, B. A., Kent, M. and Tullman-Ercek, D. (2013). “Addition of a carbohydrate-binding module enhances cellulase penetration into cellulose substrate.” Biotechnol Biofuels. 6(1): 93.

    Rodrigues JA, Ruan R, Nishimura T, Sharma MK, Sharma R, Ronald PC, Fischer RL, Zilberman. “Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm.” Proc Natl Acad Sci U S A. 2013 Apr 23. [Epub ahead of print]

    Sharma, R., De Vleesschauwer, D., Sharma, M., Ronald, P. C. (2013). “Recent advances in dissecting stress-regulatory crosstalk in rice.Molecular Plant. 6(2): 250-260.

    Sharma, R., Cao, P., Jung, K. H., Sharma, M. K. and Ronald, P. C. (2013). “Construction of a rice glycoside hydrolase phylogenomic databse and identification of targets for biofuel research.” Frontiers in Plant Biotechnology 4: 330. [epub only]

    Shi, J., Thompson, V. S., Yancey, N. A., Stavila, V., Simmons, B. A. and Singh, S. (2013). “Impact of mixed feedstocks and feedstock densification on ionic liquid pretreatment efficiency.Biofuels 4(1): 63-72.

    Shi, J., Gladden, J. M., Sathitsuksanoh, N., Kambam, P., Sandoval, L., Mitra, D., Zhang, S., George, A., Singer, S. W., Simmons, B. A. and Singh, S. (2013). “One-pot ionic liquid pretreatment and saccharification of switchgrass.” Green Chemistry. 15(9): 2579.

    Singh, S. and Simmons, B. A. (2012). “Ionic Liquid Pretreatment: Mechanism, Performance and Challenges.Aqueous pretreatment of plant biomass for biological and chemical conversion to fuels and chemicals, John Wiley & Sons, Ltd: 223-238.

    Singh, S., Varanasi, P., Singh, P., Adams, P., Auer, M. and Simmons, B. A. (2013). “Understanding the Impact of Ionic Liquid Pretreatment on Cellulose and Lignin via Thermochemical Analysis.” Biomass and Bioenergy 54: 276-283.

    Socha, A., Plummer, S., Stavila, V., Simmons, B. A. and Singh, S. (2013). “Comparison of sugar content for ionic liquid pretreated Douglas-fir woodchips and forestry residues.Biotechnol Biofuels 6(1):61.

    Sun, L., Li, C. L., Xue, Z. J., Simmons, B. A. and Singh, S. (2012). “Unveiling high-resolution, tissue specific dynamic changes in corn stover during ionic liquid pretreatment.Rsc Advances 3(6): 2017-2027.

    Sun, N., Liu, H., Sathitsuksanoh, N., Stavila, V., Sawant, M., Bonito, A., Tran, K., George, A., Sale, K., Singh, S., Simmons, B. A. and Holmes, B. (2013). “Production and Extraction of Sugars from Switchgrass Hydrolyzed in Ionic Liquids.Biotechnol Biofuels. 6(39).

    Varanasi, P., Singh, P., Arora, R., Adams, P. D., Auer, M., Simmons, B. A. and Singh, S. (2012). “Understanding changes in lignin of Panicum virgatum and Eucalyptus globulus as a function of ionic liquid pretreatment.Bioresour Technol 126C: 156-161.

    Varanasi, P., Singh, P., Auer, M., Adams, P. D., Simmons, B. A. and Singh, S. (2013). “Survey of renewable chemicals produced from lignocellulosic biomass during ionic liquid pretreatment.Biotechnol Biofuels 6(1): 14.

    Vega-Sanchez, M., Verhertbruggen, Y., Scheller, H. V. and Ronald, P. (2013). “Abundance of mixed linkage glucan in mature tissues and secondary cell walls of grasses.Plant Signal Behav 8(2).

    Xu, Y., D’Haeseleer, P., Gladden, J. M., Allgaier, M., Chain, P. S. G., Tringe, S. G., Malfatti, S. A., Aldrich, J. T., Nicora, C. D., Robinson, E. W., Paša-Toli?, L., Hugenholtz, P., Simmons, B. A. and Singer, S. W. (2013). “Proteogenomic Analysis of a Thermophilic Bacterial Consortium Adapted to Deconstruct Switchgrass.” PLoS One. 8(7): e68465.

    Yang, F., Mitra, P., Zhang, L., Prak, L., Verhertbruggen, Y., Kim, J. S., Sun, L., Zheng, K., Tang, K., Auer, M., Scheller, H. V. and Loque, D. (2012). “Engineering secondary cell wall deposition in plants.Plant Biotechnol J. 11(3): 325-35.

    Yeh, Y. C., Muller, J., Bi, C., Hillson, N. J., Beller, H. R., Chhabra, S. R. and Singer, S. W. (2013). “Functionalizing bacterial cell surfaces with a phage protein.Chem Commun (Camb) 49(9): 910-912.

    Yuan, L., Gu, R., Xuan, Y., Valle-Smith, E., Loque, D., Frommer, W. B. and von Wiren, N. (2013). “Allosteric Regulation of transport Activity by hetero-trimerization of Ammonium transporter complexes in vivo.Plant Cell 25(3): 974-984.

    Yuzawa, S., Chiba, N., Katz, L. and Keasling, J. D. (2012). “Construction of a part of a 3-hydroxypropionate cycle for heterologous polyketide biosynthesis in Escherichia coli.” Biochemistry. 51(49): 9779-9781.

    Yuzawa, S; C. Eng, L. Katz, and J. D. Keasling. 2013. “Broad substrate specificity of the loading didomain of the lipomycin polyketide synthase.Biochemistry (2013) Jun 4;52(22):3791-3. doi: 10.1021/bi400520t.

    Zhang, F., Ouellet, M., Batth, T. S., Adams, P. D., Petzold, C. J., Mukhopadhyay, A. and Keasling, J. D. (2012). “Enhancing fatty acid production by the expression of the regulatory transcription factor FadR.Metab Eng 14(6): 653-660.

    Zhang, J. Y., Lee, Y. C., Torres-Jerez, I., Wang, M., Yin, Y., Chou, W. C., He, J., Shen, H., Srivastava, A. C., Pennacchio, C., Lindquist, E., Grimwood, J., Schmutz, J., Xu, Y., Sharma, M., Sharma, R., Bartley, L. E., Ronald, P. C., Saha, M. C., Dixon, R. A., Tang, Y. and Udvardi, M. K. (2013). “Development of an integrated transcript sequence database and a gene expression atlas for gene discovery and analysis in switchgrass (Panicum virgatum L.).” Plant J. 74(1): 160-173.

  • Agrawal, G. K., Sarkar, A., Agrawal, R., Ndimba, B. K., Tanou, G., Dunn, M. J., Kieselbach, T., Cramer, R., Wienkoop, S., Chen, S., Rafudeen, M. S., Deswal, R., Barkla, B. J., Weckwerth, W., Heazlewood, J. L., Renaut, J., Job, D., Chakraborty, N., & Rakwal, R. (2012). “Boosting the globalization of plant proteomics through INPPO: current developments and future prospects”. Proteomics, 12(3), 359-368. doi, 10.1002/pmic.201290018

    Atmodjo, M. A., Sakuragi, Y., Zhu, X., Burrell, A. J., Mohanty, S. S., Atwood, J. A., 3rd, Orlando, R., Scheller, H. V., & Mohnen, D. (2011). “Galacturonosyltransferase (GAUT)1 and GAUT7 are the core of a plant cell wall pectin biosynthetic homogalacturonan:galacturonosyltransferase complex”. Proceedings of the National Academy of Sciences, 108(50), 20225-20230. doi, 1112816108 [pii]10.1073/pnas.1112816108

    Baerenfaller, K., Bastow, R., Beynon, J., Brady, S., Brendel, V., Donaldson, S., Dooley, R., Forster, M., Friesner, J., Gifford, D., Grotewold, E., Gutierrez, R., Huala, E., Jaiswal, P., Joshi, H., Kersey, P., Liu, L., Loraine, A., Lyons, E., May, S., Mayer, K., MacLean, D., Meyers, B., Mueller, L., Muller, R., Muller, H. M., Ouellette, F., Pires, J. C., Provart, N., Staiger, D., Stanzione, D., Taylor, J., Taylor, C., Town, C., Toyoda, T., Vaughn, M., Walsh, S., Ware, D., Weckwerth, W., & Int Arabidopsis, I. (2012). “Taking the Next Step: Building an Arabidopsis Information Portal”. [Editorial Material]. Plant Cell, 24(6), 2248-2256. doi, 10.1105/tpc.112.100669

    Baidoo, E. E., Benke, P. I., & Keasling, J. D. (2012). “Mass spectrometry-based microbial metabolomics”. [Research Support, U.S. Gov’t, Non-P.H.S.]. Methods Mol Biol, 881, 215-278. doi, 10.1007/978-1-61779-827-6_9

    Beller, H. R., Legler, T. C., & Kane, S. R. (2012). Genetic manipulation of the obligate chemolithoautotrophic bacterium Thiobacillus denitrificans Methods Mol Biol (2012/05/29 ed., Vol. 881, pp. 99-136).

    Bennetzen, J. L., Schmutz, J., Wang, H., Percifield, R., Hawkins, J., Pontaroli, A. C., Estep, M., Feng, L., Vaughn, J. N., Grimwood, J., Jenkins, J., Barry, K., Lindquist, E., Hellsten, U., Deshpande, S., Wang, X., Wu, X., Mitros, T., Triplett, J., Yang, X., Ye, C. Y., Mauro-Herrera, M., Wang, L., Li, P., Sharma, M., Sharma, R., Ronald, P. C., Panaud, O., Kellogg, E. A., Brutnell, T. P., Doust, A. N., Tuskan, G. A., Rokhsar, D., & Devos, K. M. (2012). “Reference genome sequence of the model plant Setaria”. [Research Support, Non-U.S. Gov’t Research Support, U.S. Gov’t, Non-P.H.S.]. Nat Biotechnol, 30(6), 555-561. doi, 10.1038/nbt.2196

    Blanch, H. W. (2012). “Bioprocessing for biofuels”. [Research Support, U.S. Gov’t, Non-P.H.S.]. Curr Opin Biotechnol, 23(3), 390-395. doi, 10.1016/j.copbio.2011.10.002

    Bokinsky, G., Groff, D., & Keasling, J. D. (2012). Synthetic biology of microbial biofuel production: From enzymes to pathways to organisms Synthetic Biologu: Tools and Applications (pp. Pages 207–223): Academic Press.

    Bokinsky, G., Peralta-Yahya, P. P., George, A., Holmes, B. M., Steen, E. J., Dietrich, J., Soon Lee, T., Tullman-Ercek, D., Voigt, C. A., Simmons, B. A., & Keasling, J. D. (2011). “Synthesis of three advanced biofuels from ionic liquid-pretreated switchgrass using engineered Escherichia coli”. Proceedings of the National Academy of Sciences, 108(50), 19949-19954. doi, 1106958108 [pii] 10.1073/pnas.1106958108,

    Borglin, S., Joyner, D., DeAngelis, K. M., Khudyakov, J., D’Haeseleer, P., Joachimiak, M. P., & Hazen, T. (2012). “Application of phenotypic microarrays to environmental microbiology”. [Review]. Current Opinion in Biotechnology, 23(1), 41-48. doi, 10.1016/j.copbio.2011.12.006

    Cao, P., Jung, K.-H., Choi, D., Hwang, D., Zhu, J., & Ronald, P. C. (2012). “The Rice Oligonucleotide Array Database: an atlas of rice gene expression”. Rice, 5(1), 17. doi, 10.1186/1939-8433-5-17

    Carothers, J. M., Goler, J. A., Juminaga, D., & Keasling, J. D. (2011). “Model-driven engineering of RNA devices to quantitatively program gene expression”. Science, 334(6063), 1716-1719. doi, 334/6063/1716 [pii] 10.1126/science.1212209

    Casler, M., Tobias, C., Kaeppler, S., Buell, C. R., Wang, Z.-Y., Cao, P., Schmutz, J., & Ronald, P. (2011). “The Switchgrass Genome: Tools and Strategies”. Plant Genome, 4(3), 273-282. doi, 10.3835/plantgenome2011.10.0026

    Chen, J., Densmore, D., Ham, T. S., Keasling, J. D., & Hillson, N. J. (2012). “DeviceEditor visual biological CAD canvas”. J Biol Eng, 6(1), 1. doi, 10.1186/1754-1611-6-1

    Chen, Z., Friedland, G. D., Pereira, J. H., Reveco, S. A., Chan, R., Park, J. I., Thelen, M. P., Adams, P. D., Arkin, A. P., Keasling, J. D., Blanch, H. W., Simmons, B. A., Sale, K. L., Chivian, D., & Chhabra, S. R. (2012). “Tracing determinants of dual substrate specificity in glycoside hydrolase family 5”. [Research Support, U.S. Gov’t, Non-P.H.S.]. J Biol Chem, 287(30), 25335-25343. doi, 10.1074/jbc.M112.362640

    Cheng, G., Datta, S., Liu, Z., Wang, C., Murton, J. K., Brown, P. A., Jablin, M. S., Dubey, M., Majewski, J., Halbert, C. E., Browning, J. F., Esker, A. R., Watson, B. J., Zhang, H., Hutcheson, S. W., Huber, D. L., Sale, K. L., Simmons, B. A., & Kent, M. S. (2012). “Interactions of endoglucanases with amorphous cellulose films resolved by neutron reflectometry and quartz crystal microbalance with dissipation monitoring”. [Research Support, U.S. Gov’t, Non-P.H.S.]. Langmuir, 28(22), 8348-8358. doi, 10.1021/la300955q

    Cheng, G., Kent, M. S., He, L., Varanasi, P., Dibble, D., Arora, R., Deng, K., Hong, K., Melnichenko, Y. B., Simmons, B. A., & Singh, S. (2012). “Effect of ionic liquid treatment on the structures of lignins in solutions: molecular subunits released from lignin”. [Research Support, U.S. Gov’t, Non-P.H.S.]. Langmuir, 28(32), 11850-11857. doi, 10.1021/la300938b

    Cheng, G., Varanasi, P., Arora, R., Stavila, V., Simmons, B. A., Kent, M. S., & Singh, S. (2012). “Impact of Ionic Liquid Pretreatment Conditions on Cellulose Crystalline Structure Using 1-Ethyl-3-methylimidazolium Acetate”. Journal of Physical Chemistry B, 116(33), 10049-10054. doi, Doi 10.1021/Jp304538v

    Christensen, U., & Scheller, H. V. (2012). “Regulation of (1,3;1,4)-?-D-glucan synthesis in developing endosperm of barley lys mutants”. Journal of Cereal Science, 55(1), 69-76. doi, 10.1016/j.jcs.2011.10.005

    Chuck, G. S., Tobias, C., Sun, L., Kraemer, F., Li, C., Dibble, D., Arora, R., Bragg, J. N., Vogel, J. P., Singh, S., Simmons, B. A., Pauly, M., & Hake, S. (2011). “Overexpression of the maize Corngrass1 microRNA prevents flowering, improves digestibility, and increases starch content of switchgrass”. Proceedings of National Academy of Sciences, 108(42), 17550-17555. doi, 1113971108 [pii] 10.1073/pnas.1113971108,

    De Michele, R., Loque, D., Lalonde, S., & Frommer, W. B. (2012). “Ammonium and urea transporter inventory of the selaginella and physcomitrella genomes”. [Original Research]. Front Plant Sci, 3(62), 62. doi, 10.3389/fpls.2012.00062

    DeAngelis, K. M., Fortney, J. L., Borglin, S., Silver, W. L., Simmons, B. A., & Hazen, T. C. (2012). “Anaerobic decomposition of switchgrass by tropical soil-derived feedstock-adapted consortia”. [Research Support, Non-U.S. Gov’t Research Support, U.S. Gov’t, Non-P.H.S.]. MBio, 3(1). doi, 10.1128/mBio.00249-11

    Deng, K., George, K. W., Reindl, W., Keasling, J. D., Adams, P. D., Lee, T. S., Singh, A. K., & Northen, T. R. (2012). “Encoding substrates with mass tags to resolve stereospecific reactions using Nimzyme”. [Research Support, U.S. Gov’t, Non-P.H.S.]. Rapid Commun Mass Spectrom, 26(6), 611-615. doi, 10.1002/rcm.6134

    Dibble, D., Li , C., Sun, L., George, A., Cheng, A., Çetinkol, O., Benke, P., Holmes, B., Singh, S., & Simmons, B. A. (2011). “A facile method for the recovery of ionic liquid and lignin from biomass pretreatment”. Green Chemistry, 13(11), 3255-3264. doi, 10.1039/C1GC15111H

    Dougherty, M. J., D’Haeseleer, P., Hazen, T. C., Simmons, B. A., Adams, P. D., & Hadi, M. Z. (2012). “Glycoside Hydrolases from a targeted Compost Metagenome, activity-screening and functional characterization”. BMC Biotechnol, 12, 38. doi, 10.1186/1472-6750-12-38

    Eudes, A., George, A., Mukerjee, P., Kim, J. S., Pollet, B., Benke, P. I., Yang, F., Mitra, P., Sun, L., Cetinkol, O. P., Chabout, S., Mouille, G., Soubigou-Taconnat, L., Balzergue, S., Singh, S., Holmes, B. M., Mukhopadhyay, A., Keasling, J. D., Simmons, B. A., Lapierre, C., Ralph, J., & Loque, D. (2012). “Biosynthesis and incorporation of side-chain-truncated lignin monomers to reduce lignin polymerization and enhance saccharification”. [Research Support, Non-U.S. Gov’t Research Support, U.S. Gov’t, Non-P.H.S.]. Plant Biotechnol J, 10(5), 609-620. doi, 10.1111/j.1467-7652.2012.00692.x

    George, A., Tran, K., Morgan, T. J., Benke, P., Berrueco, C., Lorente, E., Wu, B., Keasling, J. D., Simmon, B. A., & Holmes, B. (2011). “The effect of ionic liquid cation and anion combinations on the macromolecular structure of lignins”. Green Chemistry, 13(12), 3375-3385. doi, 10.1039/c1gc15543a

    Gladden, J. M., Eichorst, S. A., Hazen, T. C., Simmons, B. A., & Singer, S. W. (2012). “Substrate perturbation alters the glycoside hydrolase activities and community composition of switchgrass-adapted bacterial consortia”. [Research Support, U.S. Gov’t, Non-P.H.S.]. Biotechnol Bioeng, 109(5), 1140-1145. doi, 10.1002/bit.24388

    Goh, E. B., Baidoo, E. E., Keasling, J. D., & Beller, H. R. (2012). “Engineering of bacterial methyl ketone synthesis for biofuels”. Applied and Environmental Microbiology, 78(1), 70-80. doi, AEM.06785-11 [pii] 10.1128/AEM.06785-11

    Graham, D. E., Wallenstein, M. D., Vishnivetskaya, T. A., Waldrop, M. P., Phelps, T. J., Pfiffner, S. M., Onstott, T. C., Whyte, L. G., Rivkina, E. M., Gilichinsky, D. A., Elias, D. A., Mackelprang, R., VerBerkmoes, N. C., Hettich, R. L., Wagner, D., Wullschleger, S. D., & Jansson, J. K. (2012). “Microbes in thawing permafrost: the unknown variable in the climate change equation”. [Research Support, U.S. Gov’t, Non-P.H.S.]. Isme Journal, 6(4), 709-712. doi, 10.1038/ismej.2011.163

    Greving, M., Cheng, X. L., Reindl, W., Bowen, B., Deng, K., Louie, K., Nyman, M., Cohen, J., Singh, A., Simmons, B., Adams, P., Siuzdak, G., & Northen, T. (2012). “Acoustic deposition with NIMS as a high-throughput enzyme activity assay”. Analytical and Bioanalytical Chemistry, 403(3), 707-711. DOI 10.1007/s00216-012-5908-8

    Groff, D., Benke, P. I., Batth, T. S., Bokinsky, G., Petzold, C. J., Adams, P. D., & Keasling, J. D. (2012). “Supplementation of intracellular XylR leads to coutilization of hemicellulose sugars”. [Evaluation Studies Research Support, Non-U.S. Gov’t Research Support, U.S. Gov’t, Non-P.H.S.]. Appl Environ Microbiol, 78(7), 2221-2229. doi, 10.1128/AEM.06761-11

    Ham, T. S., Dmytriv, Z., Plahar, H., Chen, J., Hillson, N. J., & Keasling, J. D. (2012). “Design, implementation and practice of JBEI-ICE: an open source biological part registry platform and tools”. Nucleic Acids Res, 40(18), e141. doi, 10.1093/nar/gks531

    Hansen, S. F., Harholt, J., Oikawa, A., & Scheller, H. V. (2012). “Plant Glycosyltransferases Beyond CAZy: A Perspective on DUF Families”. [Mini Review]. Front Plant Sci, 3(59), 59. doi, 10.3389/fpls.2012.00059

    Harholt, J., Jensen, J. K., Verhertbruggen, Y., Sogaard, C., Bernard, S., Nafisi, M., Poulsen, C. P., Geshi, N., Sakuragi, Y., Driouich, A., Knox, J. P., & Scheller, H. V. (2012). “ARAD proteins associated with pectic Arabinan biosynthesis form complexes when transiently overexpressed in planta”. [Research Support, Non-U.S. Gov’t Research Support, U.S. Gov’t, Non-P.H.S.]. Planta, 236(1), 115-128. doi, 10.1007/s00425-012-1592-3

    Harholt, J., Sorensen, I., Fangel, J., Roberts, A., Willats, W. G., Scheller, H. V., Petersen, B. L., Banks, J. A., & Ulvskov, P. (2012). “The glycosyltransferase repertoire of the spikemoss Selaginella moellendorffii and a comparative study of its cell wall”. [Research Support, Non-U.S. Gov’t Research Support, U.S. Gov’t, Non-P.H.S.]. PLoS One, 7(5), e35846. doi, 10.1371/journal.pone.0035846

    Hastrup, A. C. S., Howell, C., Larsen, F. H., Sathitsuksanoh, N., Goodell, B., & Jellison, J. (2012). “Differences in crystalline cellulose modification due to degradation by brown and white rot fungi”. [Research Support, U.S. Gov’t, Non-P.H.S.]. Fungal Biology, 116(10), 1052-1063. doi, 10.1016/j.funbio.2012.07.009

    Heazlewood, J. L., & Petzold, C. J. (2012). Proteomics – Applications in Biology. Rijeka, Croatia: InTech.

    Hillson, N. J., Rosengarten, R. D., & Keasling, J. D. (2012). “j5 DNA Assembly Design Automation Software”. ACS Synthetic Biology, 1(1), 14-21. doi, Doi 10.1021/Sb2000116

    Jones, A. M., Aebersold, R., Ahrens, C. H., Apweiler, R., Baerenfaller, K., Baker, M., Bendixen, E., Briggs, S., Brownridge, P., Brunner, E., Daube, M., Deutsch, E. W., Grossniklaus, U., Heazlewood, J., Hengartner, M. O., Hermjakob, H., Jovanovic, M., Lawless, C., Lochnit, G., Martens, L., Ravnsborg, C., Schrimpf, S. P., Shim, Y. H., Subasic, D., Tholey, A., Wijk, K., Mering, C., Weiss, M., & Zheng, X. (2012). “The HUPO initiative on Model Organism Proteomes, iMOP”. Proteomics, 12(3), 340-345. doi, 10.1002/pmic.201290014

    Joshi, H. J., Christiansen, K. M., Fitz, J., Cao, J., Lipzen, A., Martin, J., Smith-Moritz, A. M., Pennacchio, L. A., Schackwitz, W. S., Weigel, D., & Heazlewood, J. L. (2012). “1001 Proteomes: a functional proteomics portal for the analysis of Arabidopsis thaliana accessions”. [Research Support, Non-U.S. Gov’t Research Support, U.S. Gov’t, Non-P.H.S.]. Bioinformatics, 28(10), 1303-1306. doi, 10.1093/bioinformatics/bts133

    Juminaga, D., Baidoo, E. E., Redding-Johanson, A. M., Batth, T. S., Burd, H., Mukhopadhyay, A., Petzold, C. J., & Keasling, J. D. (2012). “Modular Engineering of L-Tyrosine Production in Escherichia coli”. Applied and Environmental Microbiology, 78(1), 89-98. doi, AEM.06017-11 [pii] 10.1128/AEM.06017-11

    Keasling, J. D. (2012). “Synthetic biology and the development of tools for metabolic engineering”. [Research Support, U.S. Gov’t, Non-P.H.S. Review]. Metab Eng, 14(3), 189-195. doi, 10.1016/j.ymben.2012.01.004

    Khudyakov, J. I., D’Haeseleer, P., Borglin, S. E., Deangelis, K. M., Woo, H., Lindquist, E. A., Hazen, T. C., Simmons, B. A., & Thelen, M. P. (2012). “Global transcriptome response to ionic liquid by a tropical rain forest soil bacterium, Enterobacter lignolyticus”. [Research Support, Non-U.S. Gov’t Research Support, U.S. Gov’t, Non-P.H.S.]. Proc Natl Acad Sci U S A, 109(32), E2173-2182. doi, 10.1073/pnas.1112750109

    Klein-Marcuschamer, D., Oleskowicz-Popiel, P., Simmons, B. A., & Blanch, H. W. (2012). “The challenge of enzyme cost in the production of lignocellulosic biofuels”. Biotechnology and Bioengineering, 109(4), 1083-1087. doi, 10.1002/bit.24370

    Knight, R., Jansson, J., Field, D., Fierer, N., Desai, N., Fuhrman, J. A., Hugenholtz, P., van der Lelie, D., Meyer, F., Stevens, R., Bailey, M. J., Gordon, J. I., Kowalchuk, G. A., & Gilbert, J. A. (2012). “Unlocking the potential of metagenomics through replicated experimental design”. Nature Biotechnology, 30(6), 513-520. doi, Doi 10.1038/Nbt.2235

    Kumar, S., Hahn, F. M., Baidoo, E., Kahlon, T. S., Wood, D. F., McMahan, C. M., Cornish, K., Keasling, J. D., Daniell, H., & Whalen, M. C. (2012). “Remodeling the isoprenoid pathway in tobacco by expressing the cytoplasmic mevalonate pathway in chloroplasts”. [Research Support, Non-U.S. Gov’t Research Support, U.S. Gov’t, Non-P.H.S.]. Metabolic Engineering, 14(1), 19-28. doi, 10.1016/j.ymben.2011.11.005

    Lee, I., Seo, Y. S., Coltrane, D., Hwang, S., Oh, T., Marcotte, E. M., & Ronald, P. C. (2011). “Genetic dissection of the biotic stress response using a genome-scale gene network for rice”. Proceedings of National Academy of Sciences, 108(45), 18548-18553. doi, 1110384108 [pii] 10.1073/pnas.1110384108

    Li, C., Sun, L., Simmons, B. A., & Singh, S. (2012). “Comparing the Recalcitrance of Eucalyptus, Pine, and Switchgrass Using Ionic Liquid and Dilute Acid Pretreatments”. Bioenergy Research, 6(1), 14-23. doi, 10.1007/s12155-012-9220-4

    Liu, H., Cheng, G., Kent, M., Stavila, V., Simmons, B. A., Sale, K. L., & Singh, S. (2012). “Simulations Reveal Conformational Changes of Methylhydroxyl Groups during Dissolution of Cellulose I(beta) in Ionic Liquid 1-Ethyl-3-methylimidazolium Acetate”. J Phys Chem B, 116(28), 8131-8138. doi, 10.1021/jp301673h

    McAndrew, R. P., Peralta-Yahya, P. P., Degiovanni, A., Pereira, J. H., Hadi, M. Z., Keasling, J. D., & Adams, P. D. (2011). “Structure of a three-domain sesquiterpene synthase: a prospective target for advanced biofuels production”. Structure, 19(12), 1876-1884. doi, S0969-2126(11)00325-X [pii] 10.1016/j.str.2011.09.013,

    McClendon, S. D., Baath, T., Petzold, C. J., Adams, P. D., Simmons, B. A., & Singer, S. W. (2012). “Thermoascus aurantiacus is a promising source of enzymes for biomass deconstruction under thermophilic conditions”. Biotechnol Biofuels, 5(1), 54. doi, 10.1186/1754-6834-5-54

    McKee, A. E., Rutherford, B. J., Chivian, D. C., Baidoo, E. K., Juminaga, D., Kuo, D., Benke, P. I., Dietrich, J. A., Ma, S. M., Arkin, A. P., Petzold, C. J., Adams, P. D., Keasling, J. D., & Chhabra, S. R. (2012). “Manipulation of the carbon storage regulator system for metabolite remodeling and biofuel production in Escherichia coli”. Microb Cell Fact, 11(1), 79. doi, 10.1186/1475-2859-11-79

    Melnichenko, Y. B., He, L. L., Sakurovs, R., Kholodenko, A. L., Blach, T., Mastalerz, M., Radlinski, A. P., Cheng, G., & Mildner, D. F. R. (2012). “Accessibility of pores in coal to methane and carbon dioxide”. Fuel, 91(1), 200-208. doi, DOI 10.1016/j.fuel.2011.06.026

    Mukhopadhyay, A., Hillson, N. J., & Keasling, J. D. (2012). Control of Stress Tolerance in Bacterial Host Organisms for Bioproduction of Fuels. In Z. L. Liu (Ed.), Microbial Stress Tolerance: From Genomics to Biofuels (1 ed., Vol. 22, pp. 209-238). Berlin / Heidelberg: Springer-Verlag.

    Oleskowicz-Popiel, P., Kadar, Z., Heiske, S., Klein-Marcuschamer, D., Simmons, B. A., Blanch, H. W., & Schmidt, J. E. (2012). “Co-production of ethanol, biogas, protein fodder and natural fertilizer in organic farming–evaluation of a concept for a farm-scale biorefinery”. [Research Support, Non-U.S. Gov’t Research Support, U.S. Gov’t, Non-P.H.S.]. Bioresour Technol, 104(2012), 440-446. doi, 10.1016/j.biortech.2011.11.060

    Orfila, C., Degan, F. D., Jorgensen, B., Scheller, H. V., Ray, P. M., & Ulvskov, P. (2012). “Expression of mung bean pectin acetyl esterase in potato tubers: effect on acetylation of cell wall polymers and tuber mechanical properties”. Planta, 236(1), 197. doi, 10.1007/s00425-012-1596-z

    Ouellet, M., Datta, S., Dibble, D. C., Tamrakar, P. R., Benke, P., Li, C., Singh, S., Sale, K. L., Adams, P. D., Keasling, J. D., Simmons, B. A., Holmes, B. M., & Mukhopadhyay, A. (2011). “Impact of ionic liquid pretreated plant biomass on Saccharomyces cerevisiae growth and biofuel production”. Green Chemistry, 13(10), 2743-2749. doi, 10.1039/c1gc15327g,

    Papa, G., Varanasi, P., Sun, L., Cheng, G., Stavila, V., Holmes, B., Simmons, B. A., Adani, F., & Singh, S. (2012). “Exploring the effect of different plant lignin content and composition on ionic liquid pretreatment efficiency and enzymatic saccharification of Eucalyptus globulus L. mutants”. [Research Support, U.S. Gov’t, Non-P.H.S.]. Bioresour Technol, 117, 352-359. doi, 10.1016/j.biortech.2012.04.065

    Park, J. I., Steen, E. J., Burd, H., Evans, S. S., Redding-Johnson, A. M., Batth, T., Benke, P. I., D’Haeseleer, P., Sun, N., Sale, K. L., Keasling, J. D., Lee, T. S., Petzold, C. J., Mukhopadhyay, A., Singer, S. W., Simmons, B. A., & Gladden, J. M. (2012). “A thermophilic ionic liquid-tolerant cellulase cocktail for the production of cellulosic biofuels”. [Research Support, U.S. Gov’t, Non-P.H.S.]. PLoS One, 7(5), e37010. doi, 10.1371/journal.pone.0037010

    Parsons, H. T., Christiansen, K., Knierim, B., Carroll, A., Ito, J., Batth, T. S., Smith-Moritz, A. M., Morrison, S., McInerney, P., Hadi, M. Z., Auer, M., Mukhopadhyay, A., Petzold, C. J., Scheller, H. V., Loque, D., & Heazlewood, J. L. (2012). “Isolation and proteomic characterization of the Arabidopsis Golgi defines functional and novel components involved in plant cell wall biosynthesis”. [Research Support, Non-U.S. Gov’t Research Support, U.S. Gov’t, Non-P.H.S.]. Plant Physiol, 159(1), 12-26. doi, 10.1104/pp.111.193151

    Parsons, H. T., Ito, J., Park, E., Carroll, A. W., Joshi, H. J., Petzold, C. J., Drakakaki, G., & Heazlewood, J. L. (2012). The current state of the Golgi proteomes. In J. L. Heazlewood & C. J. Petzold (Eds.), Proteomics – Applications in Biology. Rijeka, Croatia: InTech.

    Peralta-Yahya, P. P., Zhang, F., del Cardayre, S. B., & Keasling, J. D. (2012). “Microbial engineering for the production of advanced biofuels”. [Research Support, U.S. Gov’t, Non-P.H.S.]. Nature, 488(7411), 320-328. doi, 10.1038/nature11478

    Perez-Gil, J., Uros, E. M., Sauret-Gueto, S., Lois, L. M., Kirby, J., Nishimoto, M., Baidoo, E. E., Keasling, J. D., Boronat, A., & Rodriguez-Concepcion, M. (2012). “Mutations in Escherichia coli aceE and ribB genes allow survival of strains defective in the first step of the isoprenoid biosynthesis pathway”. [Research Support, Non-U.S. Gov’t Research Support, U.S. Gov’t, Non-P.H.S.]. PLoS One, 7(8), e43775. doi, 10.1371/journal.pone.0043775

    Rautengarten, C., Ebert, B., Ouellet, M., Nafisi, M., Baidoo, E. E., Benke, P., Stranne, M., Mukhopadhyay, A., Keasling, J. D., Sakuragi, Y., & Scheller, H. V. (2012). “Arabidopsis Deficient in Cutin Ferulate encodes a transferase required for feruloylation of omega-hydroxy fatty acids in cutin polyester”. [Research Support, U.S. Gov’t, Non-P.H.S.]. Plant Physiol, 158(2), 654-665. doi, 10.1104/pp.111.187187

    Reindl, W., Deng, K., Cheng, X., Singh, A., Simmons, B. A., Adams, P. D., & Northen, T. (2012). Nanostructure-initiator mass spectrometry (NIMS) for the analysis of enzyme activitiesCurr protoc chem biol (Vol. 4, pp. 123-142). Retrieved from doi: 10.1002/9780470559277.ch110221

    Rennie, E. A., Hansen, S. F., Baidoo, E. E., Hadi, M. Z., Keasling, J. D., & Scheller, H. V. (2012). “Three members of the Arabidopsis glycosyltransferase family 8 are xylan glucuronosyltransferases”. [Research Support, Non-U.S. Gov’t Research Support, U.S. Gov’t, Non-P.H.S.]. Plant Physiol, 159(4), 1408-1417. doi, 10.1104/pp.112.200964

    Rutherford, B. J., & Mukhopadhyay, A. (2012). Engineering Stress Tolerance in Microbial Systems for Bioproduction of Fuels. In R. Arora (Ed.), Microbial Biotechnology: Energy and Environment. Wallingford, UK: CABI.

    Satoh, Y., Tajima, K., Munekata, M., Keasling, J. D., & Lee, T. S. (2012a). “Engineering of a tyrosol-producing pathway, utilizing simple sugar and the central metabolic tyrosine, in Escherichia coli”. [Research Support, Non-U.S. Gov’t Research Support, U.S. Gov’t, Non-P.H.S.]. J Agric Food Chem, 60(4), 979-984. doi, 10.1021/jf203256f

    Satoh, Y., Tajima, K., Munekata, M., Keasling, J. D., & Lee, T. S. (2012b). “Engineering of l-tyrosine oxidation in Escherichia coli and microbial production of hydroxytyrosol”. Metab Eng, 14(6), 603-610. doi, 10.1016/j.ymben.2012.08.002

    Schrimpf, S. P., von Mering, C., Bendixen, E., Heazlewood, J. L., Bumann, D., Omenn, G., & Hengartner, M. O. (2012). “The initiative on Model Organism Proteomes (iMOP) Session September 6, 2011, Geneva, Switzerland”. [Congresses]. Proteomics, 12(3), 346-350. doi, 10.1002/pmic.201290015

    Sharma, M. K., Sharma, R., Cao, P., Jenkins, J., Bartley, L. E., Qualls, M., Grimwood, J., Schmutz, J., Rokhsar, D., & Ronald, P. C. (2012). “A genome-wide survey of switchgrass genome structure and organization”. [Research Support, U.S. Gov’t, Non-P.H.S.]. PLoS One, 7(4), e33892. doi, 10.1371/journal.pone.0033892

    Sharma, R., Tan, F., Jung, K. H., Sharma, M. K., Peng, Z., & Ronald, P. C. (2011). “Transcriptional dynamics during cell wall removal and regeneration reveals key genes involved in cell wall development in rice”. Plant Molecular Biology, 77(4-5), 391-406. doi, 10.1007/s11103-011-9819-4,

    Sharma, V., Chiniquy, D., Baidoo, E., Keasling, J., Ronald, P., & Scheller, H. V. (2012). “Tools for Developing Glycosyl-Transferase Assays and Methods for Xylan Profiling in Plants”. Pharmaceutical Biology, 50(5), 607-607.

    Shepherd, M., Bartle, J., Lee, D. J., Brawner, J., Bush, D., Turnbull, P., Macdonel, P., Brown, T. R., Simmon, B. A., & Henry, R. (2011). “Eucalypts as a biofuel feedstock”. Biofuels, 2(6), 639-657. doi, 10.4155/bfs.11.136

    Simmons, B. A. (2011). Bioenergy from Plants and Plant Residues. In A. Altman & P. M. Hasegawa (Eds.), Plant Biotechnology and Agriculture – Prospects for the 21st Century (pp. 495-506). Oxford: Academic Press.

    Singh, P., Batth, T. S., Juminaga, D., Dahl, R. H., Keasling, J. D., Adams, P. D., & Petzold, C. J. (2012). “Application of targeted proteomics to metabolically engineered Escherichia coli”. [Research Support, U.S. Gov’t, Non-P.H.S.]. Proteomics, 12(8), 1289-1299. doi, 10.1002/pmic.201100482

    Smith-Moritz, A. M., Lao, J., Heazlewood, J. L., Ronald, P. C., & Vega-Sanchez, M. E. (2012). “Dependence of Plant Cell Wall Composition and Structure on Cellulose Synthase-Like Knock Out Mutant”. Biophysical Journal, 102(3), 590a-591a. doi, 10.1016/j.bpj.2011.11.3219

    Sogaard, C., Stenbaek, A., Bernard, S., Hadi, M., Driouich, A., Scheller, H. V., & Sakuragi, Y. (2012). “GO-PROMTO illuminates protein membrane topologies of glycan biosynthetic enzymes in the Golgi apparatus of living tissues”. [Research Support, Non-U.S. Gov’t]. PLoS One, 7(2), e31324. doi, 10.1371/journal.pone.0031324

    Sun, L., Varanasi, P., Yang, F., Loque, D., Simmons, B. A., & Singh, S. (2012). “Rapid determination of syringyl: guaiacyl ratios using FT-Raman spectroscopy”. [Research Support, U.S. Gov’t, Non-P.H.S. Validation Studies]. Biotechnol Bioeng, 109(3), 647-656. doi, 10.1002/bit.24348

    Torr, K. M., Love, K. T., Cetinkol, O. P., Donaldson, L. A., George, A., Holmes, B. M., & Simmons, B. A. (2012). “The impact of ionic liquid pretreatment on the chemistry and enzymatic digestibility of Pinus radiata compression wood”. Green Chemistry, 14(3), 778-787. doi, 10.1039/C2GC16362D

    Varanasi, P., Katsnelson, J., Larson, D. M., Sharma, R., Sharma, M. K., Vega-Sánchez, M. E., Zemla, M., Loque, D., Ronald, P. C., Simmons, B. A., Singh, S., Adams, P. D., & Auer, M. (2012). Mechanical Stress Analysis as a Method to Understand the Impact of Genetically Engineered Rice and Arabidopsis Plants Industrial Biotechnology (Vol. 8, pp. 238-244).

    Vega-Sanchez, M. E., Verhertbruggen, Y., Christensen, U., Chen, X., Sharma, V., Varanasi, P., Jobling, S. A., Talbot, M., White, R. G., Joo, M., Singh, S., Auer, M., Scheller, H. V., & Ronald, P. C. (2012). “Loss of Cellulose Synthase-Like F6 function affects mixed-linkage glucan deposition, cell wall mechanical properties and defense responses in vegetative tissues of rice”. Plant Physiology, 159, 56-69. doi, pp.112.195495 [pii] 10.1104/pp.112.195495

    Verhertbruggen, Y., Yin, L., Oikawa, A., & Scheller, H. V. (2011). “Mannan synthase activity in the CSLD family”. Plant Signaling & Behavior, 6(10), 1620-1623. doi, 17989 [pii],

    Vickers, C. E., Klein-Marcuschamer, D., & Kromer, J. O. (2012). “Examining the feasibility of bulk commodity production in Escherichia coli”. Biotechnology Letters, 34(4), 585-596. doi, 10.1007/s10529-011-0821-3

    Welz, O., Zador, J., Savee, J. D., Ng, M. Y., Meloni, G., Fernandes, R. X., Sheps, L., Simmons, B. A., Lee, T. S., Osborn, D. L., & Taatjes, C. A. (2012). “Low-temperature combustion chemistry of biofuels: pathways in the initial low-temperature (550 K-750 K) oxidation chemistry of isopentanol”. Physical Chemistry Chemical Physics, 14(9), 3112-3127. doi, 10.1039/c2cp23248k

    Wipat, A., Villalobos, A., Stan, G.-B., Smith, T., Sauro, H., Roehner, N., Pocock, M., Plahar, H., Peccoud, J., Myers, C., Misirli, G., Madsen, C., Lux, M., Kuchinsky, A., Ham, T., Grünberg, R., Gennari, J., Endy, D., Drory, O., Densmore, D., Chandran, D., Beal, J., Anderson, J. C., Adler, A., Adam, L., Rodriguez, C., Wilson, M., & Galdzicki, M. (2011). Synthetic Biology Open Language (SBOL) Version 1.0.0 BioBricks Foundation Request for Comments.

    Wipf, D., Loque, D., Lalonde, S., & Frommer, W. B. (2012). “Amino acid transporter inventory of the Selaginella genome”. [Original Research]. Frontiers in Plant Science, 3(36). doi, 10.3389/fpls.2012.00036

    Xiao, Y., Savchenko, T., Baidoo, E. E., Chehab, W. E., Hayden, D. M., Tolstikov, V., Corwin, J. A., Kliebenstein, D. J., Keasling, J. D., & Dehesh, K. (2012). “Retrograde signaling by the plastidial metabolite MEcPP regulates expression of nuclear stress-response genes”. [Research Support, U.S. Gov’t, Non-P.H.S.]. Cell, 149(7), 1525-1535. doi, 10.1016/j.cell.2012.04.038

    Yuzawa, S., Kim, W., Katz, L., & Keasling, J. D. (2012). “Heterologous production of polyketides by modular type I polyketide synthases in Escherichia coli”. [Research Support, U.S. Gov’t, Non-P.H.S. Review]. Curr Opin Biotechnol, 23(5), 727-735. doi, 10.1016/j.copbio.2011.12.029

    Zendejas, F. J., Benke, P. I., Lane, P. D., Simmons, B. A., & Lane, T. W. (2012). “Characterization of the acylglycerols and resulting biodiesel derived from vegetable oil and microalgae (Thalassiosira pseudonana and Phaeodactylum tricornutum)”. [Comparative Study Research Support, U.S. Gov’t, Non-P.H.S.]. Biotechnol Bioeng, 109(5), 1146-1154. doi, 10.1002/bit.24395

    Zhang, F., Carothers, J. M., & Keasling, J. D. (2012). “Design of a dynamic sensor-regulator system for production of chemicals and fuels derived from fatty acids”. [Research Support, Non-U.S. Gov’t Research Support, U.S. Gov’t, Non-P.H.S.]. Nat Biotechnol, 30(4), 354-359. doi, 10.1038/nbt.2149

    Zhang, F., Rodriguez, S., & Keasling, J. D. (2011). “Metabolic engineering of microbial pathways for advanced biofuels production”. Current Opinion Biotechnology, 22(6), 775-783. doi, S0958-1669(11)00087-5 [pii] 10.1016/j.copbio.2011.04.024

  • Achyuthan, K. E., Achyuthan, A. M., Adams, P. D., Dirk, S. M., Harper, J. C., Simmons, B. A., & Singh, A. K. (2010). “Supramolecular Self-Assembled Chaos: Polyphenolic Lignin’s Barrier to Cost-Effective Lignocellulosic Biofuels”. Molecules, 15(12), 8641-8688. doi, molecules15118641 [pii] 10.3390/molecules15118641,

    Banks, J. A., Nishiyama, T., Hasebe, M., Bowman, J. L., Gribskov, M., dePamphilis, C., Albert, V. A., Aono, N., Aoyama, T., Ambrose, B. A., Ashton, N. W., Axtell, M. J., Barker, E., Barker, M. S., Bennetzen, J. L., Bonawitz, N. D., Chapple, C., Cheng, C., Correa, L. G., Dacre, M., DeBarry, J., Dreyer, I., Elias, M., Engstrom, E. M., Estelle, M., Feng, L., Finet, C., Floyd, S. K., Frommer, W. B., Fujita, T., Gramzow, L., Gutensohn, M., Harholt, J., Hattori, M., Heyl, A., Hirai, T., Hiwatashi, Y., Ishikawa, M., Iwata, M., Karol, K. G., Koehler, B., Kolukisaoglu, U., Kubo, M., Kurata, T., Lalonde, S., Li, K., Li, Y., Litt, A., Lyons, E., Manning, G., Maruyama, T., Michael, T. P., Mikami, K., Miyazaki, S., Morinaga, S., Murata, T., Mueller-Roeber, B., Nelson, D. R., Obara, M., Oguri, Y., Olmstead, R. G., Onodera, N., Petersen, B. L., Pils, B., Prigge, M., Rensing, S. A., Riano-Pachon, D. M., Roberts, A. W., Sato, Y., Scheller, H. V., Schulz, B., Schulz, C., Shakirov, E. V., Shibagaki, N., Shinohara, N., Shippen, D. E., Sorensen, I., Sotooka, R., Sugimoto, N., Sugita, M., Sumikawa, N., Tanurdzic, M., Theissen, G., Ulvskov, P., Wakazuki, S., Weng, J. K., Willats, W. W., Wipf, D., Wolf, P. G., Yang, L., Zimmer, A. D., Zhu, Q., Mitros, T., Hellsten, U., Loque, D., Otillar, R., Salamov, A., Schmutz, J., Shapiro, H., Lindquist, E., Lucas, S., Rokhsar, D., & Grigoriev, I. V. (2011). “The Selaginella genome identifies genetic changes associated with the evolution of vascular plants”. Science, 332(6032), 960-963. doi, science.1203810 [pii] 10.1126/science.1203810

    Bates, J. T., Chivian, D., & Arkin, A. P. (2011). “GLAMM: Genome-Linked Application for Metabolic Maps”. Nucleic Acids Research, 39(Web Server issue), W400-405. doi, gkr433 [pii] 10.1093/nar/gkr433,

    Beller, H. R., Goh, E. B., & Keasling, J. D. (2011). “Definitive alkene identification needed for in vitro studies with ole (olefin biosynthesis) proteins”. Journal of Biological Chemistry, 286(26), le11. doi, 286/26/le11 [pii] 10.1074/jbc.L110.216127

    Bharadwaj, R., Chen, Z., Datta, S., Holmes, B. M., Sapra, R., Simmons, B. A., Adams, P. D., & Singh, A. K. (2010). “Microfluidic Glycosyl Hydrolase Screening for Biomass-to-Biofuel Conversion”. Analytical Chemistry, 82(22), 9513–9520. doi, 10.1021/ac102243f;

    Bharadwaj, R., Wong, A., Knierim, B., Singh, S., Holmes, B. M., Auer, M., Simmons, B. A., Adams, P. D., & Singh, A. K. (2011). “High-throughput enzymatic hydrolysis of lignocellulosic biomass via in-situ regeneration”. Bioresource Technology, 102(2), 1329-1337. doi, S0960-8524(10)01493-8 [pii] 10.1016/j.biortech.2010.08.108,

    Blanch, H. W., Simmons, B. A., & Klein-Marcuschamer, D. (2011). “Biomass deconstruction to sugars”. Biotechnology Journal, 6(9), 1086-1102. doi, 10.1002/biot.201000180,

    Chandrasekaran, A., Bharadwaj, R., Park, J. I., Sapra, R., Adams, P. D., & Singh, A. K. (2010). “A Microscale Platform For Integrated Cell-Free Expression And Activity Screening Of Cellulases”. Journal of Proteome Research, 9(11), 5677-5683. doi, 10.1021/pr1003938

    Cheng, G., Liu, Z., Murton, J. K., Jablin, M., Dubey, M., Majewski, J., Halbert, C., Browning, J., Ankner, J., Akgun, B., Wang, C., Esker, A. R., Sale, K. L., Simmons, B. A., & Kent, M. S. (2011). “Neutron Reflectometry and QCM-D Study of the Interaction of Cellulases with Films of Amorphous Cellulose”. Biomacromolecules, 12(6), 2216-2224. doi, 10.1021/bm200305u,

    Cheng, G., Varanasi, P., Li, C., Liu, H., Melnichenko, Y. B., Simmons, B. A., Kent, M. S., & Singh, S. (2011). “Transition of cellulose crystalline structure and surface morphology of biomass as a function of ionic liquid pretreatment and its relation to enzymatic hydrolysis”. Biomacromolecules, 12(4), 933-941. doi, 10.1021/bm101240z

    Chertkov, O., Copeland, A., Lucas, S., Lapidus, A., Berry, K. W., Detter, J. C., Del Rio, T. G., Hammon, N., Dalin, E., Tice, H., Pitluck, S., Richardson, P., Bruce, D., Goodwin, L., Han, C., Tapia, R., Saunders, E., Schmutz, J., Brettin, T., Larimer, F., Land, M., Hauser, L., Spring, S., Rohde, M., Kyrpides, N. C., Ivanova, N., Göker, M., Beller, H. R., Klenk, H.-P., & Woyke, T. (2011). “Complete genome sequence of Tolumonas auensis type strain (TA 4T)”. Standards in Genomic Sciences, 5(1). doi, 10.4056/sigs.2184986

    Chhabra, S. R., & Keasling, J. (2011). The Biological Basis | Metabolic Design and Control for Production in Prokaryotes. In M. Moo-Young (Ed.), Comprehensive Biotechnology (2 ed., Vol. 1, pp. 243–255): Elsevier.

    Datta, S., & Sapra., R. (2011). Cellulases and Hemicellulases for Biomass Degradation: An Introduction. In B. A. Simmons (Ed.), Chemical and Biochemical Catalysis for Next Generation Biofuels (pp. 115-135): Royal Society of Chemistry.

    DeAngelis, K., D’Haeseleer, P., Chivian, D., Fortney, J. L., Khudyakov, J., Simmons, B. A., Woo, H., Arkin, A. P., Davenport, K. W., Goodwin, L., Chen, A., Ivanova, N., Kyrpides, N., Mavromatis, K., Woyke, T., & Hazen, T. (2011). “Complete genome sequence of Enterobacter lignolyticus SCF1”. Standards in Genomic Sciences, 5(1), 69-85. doi, 10.4056/sigs.2104875

    DeAngelis, K. M., Allgaier, M., Chavarria, Y., Fortney, J. L., Hugenholtz, P., Simmons, B. A., Sublette, K., Silver, W. L., & Hazen, T. C. (2011). “Characterization of Trapped Lignin-Degrading Microbes in Tropical Forest Soil”. PLoS ONE 6(4), e19306. doi, 10.1371/journal.pone.0019306

    DeAngelis, K. M., Wu, C. H., Beller, H. R., Brodie, E. L., Chakraborty, R., Desantis, T. Z., Fortney, J. L., Hazen, T. C., Osman, S. R., Singer, M. E., Tom, L. M., & Andersen, G. L. (2011). “PCR amplification-independent methods for detection of microbial communities by the high-density microarray PhyloChip”. Applied and Environmental Microbiology, 77(18), 6313-6322. doi, AEM.05262-11 [pii] 10.1128/AEM.05262-11,

    Dunlop, M. J., Dossani, Z. Y., Szmidt, H. L., Chu, H. C., Lee, T. S., Keasling, J. D., Hadi, M. Z., & Mukhopadhyay, A. (2011). “Engineering microbial biofuel tolerance and export using efflux pumps”. Molecular Systems Biology, 7, 487. doi, msb201121 [pii] 10.1038/msb.2011.21,

    Eudes, A., Baidoo, E. E., Yang, F., Burd, H., Hadi, M. Z., Collins, F. W., Keasling, J. D., & Loque, D. (2011). “Production of tranilast [N-(3′,4′-dimethoxycinnamoyl)-anthranilic acid] and its analogs in yeast Saccharomyces cerevisiae”. Applied Microbiology and Biotechnology, 89(4), 989-1000. doi, 10.1007/s00253-010-2939-y

    Frear, C., Wang, Z.-W., Li, C., & Chen, S. (2011). “Biogas potential and microbial population distributions in flushed dairy manure and implications on anaerobic digestion technology”. Journal of Chemical Technology and Biotechnology, 86(1), 145-152. doi, 10.1002/jctb.2484

    Gladden, J. M., Allgaier, M., Miller, C. S., Hazen, T. C., Vandergheynst, J. S., Hugenholtz, P., Simmons, B. A., & Singer, S. W. (2011). “Glycoside hydrolase activities of thermophilic bacterial consortia adapted to switchgrass”. Applied and Environmental Microbiology, 77(16), 5804-5812. doi, AEM.00032-11 [pii] 10.1128/AEM.00032-11

    Hajimorad, M., Gray, P. R., & Keasling, J. D. (2011). “A framework and model system to investigate linear system behavior in Escherichia coli”. J Biol Eng, 5, 3. doi, 10.1186/1754-1611-5-3

    Hansen, S. F., McAndrew, R., DeGiovanni, A., McInerney, P., Pereira, J. H., Hadi, M., Adams, P., & Scheller, H. V. (2011). “Structural Comparison of Plant Glycosyltransferases”. [Meeting Abstract]. Glycobiology, 21(11), 1511-1512.

    Heazlewood, J. L. (2011). “The Green proteome: challenges in plant proteomics”. Frontiers in Plant Proteomics, 1-5. doi, 10.3389/fpls.2011.00006

    Hillson, N. J. (2011). DNA Assembly Method Standardization for Synthetic Biomolecular Circuits and Systems. In H. Koeppl, D. Densmore, M. di Bernardo & G. Setti (Eds.), Design and Analysis of Biomolecular Circuits: Engineering Approaches to Systems and Synthetic Biology (1 ed., pp. 295-314). New York: Springer-Verlag.

    Ito, J., Batth, T. S., Petzold, C. J., Redding-Johanson, A. M., Mukhopadhyay, A., Verboom, R., Meyer, E. H., Millar, A. H., & Heazlewood, J. L. (2011). “Analysis of the Arabidopsis cytosolic proteome highlights subcellular partitioning of central plant metabolism”. Journal of Proteome Research, 10(4), 1571-1582. doi, 10.1021/pr1009433;

    Joshi, H. J., Hirsch-Hoffmann, M., Baerenfaller, K., Gruissem, W., Baginsky, S., Schmidt, R., Schulze, W. X., Sun, Q., van Wijk, K. J., Egelhofer, V., Wienkoop, S., Weckwerth, W., Bruley, C., Rolland, N., Toyoda, T., Nakagami, H., Jones, A. M., Briggs, S. P., Castleden, I., Tanz, S. K., Millar, A. H., & Heazlewood, J. L. (2011). “MASCP Gator: an aggregation portal for the visualization of Arabidopsis proteomics data”. Plant Physiology, 155(1), 259-270. doi, pp.110.168195 [pii] 10.1104/pp.110.168195

    Joshua, C. J., Dahl, R., Benke, P. I., & Keasling, J. D. (2011). “Absence of Diauxie during Simultaneous Utilization of Glucose and Xylose by Sulfolobus acidocaldarius”. Journal of Bacteriology, 193(6), 1293-1301. doi, JB.01219-10 [pii] 10.1128/JB.01219-10

    Jung, K. H., Cao, P., Seo, Y. S., Dardick, C., & Ronald, P. C. (2010). “The Rice Kinase Phylogenomics Database: a guide for systematic analysis of the rice kinase super-family”. Trends in Plant Science, 15(11). doi, S1360-1385(10)00163-9 [pii] 10.1016/j.tplants.2010.08.004

    Keasling, J. D. (2010). “Manufacturing molecules through metabolic engineering”. Science, 330(6009), 1355-1358. doi, 330/6009/1355 [pii] 10.1126/science.1193990,

    Keasling, J. D. (2011). “Joint BioEnergy Institute”. Industrial Biotechnology, 7(4), 259-260. doi, 10.1089/ind.2011.7.259

    Klein-Marcuschamer, D., Holmes, B., Simmons, B. A., & Blanch, H. W. (2011). Biofuel Economics. In E. Hood, R. Powell & N. P. (Eds.), Plant Biomass Conversion (1 ed., pp. 329-348 ). New York: John Wiley & Sons.

    Klein-Marcuschamer, D., Oleskowicz-Popiel, P., Simmons, B. A., & Blanch, H. W. (2010). “Technoeconomic analysis of biofuels: A wiki-based platform for lignocellulosic biorefineries”. Biomass & Bioenergy, 34(12), 1914-1921. doi, Doi 10.1016/J.Biombioe.2010.07.033

    Klein-Marcuschamer, D., Simmons, B. A., & Blanch, H. W. (2011). “Techno-economic analysis of a lignocellulosic ethanol biorefinery with ionic liquid pre-treatment”. Biofuels, Bioproducts and Biorefining, 5(5), 562-569. doi, Doi 10.1002/Bbb.303 <Go to ISI>://000295143000018,

    Kumar, V. S., Ferry, J. G., & Maranas, C. D. (2011). “Metabolic reconstruction of the archaeon methanogen Methanosarcina Acetivorans”. [Research Support, U.S. Gov’t, Non-P.H.S.]. Bmc Systems Biology, 5, 28. doi, 10.1186/1752-0509-5-28

    Lee, T. S., Krupa, R. A., Zhang, F., Hajimorad, M., Holtz, W. J., Prasad, N., Lee, S. K., & Keasling, J. D. (2011). “BglBrick vectors and datasheets; a synthetic biology platform for gene expression”. Journal of Biological Engineering 5(1), 12. doi, 1754-1611-5-12 [pii] 10.1186/1754-1611-5-12;

    Li, C., Cheng, G., Balan, V., Kent, M. S., Ong, M., Chundawat, S. P., Sousa, L. D., Melnichenko, Y. B., Dale, B. E., Simmons, B. A., & Singh, S. (2011). “Influence of physico-chemical changes on enzymatic digestibility of ionic liquid and AFEX pretreated corn stover”. Bioresource Technology, 102(13), 6928-6936. doi, S0960-8524(11)00475-5 [pii] 10.1016/j.biortech.2011.04.005,

    Liu, H., Sale, K. L., Simmons, B. A., & Singh, S. (2011). “Molecular Dynamics Study of Polysaccharides in Binary Solvent Mixtures of an Ionic Liquid and Water”. Journal of Physical Chemistry B, 115(34), 10251-10258. doi, 10.1021/jp111738q,

    Loque, D., Eudes, A., & Yang, F. (2011). Biomass Availability and Sustainability for BioFuels. In B. A. Simmons (Ed.), Chemical and Biochemical Catalysis for Next Generation Biofuels (pp. 5-32): Royal Society of Chemistry.

    Ma, S. M., Garcia, D. E., Redding-Johanson, A. M., Friedland, G. D., Chan, R., Batth, T. S., Haliburton, J. R., Chivian, D., Keasling, J. D., Petzold, C. J., Soon Lee, T., & Chhabra, S. R. (2011). “Optimization of a heterologous mevalonate pathway through the use of variant HMG-CoA reductases”. Metabolic Engineering, 13(5), 588-597. doi, S1096-7176(11)00075-9 [pii] 10.1016/j.ymben.2011.07.001

    Manabe, Y., Nafisi, M., Verhertbruggen, Y., Orfila, C., Gille, S., Rautengarten, C., Cherk, C., Marcus, S. E., Somerville, S., Pauly, M., Knox, J. P., Sakuragi, Y., & Scheller, H. V. (2011). “Loss-of-Function Mutation of REDUCED WALL ACETYLATION2 in Arabidopsis Leads to Reduced Cell Wall Acetylation and Increased Resistance to Botrytis cinerea”. Plant Physiology, 155(3), 1068-1078. doi, pp.110.168989 [pii] 10.1104/pp.110.168989

    Miller, C. S., Baker, B. J., Thomas, B. C., Singer, S. W., & Banfield, J. F. (2011). “EMIRGE: Reconstruction of full length ribosomal genes from microbial community short read sequencing data”. Genome Biology, 12(5), R44. doi, gb-2011-12-5-r44 [pii] 10.1186/gb-2011-12-5-r44

    Muyzer, G., Sorokin, D. Y., Mavromatis, K., Lapidus, A., Clum, A., Ivanova, N., Pati, A., d’Haeseleer, P., Woyke, T., & Kyrpides, N. C. (2011). “Complete genome sequence of “Thioalkalivibrio sulfidophilus” HL-EbGr7″. Standards in Genomic Sciences, 4(1), 23-35. doi, 10.4056/sigs.1483693

    Nielsen, J., & Keasling, J. D. (2011). “Synergies between synthetic biology and metabolic engineering”. Nature Biotechnology, 29(8), 693-695. doi, 10.1038/nbt.1937 nbt.1937 [pii];

    Oikawa, A., Joshi, H. J., Rennie, E. A., Ebert, B., Manisseri, C., Heazlewood, J. L., & Scheller, H. V. (2010). “An integrative approach to the identification of Arabidopsis and rice genes involved in xylan and secondary wall development”. PLoS One, 5(11), e15481. doi, 10.1371/journal.pone.0015481

    Park, J. I., Kent, M. S., Datta, S., Holmes, B. M., Huang, Z., Simmons, B. A., Sale, K. L., & Sapra, R. (2011). “Enzymatic hydrolysis of cellulose by the cellobiohydrolase domain of CelB from the hyperthermophilic bacterium Caldicellulosiruptor saccharolyticus”. Bioresource Technology, 102(10), 5988-5994. doi, S0960-8524(11)00221-5 [pii] 10.1016/j.biortech.2011.02.036

    Peralta-Yahya, P. P., Ouellet, M., Chan, R., Mukhopadhyay, A., Keasling, J. D., & Lee, T. S. (2011). “Identification and microbial production of a terpene-based advanced biofuel”. Nature Communications 2, 483. doi, 10.1038/ncomms1494 ncomms1494 [pii]

    Pereira, J. H., Chen, Z., McAndrew, R. P., Sapra, R., Chhabra, S. R., Sale, K. L., Simmons, B. A., & Adams, P. D. (2010). “Biochemical characterization and crystal structure of endoglucanase Cel5A from the hyperthermophilic Thermotoga maritima”. Journal of Structural Biology, 172(3), 372-379. doi, S1047-8477(10)00196-6 [pii] 10.1016/j.jsb.2010.06.018

    Rautengarten, C., Ebert, B., Herter, T., Petzold, C. J., Ishii, T., Mukhopadhyay, A., Usadel, B., & Scheller, H. V. (2011). “The interconversion of UDP-arabinopyranose and UDP-arabinofuranose is indispensable for plant development in Arabidopsis”. Plant Cell, 23(4), 1373-1390. doi, tpc.111.083931 [pii] 10.1105/tpc.111.083931,

    Redding-Johanson, A. M., Batth, T. S., Chan, R., Krupa, R., Szmidt, H. L., Adams, P. D., Keasling, J. D., Soon Lee, T., Mukhopadhyay, A., & Petzold, C. J. (2011). “Targeted proteomics for metabolic pathway optimization: Application to terpene production”. Metabolic Engineering, 13(2), 194-203. doi, S1096-7176(10)00125-4 [pii] 10.1016/j.ymben.2010.12.005

    Reddy, A. P., Allgaier, M., Singer, S. W., Hazen, T. C., Simmons, B. A., Hugenholtz, P., & Vandergheynst, J. S. (2011). “Bioenergy feedstock-specific enrichment of microbial populations during high-solids thermophilic deconstruction”. Biotechnology and Bioengineering, 108(9), 2088-2098. doi, 10.1002/bit.23176

    Reindl, W., Deng, K., Gladden, J. M., Cheng, G., Wong, A., Singer, S. W., Singh, S., Lee, J. C., Yao, C. H., Hazen, T. C., Singh, A. K., Simmons, B. A., Adams, P. D., & Northen, T. R. (2011). “Colloid-based multiplexed screening for plant biomass-degrading glycoside hydrolase activities in microbial communities”. Energy & Environmental Science, 4(8), 2884-2893. doi, 10.1039/c1ee01112j <Go to ISI>://000293213600034,

    Rezaei, F., Joh, L. D., Kashima, H., Reddy, A. P., & Vandergheynst, J. S. (2011). “Selection of Conditions for Cellulase and Xylanase Extraction from Switchgrass Colonized by Acidothermus cellulolyticus”. Applied Biochemistry and Biotechnology, 164(6), 793-803. doi, 10.1007/s12010-011-9174-6,

    Ronald, P. (2011). “Plant genetics, sustainable agriculture and global food security”. Genetics, 188(1), 11-20. doi, 188/1/11 [pii] 10.1534/genetics.111.128553

    Ronald, P. C., & Beutler, B. (2010). “Plant and animal sensors of conserved microbial signatures”. Science, 330(6007), 1061-1064. doi, 330/6007/1061 [pii] 10.1126/science.1189468

    Sakuragi, Y., Norholm, M. H., & Scheller, H. V. (2011). Visual mapping of cell wall biosynthesis. In Z. A. Popper (Ed.), The Plant Cell Wall: Methods and Protocols (2011/01/12 ed., Vol. 715, pp. 153-167). Berlin, Germany: Springer Science.

    Seo, Y. S., Chern, M., Bartley, L. E., Han, M., Jung, K. H., Lee, I., Walia, H., Richter, T., Xu, X., Cao, P., Bai, W., Ramanan, R., Amonpant, F., Arul, L., Canlas, P. E., Ruan, R., Park, C. J., Chen, X., Hwang, S., Jeon, J. S., & Ronald, P. C. (2011). “Towards establishment of a rice stress response interactome”. PLoS Genet, 7(4), e1002020. doi, 10.1371/journal.pgen.1002020,

    Simmons, B. A. (2011a). Introduction to Catalysis for Biofuels. In B. A. Simmons (Ed.), Chemical and Biochemical Catalysis for Next Generation Biofuels (pp. 1-4). Cambridge Royal Society of Chemistry.

    Simmons, B. A. (2011). “Opportunities and challenges in advanced biofuel production: the importance of synthetic biology and combustion science”. Biofuels, 2(1), 5-7. doi, 10.4155/bfs.10.75

    Simmons, B. A. (2011b). “Rethinking renewable energy in Japan”. Biofuels, 2(4), 365–367. doi, 10.4155/bfs.11.117

    Simmons, B. A. (2011). “Synthetic enzymes: catalysis on demand”. Microbial Biotechnology, 4(2), 130-131.

    Singer, S. W., Reddy, A. P., Gladden, J. M., Guo, H., Hazen, T. C., Simmons, B. A., & Vandergheynst, J. S. (2011). “Enrichment, Isolation and Characterization of Fungi Tolerant to 1-Ethyl-3-Methylimadazolium Acetate”. Journal of Applied Microbiology, 110(4), 1023-1031. doi, 10.1111/j.1365-2672.2011.04959.x

    Smith-Moritz, A. M., Chern, M., Lao, J., Sze-To, W. H., Heazlewood, J. L., Ronald, P. C., & Vega-Sanchez, M. E. (2011). “Combining multivariate analysis and monosaccharide composition modeling to identify plant cell wall variations by Fourier Transform Near Infrared spectroscopy”. Plant Methods, 7, 26. doi, 10.1186/1746-4811-7-26

    Sun, L., Simmons, B. A., & Singh, S. (2011). “Understanding tissue specific compositions of bioenergy feedstocks through hyperspectral Raman imaging”. Biotechnology and Bioengineering 108(2), 286-295. doi, 10.1002/bit.22931,

    Taylor, N. L., Heazlewood, J. L., & Millar, A. H. (2011). “The Arabidopsis thaliana 2-D gel mitochondrial proteome: Refining the value of reference maps for assessing protein abundance, contaminants and post-translational modifications”. Proteomics, 11(9), 1720–1733. doi, 10.1002/pmic.201000620

    Varanasi, P., Sun, L., Knierim, B., Bosneaga, E., Sakar, P., Singh, S., & Auer, M. (2011). Quantifying Bio-Engineering: The Importance of Biophysics in Biofuel Research. In M. A. dos Santos Bernades (Ed.), Biofuel’s Engineering Process Technology (pp. 493-520): InTech.

    Yang, Y., Dec, J., Dronniou, N., & Simmons, B. A. (2010). “Characteristics of Isopentanol as a Fuel for HCCI Engines”. Society of Automobile Engineers International Journal of Fuels and Lubricants, 3(2), 725-741. doi, 2010-01-2164

    Yilmaz, S., Allgaier, M., & Hugenholtz, P. (2010). “Multiple displacement amplification compromises quantitative analysis of metagenomes”. Nature Methods, 7(12), 943-944. doi, nmeth1210-943 [pii] 10.1038/nmeth1210-943

    Yin, L., Verhertbruggen, Y., Oikawa, A., Manisseri, C., Knierim, B., Prak, L., Jensen, J. K., Knox, J. P., Auer, M., Willats, W. G., & Scheller, H. V. (2011). “The Cooperative Activities of CSLD2, CSLD3, and CSLD5 Are Required for Normal Arabidopsis Development”. Molecular Plant, 4(6), 1024-1037. doi, ssr026 [pii] 10.1093/mp/ssr026

    Zhang, F., & Keasling, J. (2011). “Biosensors and their applications in microbial metabolic engineering”. Trends in Microbiology, 19(7), 323-329. doi, S0966-842X(11)00092-8 [pii] 10.1016/j.tim.2011.05.003,

    Zhang, T., Datta, S., Eichler, J., Ivanova, N., Axen, S. D., Kerfeld, C. A., Chen, F., Kyrpides, N., Hugenholtz, P., Cheng, J.-F., Sale, K. L., Simmons, B. A., & Rubin, E. (2011). “Identification of a haloalkaliphilic and thermostable cellulase with improved ionic liquid tolerance”. Green Chemistry, 13(8), 2083-2090. doi, 10.1039/C1GC15193B <Go to ISI>://000293518300024,

    1. Achyuthan, K. E., Adams, P. D., Datta, S., Simmons, B. A., & Singh, A. K. (2010). “Hitherto unrecognized fluorescence properties of coniferyl alcohol”. Molecules, 15(3), 1645-1667. doi, 10.3390/molecules15031645
    2. Achyuthan, K. E., Adams, P. D., Simmons, B. A., & Singh, A. K. (2010). “Spectroscopic analyses of the biofuels-critical phytochemical coniferyl alcohol and its enzyme-catalyzed oxidation products”. Molecules, 14(11), 4758-4778. doi, 10.3390/molecules14114758
    3. Allgaier, M., Reddy, A., Park, J. I., Ivanova, N., D’Haeseleer, P., Lowry, S., . . . Hugenholtz, P. (2010). “Targeted discovery of glycoside hydrolases from a switchgrass-adapted compost community”. PLoS One, 5(1), e8812. doi, 10.1371/journal.pone.0008812
    4. Arora, R., Manisseri, C., Li, C. L., Ong, M. D., Scheller, H. V., Vogel, K., . . . Singh, S. (2010). “Monitoring and Analyzing Process Streams Towards Understanding Ionic Liquid Pretreatment of Switchgrass (Panicum virgatum L.)”. Bioenergy Research, 3(2), 134-145. doi, 10.1007/s12155-010-9087-1 <Go to ISI>://WOS:000278541500006.
    5. Bart, R. S., Chern, M., Vega-Sanchez, M. E., Canlas, P., & Ronald, P. C. (2010). “Rice Snl6, a cinnamoyl-CoA reductase-like gene family member, is required for NH1-mediated immunity to Xanthomonas oryzae pv. oryzae”. PLoS Genet, 6(9), e1001123. doi, 10.1371/journal.pgen.1001123
    6. Bartley, L. E., & Ronald, P. C. (2010). “Plant and microbial research seeks biofuel production from lignocellulose”. California Agriculture, 63(4), 178-184. doi, <Go to ISI>://WOS:000270705100006.
    7. Beller, H. R., Goh, E. B., & Keasling, J. D. (2010). “Genes involved in long-chain alkene biosynthesis in Micrococcus luteus”. Appl Environ Microbiol, 76(4), 1212-1223. doi, 10.1128/AEM.02312-09
    8. Brennan, T. C. R., Datta, S., Blanch, H. W., Simmons, B. A., & Holmes, B. M. (2010). “Recovery of Sugars from Ionic Liquid Biomass Liquor by Solvent Extraction”. Bioenergy Research, 3(2), 123-133. doi, Doi 10.1007/S12155-010-9091-5 <Go to ISI>://000278541500005,
    9. Cao, P. J., Jung, K. H., & Ronald, P. C. (2010). “A Survey of Databases for Analysis of Plant Cell Wall-Related Enzymes”. Bioenergy Research, 3(2), 108-114. doi, Doi 10.1007/S12155-010-9082-6 <Go to ISI>://000278541500003,
    10. Carothers, J. M., Goler, J. A., Kapoor, Y., Lara, L., & Keasling, J. D. (2010). “Selecting RNA aptamers for synthetic biology: investigating magnesium dependence and predicting binding affinity”. [Research Support, Non-U.S. Gov’t Research Support, U.S. Gov’t, Non-P.H.S.]. Nucleic Acids Res, 38(8), 2736-2747. doi, 10.1093/nar/gkq082
    11. Cetinkol, O.P., Dibble, D.C., Cheng, G., Kent, M.S., Knierim, B., Auer, M., . . . Holmes, B.M. (2010). “Understanding the impact of ionic liquid pretreatment on eucalyptus”. Biofuels, 1(1), 33-46. doi, 10.4155/BFS.09.5.
    12. Chou, H. H., Trisiriroj, A., Park, S., Hsing, Y. I. C., Ronald, P. C., & Schnable, P. S. (2010). “Direct calibration of PICKY-designed microarrays”. BMC Bioinformatics, 10(347), 1-11. doi, Artn 347 Doi 10.1186/1471-2105-10-347 <Go to ISI>://000271764200001
    13. Christensen, U., Alonso-Simon, A., Scheller, H. V., Willats, W. G. T., & Harholt, J. (2010). “Characterization of the primary cell walls of seedlings of Brachypodium distachyon – A potential model plant for temperate grasses”. Phytochemistry, 71(1), 62-69. doi, 10.1016/J.Phytochem.2009.09.019 <Go to ISI>://000274374100008
    14. Cong, Y., Baker, M. L., Jakana, J., Woolford, D., Miller, E. J., Reissmann, S., . . . Chiu, W. (2010). “4.0-A resolution cryo-EM structure of the mammalian chaperonin TRiC/CCT reveals its unique subunit arrangement”. Proceedings of the National Academy of Sciences, 107(11), 4967-4972. doi, 0913774107 [pii]10.1073/pnas.0913774107
    15. Cote, C. L., Boileau, F., Roy, V., Ouellet, M., Levasseur, C., Morency, M. J., . . . MacKay, J. J. (2010). “Gene family structure, expression and functional analysis of HD-Zip III genes in angiosperm and gymnosperm forest trees”. [Article]. Bmc Plant Biology, 10, 273. doi, 10.1186/1471-2229-10-273 <Go to ISI>://WOS:000285587200001,
    16. Datta, S., Holmes, B., Park, J. I., Chen, Z. W., Dibble, D. C., Hadi, M., . . . Sapra, R. (2010). “Ionic liquid tolerant hyperthermophilic cellulases for biomass pretreatment and hydrolysis”. Green Chemistry, 12(2), 338-345. doi, 10.1039/B916564a <Go to ISI>://000274396800025
    17. DeAngelis, K. M., Gladden, J. M., Allgaier, M., D’haeseleer, P., Fortney, J. L., Reddy, A., . . . Hazen, T. C. (2010). “Strategies for Enhancing the Effectiveness of Metagenomic-based Enzyme Discovery in Lignocellulolytic Microbial Communities”. Bioenergy Research, 3(2), 146-158. doi, 10.1007/S12155-010-9089-Z <Go to ISI>://000278541500007,
    18. Dehal, P. S., Joachimiak, M. P., Price, M. N., Bates, J. T., Baumohl, J. K., Chivian, D., . . . Arkin, A. P. (2010). “MicrobesOnline: an integrated portal for comparative and functional genomics”. Nucleic Acids Research, 38, D396-D400. doi, Doi 10.1093/Nar/Gkp919 <Go to ISI>://000276399100062,
    19. Dietrich, J. A., McKee, A. E., & Keasling, J. D. (2010). “High-throughput metabolic engineering: advances in small-molecule screening and selection”. [Research Support, U.S. Gov’t, Non-P.H.S. Review]. Annu Rev Biochem, 79, 563-590. doi, 10.1146/annurev-biochem-062608-095938
    20. Dunlop, M.J., Keasling, J.D., & Mukhopadhyay, A. (2010). “A model for improving microbial biofuel production using a synthetic feedback loop”. Synthetic and Systems Biology, 4(2), 95-104. doi, 10.1007/s11693-010-9052-5,
    21. Durek, P., Schmidt, R., Heazlewood, J. L., Jones, A., MacLean, D., Nagel, A., . . . Schulze, W. X. (2010). “PhosPhAt: the Arabidopsis thaliana phosphorylation site database. An update”. Nucleic Acids Research, 38, D828-D834. doi, 10.1093/Nar/Gkp810 <Go to ISI>://000276399100129
    22. Fedoroff, N. V., Battisti, D. S., Beachy, R. N., Cooper, P. J. M., Fischhoff, D. A., Hodges, C. N., . . . Zhu, J. K. (2010). “Radically Rethinking Agriculture for the 21st Century”. Science, 327(5967), 833-834. doi, 10.1126/Science.1186834 <Go to ISI>://000274408300051,
    23. Geshi, N., Petersen, B. L., & Scheller, H. V. (2010). “Toward tailored synthesis of functional polysaccharides in plants”. Foods for Health in the 21st Century: A Road Map for the Future, 1190, 50-57. doi, 10.1111/J.1749-6632.2009.05267.X <Go to ISI>://000277992500005
    24. Harholt, J., Bach, I. C., Lind-Bouquin, S., Nunan, K. J., Madrid, S. M., Brinch-Pedersen, H., . . . Scheller, H. V. (2010). “Generation of transgenic wheat (Triticum aestivum L.) accumulating heterologous endo-xylanase or ferulic acid esterase in the endosperm”. Plant Biotechnology Journal, 8(3), 351-362. doi, 10.1111/J.1467-7652.2009.00490.X <Go to ISI>://000275145800010,;jsessionid=E96FA6B5F9B50102409A00F130B63C73.d03t02
    25. Harholt, J., Suttangkakul, A., & Scheller, H. V. (2010). “Biosynthesis of Pectin”. Plant Physiology, 153(2), 384-395. doi, 10.1104/Pp.110.156588 <Go to ISI>://000278340200004
    26. Holtz, W. J., & Keasling, J. D. (2010). “Engineering Static and Dynamic Control of Synthetic Pathways”. Cell, 140(1), 19-23. doi, Doi 10.1016/J.Cell.2009.12.029
    27. Ito, J., Petzold, C. J., Mukhopadhyay, A., & Heazlewood, J. L. (2010). “The Role of Proteomics in the Development of Cellulosic Biofuels”. Current Proteomics, 7(2), 121-134. doi, 1570-1646/10 <Go to ISI>://000277888100006,
    28. Ju, Han, Singh, S., Lan, Sun, Simmons, B., Auer, M., & Parvin, B. (2010). “Chemical profiling of the plant cell wall through Raman microspectroscopy”. Proceedings 2010 7th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 125(1), 1273-1276. doi, 10.1109/isbi.2010.5490228 <Go to ISI>://INSPEC:11458221
    29. Jung, K. H., Seo, Y. S., Walia, H., Cao, P. J., Fukao, T., Canlas, P. E., . . . Ronald, P. C. (2010). “The Submergence Tolerance Regulator Sub1A Mediates Stress-Responsive Expression of AP2/ERF Transcription Factors”. Plant Physiology, 152(3), 1674-1692. doi, 10.1104/Pp.109.152157 <Go to ISI>://000276329500044,
    30. Keasling, Jay. (2010). “Engineering Microorganisms with Plant-derived Genes to Produce Drugs and Fuels”. In Vitro Cellular & Developmental Biology Animal, 46(Suppl. 1), 38-39. doi, <Go to ISI>://BCI:BCI201100083227.
    31. Kent, M. S., Cheng, G., Murton, J. K., Carles, E. L., Dibble, D. C., Zendejas, F., . . . Hjelm, R. P. (2010). “Study of enzymatic digestion of cellulose by small angle neutron scattering”. [Comparative Study Research Support, Non-U.S. Gov’t Research Support, U.S. Gov’t, Non-P.H.S.]. Biomacromolecules, 11(2), 357-368. doi, 10.1021/bm9008952
    32. Lacayo, C. I., Malkin, A. J., Holman, H. Y., Chen, L., Ding, S. Y., Hwang, M. S., & Thelen, M. P. (2010). “Imaging cell wall architecture in single Zinnia elegans tracheary elements”. Plant Physiology, 154(1), 121-133. doi, pp.110.155242 [pii]10.1104/pp.110.155242,
    33. Lalonde, S., Sero, A., Pratelli, R., Pilot, G., Chen, J., Sardi, M. I., . . . Frommer, W. B. (2010). “A membrane protein/signaling protein interaction network for Arabidopsis version AMPv2”. Frontiers in Physiology, 1, 24. doi, 10.3389/fphys.2010.00024
    34. Landau, A. M., Lokstein, H., Scheller, H. V., Lainez, V., Maldonado, S., & Prina, A. R. (2010). “A cytoplasmically inherited barley mutant is defective in photosystem I assembly due to a temperature-sensitive defect in ycf3 splicing”. Plant Physiology, 151, 1802-1811. doi, 10.1104/pp.109.147843
    35. Lee, Do Yup, Bowen, Benjamin P., & Northen, Trent R. (2010). “Mass spectrometry-based metabolomics, analysis of metabolite-protein interactions, and imaging”. [Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov’t Research Support, U.S. Gov’t, Non-P.H.S. Review]. Biotechniques, 49(2), 557-+. doi, 10.2144/000113451 <Go to ISI>://WOS:000287719000012
    36. Li, C., Knierim, B., Manisseri, C., Arora, R., Scheller, H. V., Auer, M., . . . Singh, S. (2010). “Comparison of dilute acid and ionic liquid pretreatment of switchgrass: Biomass recalcitrance, delignification and enzymatic saccharification”. Bioresource Technology, 101(13), 4900-4906. doi, S0960-8524(09)01442-4 [pii]10.1016/j.biortech.2009.10.066
    37. Liepman, A. H., Wightman, R., Geshi, N., Turner, S. R., & Scheller, H. V. (2010). “Arabidopsis – a powerful model system for plant cell wall research”. Plant Journal, 61(6), 1107-1121. doi, TPJ4161 [pii]10.1111/j.1365-313X.2010.04161.x
    38. Liu, H. B., Pereira, J. H., Adams, P., Simmons, B., Sapra, R., & Sale, K. (2010). “The N-Terminal Ig Domain of Endoglucanase Cel9A from the Thermoacidophilic Alicyclobacillus Acidocaldarius Enhances Protein Stability”. Biophysical Journal, 98(3), 451a-451a. doi, <Go to ISI>://WOS:000208762004259
    39. Liu, H., Pereira, J. H., Adams, P. D., Sapra, R., Simmons, B. A., & Sale, K. L. (2010). “Molecular simulations provide new insights into the role of the accessory immunoglobulin-like domain of Cel9A”. Febs Letters, 584(15), 3431-3435. doi, S0014-5793(10)00540-5 [pii]10.1016/j.febslet.2010.06.041;
    40. Liu, H., Sale, K. L., Holmes, B. M., Simmons, B. A., & Singh, S. (2010). “Understanding the interactions of cellulose with ionic liquids: a molecular dynamics study”. Journal of Physical Chemistry B, 114(12), 4293-4301. doi, 10.1021/jp9117437
    41. Lucks, J. B., Qi, L. S., Mutalik, V., & Arkin, A. P. (2010). “Engineering mRNA structural regulation of transcription using an RNA-sensing riboregulator”. [Meeting Abstract]. Faseb Journal, 24. doi, <Go to ISI>://WOS:000208675502151.
    42. Mattozzi Mde, L., & Keasling, J. D. (2010). “Rationally engineered biotransformation of p-nitrophenol”. [Research Support, Non-U.S. Gov’t Research Support, U.S. Gov’t, Non-P.H.S.]. Biotechnol Prog, 26(3), 616-621. doi, 10.1002/btpr.382
    43. Melnichenko, Yuri B., Mayama, H., Cheng, G., & Blach, T. (2010). “Monitoring Phase Behavior of Sub- and Supercritical CO2 Confined in Porous Fractal Silica with 85% Porosity”. [Research Support, Non-U.S. Gov’t Research Support, U.S. Gov’t, Non-P.H.S.]. Langmuir, 26(9), 6374-6379. doi, 10.1021/la904032p <Go to ISI>://WOS:000276969700048
    44. Morgan, T. J., George, A., Alvarez-Rodriguez, P., Millan, M., Herod, A. A., & Kandiyoti, R. (2010). “Estimating molecular masses of petroleum-derived fractions: High mass (> 2000 u) materials in maltenes and asphaltenes from Maya crude oil”. Journal of Chromatography A, 1217(24), 3804-3818. doi, 10.1016/j.chroma.2010.04.024 <Go to ISI>://WOS:000278563900012
    45. Ouellet, M., Adams, P. D., Keasling, J. D., & Mukhopadhyay, A. (2010). “A rapid and inexpensive labeling method for microarray gene expression analysis”. BMC Biotechnology, 9, 97. doi, 1472-6750-9-97 [pii]10.1186/1472-6750-9-97
    46. Peralta-Yahya, P. P., & Keasling, J. D. (2010). “Advanced biofuel production in microbes”. Biotechnology Journal, 5(2), 147-162. doi, 10.1002/biot.200900220
    47. Petzold, C.J., & Keasling, J.D. (2010). Metabolic engineering of E.coli for the production of a precursor to artemisinin, an anti-malarial drug. In Richard Balz (Ed.), The Manual of Industrial Microbiology and Biotechnology (3rd ed., pp. 364-379). Washington, DC: ASM Press.
    48. Rautengarten, C., Baidoo, E., Keasling, J. D., & Scheller, H. V. (2010). “A Simple Method for Enzymatic Synthesis of Unlabeled and Radiolabeled Hydroxycinnamate-CoA”. Bioenergy Research, 3(2), 115-122. doi, Doi 10.1007/S12155-010-9085-3 <Go to ISI>://000278541500004,
    49. Ronald, P., & Adamchak, R. (2010). “The future of sustainable food production”. Annals of the New York Academy of Sciences, 1190(1), 184-185. doi, NYAS5261 [pii]10.1111/j.1749-6632.2009.05261.x
    50. Rutherford, B. J., Dahl, R. H., Price, R. E., Szmidt, H. L., Benke, P. I., Mukhopadhyay, A., & Keasling, J. D. (2010). “Functional genomic study of exogenous n-butanol stress in Escherichia coli”. Applied and Environmental Microbiology, 76(6), 1935-1945. doi, AEM.02323-09 [pii] 10.1128/AEM.02323-09,
    51. Scheller, H. V., Singh, S., Blanch, H., & Keasling, J. D. (2010). “The Joint BioEnergy Institute (JBEI): Developing New Biofuels by Overcoming Biomass Recalcitrance”. Bioenergy Research, 3(2), 105-107. doi, Doi 10.1007/S12155-010-9086-2 <Go to ISI>://000278541500002,
    52. Scheller, H. V., & Ulvskov, P. (2010). “Hemicelluloses”. Annual Review of Plant Biology, 61, 263-289. doi, 10.1146/annurev-arplant-042809-112315
    53. Shaikh, A. S., Tang, Y. J., Mukhopadhyay, A., Martin, H. G., Gin, J., Benke, P. I., & Keasling, J. D. (2010). “Study of stationary phase metabolism via isotopomer analysis of amino acids from an isolated protein”. Biotechnology Progress, 26(1), 52-56. doi, 10.1002/btpr.325
    54. Simmons, B. A., Loque, D., & Ralph, J. (2010). “Advances in modifying lignin for enhanced biofuel production”. Current Opinion in Plant Biology, 13(3), 313-320. doi, S1369-5266(10)00019-1 [pii]10.1016/j.pbi.2010.03.001
    55. Simmons, B.A., Singh, S., Holmes, B.M., & Blanch, H.W. (2010). “Ionic liquid pretreatment”. Chemical Engineering Progress, 50-55. doi,
    56. Smith, A. M., Pradhan, P., Loque, D., Lacayo, C. I., Thelen, M., & Heazlewood, J. (2010). “Fluorescent Lifetime Imaging of Lignin in the Plant Cell Wall”. Biophysical Journal, 98(3), 581a-581a. doi, <Go to ISI>://WOS:000208762005404
    57. Steen, E. J., Kang, Y., Bokinsky, G., Hu, Z., Schirmer, A., McClure, A., . . . Keasling, J. D. (2010). “Microbial production of fatty-acid-derived fuels and chemicals from plant biomass”. Nature, 463(7280), 559-562. doi, nature08721 [pii] 10.1038/nature08721,
    58. Vega-Sanchez, M. E., & Ronald, P. C. (2010). “Genetic and biotechnological approaches for biofuel crop improvement”. Current Opinion Biotechnology, 21(2), 218-224. doi, S0958-1669(10)00017-0 [pii] 10.1016/j.copbio.2010.02.002
    59. Vogel, JP, Garvin, DF, Mockler, TC, Schmutz, J, Rokhsar, D, Bevan, MW, . . . Baxter, I. . (2010). “Genome sequence analysis of the model grass Brachypodium distachyon: insights into grass genome evolution”. Nature, 463(2), 763-768. doi, 10.1038/nature08747
    60. Wurtzel, O., Sapra, R., Chen, F., Zhu, Y., Simmons, B. A., & Sorek, R. (2010). “A single-base resolution map of an archaeal transcriptome”. Genome Research, 20(1), 133-141. doi, gr.100396.109 [pii] 10.1101/gr.100396.109
    61. Young, M., Artsatbanov, V., Beller, H. R., Chandra, G., Chater, K. F., Dover, L. G., . . . Greenblatt, C. L. (2010). “Genome sequence of the Fleming strain of Micrococcus luteus, a simple free-living actinobacterium”. Journal of Bacteriology, 192(3), 841-860. doi, JB.01254-09 [pii]10.1128/JB.01254-09,

    1. Achyuthan, K. E., McClain, J. L., & Raj, D. (2009). “Orthogonal, spectroscopic high throughput screening of laccase-catalyzed p-cresol oxidation”. [Article]. Comb Chem High Throughput Screen, 12(7), 678-689. doi,
    2. Carothers, J. M., Goler, J. A., & Keasling, J. D. (2009). “Chemical synthesis using synthetic biology”. Current Opinion in Biotechnology, 20(4), 498-503. doi, DOI 10.1016/j.copbio.2009.08.001 <Go to ISI>://000271756100017
    3. Dietrich, J. A., Yoshikuni, Y., Fisher, K. J., Woolard, F. X., Ockey, D., McPhee, D. J., . . . Keasling, J. D. (2009). “A Novel Semi-biosynthetic Route for Artemisinin Production Using Engineered Substrate-Promiscuous P450(BM3)”. Acs Chemical Biology, 4(4), 261-267. doi, Doi 10.1021/Cb900006h <Go to ISI>://000265444200005,
    4. Dueber, J. E., Wu, G. C., Malmirchegini, G. R., Moon, T. S., Petzold, C. J., Ullal, A. V., . . . Keasling, J. D. (2009). “Synthetic protein scaffolds provide modular control over metabolic flux”. Nature Biotechnology, 27(8), 753-U107. doi, Doi 10.1038/Nbt.1557 <Go to ISI>://000268774500026,
    5. Eudes, Aymerick, Pradhan, Prajakta, & Loque, Dominique. (2009). “Synthesis of phenylpropanoid-esters and -amides in Arabidopsis thaliana to engineer a cleavable lignin”. Plant Biology (Rockville), 2009(Suppl. S), 175-175. doi, <Go to ISI>://BCI:BCI201000265477.
    6. Harper, J. C., Brozik, S. M., Flemming, J. H., McClain, J. L., Polsky, R., Raj, D., . . . Achyuthan, K. E. (2009). “Fabrication and testing of a microneedles sensor array for p-cresol detection with potential biofuel applications”. ACS Applied Materials & Interfaces, 1(7), 1591-1598. doi, 10.1021/am900259u,
    7. Ito, J., Taylor, N. L., Castleden, I., Weckwerth, W., Millar, A. H., & Heazlewood, J. L. (2009). “A survey of the Arabidopsis thaliana mitochondrial phosphoproteome”. Proteomics, 9(17), 4229-4240. doi, 10.1002/pmic.200900064
    8. Jung, K. H., Bartley, L. E., Cao, P. J., Canlas, P. E., & Ronald, P. C. (2009). “Analysis of Alternatively Spliced Rice Transcripts Using Microarray Data”. Rice, 2(1), 44-55. doi, DOI 10.1007/s12284-008-9020-9 <Go to ISI>://WOS:000282786200004
    9. Jung, K. H., Dardick, C., Bartley, L. E., Cao, P. J., Phetsom, J., Canlas, P., . . . Ronald, P. C. (2009). “Refinement of Light-Responsive Transcript Lists Using Rice Oligonucleotide Arrays: Evaluation of Gene-Redundancy”. PLoS One, 3(10), e3337. doi, ARTN e3337 DOI 10.1371/journal.pone.0003337 <Go to ISI>://000265113500005
    10. Kent, M.S., Murton, J. K., Dibble, D. C., Zendejas, F., Banuelos, J. L., Urquidi, J., . . . Simmons, B. A. (2009). “Effect of Agitation/Flow on the Enzymatic Digestion of Cellulose: a Structural Study by SANS”. Polymer Preprints, ACS-PMSE symposium on Small Angle Neutron Scattering from Polymers and Complex Fluids, 238th ACS National Meeting, Washington DC, Aug 16-20, 2009., 2. doi.
    11. Kirby, J., & Keasling, J. D. (2009). “Biosynthesis of plant isoprenoids: perspectives for microbial engineering”. Annual Review of Plant Biology, 60, 335-355. doi, 10.1146/annurev.arplant.043008.091955;
    12. Lee, S. K., Chou, H., Ham, T. S., Lee, T. S., & Keasling, J. D. (2009). “Metabolic engineering of microorganisms for biofuels production: from bugs to synthetic biology to fuels”. Curr Opin Biotechnol, 19(6), 556-563. doi, 10.1016/j.copbio.2008.10.014
    13. Loque, D., Mora, S. I., Andrade, S. L., Pantoja, O., & Frommer, W. B. (2009). “Pore mutations in ammonium transporter AMT1 with increased electrogenic ammonium transport activity”. Journal of Biological Chemistry, 284(37), 24988-24995. doi, M109.020842 [pii] 10.1074/jbc.M109.020842,
    14. Marner, W. D., 2nd, Shaikh, A. S., Muller, S. J., & Keasling, J. D. (2009). “Enzyme immobilization via silaffin-mediated autoencapsulation in a biosilica support”. Biotechnology Progress, 25(2), 417-423. doi, 10.1002/btpr.136
    15. Meng, M., Geisler, M., Johansson, H., Harholt, J., Scheller, H. V., Mellerowicz, E. J., & Kleczkowski, L. A. (2009). “UDP-glucose pyrophosphorylase is not rate limiting, but is essential in Arabidopsis”. Plant Cell Physiology, 50(5), 998-1011. doi, pcp052 [pii] 10.1093/pcp/pcp052
    16. Pereira, J. H., Sapra, R., Volponi, J. V., Kozina, C. L., Simmons, B., & Adams, P. D. (2009). “Structure of endoglucanase Cel9A from the thermoacidophilic Alicyclobacillus acidocaldarius”. Acta Crystallographica Section D Biological Crystallography, 65(Pt 8), 744-750. doi, S0907444909012773 [pii] 10.1107/S0907444909012773
    17. Petersen, B. L., Egelund, J., Damager, I., Faber, K., Jensen, J. K., Yang, Z., . . . Ulvskov, P. (2009). “Assay and heterologous expression in Pichia pastoris of plant cell wall type-II membrane anchored glycosyltransferases”. Glycoconjugate Journal, 26(9), 1235-1246. doi, 10.1007/s10719-009-9242-0
    18. Sarkar, P., Bosneaga, E., & Auer, M. (2009). “Plant cell walls throughout evolution: towards a molecular understanding of their design principles”. Journal of Experimental Botany, 60(13), 3615-3635. doi, erp245 [pii] 10.1093/jxb/erp245
    19. Simmons, B. A., Loque, D., & Blanch, H. W. (2009). “Next-generation biomass feedstocks for biofuel production”. Genome Biology, 9(12), 242. doi, gb-2008-9-12-242 [pii]10.1186/gb-2008-9-12-242
    20. Singh, S., Simmons, B. A., & Vogel, K. P. (2009). “Visualization of biomass solubilization and cellulose regeneration during ionic liquid pretreatment of switchgrass”. Biotechnology and Bioengineering, 104(1), 68-75. doi, 10.1002/bit.22386
    21. Steen, E. J., Chan, R., Prasad, N., Myers, S., Petzold, C. J., Redding, A., . . . Keasling, J. D. (2009). “Metabolic engineering of Saccharomyces cerevisiae for the production of n-butanol”. Microbial Cell Factories, 7, 36. doi, 1475-2859-7-36 [pii]10.1186/1475-2859-7-36;
    22. Tang, Y. J., Martin, H. G., Dehal, P. S., Deutschbauer, A., Llora, X., Meadows, A., . . . Keasling, J. D. (2009). “Metabolic flux analysis of Shewanella spp. reveals evolutionary robustness in central carbon metabolism”. [Research Support, U.S. Gov’t, Non-P.H.S.]. Biotechnol Bioeng, 102(4), 1161-1169. doi, 10.1002/bit.22129
    23. Tang, Y. J., Martin, H. G., Deutschbauer, A., Feng, X., Huang, R., Llora, X., . . . Keasling, J. D. (2009). “Invariability of central metabolic flux distribution in Shewanella oneidensis MR-1 under environmental or genetic perturbations”. [Research Support, Non-U.S. Gov’t Research Support, U.S. Gov’t, Non-P.H.S.]. Biotechnol Prog, 25(5), 1254-1259. doi, 10.1002/btpr.227
    24. Tang, Y. J., Martin, H. G., Myers, S., Rodriguez, S., Baidoo, E. E., & Keasling, J. D. (2009). “Advances in analysis of microbial metabolic fluxes via (13)C isotopic labeling”. Mass Spectrometry Reviews, 28(2), 362-375. doi, 10.1002/mas.20191
    25. Tang, Y. J., Sapra, R., Joyner, D., Hazen, T. C., Myers, S., Reichmuth, D., . . . Keasling, J. D. (2009). “Analysis of metabolic pathways and fluxes in a newly discovered thermophilic and ethanol-tolerant Geobacillus strain”. Biotechnology and Bioengineering, 102(5), 1377-1386. doi, 10.1002/bit.22181
    26. Tang, Y. J., Yi, S., Zhuang, W. Q., Zinder, S. H., Keasling, J. D., & Alvarez-Cohen, L. (2009). “Investigation of carbon metabolism in “Dehalococcoides ethenogenes” strain 195 by use of isotopomer and transcriptomic analyses”. Journal of Bacteriology, 191(16), 5224-5231. doi, JB.00085-09 [pii]10.1128/JB.00085-09
    27. Weckwerth, W., Baginsky, S., van Wijk, K., Heazlewood, J. L., & Millar, H. (2009). “The multinational Arabidopsis steering subcommittee for proteomics assembles the largest proteome database resource for plant systems biology”. Journal of Proteome Research, 7(10), 4209-4210. doi, 10.1021/pr800480u
    28. Yang, Fan, Zheng, Kejian, Zhang, Ling, & Loque, Dominique. (2009). “Monolignol Transporters and Cell Wall Oxidases Screens”. Plant Biology (Rockville), 2009(Suppl. S), 275-275. doi, <Go to ISI>://BCI:BCI201000265909.

    1. Bernal, A. J., Yoo, C. M., Mutwil, M., Jensen, J. K., Hou, G., Blaukopf, C., . . . Willats, W. G. (2008). “Functional analysis of the cellulose synthase-like genes CSLD1, CSLD2, and CSLD4 in tip-growing Arabidopsis cells”. [Research Support, Non-U.S. Gov’t Research Support, U.S. Gov’t, Non-P.H.S.]. Plant Physiol, 148(3), 1238-1253. doi, 10.1104/pp.108.121939
    2. Blanch, H. W., Adams, P. D., Andrews-Cramer, K. M., Frommer, W. B., Simmons, B. A., & Keasling, J. D. (2008). “Addressing the need for alternative transportation fuels: the Joint BioEnergy Institute”. Acs Chemical Biology, 3(1), 17-20. doi, 10.1021/cb700267s
    3. Cao, P. J., Bartley, L. E., Jung, K. H., & Ronald, P. C. (2008). “Construction of a rice glycosyltransferase phylogenomic database and identification of rice-diverged glycosyltransferases”. Molecular Plant, 1(5), 858-877. doi, Doi 10.1093/Mp/Ssn052 <Go to ISI>://000259104500014,
    4. Fortman, J. L., Chhabra, S., Mukhopadhyay, A., Chou, H., Lee, T. S., Steen, E., & Keasling, J. D. (2008). “Biofuel alternatives to ethanol: pumping the microbial well”. Trends Biotechnol, 26(7), 375-381. doi, 10.1016/j.tibtech.2008.03.008
    5. Garcia, D. E., Baidoo, E. E., Benke, P. I., Pingitore, F., Tang, Y. J., Villa, S., & Keasling, J. D. (2008). “Separation and mass spectrometry in microbial metabolomics”. Current Opinion in Microbiology, 11(3), 233-239. doi, 10.1016/J.Mib.2008.04.002 <Go to ISI>://000257974900007,
    6. Geshi, N., Oikawa, A., Yin, L., Motawia, M. S., & Scheller, H. V. (2008). “Glycosyltranfserases Involved in the Plant Cell Wall Polysaccharides Biosynthesis”. Glycobiology, 18(11), 973-973. doi, <Go to ISI>://WOS:000260141400144.
    7. Jensen, J. K., Sorensen, S. O., Harholt, J., Geshi, N., Sakuragi, Y., Moller, I., . . . Scheller, H. V. (2008). “Identification of a xylogalacturonan xylosyltransferase involved in pectin biosynthesis in Arabidopsis”. Plant Cell, 20(5), 1289-1302. doi, 10.1105/Tpc.107.050906 <Go to ISI>://000257320600010,
    8. Keasling, J. D. (2008). “Synthetic biology for synthetic chemistry”. Acs Chemical Biology, 3(1), 64-76. doi, Doi 10.1021/Cb7002434 <Go to ISI>://000252515200017,
    9. Keasling, J. D., & Chou, H. (2008). “Metabolic engineering delivers next-generation biofuels”. Nature Biotechnology, 26(3), 298-299. doi, Doi 10.1038/Nbt0308-298 <Go to ISI>://000254123400021,
    10. Mukhopadhyay, A., Redding, A. M., Rutherford, B. J., & Keasling, J. D. (2008). “Importance of systems biology in engineering microbes for biofuel production”. Current Opinion in Biotechnology, 19(3), 228-234. doi, S0958-1669(08)00056-6 [pii] 10.1016/j.copbio.2008.05.003
    11. Okumoto, Sakiko, Takanaga, Hitomi, & Frommer, Wolf B. (2008). “Quantitative imaging for discovery and assembly of the metabo-regulome”. [Research Support, N.I.H., Extramural Research Support, U.S. Gov’t, Non-P.H.S. Review]. New Phytologist, 180(2), 271-295. doi, 10.1111/j.1469-8137.2008.02611.x <Go to ISI>://WOS:000259526300006
    12. Shaikh, A. S., Tang, Y. J., Mukhopadhyay, A., & Keasling, J. D. (2008). “Isotopomer distributions in amino acids from a highly expressed protein as a proxy for those from total protein”. Analytical Chemistry, 80(3), 886-890. doi, 10.1021/ac071445+