Case Study Education

CBiRC Overview Video.

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 Joseph Noel *  Nancy Da Silva *  Robert Davis *  Rob Anex *
 Basil Nikolau  Laura Jarboe  Brent Shanks  Raj Raman
 Eran Pichersky  Jackie Shanks  James Dumesic  Peter Keeling
 Eve Wurtele  Julie Dickerson  George Kraus  Adam Okerlund
 Adam Barb  Ramon Gonzalez  Matthew Neurock
 Marna Yandeau-Nelson  Ka-Yiu San  Abhaya Datye
 Costas Maranas  Jean-Philippe Tessonnier
 Suzanne Sandmeyer  Klaus Schmidt-Rohr
 Zengyi Shao


JOURNAL ARTICLES (Alphabetic Listing)

Any opinions, findings, and conclusions or recommendations expressed in these materials are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.

Akshay, Patel, Juan Carlos Serrano-Ruiz, James A. Dumesic, and Robert P. Anex. “Technoeconomic Analysis of Dimethylfuran (DMF) and Hydroxymethylfurfural (HMF) Production from Pure Fructose in Catalytic Processes.” Chemical Engineering Journal 169 (2011): 329.

Alonso, D. M., J. Q. Bond, J. A. Dumesic, Green Chemistry, 12, 1493 (2010).

Alonso, D. M., J. Q. Bond, J. C. Serrano-Ruiz, J. A. Dumesic, Green Chemistry, 12, 992 (2010).

Alonso, David Martin, Stephanie G. Wettstein, Jesse Q. Bond, Thatcher W. Root, and James A. Dumesic. “Production of Biofuels from Cellulose and Corn Stover Using Alkylphenol Solvents.” Chemistry and Sustainability 4 (2011): 1078.

Anex, R.P., L.R. Lynd, M.S. Laser, A.H. Heggenstaller, M. Liebman (2007). Growing energy, closing cycles: the potential for enhanced nutrient cycling through the coupling of agricultural and bioenergy systems. Crop Science Journal47:1327-1335.

Auldridge, M. E., Y. Guo, M. B. Austin, J. Ramsey, E. Fridman, E. Pichersky, J. P. Noel. “Emergent Decarboxylase Activity and Attenuation of /β Hydrolase Activity During the Evolution of Methylketone Biosynthesis in Tomato.” Plant Cell 4 (2012): 1596-1607 (DOI: 10.1105/tpc.111.093997; Epub PubMed PMID: 22523203; PubMed Central PMCID: PMC3398566).

Azadi, Pooya, Ronald Carrasquillo-Flores, Yomaira J. Pagan-Torres, Elif I. Guerbuez, Ramin Farnood, and James A. Dumesic. “Catalytic Conversion of Biomass Using Solvents Derived from Lignin” Green Chemistry 14(6) (2012): 1573-1576 (DOI: 10.1039/C2GC35203F).

Bais, P., Moon S.M., He K., Leitao R., Dreher K., Walk T., Sucaet Y., Barkan L., Wohlgemuth G., Roth R.M., Wurtele E.S., Dixon P., Fiehn O., Lange BM., Shulaev V., Sumner L.W., Welti R., Nikolau B.J., Rhee S.Y., and Dickerson J.A. (2010). A web portal for Plant Metabolomics Experiments. Plant Physiology.

Bais, P., S. M. Moon-Quanbeck, B. J. Nikolau, and J. A. Dickerson. “ Mass Spectrometry-based Arabidopsis Metabolomics–Database and Tools Update.” Nucleic Acids Research 40, D1216-1220 (2012).

Behrens, Malte and Abhaya Datye, Eds. “Catalysis for the Conversion of Biomass and Its Derivatives.” Max Planck Research Library for the History and Development of Knowledge, Proceedings 2. Berlin: Edition Open Access (2013) (ISBN 978-3-8442-4282-9).

Benavidez, A. D., L. Kovarik, A. Genc, N. Agrawal, E. M. Larsson, T. W. Hansen, A. M. Karim, and A. K. Datye. “Environmental Transmission Electron Microscopy Study of the Origins of Anomalous Particle Size Distributions in Supported Metal Catalysts.” ACS Catalysis 2(11) (2012): 2349-2356 (DOI: 10.1021/cs3005117).

Ben-Israel, I., G. Yu, M.B. Austin, N. Bhuiyan, M. Auldridge, T. Nguyen, I. Schauvinhold, J. P. Noel, E. Pichersky, and E. Fridman (2009).  Multiple biochemical and morphological factors underlie the production of methylketones in tomate trichomes.  Plant Physiology 151:1952-1964.

Birky, T. W., Joseph T. Kozlowski, and Robert J. Davis. “Isotopic Transient Analysis of the Ethanol Coupling Reaction over Magnesia.” Journal of Catalysis 298 (2013): 130-137 (DOI: 10.1016/j.jcat.2012.11.014).

Blankschien, M. D., Clomburg, J. M., and Gonzalez, R. (2010). Metabolic engineering of Escherichia coli for the production of succinate from glycerol. Metab. Eng. 12 (5): 409-419.

Bond, J. Q., D. M. Alonso, R. M. West, J. A. Dumesic, Langmuir, 26, 16291 (2010).

Bond, J. Q., D. Martin-Alonso, R. M. West, D. Wang, J.A. Dumesic, Science, 327, 1110 (2010).

Bond, Jesse Q., David Martin Alonso, Dong Wang, and James A. Dumesic. “Activation of Amberlyst-70 for Alkene Oligomerization in Hydrophobic Media.” Topics in Catalysis 54 (2011): 447.

Bond, Jesse Q., Dong Wang, David Martin Alonso, and James A. Dumesic. “Inter-conversion Between g-valerolactone and Pentenoic acid Combined with Decarboxylation to form Butene over Silica/alumina.” Journal of Catalysis 281 (2011): 290.

Braden, Drew J., Carlos A. Henao, Jacob Heltzel, Christos C. Maravelias, and James A. Dumesic. “Production of liquid hydrocarbon fuels by catalytic conversion of biomass derived levulinic acid.” Green Chemistry 7 (2011): 1755.

Brown M. and J. V. Shanks, “Linear Hydrocarbon Producing Pathways in Plants, Algae and Microbes.” Sustainable Bioenergy and Bioproducts. K. Gopalakrishnan, J. H. van Leeuwen, R. L. Brown, Eds.  Springer-Verlag (© 2012): 1-12 (DOI: 10.1007/978-1-4471-2324-8).

Buitrango-Sierra, R., J. C. Serrano-Ruiz, F. Rodriguez-Reinoso, A. Sepulveda-Escribando, James A. Dumesic. “Ce promoted Pd-Nb Catalysts for Gamma-valerolactone Ring opening and Hydrogenation.” Green Chemistry 14(12) (2012): 3318-3324 (DOI: 10.1039/C2GC36161B).

Burton, P. D., T. J. Boyle, and A. K. Datye. “Facile, Surfactant-free Synthesis of Pd Nanoparticles for Heterogeneous Catalysts.” Journal of Catalysis 280(2) (2011): 145-149.

Burton, P.D., E.J. Peterson, T.J. Boyle, and A.K. Datye, Synthesis of High Surface Area ZnO(0001) Plates as Novel Oxide Supports for Heterogeneous Catalysts. Catalysis Letters, 2010. 139(1-2): p. 26-32.

Burton, Patrick. Novel Routes for the Synthesis of Pd Nanoparticles and Faceted ZnO Supports for Heterogeneous Catalysts. Ph.D. Dissertation. University of New Mexico, 2011.

Cantu, D. C., Tingsong Dai, Zachary S. Beversdorf, and Peter J. Reilly. “Structural Classification and Properties of Ketoacyl Reductases, Hydroxyacyl Dehydratases, and Enoyl Reductases.” Protein Engineering Design & Selection 25(12) (2012): 803-811 (DOI: 10.1093/protein/gzs050).

Cantu, D. C., Y. Chen, and P. J. Reilly. Thioesterases: A New Perspective Based on Their Primary and Tertiary Structures. Protein Sci., 19, 1281 (2010).

Cantu, D. C., Y. Chen, M. L. Lemons, and P. J. Reilly. ThYme: A Database for Thioester-Active Enzymes. Nucleic Acids Res., 39, D342 (2011).

Cantu, D.C, Michael J. Forrester, Katherine Charov, and Peter J. Reilly. “Acyl Carrier Protein Structural Classification and Normal Mode Analysis.” Protein Science 21(5) (2012): 655-666 (DOI: 10.1002/pro.2052).

Cha, S., Song, Z., Nikolau, B.J., Yeung, E.S. (2009).  Direct profiling and imaging of epicuticular waxes on arabidopsis thaliana by laser desorption/ionization mass spectrometry using silver colloid as a matrix. Analytical Chemistry 81: 2991-3000.

Challa, S. R., A. T. Delariva, T. W. Hansen, S. Helveg, J. Sehested, P. L. Hansen, F. Garzon, and A. K. Datye. “Relating Rates of Catalyst Sintering to the Disappearance of Individual Nanoparticles during Ostwald Ripening.” Journal of the American Chemical Society 133(51) (2011): 20672-20675.

Chen, Y., Armando Elizondo-Noriega, David C. Cantu, and Peter J. Reilly. “Structural Classification of Biotin Carboxyl Carrier Proteins.” Biotechnology Letters 34(10) (2012): 1869-1875 (DOI: 10.1007/s10529-012-0978-4).

Chen, Y., E. E. Kelly, R. P. Masluk, C. L. Nelson, D. C. Cantu, and P. J. Reilly. “Structural Classification and Properties of Ketoacyl Synthases.” Protein Science 20 (2011): 1659.

Chen, Yihong, Ethel Apolinario, Libuse Brachova, Zvi Kelman, Zhuo Li, Basil J. Nikolau, Lucas Showman, Kevin Sowers and John Orban. “A Nuclear Magnetic Resonance Based Approach to Accurate Functional Annotation of Putative Enzymes in the Methanogen Methanosarcina acetivorans.” BMC Genomics 12 (Suppl 1) (2011): S7 (DOI: 10.1186/1471-2164-12-S1-S7).

Chia, M., T. J. Schwartz, B. H. Shanks, and J. A. Dumesic. “Triacetic Acid Lactone as a Biorenewable Platform Chemical.” Green Chemistry 14(7) (2012): 1850-1853 (DOI: 10.1039/C2GC35343A).

Chia, M., Y. J. Pagan-Torres, D. Hibbitts, Q. H. Tan, H. N. Pham, A. K. Datye, M. Neurock, R. J. Davis, and J. A. Dumesic. “Selective Hydrogenolysis of Polyols and Cyclic Ethers over Bifunctional Surface Sites on Rhodium-Rhenium Catalysts.” Journal of the American Chemical Society 133(32) (2011): 12675-12689.

Chia, Mei and James A. Dumesic. “Liquid-phase catalytic transfer hydrogenation and cyclization of levulinic acid and its esters to γ-valerolactone over metal oxide catalysts.” Chemical Communications 47(44) (2011): 12233.

Choudhary, M. K., J. M. Yoon, R. Gonzalez, and J. V. Shanks. “Re-examination of Metabolic Fluxes in Escherichia coli During Anaerobic Fermentation of Glucose Using 13C Labeling Experiments and 2-Dimensional Nuclear Magnetic Resonance (NMR) Spectroscopy.” Biotechnology and Bioprocess Engineering 16 (2011): 419-437 (DOI 10.1007/s12257-010-0449-5).

Christiansen, K. L., D. R. Raman, and R. P. Anex. “Predicting Cost Growth and Performance of First-Generation Algal Production Systems.” Energy Policy 51 (2012): 382-391 (DOI:  0.1016/j.bbr.2011.03.031).

Cinlar, B. and B. H. Shanks. “Characterization of the Acidic Sites in Organic Acid Functionalized Mesoporous Silica in the Aqueous Phase.” Applied Catalysis A-General 396 (2011): 76-84.

Cinlar, Basak. Acid Catalyzed Carbohydrate Degradation and Dehydration. Ph.D. Dissertation. Iowa State University, 2010.

Cintolesi, A., J. M. Clomburg, V. Rigou, K. Zygourakis, and R. Gonzalez. “Quantitative Analysis of the Fermentative Metabolism of Glycerol in Escherichia coli.” Biotechnology and Bioengineering 109 (1) (2012): 187-198.

Clomburg, J. and R. Gonzalez. “Metabolic Engineering of Escherichia coli for the Production of 1,2-Propanediol from Glycerol.” Biotechnology and Bioengineering 108 (4) (2011): 867-879.

Clomburg, J. M., and Gonzalez, R. (2010). Biofuel production in Escherichia coli: the role of metabolic engineering and synthetic biology. App. Microbiol. Biotechnol. 86 (2): 419-434.

Clomburg, J. M., J. E. Vick, M. D. Blankschien, M. Rodriguez-Moya, and R. Gonzalez. “A Synthetic Biology Approach to Engineer a Functional Reversal of the Beta-oxidation Cycle.” ACS Synthetic Biology 1(11) (2012): 541-554 (DOI: 10.1021/sb3000782).

Combs, E., B. Cinlar, Y. J. Pagan-Torres, J. A. Dumesic, and B. H. Shanks. “Influence of Alkali and Alkaline Earth Metal Salts on Glucose Conversion to 5-Hydroxymethylfurfural in an Aqueous System.” Catalysis Communications 30 (2013): 1-4 (DOI: 10.1016/j.catcom.2012.10.011).

Conant, T., A.M. Karim, V. Lebarbier, Y. Wang, F. Girgsdies, R. Schloegl, and A. Datye, Stability of bimetallic Pd-Zn catalysts for the steam reforming of methanol. Journal of Catalysis, 2008. 257(1): p. 64-70.

Crisci, A. J., M. H. Tucker, J.A., Dumesic, S. L. Scott., Topics in Catalysis, 53, 1185 (2010).

Crispin, M. C. and E. S. Wurtele. “Use of Metabolomics and Transcriptomics to Gain Insights into the Regulation and Biosynthesis of Medicinal Compounds: Hypericum as a Model.” Biotechnology for Medicinal Plants (2013): 395-411 (DOI: 10.1007/978-3-642-29974-2_17).

Daniel, O.M., A. DeLaRiva, E.L. Kunkes, A.K. Datye, J.A. Dumesic, and R.J. Davis, X-ray Absorption Spectroscopy of Bimetallic Pt-Re Catalysts for Hydrogenolysis of Glycerol to Propanediols. Chemcatchem, 2010. 2(9): p. 1107-1114.

Daniel, Oliver. Synthesis, Characterization and Reactivity of Bimetallic PtRe Catalysis for Hydrogenolysis of Glycerol to Propanediols. M.S. Thesis. University of Virginia, 2010.

Davis, Robert. “Reaction Engineering Concepts for the Catalytic Conversion of Biorenewable Molecules.” Heterogeneous Catalysis for the Conversion of Biomass and Its Derivatives, M. Behrens and A. Datye, Eds. Printed in Germany by epubli, Oranienstraße 183, 10999 Berlin (2012): 247-282  (

Davis, S. E., B. N. Zope, and R. J. Davis. “On the Mechanism of Selective Oxidation of 5-Hydroxymethylfurfural to 2,5-Furandicarboxylic Acid over Supported Pt and Au Catalysts.” Green Chemistry 14 (2012): 143-147.

Davis, S. E., L. R. Houk, E. C. Tamargo, A. K. Datye, and R. J. Davis. “Oxidation of 5-Hydroxymethylfurfural over Supported Pt, Pd and Au Catalysts.” Catalysis Today 160(1) (2011): 55-60.

Davis, S.E., L.R. Houk, E.C. Tamargo, A.K. Datye, and R.J. Davis, Oxidation of 5-hydroxymethylfurfural over supported Pt, Pd and Au catalysts. Catalysis Today, 2011. 160(1): p. 55-60.

Davis, S.E., Matthew S. Ide, and Robert J. Davis. “Selective Oxidation of Alcohols and Aldehydes over Supported Metal Nanoparticles.” Green Chemistry 15(1) (2013): 17-45 (DOI: 10.1039/C2GC36441G).

Dawson, Noel. Plan II (Professinoal Science Masters) – Non Thesis Option with Technology Business Plan. M.S. Thesis. University of New Mexico, 2011.

Degirmenci, V., Cinlar, B., Yilmaz, A., van Santen, R.A., Shanks, B.H., Hensen, E.J.M., and Uner,  D., “Sulfated zirconia modified SBA-15 catalysts for cellobiose hydrolysis,” Catal. Lett., 141, 33-42 (2011).

Dellomonaco, C., and Gonzalez, R. (2010). The path to next generation biofuels: successes and challenges in the era of metabolic engineering and synthetic biology. Microbial Cell Factories 9:3.

Dellomonaco, C., J. M. Clomburg, E. N. Miller, and R. Gonzalez. “Engineered Reversal of the β-oxidation Cycle for the Synthesis of Fuels and Chemicals.” Nature 476 (2011): 355-359.

Dellomonaco, C., Rivera, C., Campbell, P., and R. Gonzalez. (2010). Engineered respiro-fermentative metabolism for the production of biofuels and biochemicals from fatty acid-rich feedstocks. Applied and Environmental Microbiology, 76 (15), 5067-5078.

Deutsch, K. L. and B. H. Shanks. “Active Species of Copper Chromite Catalyst in C-O Hydrogenolysis of 5-Methylfurfuryl Alcohol.” Journal of Catalysis 285 (2012): 235-241.

Deutsch, K. L. and Brent H. Shanks. “Hydrodeoxygenation of Lignin Model Compounds Over a Copper Chromite Catalyst.” Applied Catalysis A: General, Volumes 447-448 (2012): 144-150 (; ISSN 0926-860X).

Deutsch, K. L., D. G. Lahr, and B. H. Shanks. “Probing the Ruthenium-catalyzed Higher Polyol Hydrogenolysis Reaction Through the use of Stereoisomers.” Green Chemistry 14(6) (2012): 1635-1642 (DOI: 10.1039/C2GC00026A).

Dietrich, Paul J., Rodrigo J. Lobo-Lapidus, Tianpin Wu, Aslihan Sumer, M. Cem Akaty, Bradley R. Fingland, Neng Guo, James A. Dumesic, Christopher L. Marshall, Eric Stach, Julius Jellinek, W. Nicholas Delgass, Fabio H. Riberio, and Jeffrey T. Miller. “Aqueous Phase Glycerol Reforming by PtMo Bimetallic Nano-particle Catalyst: Product Selectivity and Structural Characterization.” Topics in Catalysis 55(1-2) (2012): 53-69 (2012) (DOI: 10.1007/s11244-012-9775-5).

Ding, G., P. Che, H. Ilarslan, E. S. Wurtele, and B. J. Nikolau. “Genetic Dissection of Methylcrotonyl CoA Carboxylase Indicates a Complex Role for Mitochondrial Leucine Catabolism During Seed Development and Germination.” The Plant Journal (2011) (DOI: 10.1111/j.1365-313X.2011.04893.x).

Durnin, G., Clomburg, J., Yeates, Z., Alvarez, P.J.J., Zygourakis, K., Campbell, P., and Gonzalez, R. (2009). Understanding and harnessing the microaerobic metabolism of glycerol in Escherichia coli. Biotechnol. Bioeng. 103 (1): 148-161.

Falara, V., R. Amarasinghe, J. Poldy, E. Pichersky, R. Barrow, and R. Peakall. “The Production of a Key Floral Volatile is Dependent on UV Light in a Sexually Deceptive Orchid.” Annals of Botany 111.1 (2013): 21-30 (DOI: 10.1093/aob/mcs228).

Fang, F., Salmon, K., Shen, M., Aeling, K, Ito, E.,  Irwin, B., Tran, U., Hatfield, G.W., Da Silva, N.*, and Sandmeyer, S.* (2011) A combinatorial vector set for metabolic engineering in Saccharomyces cerevisiae.  Yeast 28:123-136.  (*=co-corresponding authors)

Faraldos, J.A., O’Maille, P.E., Dellas, N., Noel, J.P. and Coates, R.M. (2010) Bisabolyl-Derived Sesquiterpenes from Tobacco 5-Epi-aristolochene Synthase-Catalyzed Cyclization of (2Z,6E)-Farnesyl Diphosphate. J. Am. Chem. Soc. 132: 4281-4289. Epub 2010 Mar 4. PubMed PMID: 20201526.

Faulhaber, Carol. Developing Models for Analyzing Cost Structures in Fermentative Bioprocesses. M.S. Thesis. Iowa State University, 2011. Ann Arbor: UMI, 2011. 1494664.

Feng, Yaping, Jonathan Hurst, Marcia Almeida-De-Macedo, Xi Chen, Ling Li, Nick Ransom, and Eve Syrkin Wurtele. “Massive Human Co-Expression Network and Its Medical Applications.” Chemistry &  Biodiversity 9(5) (2012): 868-887 (DOI: 10.1002/cbdv.201100355).

Ferrin, P., D. Simonetti, S. Kandoi, E. L. Kunkes, J. A. Dumesic, J. K. Nørskov, M. Mavrikakis, Modeling ethanol decomposition on transition metals: a combined application of scaling and Brønsted-Evans-Polanyi relations, J. Am. Chem. Soc., 131, 5809-5815 (2009).

Fu, J., S. H. Hakim, and B. H. Shanks. “Aqueous-Phase Processing of Bio-oil Model Compounds over Pt-Re Supported on Carbon.” Topics in Catalysis 55(3-4) (2012): 140-147 (DOI: 10.1007/s11244-012-9784-4).

Fu, Yanfen. Metabolic Flux Analysis of Escherichia coli MG1655 Under Aerobic Conditons. M.S. Thesis. Iowa State University, 2011.

Fu, Yao, Laura R Jarboe, Julie Dickerson,(2010). Gene Regulatory Network Reconstruction based on Gene Expression and Transcription Factor Activities, In Proceedings of the  International Conference on Bioinformatics & Computational Biology (BIOCOMP’10),July 12-15, Las Vegas, Nevada, USA, Volume I, 113-119, CSREA Press 2010, ISBN:1-60132-132-5.

Fu, Yao, Laura R. Jarboe, and Julie A Dickerson. “Reconstructing Genome-wide Regulatory Network of E. coli using Transcriptome Data and Predicted Transcription Factor Activities.” BMC Bioinformatics 12:233 (2011).

Gaertner, C. A., J. C. Serrano-Ruiz, D. J. Braden, J.A. Dumesic, Ind. Eng. Chem. Res., 49, 6027 (2010).

Gaertner, C.A., J. C. Serrano-Ruiz, D. J. Braden, J. A. Dumesic, Catalytic coupling of carboxylic acids by ketonization as a processing step in biomass conversion, J. Catal., 266, 71-78 (2009).

Gallo, Jean Marcel R.; David Martin Alonso, Max A. Mellmer, and James A. Dumesic. “Production and Upgrading of 5-hydroxymethylfurfural Using Heterogeneous Catalysts and Biomass-derived Solvents.” Green Chemistry 15(1) (2013): 85-90 (DOI: 10.1039/C2GC36536G).

Gärtner, C. A., J. C. Serrano-Ruiz, D. J. Braden, J. A. Dumesic, Catalytic upgrading of bio-oils by ketonization, ChemSusChem, 2, 1121-1121 (2009).

Geisinger, B. N., D. R. Raman, K. M. Haen, M. R. Kemis, M. R., and M. L. Pate. “Virtual Education Center for Biorenewable Resources: Building Capacity and Humanizing Distance Education.” NACTA Journal 56(4) (2012): 13-21.

Goeke, R.S., A.K. Datye, P. Atanassov, and J. St-Pierre, Nanoparticle size effects on the electrochemical dissolution rate of Pt. ECS Trans., 2009. 25(Copyright (C) 2010 American Chemical Society (ACS). All Rights Reserved.): p. 593-600.

Goeke, Ronald S. Model Electrode Structures for Studies of Electrocatalyst Degradation. Ph.D. Dissertation. University of New Mexico, 2010.

Gogate, M.R. and Davis, R.J., X-ray Absorption Spectroscopy of Fe-Promoted Rh/TiO2 Catalyst for Synthesis of Ethanol from Synthesis Gas. ChemCatChem, 1 (2009) 295-303.

Gonzalez, R., Campbell, P., and Wong, M. (2010). Production of ethanol from thin stillage by metabolically engineeredEscherichia coli. Biotechol. Letters 32 (3): 405-411.

Goyal, G, S.-L. Tsai, B. Madan, N. Da Silva, and W. Chen. “Simultaneous Cell Growth and Ethanol Production from Cellulose by an Engineered Yeast Consortium Displaying a Functional Mini-cellulosome.” Microbial Cell Factories 10:89 (2011).

Gupta, A., Murarka, A., Campbell, P., and Gonzalez, R. (2009). Anaerobic fermentation of glycerol in Paenibacillus macerans: metabolic pathways and environmental determinants. Appl. Environ. Microbiol. 75 (18): 5871-5883.

Gürbüz, E. I., D. M. Alonso, J. Q. Bond, J.A. Dumesic, ChemSusChem, n/a.

Gürbüz, E. I., E. L. Kunkes, J.A. Dumesic, Appl. Catal. B Environ., 94, 134 (2010).

Gürbüz, E. I., E. L. Kunkes, J.A. Dumesic, Green Chemistry, 12, 223 (2010).

Gürbüz, Elif I., David Martin Alonso, Jesse Q. Bond, and James A. Dumesic. “Reactive Extraction of Levulinate Esters and Conversion to g-valerolactone for Production of Liquid Fuels.” Chemistry and Sustainability (ChemSusChem) 4 (2011): 357.

Gürbüz, Elif I., Stephanie G. Wettstein, and James A. Dumesic. “Conversion of Hemicellulose to Furfural and Levulinic Acid using Biphasic Reactors with Alkylphenol Solvents.” Chemistry and Sustainability (ChemSusChem) 5(2) (2012): 383-387. (DOI:10.1002/cssc.201100608).

Haen, K. M., D. R. Raman, E. Polush, and M. R. Kemis. “Training the Next Generation of Creative, Innovative and Adaptive Scientists and Engineers: The NSF Engineering Research Center for Biorenewable Chemicals (CBiRC) Research Experience for Undergraduates.” Education for Chemical Engineers 7(4) (2012): e230-240 (

Haider, M.A., M.R. Gogate, and R.J. Davis, Fe-Promotion of Supported Rh Catalysts for Direct Conversion of Syngas to Ethanol. J. Catal. 261 (2009 ) 9-16.

Halevi, B., E. J. Peterson, A. Roy, A. Delariva, E. Jeroro, F. Gao, Y. Wang, J. M. Vohs, B. Kiefer, E. Kunkes, M. Hävecker, M. Behrens, R. Schlögl, and A. K. Datye. “Catalytic Reactivity of Face Centered Cubic PdZn  for the Steam Reforming of Methanol.” Journal of Catalysis 291 (2012): 44-54 (DOI: 10.1016/j.jcat.2012.04.002).

Halevi, B., E.J. Peterson, A. Delariva, E. Jeroro, V.M. Lebarbier, Y. Wang, J.M. Vohs, B. Kiefer, E. Kunkes, M. Havecker, M. Behrens, R. Schlogl, and A.K. Datye, Aerosol-Dearived Bimetallic Alloy Powders: Bridging the Gap. Journal of Physical Chemistry C, 2010. 114(40): p. 17181-17190.

Heggenstaller, A.H., K.J. Moore, M. Liebman, D.N. Sundberg, and R.P. Anex (2009). Nitrogen influences productivity, resource partitioning, and carbon storage by perennial, warm-season grasses. Agronomy Journal 101(6):1363-1371.

Heggenstaller, A.H., M. Liebman, and R.P. Anex (2009). Growth analysis of biomass production in sole-crop and double-crop corn systems. Crop Science 49: 2215-2224.

Heggenstaller, A.H., R.P. Anex, M. Liebman, D.N. Sundberg, and L.R. Gibson (2008). Productivity and nutrient dynamics in bioenergy double-cropping systems. Agronomy Journal 100(6):1740-1748.

Hothorn, M., Y. Belkhadir, M. Dreux, T. Dabi, J. P. Noel, I. A. Wilson, and J. Chory. “Structural Basis of Steroid Hormone Perception by the Receptor Kinase BRI1.” Nature 474 (2011): 467-471. PubMed PMID: 21666665.

Houk, L.R., S.R. Challa, B. Grayson, P. Fanson, and A.K. Datye, The Definition of “Critical Radius” for a Collection of Nanoparticles Undergoing Ostwald Ripening. Langmuir, 2009. 25(19): p. 11225-11227.

Houk, Levi R. Sintering of Metal Nanoparticles on Model Substrates. M.S. Thesis. University of New Mexico, 2010.

Hruby, S.L. and Shanks, B.H., Acid-Base Cooperativity in Condensation Reactions with Functionalized Mesoporous Silica Catalysts. J. Catal., 263, 181-188 (2009).

Hu, E. L., S. M. Davis, R. Davis, and E. Scher. “Applications: Catalysis by Nanostructured Materials”. Chapter 10: Nanotechnology Research Directions for Societal Needs in 2020. Retrospective and Outlook, M. C. Roco, C. A. Mirkin, and M. C. Hersam, Eds., Springer (Berlin and Boston) (2011): 341-360.

Hummelshoj, J.S., D.D. Landis, J. Voss, T. Jiang, A. Tekin, N. Bork, M. Dulak, J.J. Mortensen, L. Adamska, J. Andersin, J.D. Baran, G.D. Barmparis, F. Bell, A.L. Bezanilla, J. Bjork, M.E. Bjorketun, F. Bleken, F. Buchter, M. Burkle, P.D. Burton, B.B. Buus, A. Calborean, F. Calle-Vallejo, S. Casolo, B.D. Chandler, D.H. Chi, I. Czekaj, S. Datta, A. Datye, A. DeLaRiva, V. Despoja, S. Dobrin, M. Engelund, L. Ferrighi, P. Frondelius, Q. Fu, A. Fuentes, J. Furst, A. Garcia-Fuente, J. Gavnholt, R. Goeke, S. Gudmundsdottir, K.D. Hammond, H.A. Hansen, D. Hibbitts, J.E. Hobi, J.G. Howalt, S.L. Hruby, A. Huth, L. Isaeva, J. Jelic, I.J.T. Jensen, K.A. Kacprzak, A. Kelkkanen, D. Kelsey, D.S. Kesanakurthi, J. Kleis, P.J. Klupfel, I. Konstantinov, R. Korytar, P. Koskinen, C. Krishna, E. Kunkes, A.H. Larsen, J.M.G. Lastra, H. Lin, O. Lopez-Acevedo, M. Mantega, J.I. Martinez, I.N. Mesa, D.J. Mowbray, J.S.G. Myrdal, Y. Natanzon, A. Nistor, T. Olsen, H. Park, L.S. Pedroza, V. Petzold, C. Plaisance, J.A. Rasmussen, H. Ren, M. Rizzi, A.S. Ronco, C. Rostgaard, S. Saadi, L.A. Salguero, E.J.G. Santos, A.L. Schoenhalz, J. Shen, M. Smedemand, O.J. Stausholm-Moller, M. Stibius, M. Strange, H.B. Su, B. Temel, A. Toftelund, V. Tripkovic, M. Vanin, V. Viswanathan, A. Vojvodic, S. Wang, J. Wellendorff, K.S. Thygesen, J. Rossmeisl, T. Bligaard, K.W. Jacobsen, J.K. Norskov and T. Vegge, Density functional theory based screening of ternary alkali-transition metal borohydrides: A computational material design project. The Journal of Chemical Physics, 2009. 131(1): p. 014101-9.

Hur, M., A. A. Cambell, M. Almeida-de-Macedo, L. Li, N. Ransom, A. Jose, B. J. Nikolau, E. S. Wurtele. “A Global Approach to Analysis and Interpretation of Metabolomic Data for Plant Natural Product Discovery.” Natural Product Reports 30(4) (2013): 565-583 (DOI: 10.1039/C3NP20111B).

Ide, M. S., Bing Hao, Matthew Neurock, and Robert J. Davis. “Mechanistic Insights on the Hydrogenation of alpha,beta-Unsaturated Ketones and Aldehydes to Unsaturated Alcohols over Metal Catalysts.” ACS Catalysis 2(4) (2012): 671-683 (DOI: 10.1021/cs200567z).

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Isci, A., J.N. Himmelsbach, J. Strohl, A.L. Pometto III, D.R. Raman, R.P. Anex (2008). Pilot scale fermentation of aqueous ammonia soaked switchgrass. Applied Biochemistry and Biotechnology 157(3): 453-462.

Isci, A., P.T. Murphy, R.P. Anex, K.J. Moore (2008). A rapid simultaneous saccharification and fermentation (SSF) technique to determine ethanol yields. BioEnergy Research 1(2): 163-169.

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Jin, H. N. and B. J. Nikolau. “Role of Genetic Redundancy in Polyhydroxyalkanoate (PHA) Polymerases in PHA Biosynthesis in Rhodospirillum rubrum.” Journal of Bacteriology 194(20) (2012): 5522-5529 (DOI: 10.1128/JB.01111-12).

Jin, H., Z. Song, and B. J. Nikolau. “Reverse Genetic Characterization of Two Paralogous Acetoacetyl-CoA Thiolase Genes in Arabidopsis Reveals Their Importance in Plant Growth and Development.” The Plant Journal: for Cell and Molecular Biology (2012).

Jing, F., D C. Cantu, J. Tvaruzkova, J. P. Chipman, B. J. Nikolau, M. D. Yandeau-Nelson, and P. J. Reilly. “Phylogenetic and Experimental Characterization of an Acyl-ACP Thioesterase Family Reveals Significant Diversity in Enzymatic Specificity and Activity.” BMC Biochemistry 12 (2011): 44.

Johansson, R., S.L. Hruby, J. Rass-Hansen, and C.H. Christensen, The Hydrocarbon Pool in Ethanol-to-Gasoline over HZSM-5 Catalysts. Catalysis Letters, 2009. 127(1-2): p. 1-6.147, 115-125 (2009).

Jun, Ji Hyun, Zhihong Song, Zhenjiu Liu, Basil J. Nikolau, Edward S. Yeung and Young Jin Lee. High-Spatial and High-Mass Resolution Imaging of Surface Metabolites of Arabidopsis thaliana by Laser Desorption-Ionization Mass Spectrometry Using Colloidal Silver. Analytical Chemistry. 2010, 82, 3255–3265.

Kandoi, S., J. Greeley, D. Simonetti, J. Shabaker, J. A. Dumesic, M. Mavrikakis, J. Phys. Chem. C, 115, 961 (2011).

Kandoi, Shampa Kandoi, Jeff Greeley, Dante Simonetti, John Shabaker, James A. Dumesic, and Manos Mavrikakis. “Reaction Kinetics of Ethylene Glycol Reforming over Platinum in the Vapor versus Aqueous Phases.” Journal of Physical Chemistry C 115 (2011: 961.

Karim, A.M., T. Conant, and A.K. Datye, Controlling ZnO morphology for improved methanol steam reforming reactivity. Physical Chemistry Chemical Physics, 2008. 10(36): p. 5584-5590.

Kautharapu, K. B. and L. R. Jarboe. “Genome Sequence of Psychrophilic Deep Sea Bacterium Moritella marina MP-1.” Journal of Bacteriology 194(22) (2012): 6296-6297 (DOI: 10.1128/JB.01382-12).

Kautharapu, K. B., J. Rathmacher, and L. R. Jarboe. “Growth Condition Optimization for Docosahexaenoic Acid (DHA) Production by Moritella marina MP-1.” Journal Applied Microbiology and Biotechnology (2012) (DOI: 10.1007/s00253-012-4529-7).

Klitgaard, S.K., A.T. DeLa Riva, S. Helveg, R.M. Werchmeister, and C.H. Christensen, Aerobic Oxidation of Alcohols over Gold Catalysts: Role of Acid and Base. Catalysis Letters, 2008. 126(3-4): p. 213-217.

Klobukowski, Erik R. Bulk Gold Catalyzed Oxidation Reactions of Amines and Isocyanides and Iron Porphyrin Catalyzed N-H and O-H Bond Insertion/cyclization Reactions of Diamines and Aminoalcohols. Ph.D. Dissertation. Iowa State University, 2011.

Korte, A. R., Z. Song, B. J. Nikolau, and Y. L. Lee. “Mass Spectrometric Imaging as a High-Spatial Resolution Tool for Functional Genomics: Tissue-Specific Gene Expression of TT7 Inferred from Heterogeneous Distribution of Metabolites in Arabidopsis Flowers” Analytical Methods 4 (2012): 474-481.

Kozlowski, J. T. and Robert J. Davis. “Sodium Modification of Zirconia Catalysts for Ethanol Coupling to 1-Butanol.” Journal of Energy Chemistry 22(1) (2013): 58-64 (

Kozlowski, J.T., M.T. Aronson and Robert Davis, “Transesterification of tributyrin with methanol over basic Mg:Zr mixed oxide catalysts” Appl. Catal. B: Environ., 96 (2010) 508-515.

Kraus, G. A. and J. J. Lee. “A Direct Synthesis of Renewable Sulfonate-Based Surfactants.” Journal of Surfactants and Detergents (2012) (DOI: 10.1007/s11743-012-1408-2). Kraus, G.A. and Tezcan Guney. “A Direct Synthesis of 5-alkoxymethylfurfural Ethers from Fructose via Sulfonic Acid-functionalized Ionic Liquids.” Green Chemistry 14(6) (2012): 1593-1596 (DOI: 10.1039/C2GC35175G).

Kraus, G. A. and Sean Riley. “A Large Scale Synthesis of -Olefins and ,ω-Dienes.” Synthesis 44(19) (2012): 3003-3005 (DOI: 10.1055/s-0031-1290400). Maldonando, Gretchen M. Gonzalez, Rajeev S. Assary, James A. Dumesic, and Larry A. Curtiss. “Acid-catalyzed Conversion of Furfuryl Alcohol to Ethyl Levulinate in Liquid Ethanol.” Energy and Environmental Science 5(10) (2012): 8990-8997 (DOI: 10.1039/C2EE22486K).

Kraus, G. A., S. Riley, and T. Cordes. “Aromatics from Pyrones: Para-Substituted Alkyl Benzoates from Alkenes and Coumalic Acid and Methyl Coumalate.” Green Chemistry (2011): 2734-2736.

Kunkes, E. L., D. A. Simonetti, W. D. Pyrz, L. Murillo, W. Lonergan, J. G. Chen,  D. J. Buttrey, J. A. Dumesic The role of rhenium in the conversion of glycerol to synthesis gas over carbon supported platinum-rhenium catalysts, J. Catal., 260, 164-177 (2008).

Kunkes, E. L., E. I. Gürbüz, J. A. Dumesic, Vapor-Phase C-C Coupling Reactions of Biomass-Derived Oxygenates over Pd/CeZrOx Catalysts, J. Catal., 266, 236-249 (2009).

Kunkes, E. L., R. R. Soares, D. A. Simonetti, J. A. Dumesic, An integrated catalytic approach for production of hydrogen by vapor-phase reforming of glycerol coupled with water-gas-shift, Appl. Catal. B: Environ., 90, 693-698 (2009).

Laser, M., E. Larson, B. Dale, M. Wang, N. Greene, and L.R. Lynd (2009). Comparative Analysis of Efficiency, Environmental Impact, and Process Economics for Mature Biomass Refining Scenarios. Biofuels, Bioprod. Bioref.3:247–270.

Lebarbier, V. M., A. M . Karim, M. H. Engelhard, Y. Wu, B. Q. Xu, E. J. Petersen, A. K. Datye, and Y. Wang. “The Effect of Zinc Addition on the Oxidation State of Cobalt in Co/ZrO2 Catalysts.” Chemsuschem 4(11) (2011): 1679-1684.

Li X, Ilarslan H, Brachova L, Qian HR, Li L, Che P, Wurtele ES, Nikolau BJ. 2011  Reverse genetic analysis of the two biotin-containing subunit genes of the heteromeric acetyl-CoA carboxylase in Arabidopsis thaliana indicates a unidirectional functional redundancy. Plant Physiol. 155:293-314.  PubMed PMID: 21030508.

Li, Mai, Xiujun Zhang, Arpita Agrawal, Ka-Yiu San. “Effect of Acetate Formation Pathway and Long Chain Fatty Acid CoA-ligase on the Free Fatty Acid Production in E. coli Expressing acyl-ACP Thioesterase from Ricinus communis,” Metabolic Engineering 14(4) (2012): 380-387 (ISSN 1096-7176; DOI: 10.1016/j.ymben.2012.03.007).

Liscombe, D. K., G. V. Louie, and J. P. Noel. “Architectures, Mechanisms and Molecular Evolution of Natural Product Methyltransferases.” Natural Product Reports 10 (2012): 1238-50 (DOI: 10.1039/c2np20029e; Epub 2012 Aug 1. Review; PubMed PMID: 22850796).

Liu, Ping and Laura R Jarboe. “Metabolic Engineering of Biocatalysts for Carboxylic Acids Production.” Computational and Structural Biotechnology Journal 3(4) (2012): e201210011 (

Liu, Ping, Andriy Chernyshov, Tarek Najdi, Yao Fu, Julie Dickerson, Suzanne Sandmeyer, and Laura Jarboe. 2013. “Membrane Stress Caused by Octanoic Acid in Saccharomyces cerevisiae,” Applied Microbiology Biotechnology (2013) (DOI: 10.1007/s00253-013-4773-5).

Lohitharn, N. and Shanks, B.H., Upgrading of Bio-oil:  Effect of Light Aldehydes on Acetic Acid Removal via Esterification. Catal. Commun., 11, 96-99 (2009).

Louie, G.V., Bowman, M.E., Tu, Y., Mouradov, A., Spangenberg, G. and Noel, J.P. (2010) Structure-function analyses of a Caffeic Acid O-methyltransferase from Perennial Ryegrass Reveal the Molecular Basis for Substrate Preference. Plant Cell 22: 4114-4127. Epub 2010 Dec 21. PubMed PMID: 21177481; PubMed Central PMCID: PMC3027180.

Louie, G.V., M. E. Bowman, Y. Tu, A. Mouradov, G. Spangenberg, and J. P. Noel. “Structurefunction Analyses of a Caffeic Acid O-methyltransferase from Perennial Ryegrass Reveal the Molecular Basis for Substrate Preference.” Plant Cell 22 (Epub 2010 Dec 21): 4114-4127. PubMed PMID: 21177481; PubMed Central PMCID: PMC3027180.

Madon, Rostam J., Drew Braden, Shampa Kandoi, Peter Nagel, Manos Mavrikakis, and James A. Dumesic. “A Microkinetic Analysis and Mechanism for the Water Gas Shift Reaction over Copper Catalysts.” Journal of Catalysis 281 (2011); 1.

Martínez, I, G. N. Bennett, and K-Y San. “Culture Conditions’ Impact on Succinate Production by a High Succinate Producing Escherichia coli Strain.” Biotechnology Progress, 27 (2011): 1225-1231 (DOI: 10.1002/btpr.641).

Mazumdar, S., Clomburg, J. M., and Gonzalez, R. (2010). Engineered Escherichia coli strains for the homofermentative production of D-lactic acid from glycerol. Applied and Environmental Microbiology, 76(13): 4327-4336.

Mentzel, U.V., S. Shunmugavel, S.L. Hruby, C.H. Christensen, and M.S. Holm, High Yield of Liquid Range Olefins Obtained by Converting i-Propanol over Zeolite H-ZSM-5. Journal of the American Chemical Society, 2009. 131(46): p. 17009-17013.

Miao, S. and Shanks, B. H. “On the Mechanism of Acetic Acid Esterification over Sulfonic Acid Functionalized Mesoporous Silica.” Journal of Catalysis 279 (2011): 136-143.

Miao, S. and Shanks, B.H., Esterification of Biomass Pyrolysis Model Acids over Sulfonic Acid-Functionalized Mesoporous Silicas. Appl. Catal. A: Gen., 359, 113-120 (2009).

Miller, Elliot. Engineering Escherichia coli for the Production of Platform Chemicals from Betaoxidation Reversal. Ph.D. Dissertation. Rice University, 2012.

Ming J. *, D. Reiners, E.S. Wurtele, J.A. Dickerson, “MetNetGE: Visualizing Biological Networks in Hierarchical Views and 3D Tiered Layouts,” BMC Bioinformatics 2010, 11:469 doi:10.1186/1471-2105-11-469, 2010.

Moon, S., L. Brachova, A. A. Campbell, X. Guan, M. A. Perera, K. He, S. Y. Rhee, P. Bais, J. A. Dickerson, P. M. Dixon, G. Wohlgemuth, O. Fiehn, L. Barkan, B. M. Lange, I. Lee, D. Cortes, C. Salazar, J. Shuman, V. Shulaev, D. V. Huhman, L. W. Sumner, M. Roth, R. Welti, H. Ilarslan, E. S. Wurtele, and B. J. Nikolau. “Metabolomics as a Hypothesis generating Functional Genomics Tool for the Annotation of Arabidopsis Thaliana Genes of Unknown Function.” Frontiers in Plant Science 3 (2012): 15.

Murarka, A., Clomburg, J. M., Moran, S., Shanks, J.V., and Gonzalez, R. (2010). Metabolic analysis of wild-type Escherichia coli and a pyruvate dehydrogenase (PDH)-deficient derivative reveals the role of PDH in the fermentative metabolism of glucose. Journal of Biologial Chemistry, 285 (41): 31548-31558.

Murat Sen, S., Carlos A. Henao, Drew J. Braden, Christos T. Maravelias, and James A. Dumesic. “Catalytic Conversion of Lignocellulosic Biomass to Fuels: Process Development and Technoeconomic Evaluation.” Chemical Engineering Science 67 (2012): 57.

Neurock, M., Engineering Molecular Transformations, Ind. Eng. Chem., 49, 21, 10183-10199, 2010.

Neves do Amaral, W. A. and R. P. Anex. 2010. Life cycle analysis and indicators of sustainability of sugarcane production. In T. R. Coser and M. J. Davis (Eds.), BIOFUELS: Reasonable Steps Towards a Renewable Energy Future (pp. 187-205), 1st ed. Brasilia, Brazil: Fulbright Commission Brazil.

Ngaki, M. N., G. V. Louie, R. N. Philippe, G. Manning, F. Pojer, M. E. Bowman, L. Li, E. Larsen, E. S. Wurtele, and J. P. Noel. “Evolution of the Chalcone-isomerase Fold from Fatty-acid Binding to Stereospecific Catalysis.” Nature 485(7399) (2012): 530-533 (DOI: 10.1038/nature11009; PubMed PMID: 22622584).

Noel, J.P., Dellas, N., Faraldos, J.A., Zhao, Y., Hess, B.A., Smentek, L., Coates, R.M. and O’Maille, P.E. (2010) Structural Elucidation of Cisoid and Transoid Cyclization Pathways of a Sesquiterpene Synthase Using 2-Fluorofarnesyl Diphosphates. ACS Chem. Biol. 5: 377-392. Epub 2010 Feb 22. PubMed PMID: 20175559; PubMed Central PMCID: PMC2860371.

O’Neill, Brandon J., Elif I. Gurbuz, and James A. Dumesic. “Reaction Kinetics Studies of the Conversions of Formic Acid and Butyl Formate over Carbon-supported Palladium in the Liquid Phase.” Journal of Catalysis 290 (2012): 193-201 (DOI: 10.1016/j.jcat.2012.03.014).

Olcay, Hakan; Ayyagari V. Subrahmanyam, Rong Xing, Jason Jajoie, James A. Dumesic, and George W. Huber. “Production of Renewable Petroleum Refinery Diesel and Jet Fuel Feedstocks from Hemicellulose Sugar Streams.” Energy and Environmental Science 6(1) (2013): 205-216 (DOI: 10.1039/C2EE23316A).

Oliver, D.J., Nikolau B.J., Wurtele, E.S. (2009).  Acetyl-CoA – life at the metabolic nexus. Plant Science 176: 597-601

Ortiz-Toral, P. J., J. Satrio, R. C. Brown, and B. H. Shanks. “Steam Reforming of Bio-oil Fractions: Effect of Composition and Stability.” Energy Fuels 25 (2011): 3289-3297.

Ortiz-Toral, Pedro. Steam Reforming of Water-Soluble Fast Pyrolysis Bio-oil: Studies on Biooil Composition, Carbon Deposition and Catalyst Modifications. Ph.D. Dissertation. Iowa State University, 2011.

Pagan-Tores, Yomaira. Catalytic Strategies and Catalyst Design for the Conversion of Biomassderived Carbohydrates to Chemicals. Ph.D. Dissertation. University of Wisconsin, 2011.

Pagan-Torres, Y. J., J. M. R. Gallo, D. Wang, H. N. Pham, J. A. Libera, C. L. Marshall, J. W. Elam, A. K. Datye, and J. A. Dumesic. “Synthesis of Highly Ordered Hydrothermally Stable Mesoporous Niobia Catalysts by Atomic Layer Deposition.” ACS Catalysis 1(10) (2011): 1234-1245.

Pagan-Torres, Y.J., T. Wang, J. M. R. Gallo, B. H. Shanks, and J. A. Dumesic. “Production of 5-Hydroxymethylfurfural from Glucose Using a Combination of Lewis and Brønsted Acid Catalysts in Water in a Biphasic Reactor with an Alkylphenol Solvent.” ACS Catalysis 2(6) (2012): 930–934 (DOI: 10.1021/cs300192z).

Park, J., M. Rodriguez-Moya, M. Li, E. Pichersky, K.-Y. San, and R. Gonzalez. “Synthesis of Methyl Ketones by Metabolically Engineered Escherichia coli.” Journal of Industrial Microbiology and Biotechnology 39(11) (2012): 1703-1712 (DOI: 10.1007/s10295-012- 1178-x).

Park, John. Engineering Escherichia coli for the Production of Polyketide-based Platform Chemicals. M.S. Thesis. Rice University, 2011.

Patel, A. D., J. C. Serrano-Ruiz, J. A. Dumesic, R. P. Anex, Chemical Engineering Journal, 160, 311 (2010).

Patel, Akshay. Techno-economic Analysis of Di-butyl Ketone, Di-methyl Furan and Hydroxymethyl Furfural Production from Biomass Based Resources. M.S. Thesis. Iowa State University, 2011.

Perera MADN, Qin W, Yandau-Nelson M, Fan L, Dixon P, Nikolau BJ. 2010  Biological origins of normal-chain hydrocarbons.  The Plant Journal. 64:618-632.

Perera, MADN, Choi, S-Y, Wurtele, E.S., Nikolau, B.J. (2009). Quantitative analysis of acyl-Coenzyme-As in plant tissues by an LC-MS-MS electrospray ionization method. Journal of Chromatography B 877: 482-488.

Peterson, E. J., B. Halevi, B. Kiefer, M. N. Spilde, A. K. Datye, J. Peterson, L. Daemen, A. Llobet, and H. Nakotte. “Aerosol synthesis and Rietveld analysis of tetragonal (beta(1)) PdZn.” Journal of Alloys and Compounds 509(5) (2011): 1463-1470.

Peterson, E.J., B. Halevi, B. Kiefer, M.N. Spilde, A.K. Datye, J. Peterson, L. Daemen, A. Llobet, and H. Nakotte, Aerosol synthesis and Rietveld analysis of tetragonal ([beta]1) PdZn. Journal of Alloys and Compounds, 2011. 509(5): p. 1463-1470.

Pfister, D. P.; Larock, R. C. “Thermophysical Properties of Conjugated Soybean Oil/Corn Stover Biocomposites,” Bioresour. Technol. 2010, 101(15), 6200-6206.

Pfister, Daniel. Green Composite and Coatings from Agricultural Feed Stock. Ph.D. Dissertation. Iowa State University, 2010.

Pham, H. N., A. E. Anderson, R. L. Johnson, K. Schmidt-Rohr, and A. K. Datye. “Improved Hydrothermal Stability of Mesoporous Oxides for Reactions in the Aqueous Phase.” Angewandte Chemie International Edition 51(52) (2012): 13163-13167 (DOI: 10.1002/anie.201206675).

Pham, H. N., Y. J. Pagan-Torres, J. C., Serrano-Ruiz, D. Wang, J. A. Dumesic, and A. K. Datye. “Improved Hydrothermal Stability of Niobia-supported Pd Catalysts.” Applied Catalysis A-General 397 (1-2) (2011): 153-162.

Portle, S., Iadevaia1, S., K.-Y., Bennett, G.N., Mantzaris, N., Environmentally-modulated changes in fluorescence distribution in cells with oscillatory network dynamics. J Biotechnology, 140(3-4):203-17 (2009).

Posada, J. A., C. A. Cardona, and R. Gonzalez. “Analysis of the Production Process of Optically Pure D-lactic Acid from Raw Glycerol using Engineered Escherichia coli Strains.” Applied Biochemistry and Biotechnology 166 (3): (2012): 680-699.

Quirino, R. L. and R. C. Larock. “Rh-based Biphasic Isomerization of Carbon–Carbon Double Bonds in Natural Oils.” Journal of the American Oil Chemists’ Society (2011).

Quirino, Rafael Lopes. Natural Oil-Based Composites Reinforced with Natural Fillers, and Conjugation/Isomerization of Carbon-carbon Double Bonds. Ph.D. Dissertation. Iowa State University, 2011.

Raman, D. R. and R. P. Anex. “Conceptual and Mathematical Models of Batch Simultaneous Saccharification and Fermentation: Dimensionless Groups for Predicting Process Dynamics.” Journal of Biological Systems 20(2) (2012): 195-211 (DOI: 10.1142/S0218339012500064).

Ranganathan, Sridhar, Ting Wei Tee, Anupam Chowdhury, Ali R. Zomorrodi, Jong Moon Yoon, Yanfen Fu, Jacqueline V. Shanks, and Costas D. Maranas. “An Integrated Computational and Experimental Study for Overproducing Fatty Acids in Escherichia coli.” Metabolic Engineering 14(6) (2012): 687-704 (DOI: 10.1016/j.ymben.2012.08.008).

Research Thrust 3 – Chemical Catalyst Design Alonso, David Martin, Stephanie G. Wettstein, Max A. Mellmer, Elif I. Gurbuz, and James A. Dumesic. “Integrated Conversion of Hemicellulose and Cellulose from Lignocellulosic Biomass.” Energy and Environmental Science, 6 (2013): 76-80 (DOI: 10.1039/C2EE23617F).

Riley, Sean. Chemistry from Nature: From Natural Products to Biorenewables. Ph.D. Dissertation. Iowa State University, 2011.

Roberts, G. M., Philip J. Pierce, and L. Keith Woo. “Palladium Complexes with N-heterocyclic Carbene Ligands as Catalysts for the Alkoxycarbonylation of Olefins.” Organometallics 32 (2013): 2033-2036 (DOI: 10.1021/om300959f).

Rodriguez-Moya, M., and Gonzalez, R. (2010). Systems biology approaches for the microbial production of biofuels.Biofuels 1(2), 291–310.

Roman-Leshkov, Y., J. A. Dumesic, Solvent effects on fructose dehydration to 5-hydroxymethylfurfural in biphasic systems saturated with inorganic salts, Top. Catal., 52, 297-303 (2009).

Roy, B., K. Artyushkova, H. N. Pham, L. Li, A. K. Datye, and C. A. Leclerc. “Effect of Preparation Method on the Performance of the Ni/Al2O3 Catalysts for Aqueous-phase Reforming of Ethanol: Part II-characterization.” International Journal of Hydrogen Energy 37(24) (2012): 18815-18826 (DOI: 10.1016/j.ijhydene.2012.09.098).

Roy, B., K. Loganathan, H.N. Pham, A.K. Datye, and C.A. Leclerc, Surface modification of solution combustion synthesized Ni/Al2O3 catalyst for aqueous-phase reforming of ethanol. International Journal of Hydrogen Energy, 2010. 35(21): p. 11700-11708.

Roy, B., U. Martinez, K. Loganathan, A. K. Datye, and C. A. Leclerc. “Effect of Preparation Methods on the Performance of Ni/Al2O3 Catalysts for Aqueous-phase Reforming of Ethanol: Part I-catalytic Activity.” International Journal of Hydrogen Energy 37(10) (2012): 8143-8153 (DOI: 10.1016/j.ijhydene.2012.02.056).

Royce, Liam , Erin Boggess, Tao Jin, Julie Dickerson, and Laura Jarboe. “Identification of Mutations in Evolved Bacterial Genomes.” Systems Metabolic Engineering: Methods in Molecular Biology, Hal S. Alper, Ed., 985 (2013) (DOI: 10.1007/978-1-62703-299-5_13; ISBN: 978-1-62703-298-8).

Schneller ,W, P. J. Campbell, D. Bassham, and E. S. Wurtele. “Meta!Blast Computer Game: A Pipeline from Science to 3D Art to Education.” Proceedings SPIE 8289, 828905 (2011) (

Sen, S. Murat, David Martin Alonso, Stephanie G. Wettstein, Elif I. Gurbux, Carlos A. Heano, James A. Dumesic, and Christos T. Maravelias. “A Sulfuric Acid Management Strategy for the Production of Liquid Hydrocarbon Fuels via Catalytic Conversion of Biomass-derived Levulinic Acid.” Energy and Environmental Science 5(12) (2012): 9690-9697 (DOI: 10.1039/C2EE22526C).

Sen, S. Murat, Elif I. Gurbuz, Stephanie G. Wettstein, David Martin Alonso, James A. Dumesic, and Christos T. Maravelias. “Production of Butene Oligomers as Transportation Fuels using Butene for Esterification of Levulinic Acid from Lignocellulosic Biomass: Process Synthesis and Technoeconomic Evaluation.” Green Chemistry 14(12) (2012): 3289-3294 (DOI: 10.1039/C2GC35881F).

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Serrano-Ruiz, J. C., R. M. West, J.A. Dumesic, Annual Review of Chemical and Biomolecular Engineering,  1, 79 (2010).

Serrano-Ruiz, J.C., D. J. Braden, R. M. West, J. A. Dumesic, Appl. Catal. B Environ., 100, 184, 2010.

Serrano-Ruiz, J.C., J. A. Dumesic, Catalytic processing of lactic acid over Pt/Nb2O5, ChemSusChem, 2, 581-586 (2009).

Serrano-Ruiz, J.C., J. A. Dumesic, Catalytic upgrading of biomass-derived lactic acid to fuels and chemicals by dehydration/hydrogenation and C-C coupling reactions, Green Chem., 8, 1101-1104 (2009).

Serrano-Ruiz, Juan Carlos, and James A. Dumesic. “Catalytic Routes for the Conversion of Biomass into Liquid Hydrocarbon Transportation Fuels.” Energy and Environmental Science 4 (2011): 83.

Shanks, B. H. “Design of Heterogeneous Catalysts for the Conversion of Biorenewable Feedstocks.” Catalysis for the Conversion of Biomass and Its Derivatives, Behrens, M. and A. K. Datye, Eds., Max Planck Research Library, Germany (2013): 349-396 (ISBN: 9783844242829;

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Simonetti, D. A., J. A. Dumesic, Catalytic strategies for changing the energy content and achieving C-C coupling in biomass-derived oxygenated hydrocarbons, ChemSusChem., 1, 725-733 (2008).

Sinha, Nishant K. and Matthew Neurock. “A First Principles Analysis of the Hydrogenation of C1-C4 Aldehydes and Ketones over Ru(0001).” Journal of Catalysis 295 (2012): 31-44 (DOI: 10.1016/j.jcat.2012.07.018).

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Snell, R.W. and B. H. Shanks. “Ceria Calcination Temperature Influence on Acetic Acid Ketonization: Mechanistic Insights.” Applied Catalysis A: General 451 (2013): 86-93 (DOI: 10.1016/j.apcata.2012.08.043).

Snell, R.W., Combs, E. and Shanks, B.H., “Aldol Condensations using Bio-oil Model Compounds: The Role of Acid-Base Bi-functionality,” Catal. Today, 53, 1248-1253 (2010).

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Staker, Amanda. Carbon Coating for Improved Hydrotehrmal Stability of Silica Supports. M.S. Thesis. University of New Mexico, 2010.

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Tang, Y., Miao, S., Shanks, B.H., and Zheng, X., “Bifunctional Mesoporous Organic–Inorganic Hybrid Silica for Combined One-step Hydrogenation Esterification,” Appl. Catal A: Gen., 375, 310-317 (2010).

Tang, Y., S. J. Miao, H. N. Pham, A. Datye, X. M. Zheng, and B. H. Shanks. “Enhancement of Pt catalytic activity in the hydrogenation of aldehydes.” Applied Catalysis A-General 406(1-2) (2011): 81-88.

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Thakker, Chandresh, Ka-Yiu San, and George N. Bennett. “Production of Succinic Acid by Engineered E. coli Strains Using Soybean Carbohydrates as Feedstock Under Aerobic Fermentation Conditions.” Bioresource Technology 130 (2013): 398-405 (DOI: 10.1016/j.biortech.2012.10.154; ISSN 0960-8524).

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Tucker, Mark H., Anthony J. Crisci, Bethany N. Wigington, Neelay Phadke, Ricardo Alamillo, Jinping Zhang, Susannah L.Scott, and James A. Dumesic. “Acid-Functionalized SBA-15-Type Periodic Mesoporous Organosilicas and Their Use in the Continuous Production of 5-Hydroxymethylfurfural.” ACS Catalysis 2(9) (2012): 1865-1876 (DOI: 10.1021/cs300303v).

Tucker, Mark. Selective Production of Value Added Chemicals from Fructose Using Heterogeneous Catalysis. Ph.D. Dissertation. University of Wisconsin, 2011.

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Wang, J., J. Zhu, G. N. Bennett, and K-Y San. “Succinate Production from Different Carbon Sources Under Anaerobic Conditions by Metabolic Engineered Escherichia coli Strains.” Metabolic Engineering 13 (2011): 328-335.

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Wettstein, Stephanie G., David Martin Alonso, and James A. Dumesic. “Bimetallic Catalysts for Upgrading of Biomass to Fuels and Chemicals.” Chemical Society Reviews 41(24) (2012): 8075-8098 (DOI: 10.1039/C2CS35188A).

Wettstein, Stephanie G., David Martin Alonso, Elif I. Gurbuz, and James A. Dumesic. “A Roadmap for Conversion of Lignocellulosic Biomass to Chemicals and Fuels.” Current Opinion in Chemical Engineering, 1(3) (2012): 218-224 (DOI: 10.1016/j.coche.2012.04.002).

Wettstein, Stephanie G., David Martin Alonso, Y. X. Chong, and James A. Dumesic. “Production of Levulinic acid and Gamma-valerolactone (GVL) from Cellulose using GVL as a Solvent in Biphasic Systems.” Energy and Environmental Science 5(8) (2012): 8199- 8203 (DOI: 10.1039/C2EE22111J).

Wettstein, Stephanie G., Jesse Q. Bond, David Martin Alonso, Hien N. Pham, Abhaya K. Datye, James A. Dumesic. “RuSn Bimetallic Catalysts for Selective Hydrogenation of Levulinic Acid to γ-valerolactone.” Applied Catalysis B: Environmental 117-118 (2012): 321-329 (DOI: j.apcatb.2012.01.033).

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Wiedmann, Monika K., David H. K. Jackson, Yomaira J. Pagan-Torres, James A. Dumesic, and T. F. Kuech. “Atomic Layer Deposition of Titanium Phosphate on Silica Nanoparticles.” Journal of Vacuum Science and Technology 30(1), 01A134 (2012).

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Any opinions, findings, and conclusions or recommendations expressed in these materials are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.