Updated 2/8/10.

1. ALLEN, D. K., LIBOUREL, I. G. L. & SHACHAR-HILL, Y. (2009) Metabolic flux analysis in plants: coping with complexity. Plant, Cell & Environment, 32, 1241-1257
2. ALLEN, D. K., OHLROGGE, J. B. & SHACHAR-HILL, Y. (2009) The role of light in soybean seed filling metabolism. Plant J, 58, 220-34
3. BALAN, V., BALS, B., CHUNDAWAT, S. P., MARSHALL, D. & DALE, B. E. (2009) Lignocellulosic Biomass Pretreatment Using AFEX.
4. BALAN, V., SOUSA LDA, C., CHUNDAWAT, S. P., MARSHALL, D., SHARMA, L. N., CHAMBLISS, C. K. & DALE, B. E. (2009) Enzymatic digestibility and pretreatment degradation products of AFEX-treated hardwoods (Populus nigra). Biotechnol Prog, 25, 365-75.
5. BANERJEE, G., SCOTT-CRAIG, J. S. & WALTON, J. D. Improving Enzymes for Biomass Conversion: A Basic Research Perspective. BioEnergy Research.
6. BATES, P. D., DURRETT, T. P., OHLROGGE, J. B. & POLLARD, M. (2009) Analysis of Acyl Fluxes through Multiple Pathways of Triacylglycerol Synthesis in Developing Soybean Embryos. Plant Physiol., 150, 55-72.
7. BENNING, C. & PICHERSKY, E. (2008) Harnessing plant biomass for biofuels and biomaterials. The Plant Journal, 54, 533-535.
8. BINDER, J. B. & RAINES, R. T. (2009) Simple Chemical Transformation of Lignocellulosic Biomass into Furans for Fuels and Chemicals. Journal of the American Chemical Society, 131, 1979-1985.
9. CALDERA, E. J., POULSEN, M., SUEN, G. & CURRIE, C. R. (2009) Insect Symbioses: A Case Study of Past, Present, and Future Fungus-Growing Ant Research*. Environmental Entomology, 38, 78-92.
10. ÇETINKOL, Ö. P., DIBBLE, D. C., CHENG, G., KENT, M. S., KNIERIM, B., AUER, M., WEMMER, D. E., PELTON, J. G., MELNICHENKO, Y. B., RALPH, J., SIMMONS, B. A. & HOLMES, B. M. Understanding the impact of ionic liquid pretreatment on Eucalyptus. Biofuels, 2009, 1, 33-46.
11. CHUNDAWAT, S. P. S., BALAN, V., DACOSTA SOUSA, L. & DALE, B. (2009) Characteristics of an ideal thermochemical pretreatment for reducing recalcitrance of lignocellulosic biomass to biological processing.  . Bioalcohol production., Chapter 13 (Chemical pretreatments)
12. COLE, J. R., WANG, Q., CARDENAS, E., FISH, J., CHAI, B., FARRIS, R. J., KULAM-SYED-MOHIDEEN, A. S., MCGARRELL, D. M., MARSH, T., GARRITY, G. M. & TIEDJE, J. M. (2009) The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res, 37, D141-5.
13. DA COSTA SOUSA, L., CHUNDAWAT, S. P. S., BALAN, V. & DALE, B. E. (2009) [`]Cradle-to-grave’ assessment of existing lignocellulose pretreatment technologies. Current Opinion in Biotechnology, 20, 339-347.
14. DELISA, M. P. & CONRADO, R. J. (2009) Synthetic metabolic pipelines. Nat Biotech, 27, 728-729.
15. DURRETT, T. P., BENNING, C. & OHLROGGE, J. (2008) Plant triacylglycerols as feedstocks for the production of biofuels. Plant J, 54, 593-607.
16. FORTENBERY, T. R., DONOHUE, T. J., KLEINMAN, D., DELBORNE, J., CLOUD‐HANSEN, K. & HANDELSMAN, J. (2009) Opportunities and challenges for next generation biofuels. Controversies in Science and Technology., Vol. 3.
17. GAO, D., CHUNDAWAT, S. P. S., LIU, T., HERMANSON, S., GOWDA, K., BRUMM, P., DALE, B. E. & BALAN, V. Strategy for Identification of Novel Fungal and Bacterial Glycosyl Hydrolase Hybrid Mixtures that can Efficiently Saccharify Pretreated Lignocellulosic Biomass. BioEnergy Research, 1939-1234.
18. GAO, D., CHUNDAWATA, S. P. S., KRISHNANC, C., BALANA, V. & DALE, B. E. 2010. Mixture optimization of six core glycosyl hydrolases for maximizing saccharification of ammonia fiber expansion (AFEX) pretreated corn stover. Bioresource Technology, 101, 2770-2781.
19. Gao D., Krishnan C., Chundawat S.P.S., Balan V., and Dale B.E. Demonstration of synergistic interactions between purified cellulases and hemicellulases on ammonia fiber expansion (AFEX) treated corn stover. Enzyme and Microbial Technology. (communicated in March 2009)
20. GAO, J., HAO, X., THELEN, K. D. & ROBERTSON, G. P. (2009) Agronomic Management System and Precipitation Effects on Soybean Oil and Fatty Acid Profiles. Crop Sci, 49, 1049-1057.
21. GREGG, J. S. & IZAURRALDE, R. C. S. 2010. Effect of crop residue harvest on long-term crop yield, soil erosion and nutrient balance: trade-offs for a sustainable bioenergy feedstock. Biofuels, 1, 69-83.
22. GÜRBÜZ, E. I., KUNKES, E. L. & DUMESIC, J. A. 2010. Dual-bed catalyst system for C–C coupling of biomass-derived oxygenated hydrocarbons to fuel-grade compounds. Green Chemistry.
23. H., F. & BABCOCK, B. A. (2008) Impacts of ethanol on planted acreage in market equilibrium. CARD Working Paper 08-WP 472, Iowa State University.
24. HANSEY, C. N., LORENZ, A. J. & LEON, N. D. Cell Wall Composition and Ruminant Digestibility of Various Maize Tissues Across Development. BioEnergy Research.
25. HEDENSTROM, M., WIKLUND-LINDSTROM, S., OMAN, T., LU, F., GERBER, L., SCHATZ, P., SUNDBERG, B. & RALPH, J. (2009) Identification of Lignin and Polysaccharide Modifications in Populus Wood by Chemometric Analysis of 2D NMR Spectra from Dissolved Cell Walls. Mol Plant, 2, 933-942.
26. JEFFRIES, T. W. & VAN VLEET, J. R. (2009) Pichia stipitis genomics, transcriptomics, and gene clusters. FEMS Yeast Res, 9, 793-807.
27. JIANG, Y. & SWINTON, S. M. (2009) Market interactions, farmers’ choices, and the sustainability of growing advanced biofuels: a missing perspective? International Journal of Sustainable Development & World Ecology, 16, 438 – 450.
28. JIANG, Y. & SWINTON, S. M. (2009) Market interactions, farmer choices, and the sustainability of growing advanced biofuels. Staff Paper No. 2008-03. Department of Agricultural, Food and Resource Economics, Michigan State University.
29. KIM, H., KIM, S. & DALE, B. E. (2009) Biofuels, Land Use Change, and Greenhouse Gas Emissions: Some Unexplored Variables. Environmental Science & Technology, 43, 961-967.
30. KIM, H. & RALPH, J. Solution-state 2D NMR of ball-milled plant cell wall gels in DMSO-d6/pyridine-d5. Organic & Biomolecular Chemistry, 2009.
31. KIM, S. & DALE, B. (2009) Regional variations in greenhouse gas emissions of biobased products in the United States—corn-based ethanol and soybean oil. The International Journal of Life Cycle Assessment, 14, 540-546.
32. KO, J. H., KIM, W. C. & HAN, K. H. (2009) Ectopic expression of MYB46 identifies transcriptional regulatory genes involved in secondary wall biosynthesis in Arabidopsis. Plant J, 60, 649-65.
33. KUMAR, R., MAGO, G., BALAN, V. & WYMAN, C. E. (2009) Physical and chemical characterizations of corn stover and poplar solids resulting from leading pretreatment technologies. Bioresour Technol, 100, 3948-62.
34. KUNKES, E. L., GÜRBÜZ, E. I. & DUMESIC, J. A. (2009) Vapor-Phase C-C Coupling Reactions of Biomass-Derived Oxygenates over Pd/CeZrOx Catalysts.  Journal of Catalysis , 266, 2009, 236-249.
35. LANDIS, D. A., GARDINER, M. M., VAN DER WERF, W. & SWINTON, S. M. (2008) Increasing corn for biofuel production reduces biocontrol services in agricultural landscapes. Proc Natl Acad Sci U S A, 105, 20552-7.
36. LAU, M., GUNAWAN, C. & DALE, B. 2009. The impacts of pretreatment on the fermentability of pretreated lignocellulosic biomass: a comparative evaluation between ammonia fiber expansion and dilute acid pretreatment. Biotechnology for Biofuels, 2, 30.
37. LAU, M. W. & DALE, B. E. (2009) Cellulosic ethanol production from AFEX-treated corn stover using Saccharomyces cerevisiae 424A(LNH-ST). Proceedings of the National Academy of Sciences, 106, 1368-1373.
38. LI, B. Z., BALAN, V., YUAN, Y. J. & DALE, B. E. Process optimization to convert forage and sweet sorghum bagasse to ethanol based on ammonia fiber expansion (AFEX) pretreatment. Bioresour Technol, 101, 1285-92.
39. LIANG, C., PEDERSEN, J. A. & BALSER, T. C. (2009) Aminoglycoside antibiotics may interfere with microbial amino sugar analysis. Journal of Chromatography A, 1216, 5296-5301.
40. MARNER, W. D., 2ND (2009) Practical application of synthetic biology principles. Biotechnol J, 4, 1406-19.
41. NAGENDRAN, S., HALLEN-ADAMS, H. E., PAPER, J. M., ASLAM, N. & WALTON, J. D. (2009) Reduced genomic potential for secreted plant cell-wall-degrading enzymes in the ectomycorrhizal fungus Amanita bisporigera, based on the secretome of Trichoderma reesei. Fungal Genet Biol, 46, 427-35.
42. OHLROGGE, J., ALLEN, D., BERGUSON, B., DELLAPENNA, D., SHACHAR-HILL, Y. & STYMNE, S. (2009) Driving on Biomass. Science 22 May 2009 324: 1019-1020.
43. PAULY, M. & KEEGSTRA, K. (2008) Cell-wall carbohydrates and their modification as a resource for biofuels. Plant J, 54, 559-68.
44. PAULY, M. & KEEGSTRA, K. (2008) Physiology and metabolism ‘Tear down this wall’. Curr Opin Plant Biol, 11, 233-5.
45. PERRSON, S., WILLATS, W. & PAULY, M. (2008) Dissection of the Plant Cell Wall by High Through-put Methods. Plant Cell Walls, Udskov editor, In Press.
46. PHILLIPS, G. N., JR.  (2009) Describing protein conformational ensembles:  Beyond static snapshots.  F1000 Biology Reports, 1:38-41
47. PINTO-TOMAS, A. A., ANDERSON, M. A., SUEN, G., STEVENSON, D. M., CHU, F. S. T., CLELAND, W. W., WEIMER, P. J. & CURRIE, C. R. (2009) Symbiotic Nitrogen Fixation in the Fungus Gardens of Leaf-Cutter Ants. Science, 326, 1120-1123.
48. POLLARD, M., BEISSON, F., LI, Y. & OHLROGGE, J. B. (2008) Building lipid barriers: biosynthesis of cutin and suberin. Trends Plant Sci, 13, 236-46.
49. RALPH, J. Hydroxycinnamates in lignification. Phytochemistry Reviews.
50. ROBERTSON, G. P., DALE, V. H., DOERING, O. C., HAMBURG, S. P., MELILLO, J. M., WANDER, M. M., PARTON, W. J., ADLER, P. R., BARNEY, J. N., CRUSE, R. M., DUKE, C. S., FEARNSIDE, P. M., FOLLETT, R. F., GIBBS, H. K., GOLDEMBERG, J., MLADENOFF, D. J., OJIMA, D., PALMER, M. W., SHARPLEY, A., WALLACE, L., WEATHERS, K. C., WIENS, J. A. & WILHELM, W. W. (2008) Agriculture. Sustainable biofuels redux. Science, 322, 49-50.
51. ROBERTSON, G. P., HAMILTON, S. K. & PARTON, W. J. (2009) The biogeochemistry of bioenergy landscapes: Carbon, nitrogen, and water considerations. Ecological Applications, In Press.
52. ROBERTSON, G. P. & VITOUSEK, P. M. 2009. Nitrogen in Agriculture: Balancing the Cost of an Essential Resource. Annual Review of Environment and Resources, 34, 97-125.
53. S., P., W., W. & M., P. 2008. Dissection of the Plant Cell Wall by High Through-put Methods. Plant Cell Walls, Udskov editor, In Press.
54. SANTORO, N., CANTU, S. L., TORNQVIST, C.-E., FALBEL, T. G., BOLIVAR, J. L., PATTERSON, S. E., PAULY, M. & WALTON, J. D. 2010. A High-Throughput Platform for Screening Milligram Quantities of Plant Biomass for Lignocellulose Digestibility. BioEnergy Research.
55. SCIENCE, U. S. D. O. E. O. O. & AGRICULTURE, U. S. D. O. (2009) Sustainability of Biofuels: Future Research Opportunities; Report from the October 2208 Workshop.  (http://genomicsgtl.energy.gov/biofuels/sustainability/)  42 pp.  [D.A. Landis drafted sections of “2.3 Biodiversity and Ecosystem Services” and “2.4 Integrated Landscape Ecology and Feedstock Production Analysis.”]
56. SEARCHINGER, T. D., HAMBURG, S. P., MELILLO, J., CHAMEIDES, W., HAVLIK, P., KAMMEN, D. M., LIKENS, G. E., LUBOWSKI, R. N., OBERSTEINER, M., OPPENHEIMER, M., PHILIP ROBERTSON, G., SCHLESINGER, W. H. & DAVID TILMAN, G. 2009. Fixing a Critical Climate Accounting Error. Science, 326, 527-528.
57. SENDICH, E. D. & DALE, B. E. 2009. Environmental and economic analysis of the fully integrated biorefinery. GCB Bioenergy, 1, 331-345.
58. SENDICH, E. N., LASER, M., KIM, S., ALIZADEH, H., LAUREANO-PEREZ, L., DALE, B. & LYND, L. (2008) Recent process improvements for the ammonia fiber expansion (AFEX) process and resulting reductions in minimum ethanol selling price. Bioresour Technol, 99, 8429-35.
59. STEWART, J. J., AKIYAMA, T., CHAPPLE, C., RALPH, J. & MANSFIELD, S. D. (2009) The Effects on Lignin Structure of Overexpression of Ferulate 5-Hydroxylase in Hybrid Poplar1. Plant Physiol., 150, 621-635.
60. TERASHIMA, N., AKIYAMA, T., RALPH, S. A., EVTUGUIN, D., PASCOAL NETO, C., PARKÅS, J., PAULSSON, M., WESTERMARK, U. & RALPH, J. (2009) 2D-NMR difference spectra between specifically 13C-enriched and unenriched ginkgo protolignin by solution-state whole-cell-wall NMR. Holzforschung, 63, 379-384.
61. TIEDJE, J. & DONOHUE, T. (2008) Microbes in the Energy Grid. Science, 320, 985-.
62. VAN VLEET, J. H. & JEFFRIES, T. W. (2009) Yeast metabolic engineering for hemicellulosic ethanol production. Curr Opin Biotechnol, 20, 300-6.
63. WAGNER, A., DONALDSON, L., KIM, H., PHILLIPS, L., FLINT, H., STEWARD, D., TORR, K., KOCH, G., SCHMITT, U. & RALPH, J. (2009) Suppression of 4-Coumarate-CoA Ligase in the Coniferous Gymnosperm Pinus radiata. Plant Physiol., 149, 370-383.
64. WISE, M., CALVIN, K., THOMSON, A., CLARKE, L., BOND-LAMBERTY, B., SANDS, R., SMITH, S. J., JANETOS, A. & EDMONDS, J. (2009) Implications of Limiting CO2 Concentrations for Land Use and Energy. Science, 324, 1183-1186.
65. YANG, Z. & OHLROGGE, J. B. (2009) Turnover of fatty acids during natural senescence of Arabidopsis, Brachypodium, and switchgrass and in Arabidopsis beta-oxidation mutants. Plant Physiol, 150, 1981-9.
66. ZHANG, A., LU, F., SUN, R. & RALPH, J. (2009) Ferulate-coniferyl alcohol cross-coupled products formed by radical coupling reactions. Planta, 229, 1099-1108.
67. ZHANG, M., FAN, J., TAYLOR, D. C. & OHLROGGE, J. B. 2009. DGAT1 and PDAT1 acyltransferases have overlapping functions in Arabidopsis triacylglycerol biosynthesis and are essential for normal pollen and seed development. Plant Cell, 21, 3885-901.