Publications

Aqueous Phase Catalytic Processing in Biomass Valorization to H2 and Liquid Fuels
2012. CRC PRESS. Gürbüz, Elif I.; Braden, D; Dumesic, James A

Effectiveness of summer mowing for weed control in plantings of native C4 prairie grasses
2011. Michigan State University. Phillippo, C.

Prairie grasses for biofuels and ecological restoration: Modifications to native species and their place in human-modified landscapes
2011. Michigan State University. Schrotenboer, A. C.

Differences in drought sensitivity among prairie communities and among management histories: a remote sensing analysis of 221 prairies in the northern Great Plains
2011. Michigan State University. Morrice, J.

Lignin composition and structure in young versus adult Eucalyptus globulus plants
2011. AMER SOC PLANT BIOLOGISTS. Rencoret, Jorge; Gutierrez, Ana; Nieto, Lidia; Jimenez-Barbero, Jesus; Faulds, Craig B.; Kim, Hoon; Ralph, John; Martinez, Angel T.; del Rio, Jose C.

Controls over soil microbial biomass responses to carbon amendments in agricultural systems: A meta-analysis
2011. Agriculture, Ecosystems, and Environment. Kallenbach, Cynthia; Grandy, A. Stuart

Future of metagenomics, metatranscriptomics, metabolomics, metaproteomics and single cell analysis: A perspective
2011. Wiley-Blackwell. Brown, C. Titus; Tiedje, J. M.

Facile synthesis of 4-hydroxycinnamaldehydes
2011. BioEnergy Research. Zhu, Y.; Mohammadi, A.; Ralph, J.

Identifying protein-protein interactions in Arabidopsis by co-immunoprecipitation of GFP-tagged proteins and proteomic detection
2011. Fluorescent Proteins. Held, Michael A.; Danhof, Linda; Brandizzi, Federica

Isolation of improved free fatty acid overproducing strains of Escherichia coli via Nile red based high-throughput screening
2011. Environmental Progress & Sustainable Energy. Hoover, Spencer W.; Youngquist, J. Tyler; Angart, Phil A.; Withers, Sydnor T.; Lennen, Rebecca M.; Pfleger, Brian F.

Large-scale bi-level strain design approaches and mixed-integer programming solution techniques
2011. Public Library of Science ONE. Kim, Joonhoon; Reed, Jennifer L.; Maravelias, Christos T.

Utility of RNA-seq for analysis of maize reproductive transcriptomes
2011. The Plant Genome. Davidson, R.M.; Hansey, Candice N.; Gowda, M.; Childs, Kevin L.; Lin, Haining; Vailancourt, B.; Sekhon, Rajandeep S.; de Leon, Natalia; Kaeppler, Shawn M.; Jiang, N.; Buell, C. Robin

Pathways involved in reductant distribution during photobiological H2 production by Rhodobacter sphaeroides
2011. AMER SOC MICROBIOLOGY. Kontur, W. S.; Ziegelhoffer, E. C.; Spero, M.; Imam, S.; Noguera, Daniel R.; Donohue, Timothy J.

Low Temperature and Long Residence Time AFEX Pretreatment of Corn Stover
2011. BioEnergy Research. Bals, Bryan; Teymouri, Farzaneh; Campbell, Tim; Jin, Mingjie; Dale, Bruce

Identification, Cloning and Characterization of Dictyoglomus turgidum CelA, an Endoglucanase with Cellulase and Mannanase Activity
2011. Journal of Life Sciences. Brumm, P. J.; Hermanson, Spencer; Luedtke, Joshua; Mead, D. A.

HPC-EPIC for High Resolution Simulations of Environmental and Sustainability Assessment
2011. Computers and Electronics in Agriculture. Nichols, J.; Kang, S.; Post, W.M.; Wang, D.; Bandaru, V.P.; Manowitz, D.; Zhang, X.; Izaurralde, R. C.

Bioprospecting metagenomics of decaying wood: mining for new glycoside hydrolases
2011. Biotechnology for Biofuels. Li, Luen-Luen; Taghavi, Safiyh; McCorkle, Sean; Zhang, Yian-Biao; Blewitt, Michael; Brunecky, Roman; Adney, William; Himmel, Michael; Brumm, Phillip; Drinkwater, Colleen; Mead, David; Tringe, Susannah; van der Lelie, Daniel

Land-use history has a stronger impact on soil microbial community composition than aboveground vegetation and soil properties
2011. Soil Biology and Biochemistry. Jangid, Kamlesh; Williams, Mark A.; Franzluebbers, Alan J.; Schmidt, Thomas M.; Coleman, David C.; Whitman, William B.

Combined Computational and Experimental Approaches to Sequence-Based Design of Protein Thermal Stability
2011. CRC Press. Mitchell JC, Rutkoski TJ, Bannen RM, & Phillips GNJ

Catalytic Conversion of Lignocellulosic Biomass to Fuels: Process Development and Technoeconomic Evaluation
2011. PERGAMON-ELSEVIER SCIENCE LTD. Murat Sen, S.; Henao, Carlos A.; Braden, Drew J.; Dumesic, James A.; Maravelias, Christos T.

Comparative Genomics of Xylose-Fermenting Fungi for Enhanced Biofuel Production
2011. Proceedings of the National Academies of Science. D.J. Wohlbach; A. Kuo; T.K. Sato; K.M. Potts; A.A. Salamov; K.M. LaButti; H. Sun; A. Clum; J.L. Pangilinan; E.A. Lindquist; S. Lucas; A. Lapidus; M. Jin; C. Gunawan; V. Balan; B.E. Dale; T.W. Jeffries; R. Zinkel; K.W. Barry; I.V. Grigoriev; A.P. Gasch

Post-glacial evolution of Panicum virgatum: centers of diversity and gene pools revealed by SSR markers and cpDNA sequences
2011. Springer Netherlands. Zhang, Yunwei; Zalapa, Juan; Jakubowski, Andrew; Price, David; Acharya, Ananta; Wei, Yanling; Brummer, E.; Kaeppler, Shawn; Casler, Michael

iRsp1095: A Genome-scale reconstruction of the Rhodobacter sphaeroides metabolic network
2011. BMC Systems Biology. Saheed Imam; Safak Yilmaz; Ugur Sohmen; Alexander S Gorzalski; Jennifer L Reed; Daniel R Noguera; Timothy J Donohue

Agricultural landscape simplification and insecticide use in the Midwestern United States
2011. Proceedings of the National Academy of Sciences. Meehan, Timothy D.; Werling, Ben P.; Landis, Douglas A.; Gratton, Claudio

Carbon debt of CRP grasslands converted to bioenergy production
2011. Proceeding of the National Academy of Sciences. Gelfand, Ilya; Zenone, T.; Jasrotia, P.; Chen, J.; Hamilton, S.K.; Robertson, G Philip

Advanced Regional Biomass Processing Depots: a key to the logistical challenges of the cellulosic biofuel industry
2011. Biofuels Bioproducts & Biorefining. Eranki, Pragnya; Bals, Bryan D.; Dale, Bruce E.

Advanced Regional Biomass Processing Depots: a key to the logistical challenges of the cellulosic biofuel industry
2011. WILEY-BLACKWELL. Eranki, Pragnya; Bals, Bryan D.; Dale, Bruce E.

Independent Recruitment of an O-Methyltransferase for Syringyl Lignin Biosynthesis in Selaginella moellendorffii
2011. AMER SOC PLANT BIOLOGISTS . Weng, Jing-Ke; Akiyama, Takuya; Ralph, John; Chapple, Clint

Production of Biofuels from Cellulose and Corn Stover Using Alkylphenol Solvents
2011. ChemSusChem. Alonso DM, Wettstein SG, Bond JQ, Root TW, & Dumesic JA

Comparative transcriptome and metabolite analysis of oil palm and date palm mesocarp that differ dramatically in carbon partitioning
2011. NATL ACAD SCIENCES. Bourgis, Fabienne; Kilaru, Aruna; Cao, Xia; Ngando-Ebongue, George-Frank; Drira, Noureddine; Ohlrogge, John B.; Arondel, Vincent

The Charophycean green algae provide insights into the early origins of plant cell walls
2011. The Plant Journal. Sørensen, Iben; Pettolino, Filomena A.; Bacic, Antony; Ralph, John; Lu, Fachuang; O'Neill, Malcom A.; Fei, Zhangzhun; Rose, Jocelyn K.; Domozych, David S.; Willats, William G.T.

Influence of habitat and landscape perenniality on insect natural enemies in three candidate biofuel crops
2011. Biological Control. Werling, Ben P.; Meehan, Timothy D.; Gratton, Claudio; Landis, Douglas A.

Switching to Perennial Energy Crops under Uncertainty and Costly Reversibility
2011. American Journal of Agricultural Economics. Song, F. Zhao, J. Swinton, S. M.

Reactions of Dehydrodiferulates with Ammonia
2011. Org Biomol Chem. Azarpira, Ali; Lu, Fachuang; Ralph, J.

Comment on “Modeling Miscanthus in the Soil and Water Assessment Tool (SWAT) to Simulate Its Water Quality Effects As a Bioenergy Crop”
2011. American Chemical Society. Zhang, Xuesong; Izaurralde, R. César; Arnold, Jeffrey G.; Sammons, Nancy B.; Manowitz, David H.; Thomson, Allison M.; Williams, Jimmy R.

Proteomics-based Compositional Analysis of Complex Cellulase–Hemicellulase Mixtures
2011. Journal of Proteome Research. Chundawat, Shishir P. S.; Lipton, Mary S.; Purvine, Samuel O.; Uppugundla, Nirmal; Gao, Dahai; Balan, Venkatesh; Dale, Bruce E.

Higher US crop prices trigger little area expansion so marginal land for biofuel crops is limited
2011. Energy Policy. Swinton, Scott M.; Babcock, Bruce A.; James, Laura K.; Bandaru, Varaprasad

Restructuring the Crystalline Cellulose Hydrogen Bond Network Enhances Its Depolymerization Rate
2011. American Chemical Society. Chundawat, Shishir P. S.; Bellesia, Giovanni; Uppugundla, Nirmal; da Costa Sousa, Leonardo; Gao, Dahai; Cheh, Albert M.; Agarwal, Umesh P.; Bianchetti, Christopher M.; Phillips, George N.; Langan, Paul; Balan, Venkatesh; Gnanakaran, S.; Dale, Bruce E.

Alkaline peroxide pretreatment of corn stover: effects of biomass, peroxide, and enzyme loading and composition on yields of glucose and xylose
2011. Biotechnology for Biofuels. Banerjee, Goutami; Car, Suzana; Scott-Craig, John; Hodge, D.B.; Walton, J. D.

Bacterial production of free fatty acids from freshwater macroalgal cellulose
2011. Applied Microbiology and Biotechnology. Hoover, Spense W.; Marner, Wesley D., 2nd; Brownson, Amy K.; Lennen, Rebecca M.; Wittkopp, Tyler M.; Yoshitani, un.; Zulkifly, Shahrizim; Graham, Linda E.; Chaston, Sheena D.; McMahon, Katherine D.; Pfleger, Brian F.

De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera)
2011. Nature Biotechnology. Al-Dous, E K; George, B; Al-Mahmoud, M E; Al-Jaber, M Y; Wang, H; Salameh, Y M; Al-Azwani, E K; Chaluvadi, S; Pontaroli, A C; Debarry, J; Arondel, V; Ohlrogge, J B; Saie, I J; Suliman-Elmeer, K M; Bennetzen, J; Kruegger, R; Malek, J A

The expanding field of plant virus ecology: Historical foundations, knowledge gaps, and research directions
2011. Virus Research. Malmstrom, Carolyn M.; Melcher, Ulrich; Bosque-Pérez, Nilsa A.

Investigation of the molecular ion structure for aldononitrile acetate derivatized muramic acid
2011. Journal of Microbiological Methods. Liang, Chao; Zhang, Xudong; Wei, Liping; He, Hongbo; Higbee, Alan J.; Balser, Teri C.

Stereoselective synthesis of 1-O-β-feruloyl and 1-O-β-sinapoyl glucopyranoses
2011. Tetrahedron Letters. Zhu Y & Ralph J

SWAT ungauged: Hydrological budget and crop yield predictions in the Upper Mississippi River Basin.
2011. ASABE. Srinivasan, R.; X. Zhang; and J. Arnold

Conversion for Avicel and AFEX pretreated corn stover by Clostridium thermocellum and simultaneous saccharification and fermentation: Insights into microbial conversion of pretreated cellulosic biomass
2011. Bioresource Technology. Shao, Xiongjun; Jin, Mingjie; Guseva, Anna; Liu, Chaogang; Balan, Venkatesh; Hogsett, David; Dale, Bruce E.; Lynd, Lee

Indirect land use change for biofuels: Testing predictions and improving analytical methodologies
2011. Biomass and Bioenergy. Kim, Seungdo; Dale, Bruce E.

Significant Alteration of Gene Expression in Wood Decay Fungi Postia placenta and Phanerochaete chrysosporium by Plant Species
2011. Applied and environmental microbiology. Vanden Wymelenberg A, et al.

Potential legacy effects of biofuel cropping systems on soil microbial communities in southern Wisconsin
2011. Agricultural Sciences. Liang, C.; Sanford, G. R.; Jackson, R.D.; Balser, T. C.