Publications

When it comes to interdisciplinary collaboration, the titles of GLBRC publications speak for themselves. Each new year of operation has seen more publications from multiple labs that span our research themes, accelerating the Center's production of the basic research that generates technology to convert cellulosic biomass to advanced biofuels and bioproducts.

Year	Publication	Keywords
2013	Chung, D., Park, D., Myers, K., Grass, J., Kiley, P., Landick, R. & Keleş, S. "dPeak: High resolution identification of transcription factor binding sites from PET and SET ChIP-Seq data." PLOS Computational Biology 9,10, (2013). [DOI: 10.1371/journal.pcbi.1003246] DOI Google Scholar	Conversion
2013	Chylla, R., Van Acker, R., Kim, H., Azarpira, A., Mukerjee, P., Markley, J.L., Storme, V., Boerjan, W. & Ralph, J. "Plant cell wall profiling by fast maximum likelihood reconstruction (FMLR) and region-of-interest (ROI) segmentation of solution-state 2D 1H–13C NMR spectra." Biotechnology for Biofuels 6,45, 1-14+ (2013). [DOI: 10.1186/1754-6834-6-45] DOI Google Scholar	Feedstocks
2013	Cotten, C. & Reed, J.L. "Mechanistic analysis of multi-omics datasets to generate kinetic parameters for constraint-based metabolic models." BMC Bioinformatics 14, 32+ (2013). [DOI: 10.1186/1471-2105-14-32] DOI Google Scholar	Conversion
2013	Cotten, C. & Reed, J.L. "Constraint-based strain design using continuous modifications (CosMos) of flux bounds finds new strategies for metabolic engineering." Biotechnology Journal 8,5, 595-604+ (2013). [DOI: 10.1002/biot.201200316] DOI Google Scholar	Conversion
2013	Culbertson, A., Jin, M., Sousa, L. da C., Dale, B.E. & Balan, V. "In-house cellulase production from AFEX™ pretreated corn stover using Trichoderma reesei RUT C-30." RSC Advances 3,48, 25960-25969+ (2013). [DOI: 10.1039/c3ra44847a] DOI Google Scholar	Deconstruction
2013	de Leon, N., Kaeppler, S.M. & Lauer, J.G. "Breeding maize for lignocellulosic biofuel production." in Bioenergy Feedstocks: Breeding and Genetics. 151-172+ (Wiley Blackwell, 2013). [DOI: 10.1002/9781118609477.ch8] DOI Google Scholar	Feedstocks
2013	Decanio, M.S., Landick, R. & Haft, R.J. "The non-pathogenic Escherichia coli strain W secretes SslE via the virulence-associated type II secretion system beta." BioMed Central Microbiology 13,1, 130+ (2013). [DOI: 10.1186/1471-2180-13-130] DOI Google Scholar	Conversion
2013	Donohue, T.J. "Interview with Professor Timothy Donohue." Biofuels 4,3, 255-258+ (2013). [DOI: 10.4155/bfs.13.11] DOI Google Scholar
2013	Duran, B.E.L. & Kucharik, C.J. "Comparison of two chamber methods for measuring soil trace-gas fluxes in bioenergy cropping systems." Soil Science Society of America Journal 77,5, 1601-1612+ (2013). [DOI: 10.2136/sssaj2013.01.0023] DOI Google Scholar	Sustainability
2013	Egbendewe-Mondzozo, A., Swinton, S.M., Bals, B.D. & Dale, B.E. "Can dispersed biomass processing protect the environment and cover the bottom line for biofuel?" Environmental Science & Technology 47,3, 1695-1703+ (2013). [DOI: 10.1021/es303829w] DOI Google Scholar	Sustainability
2013	Egbendewe-Mondzozo, A., Swinton, S.M., Izaurralde, C., Manowitz, D.H. & Zhang, X. "Maintaining environmental quality while expanding biomass production: sub-regional U.S. policy simulations." Energy Policy 58,June 2013, 518-531+ (2013). [DOI: 10.1016/j.enpol.2013.02.021] DOI Google Scholar	Sustainability
2013	Eranki, P.L., Manowitz, D.H., Bals, B.D., Izaurralde, C., Kim, S. & Dale, B.E. "The watershed-scale optimized and rearranged landscape design (WORLD) model and local biomass processing depots for sustainable biofuel production: integrated life cycle assessments." Biofuels, Bioproducts and Biorefining 7,5, 537-550+ (2013). [DOI: 10.1002/bbb.1426] DOI Google Scholar	Sustainability
2013	Fish, J.A., Chai, B., Wang, Q., Sun, Y., Brown, T., Tiedje, J.M. & Cole, J.R. "FunGene: the functional gene pipeline and repository." Frontiers in Microbiology 4, 291+ (2013). [DOI: 10.3389/fmicb.2013.00291] DOI Google Scholar	Sustainability
2013	Gall, D.L., Ralph, J., Donohue, T.J. & Noguera, D.R. "Benzoyl coenzyme A pathway-mediated metabolism of meta-hydroxy-aromatic acids in Rhodopseudomonas palustris." Journal of Bacteriology 195,18, 4112-4120+ (2013). [DOI: 10.1128/JB.00634-13] DOI Google Scholar	Feedstocks, Conversion
2013	Gallo, J.M.R., Alonso, D.M., Mellmer, M.A., Yeap, J.H., Wong, H.C. & Dumesic, J.A. "Production of furfural from lignocellulosic biomass using Beta Zeolite and biomass-derived solvent." Topics in Catalysis 56, 1775-1781+ (2013). [DOI: 10.1007/s11244-013-0113-3] DOI Google Scholar	Conversion
2013	Gao, D., Chundawat, S.P.S., Sethi, A., Balan, V., Gnanakaran, S. & Dale, B.E. "Increased enzyme binding to substrate is not necessary for more efficient cellulose hydrolysis." Proceedings of the National Academy of Sciences of the United States of America 110,27, 10922-10927+ (2013). [DOI: 10.1073/pnas.1213426110] DOI Google Scholar	Deconstruction
2013	Gao, J., Thelen, K.D. & Hao, X. "Life cycle analyses of corn harvest strategies for bioethanol production." Agronomy Journal 105,3, 705-712+ (2013). [DOI: 10.2134/agronj2012.0420] DOI Google Scholar	Sustainability
2013	Gelfand, I., Sahajpal, R., Zhang, X., Izaurralde, C., Gross, K.L. & Robertson, P. "Sustainable bioenergy production from marginal lands in the US Midwest." Nature 493, 514-517+ (2013). [DOI: 10.1038/nature11811] DOI Google Scholar	Sustainability
2013	Gidda, S.K., Watt, S., Collins-Silva, J., Kilaru, A., Arondel, V., Yurchenko, O., Horn, P.J., James, C.N., Shintani, D., Ohlrogge, J.B., et al. "Lipid droplet-associated proteins (LDAPs) are involved in the compartmentalization of lipophilic compounds in plant cells." Plant Signaling & Behavior 8,11, (2013). [DOI: 10.4161/psb.27141] DOI Google Scholar	Feedstocks
2013	Góngora-Castillo, E. & Buell, R. "Bioinformatics challenges in de novo transcriptome assembly using short read sequences in the absence of a reference genome sequence." Natural Product Reports 30,4, 490-500+ (2013). [DOI: 10.1039/C3NP20099J] DOI Google Scholar	Feedstocks
2013	Gurbuz, E.I., Gallo, J.M.R., Alonso, D.M., Wettstein, S.G., Lim, W.Y. & Dumesic, J.A. "Conversion of hemicellulose into furfural using solid acid catalysts in γ-valerolactone." Angewandte Chemie (International Edition) 53,4, 1270-1274+ (2013). [DOI: 10.1002/anie.201207334] DOI Google Scholar	Conversion
2013	Harun, S., Balan, V., Takriff, M.S., Hassan, O., Jahim, J. & Dale, B.E. "Performance of AFEX™ pretreated rice straw as source of fermentable sugars: the influence of particle size." Biotechnology for Biofuels 6, 40+ (2013). [DOI: 10.1186/1754-6834-6-40] DOI Google Scholar	Deconstruction
2013	Hirsch, C.N. & Buell, R. "Tapping the promise of genomics in species with complex, non-model genomes." Annual Review of Plant Biology 64, 89-110+ (2013). [DOI: 10.1146/annurev-arplant-050312-120237] DOI Google Scholar	Feedstocks
2013	Hoagland, K.C., Ruark, M.D., Renz, M.J. & Jackson, R.D. "Agricultural management of switchgrass for fuel quality and thermal energy yield on highly erodible land in the Driftless Area of southwest Wisconsin." BioEnergy Research 6, 1012-1021+ (2013). [DOI: 10.1007/s12155-013-9335-2] DOI Google Scholar	Sustainability
2013	Horn, P.J., James, C.N., Gidda, S.K., Kilaru, A., Dyer, J.M., Mullen, R.T., Ohlrogge, J.B. & Chapman, K.D. "Identification of a new class of lipid droplet-associated proteins in plants." Plant Physiology 162,4, 1926-1936+ (2013). [DOI: 10.1104/pp.113.222455] DOI Google Scholar	Feedstocks