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	Beissinger, T.M., Hirsch, C.N., Sekhon, R.S., Foerster, J.M., Johnson, J.M., Muttoni, G., Vaillancourt, B., Buell, R., Kaeppler, S.M. & de Leon, N. "Marker density and read-depth for genotyping populations using genotyping-by-sequencing." Genetics 193,4, 1073-1081+ (2013). [DOI: 10.1534/genetics.112.147710] DOI Google Scholar	Feedstocks
2013	Bianchetti, C.M., Brumm, P., Smith, R.W., Dyer, K., Hura, G.L., Rutkoski, T.J. & Phillips, G.N. "Structure, dynamics, and specificity of endoglucanase D from Clostridium cellulovorans." Journal of Molecular Biology 425,22, 4267-4285+ (2013). [DOI: 10.1016/j.jmb.2013.05.030] DOI Google Scholar	Deconstruction
2013	Bianchetti, C.M., Harmann, C.H., Takasuka, T.E., Hura, G.L., Dyer, K. & Fox, B.G. "Fusion of dioxygenase and lignin-binding domains in a novel secreted enzyme from cellulolytic Streptomyces sp. SirexAA-E." Journal of Biological Chemistry 288,25, 18574-18587+ (2013). [DOI: 10.1074/jbc.M113.475848] DOI Google Scholar	Deconstruction
2013	Brumm, P.J. "Bacterial genomes: what they teach us about cellulose degradation." Biofuels 4,6, 669-681+ (2013). [DOI: 10.4155/bfs.13.44] DOI Google Scholar	Deconstruction
2013	Caes, B.R., Van Oosbree, T.R., Lu, F., Ralph, J., Maravelias, C.T. & Raines, R.T. "Simulated moving bed chromatography: separation and recovery of sugars and ionic liquid from biomass hydrolysates." ChemSusChem 6, 2083-2089+ (2013). [DOI: 10.1093/bioinformatics/btt357] DOI Google Scholar	Feedstocks, Deconstruction, Conversion
2013	Chandrasekaran, A., Deng, K., Koh, C.-Y., Takasuka, T.E., Bergeman, L.F., Fox, B.G., Adams, P.D. & Singh, A.K. "A universal flow cytometry assay for screening carbohydrate-active enzymes using glycan microspheres." Chemical Communications 49, 5441-5443+ (2013). [DOI: 10.1039/C3CC39155H] DOI Google Scholar	Deconstruction
2013	Chen, X., Alonso, A.P. & Shachar-Hill, Y. "Dynamic metabolic flux analysis of plant cell wall synthesis." Metabolic Engineering 18, 78-85+ (2013). [DOI: 10.1016/j.ymben.2013.04.006] DOI Google Scholar	Feedstocks
2013	Christopherson, M.R. & Suen, G. "Nature's bioreactor: the rumen as a model for biofuel production." Biofuels 4,5, 511-521+ (2013). [DOI: 10.4155/bfs.13.36] DOI Google Scholar	Deconstruction
2013	Christopherson, M.R., Suen, G., Bramhacharya, S., Jewell, K.A., Aylward, F.O., Mead, D. & Brumm, P.J. "The genome sequences of Cellulomonas fimi and “Cellvibrio gilvus” reveal the cellulolytic strategies of two facultative anaerobes, transfer of “Cellvibrio gilvus” to the genus Cellulomonas, and proposal of Cellulomonas gilvus sp. nov." PLOS ONE 8,1, (2013). [DOI: 10.1371/journal.pone.0053954] DOI Google Scholar	Deconstruction
2013	Chundawat, S.P.S., Bals, B., Campbell, T., Sousa, L., Gao, D., Jin, M., Eranki, P.L., Garlock, R., Teymouri, F., Balen, V., et al. "Primer on ammonia fiber expansion pretreatment." in Aqueous Pretreatment of Plant Biomass for Biological and Chemical Conversion to Fuels and Chemicals. 173-204+ (John Wiley & Sons, Ltd., 2013). [DOI: 10.1002/9780470975831.ch9] DOI Google Scholar	Deconstruction
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