Publications

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, e1003246+ (2013). [DOI: 10.1371/journal.pcbi.1003246]

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]

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]

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]

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]

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]

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]

Donohue, T.J. "Interview with Professor Timothy Donohue." Biofuels 4,3, 255–258+ (2013). [DOI: 10.4155/bfs.13.11]

Duran, B.E. & 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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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, e27141+ (2013). [DOI: 10.4161/psb.27141]

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]

Gürbüz, E.I., Gallo, J.M., 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]

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]

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]

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]

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]