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
2020
Myers, K.S., Place, M., Noguera, D.R. & Donohue, T.J. "COnTORT: COmprehensive Transcriptomic ORganizational Tool for simultaneously retrieving and organizing numerous gene expression data sets from the NCBI Gene Expression Omnibus database." Microbiology Resource Announcements 9,25, (2020). [DOI: 10.1128/MRA.00587-20]
2020
Myers, K.S., Vera, J.M., Lemmer, K.C., Linz, A.M., Landick, R., Noguera, D.R. & Donohue, T.J. "Genome-wide identification of transcription start sites in two Alphaproteobacteria, Rhodobacter sphaeroides 2.4.1 and Novosphingobium aromaticivorans DSM 12444." Microbiology Resource Announcements 9,36, (2020). [DOI: 10.1128/MRA.00880-20]
2020
Ong, W.K., Courtney, D.K., Pan, S., Andrade, R.B., Kiley, P.J., Pfleger, B.F. & Reed, J.L. "Model-driven analysis of mutant fitness experiments improves genome-scale metabolic models of Zymomonas mobilis ZM4." PLOS Computational Biology 16,8, (2020). [DOI: 10.1371/journal.pcbi.1008137]
2020
Collaborative, O.C.B.E. "1.21: BioFuel Project." in Lab Manual: Introduction to Biotechnology. (Academic Senate for California Community Colleges Online Educational Resource Initiative (ASCCC-OERI), 2020). [DOI: none will be provided]
2020
Oshlag, Z., Ma, Y., Morse, K., Burger, B.T., Lemke, R.A., Karlen, S.D., Myers, K.S., Donohue, T.J. & Noguera, D.R. "Anaerobic degradation of syringic acid by an adapted strain of Rhodopseudomonas palustris." Applied and Environmental Microbiology 86,3, (2020). [DOI: 10.1128/AEM.01888-19]
Conversion
2020
Panchy, N.L., Lloyd, J.P. & Shiu, S.-H. "Improved recovery of cell-cycle gene expression in Saccharomyces cerevisiae from regulatory interactions in multiple omics data." BMC Genomics 21,1, 159+ (2020). [DOI: 10.1186/s12864-020-6554-8]
2020
Park, S. & Ding, S.-Y. "The N-terminal zinc finger of CELLULOSE SYNTHASE6 is critical in defining its functional properties by determining the level of homodimerization in Arabidopsis." The Plant Journal 103,5, 1826-1838+ (2020). [DOI: 10.1111/tpj.14870]
2020
Peris, D., Alexander, W.G., Fisher, K.J., Moriarty, R.V., Basuino, M.G., Ubbelohde, E.J., Wrobel, R.L. & Hittinger, C.T. "Synthetic hybrids of six yeast species." Nature Communications 11,1, 2085+ (2020). [DOI: 10.1038/s41467-020-15559-4]
2020
Petipas, R.H., Bowsher, A.W., Bekkerring, C., Jack, C.N., McLachlan, E.E., White, R.A., Younginger, B.S., Tiemann, L.K., Evans, S.E. & Friesen, M.L. "Interactive effects of microbes and nitrogen on Panicum virgatum root functional traits and patterns of phenotypic selection." International Journal of Plant Sciences 181,1, 20-32+ (2020). [DOI: 10.1086/706198]
Sustainability
2020
Poe, J., Reed, D.E., Abraha, M., Chen, J., Dahlin, K.M. & Desai, A.R. "Geospatial coherence of surface-atmosphere fluxes in the upper Great Lakes region." Agricultural and Forest Meteorology 295, 108188+ (2020). [DOI: 10.1016/j.agrformet.2020.108188]
Sustainability
2020
Ralph, J. "Tricin and tricin-lignins in Medicago versus in monocots." New Phytologist 228,1, 11-14+ (2020). [DOI: 10.1111/nph.16827]
2020
Reed, D.E., Chen, J., Abraha, M., Robertson, P. & Dahlin, K.M. "The shifting role of mRUE for regulating ecosystem production." Ecosystems 23, 359–369+ (2020). [DOI: 10.1007/s10021-019-00407-4]
Sustainability
2020
Ruan, L. & Robertson, P. "No-till establishment improves the climate benefit of bioenergy crops on marginal grasslands." Soil Science Society of America Journal 84,4, 1280-1295+ (2020). [DOI: 10.1002/saj2.20082]
2020
Ryu, J., Kong, L., de Lima, A.E.P. & Maravelias, C.T. "A generalized superstructure-based framework for process synthesis." Computers & Chemical Engineering 133, 106653+ (2020). [DOI: 10.1016/j.compchemeng.2019.106653]
2020
Ryu, J. & Maravelias, C.T. "Efficient generalized shortcut distillation model with improved accuracy for superstructure-based process synthesis." AIChE Journal 66,11, (2020). [DOI: 10.1002/aic.16994]
Deconstruction
2020
Ryu, J. & Maravelias, C.T. "Computationally efficient optimization models for preliminary distillation column design and separation energy targeting." Computers & Chemical Engineering 143, 107072+ (2020). [DOI: 10.1016/j.compchemeng.2020.107072]
Sustainability
2020
Scarborough, M.J., Hamilton, J.J., Erb, E.A., Donohue, T.J. & Noguera, D.R. "Diagnosing and predicting mixed-culture fermentations with unicellular and guild-based metabolic models." mSystems 5,5, (2020). [DOI: 10.1128/mSystems.00755-20]
2020
Scarborough, M.J., Myers, K.S., Donohue, T.J. & Noguera, D.R. "Medium-chain fatty acid synthesis by Candidatus Weimeria bifida, gen. nov., sp. nov., and Candidatus Pseudoramibacter fermentans, sp. nov." Applied and Environmental Microbiology 86,3, (2020). [DOI: 10.1128/AEM.02242-19]
2020
Schwarz, B., Azodi, C.B., Shiu, S.-H. & Bauer, P. "Putative cis-regulatory elements predict iron deficiency responses in Arabidopsis roots." Plant Physiololgy 182,3, 1420-1439+ (2020). [DOI: 10.1104/pp.19.00760]
2020
Sciusco, P., Chen, J., Abraha, M., Lei, C., Robertson, P., Lafortezza, R., Shirkey, G., Ouyang, Z., Zhang, R. & John, R. "Spatiotemporal variations of albedo in managed agricultural landscapes: inferences to global warming impacts (GWI)." Landscape Ecology 35, 1385-1402+ (2020). [DOI: 10.1007/s10980-020-01022-8]
Sustainability
2020
Sharkey, T.D., Preiser, A.L., Weraduwage, S.M. & Gog, L. "Source of 12C in Calvin-Benson cycle intermediates and isoprene emitted from plant leaves fed with 13CO2." Biochemical Journal 477,17, 3237-3252+ (2020). [DOI: 10.1042/BCJ20200480]
2020
Shen, A., Sakai, S. & Rothamer, D. "Parameters for screening SI engine alternative fuels for mixture formation behavior related to particulate matter formation: application to 2-methyl-3-buten-2-ol (methyl butenol, MBO)." in Spring Technical Meeting of the Central States Section of the Combustion Institute. (2020).
Sustainability
2020
Shen, X.-X., Li, Y., Hittinger, C.T., Chen, X.-xin & Rokas, A. "An investigation of irreproducibility in maximum likelihood phylogenetic inference." Nature Communications 11, 6096+ (2020). [DOI: 10.1038/s41467-020-20005-6]
2020
Shen, X.-X., Steenwyk, J.L., Labella, A.L., Opulente, D.A., Zhou, X., Kominek, J., Li, Y., Groenewald, M., Hittinger, C.T. & Rokas, A. "Genome-scale phylogeny and contrasting modes of genome evolution in the fungal phylum Ascomycota." Science Advances 6,45, (2020). [DOI: 10.1126/sciadv.abd0079]
2020
Shen, Z. & Van Lehn, R.C. "Solvent selection for the separation of lignin-derived monomers using the conductor-like screening model for real solvents." Industrial & Engineering Chemistry Research 59,16, 7755-7764+ (2020). [DOI: 10.1021/acs.iecr.9b06086]