Keasling Lab plants

PUBLICATIONS BY YEAR

2012201120102009 2008 2007 2006 2005 2004 2003 2002 2001more

2012

E. B. Goh, E. E. Baidoo, J. D. Keasling, and H. R. Beller.  2012.  “Engineering of bacterial methyl ketone synthesis for biofuels.”  Appl. Environ. Microbiol. 78:70-80.

D. Juminaga, E. E. Baidoo, A. M. Redding-Johanson, T. S. Batth, H. Burd, A. Mukhopadhyay, C. J. Petzold, and J. D. Keasling.  2012.  “Modular engineering of L-tyrosine production in Escherichia coli.”  Appl. Environ. Microbiol. 78:89-98.

D. Groff, P. I. Benke, T. S. Batth, G. Bokinsky, C. J. Petzold, P. D. Adams, and J. D. Keasling.  2012.  “Supplementation of intracellular XylR leads to coutilization of hemicellulose sugars.”  Appl. Environ. Microbiol. 78:2221-2229.

Y. Satoh, K. Tajima, M. Munekata, J. D. Keasling, and T. S. Lee.  2012.  “Engineering of a tyrosol-producing pathway, utilizing simple sugar and the central metabolite tyrosine, in Escherichia coli.”  J. Agric. Food Chem. 60:979-984.

P. J. Westfall, D. J. Pitera, J. R. Lenihan, D. Eng, F. Woolard, R. Regentin, T. Horning, Hiroko Tsuruta, D. Melis, A. Owens, S. Fickes, D. Diola, J. D. Keasling, M. D. Leavell, D. McPhee, N. S. Renninger, J. D. Newman, C. J. Paddon.  2012.  “Production of Amorpha-4,11-diene in yeast, and its conversion to dihydroartemisinic acid, precursor to the antimalarial agent artemisinin.”  Proc. Natl. Acad. Sci. USA 109:E111-E118.

Z. Li, J. D. Keasling, and K. Niyogi. 2012. “Overlapping photoprotective function of vitamin E and carotenoids in Chlamydomonas.” Plant Phys. 158:313-323.

S. Kumar, F. M. Hahn, E. Baidoo, T. S. Kahlon, D. F. Wood, C. M. McMahan, K. Cornish, J. D. Keasling, H. Daniell, and M. C. Whalen.  2012.  “Remodeling the isoprenoid pathway in tobacco by expressing the cytoplasmic mevalonate pathway in chloroplasts.”  Met. Eng. 14:19-28.

C. Rautengarten, B. Ebert, M. Ouellet, M. Nafisi, E. E.K. Baidoo, P. Benke, M. Stranne, A. Mukhopadhyay, J. D. Keasling, Y. Sakuragi, and H. V. Scheller.  2012.  “The Arabidopsis deficient in cutin ferulate (DCF) encodes a transferase required for feruloylation of ω-hydroxy fatty acids in cutin polyester.” Plant Phys. 158:654-665.

K. Deng, K. W. George, W. Reindl, J. D. Keasling, P. D. Adams, T. S. Lee, A. K. Singh, and T. R. Northen.  2012.  “Encoding substrates with mass tags to resolve stereospecific reactions using Nimzyme.” Rapid Commun. Mass Spectrom. 26:611-615.

J. Chen, D. Densmore, T. S. Ham, J. D. Keasling, and N. J. Hillson.  2012.  “DeviceEditor visual biological CAD canvas.”  J. Biol. Eng. 6:1. 

J. D. Keasling.  2012.  “Synthetic biology and the development of tools for metabolic engineering.”  Met. Eng. 14:189-195.

F. Zhang, J. M. Carothers, and J. D. Keasling.  2012.  “Design of a dynamic sensor-regulator system for production of chemicals and fuels derived from fatty acids.”  Nat. Biotechnol. 30:354-359.

A. Eudes, A. George, P. Mukerjee, J. S. Kim, B. Pollet, P. I. Benke, F. Yang, P. Mitra, L. Sun, O. P. Cetinkol, S. Chabout, G. Mouille, L. Soubigou-Taconnat, S. Balzergue, S. Singh, B. M. Holmes, A. Mukhopadhyay, J. D. Keasling, B. A. Simmons, C. Lapierre, J. Ralph, D. Loqué.  2012.  “Biosynthesis and incorporation of side-chain-truncated lignin monomers to reduce lignin polymerization and enhance saccharification.”  Plant Biotechnol J.  10:609-620.

X. Xie, J. Kirby, and J. D. Keasling.  2012.  “Functional characterization of four sesquiterpene synthases from Ricinus communis (Caster Bean).”  Phytochemistry 78:20-28.

P. Singh, T. S. Batth, D. Juminaga, R. H. Dahl, J. D. Keasling, P. D. Adams, and C. J. Petzold.  2012.  “Application of targeted proteomics to metabolically engineered Escherichia coli.”  Proteomics 12:1289-1299.

J. L. Park, E. J. Steen, H. Burd, S. S. Evans, A. M. Redding-Johanson, T. Batth, P. I. Benke, P. D’haeseleer, N. Sun, K. L. Sale, J. D. Keasling, C. J. Petzold, A. Mukhopadhyay, S. W. Singer, B. A. Simmons, and J. M. Gladden.  2012.  “A thermophilic ionic liquid-tolerant cocktail for the production of cellulosic biofuels.”  PLoS One 7:e37010. 

Z. Chen, G. D. Friedland, J. H. Pereira, S. A. Reveco, R. Chan, J. I. Park, M. P. Thelen, P. D. Adams, A. P. Arkin, J. D. Keasling, H. W. Blanch, B. A. Simmons, D. Chivian, and S. R. Chhabra.  2012.  “Tracing determinants of dual-substrate specificity in glycoside hydrolase family 5.”  J. Biol. Chem. 287:25335-25343.

Y. Xiao, T. Savchenko, E. E. Baidoo, W. E. Chehab, D. M. Hayden, V. Tolstikov, J. A. Corwin, D. J. Kliebenstein, J. D. Keasling, and K. Dehesh.  2012.  “Retrograde signaling by the plastidial metabolite MEcPP regulates expression of nuclear stress-response genes.”  Cell 149:1525-1535.

M. E. Clark, Z. He, A. M. Redding, M. P. Joachimiak, J. D. Keasling, J. Zhou, A. P. Arkin, A. Mukhopadhyay, and M. W. Fields.  2012.  “Transcriptomic and proteomic analyses of Desulfovibrio vulgaris biofilms: carbon and energy flow contribute to the distinct biofilm growth state.”  BMC Genomics 13:138.

P. P. Peralta-Yahya, F. Zhang, S. B. del Cardayre, and J. D. Keasling.  2012.  “Microbial engineering for the production of advanced biofuels.”  Nature 488:320-328.

J. Perez-Gil, E. M. Uros, S. Sauret-Gueto, L. M. Lois, J. Kirby, M. Nishimoto, E. E. K. Baidoo, J. D. Keasling, A. Boronat, and M. Rodriguez-Concepcion.  2012.  “Mutations in Escherichia coli aceE and rib genes allow survival of strains defective in the first step of the isoprenoid biosynthesis pathway.” PLoS One 7(8):e43775. 

E. A. Rennie, S. F. Hansen, E. Baidoo, M. Hadi, J. D. Keasling, H. Scheller.  2012.  “Three members of the Arabidopsis glycosyltransferase family 8 are xylan glucuronosyltransferases.” Plant Physiol. 159:1408-1417.  

N. J. Hillson, R. D. Rosengarten, and J. D. Keasling.  2012.  “j5 DNA assembly design automation software.”  ACS Syn. Biol. 1:14-21.

J. H. Pereira, E.-B. Goh, J. D. Keasling, H. R. Beller, and P. D. Adams.  2012.  “Structure of FabH and factors affecting the distribution of branched fatty acids in Micrococcus luteus.”  Acta Crystallographica D. 68:1320-1328.

S. Yuzawa, W. Kim, L. Katz, and J. D. Keasling.  2012. “Heterologous production of polyketides by modular type I polyketide synthases in Escherichia coli.Curr. Opin. Biotechnol. 23:725-735.

C. B. Walker, A. M. Redding-Johanson, E. Baidoo, L. Rajeev, Z. He, E. L Hendrickson, M.P. Joachimiak, S. Stolyar, A. P. Arkin, J. A. Leigh, J. Zhou, J. D. Keasling, A. Mukhopadhyay, and D. A. Stahl.  2012.  “Functional response of methanogenic archaea to syntrophic growth.”  ISME J. 6:2045-2055.

H. H. Chou and J. D. Keasling.  2012.  “Five-carbon alcohols are produced from isopentenyl diphosphate using a synthetic pathway.”  Appl. Environ. Microbiol. 78:7829-7855.

D. Chiniquy, V. Sharma, A. Schultink, E. E. Baidoo, C. Rautengarten, K. Cheng, A. Carroll, P. Ulvskov, J. Harholt, J. D. Keasling, M. Pauly, H. V. Scheller, and P. C. Ronald.  2012.  “XAX1 from glycosyltransferase family 61 mediates xylosyltransfer to rice xylan.”  Proc. Natl. Acad. Sci. USA 109:17117-17122.

T. S. Ham, Z. Dmytriv, H. Plahar, J. Chen, N. J. Hillson, and J. D. Keasling.  2012.  “Design, implementation and practice of JBEI-ICE: an open source biological part registry platform and tools.”  Nucl. Acids Res. 40:e141 (doi: 10.1093/nar/gks531).

F. Zhang, M. Ouellet, T. Batth, P. D. Adams, C. J. Petzold, A. Mukhopadhyay, and J. D. Keasling.  2012.  “Enhancing fatty acid production by the expression of the regulatory transcription factor FadR.”  Met. Eng. 14:653-660.

A. E. Mckee, B. J. Rutherford, D. C. Chivian, E. K. Baidoo, D. Juminaga, D. Kuo, P. I. Benke, J. A. Dietrich, S. M. Ma, A. P. Arkin, C. J. Petzold, P. D. Adams, J. D. Keasling and S. R. Chhabra.  2012.  “Manipulation of the carbon storage regulator system for metabolite remodeling and biofuel production in Escherichia coli.”  Microb. Cell Fact. 11:79 (doi:10.1186/1475-2859-11-79). 

J. D. Keasling, A. Mendoza, and P. S. Baran. 2012. “Synthesis: A constructive debate.”  Nature 492:188-189. 

Y. Satoh, K. Tajima, M. Munekata, J. D. Keasling, and T. S. Lee.  2012.  “Engineering of L-tyrosine oxidation in Escherichia coli and microbial production of hydroxytyrosol.”  Met. Eng. 14:603-610.

J. D. Keasling. 2012. “Engineering biology for drugs and fuels.” Proc. Amer. Philosoph. Soc. 156:283-294. 

Y. Kung, W. Runguphan, and J. D. Keasling. 2012. “From fields to fuels: recent advances in the microbial production of biofuels.”  ACS Synth. Biol. 1:498-513.

S. M. Paap, T. H. West, D. K. Manley, E. J. Steen, H. R. Beller, J. D. Keasling, D. C. Dibble, S. Chana, and B. A. Simmons.  2013.  “Biochemical production of ethanol and fatty acid ethyl esters from switchgrass: A comparative analysis of environmental and economic performance.”  Biomass Bioenergy 49:49-62.

B. Ozaydin, H. Burd, T. S. Lee, and J. D. Keasling.  2013.  “Carotenoid-based phenotypic screen of the yeast deletion collection reveals new genes with roles in isoprenoid production.”  Met. Eng15:174-183.

J. A. Dietrich, D. L. Shis, A. Alikhani, and J. D. Keasling.  2013.  “Transcription factor-based screens and synthetic selections for microbial small-molecule biosynthesis.”  ACS Synth. Biol. 2:47-58. 

S. Yuzawa, N. Chiba, L. Katz, and J. D. Keasling.  2012.  “Construction of a part of a 3-hydroxypropionate cycle for heterologous polyketide biosynthesis in Escherichia coli.” Biochemistry in press.

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