PUBLICATIONS BY YEAR

2012 2011 2010 2009 2008 2007 2006 2005 2004 2003 2002 2001 more

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. Eng. 15:174-183.

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.

2011

W. Shui, C. J. Petzold, A. M. Redding, J. Liu, A. Pitcher, L. Sheu, C. R. Bertozzi, and J. D. Keasling. 2011. “Organelle membrane proteomics reveals differential influence of mycobacterial lipoglycans on macrophage phagosome maturation and autophagosome accumulation.” J. Proteome Res. 10:339-348.
C. J. Joshua, R. Dahl, P. I. Benke, and J. D. Keasling. 2011. “Absence of diauxie during simultaneous utilization of glucose and xylose by Sulfolobus acidocaldarius.” J. Bacteriol. 193:1293-1301.
A. M. Redding-Johanson, T. S. Batth, R. Chan, R. Krupa, H. L. Szmidt, P. D. Adams, J. D. Keasling, T. S. Lee, A. Mukhopadhyay, C. J. Petzold. 2011. “Targeted proteomics for metabolic pathway optimization: application to terpene production.” Metab. Eng. 13:194-203.
M. J. Dunlop, H. L. Szmidt, H. C. Chu, J. D. Keasling, M. Hadi, A. Mukhopadhyay. 2011. “A targeted bioprospecting approach for engineering microbial biofuel tolerance.” Mol. Sys. Biol. 7:487.
M. Hajimorad, P. R. Gray, J. D. Keasling. 2011. “A framework and model system to investigate linear system behavior in Escherichia coli.” J. Biol. Eng. 5:3.
F. Zhang and J. D. Keasling. 2011. “Biosensors and their applications in microbial metabolic engineering.” Trends Microbiol. 19:323-329.
S. R. Chhabra, M. P. Joachimiak, C. J. Petzold, G. M. Zane, M. N. Price, S. A. Reveco, V. Fok, A. R. Johanson, T. S. Batth, M. Singer, J. M. Chandonia, D. Joyner, T. C. Hazen, A, P. Arkin, J. D. Wall, A. K. Singh, and J. D. Keasling. 2011. “Towards a rigorous network of protein-protein interactions of the model sulfate reducer Desulfovibrio vulgaris Hildenborough.” PLoS One 6:e21470.
J. Nielsen and J. D. Keasling. 2011. “Synergies between synthetic biology and metabolic engineering.” Nat. Biotechnol. 29:693-695.
T. S. Lee, R. A. Krupa, F. Zhang, M. Hajimorad, W. J. Holtz, N. Prasad, S. K. Lee, and J. D. Keasling. 2011. “BglBrick vectors and datasheets: a synthetic biology platform for gene expression.” J. Biol. Eng. 5:12.
P. P. Peralta-Yahya, M. Ouellet, R. Chan, A. Mukhopadhyay, J. D. Keasling, and T. S. Lee. 2011. “Identification and microbial production of a terpene-based advanced biofuel.” Nat. Comm. 2:483.
S. M. Ma, D. E. Garcia, A. M. Redding-Johanson, G. D. Friedland, R. Chan, T. S. Batth, J. R. Haliburton, D. Chivian, J. D. Keasling, C. J. Petzold, T. S. Lee, S. R. Chhabra. 2011. “Optimization of a heterologous mevalonate pathway through use of variant HMG-CoA reductases.” Met. Eng. 13:588-597.
S. R. Chhabra, G. Butland, D. Elias, J.-M. Chandonia, O.-Y. Fok, T. Juba, A. Gorur, S. Allen, C. M. Leung, K. Keller, S. Reveco, G. Zane, E. Semkiw, R. Prathapam, B. Gold, M. Singer, M. Ouellet, E. Szakal, D. Jorgens, M. Price, E. Witkowska, H. Beller, T. C. Hazen, M. D. Biggin, M. Auer, J. Wall, and J. D. Keasling. 2011. "Generalized schemes for high throughput manipulation of the Desulfovibrio vulgaris Hildenborough genome". Appl. Environ. Microbiol. 77:7595-7604.
H. R. Beller, E. B. Goh, and J. D. Keasling. 2011. “Definitive alkene identification needed for in vitro studies with ole (olefin biosynthesis) proteins.” J. Biol. Chem. 286:1e11.
M. Ouellet, S. Datta, D. C. Dibble, P. R. Tamrakar, P. I. Benke, C. Li, S. Singh, K. L. Sale, P. D. Adams, J. D. Keasling, B. A. Simmons, B. M. Holmes and A. Mukhopadhyay. 2011. “Impact of ionic liquid pretreated plant biomass on Saccharomyces cerevisiae growth and biofuel production.” Green Chem. 13:2743-2749.
F. Zhang, S. Rodriquez, and J. D. Keasling. 2011. “Metabolic engineering of microbial pathways for advanced biofuels production.” Curr. Opin. Biotechnol. 22:775-783.
R. P. McAndrew, P. P. Peralta-Yahya, A. DeGiovanni, J. H. Pereira, M. Z. Hadi, J. D. Keasling, and P. D. Adams. 2011. “Structure of a three-domain sesquiterpene synthase: a prospective target for advanced biofuels production.” Structure 19:1876-1884.
G. Bokinsky, P. Peralta-Yahya, A. George, B. M. Holmes, E. J. Steen, J. Dietrich, T. S. Lee, D. Tullman-Ercek, C. Voigt, B. A. Simmons, J. D. Keasling. 2011. “Synthesis of three advanced biofuels from ionic liquid-pretreated switchgrass using engineered Escherichia coli.” Proc. Natl. Acad. Sci. USA 108:19949-19954.
J. M. Carothers, J. A. Goler, D. Juminaga, and J. D. Keasling. 2011. “Model-driven engineering of RNA devices to quantitatively program gene expression.” Science 334:1716-1719.
A. George, K. Tran, T. J. Morgan, P. Benke, C. Berrueco, E. Lorente, B. Wu, J. D. Keasling, B. A. Simmon, and B. Holmes. 2011. "The effect of ionic liquid cation and anion combinations on the macromolecular structure of lignins." Green Chemistry 13:3375-3385.

2010

M. Ouellet, P. D. Adams, J. D. Keasling, and A. Mukhopadhyay. 2010. “A rapid and inexpensive method for microarray gene expression analysis.” BMC Biotechnol. 9:97 (doi:10.1186/1472-6750-9-97).
E. J. Steen, Y. Kang, G. Bokinsky, Z. Hu, A. Schirmer, A. McClure, S. B. del Cardayre, and J. D. Keasling. 2010. “Microbial production of fatty acid-derived fuels and chemicals from plant biomass.” Nature 463:559-562.
W. J. Holtz and J. D. Keasling. 2010. “Engineering static and dynamic control of synthetic pathways.” Cell 140:19-23.
H. R. Beller, E.-B. Goh, and J. D. Keasling. 2010. “Genes involved in long-chain alkene biosynthesis in Micrococcus luteus.” Appl. Environ. Microbiol. 76:1212-1223.
J. Anderson, J. E. Dueber, M. Leguia, G. C. Wu, J. A Goler, A. P. Arkin, J. D. Keasling. 2010. “BglBricks: A flexible standard for biological part assembly.” J. Biol. Eng. 4:1-12.
Z. He, A. Zhou, E. Baidoo, Q. He, M. P. Joachimiak, P. Benke, R. Phan, A. Mukhopadhyay, C. L. Hemme, K. Huang, E. J. Alm, M. W. Fields, J. Wall, D. Stahl, T. C. Hazen, J. D. Keasling, A. P. Arkin, and J. Zhou. 2010. “Global transcriptional, physiological and metabolite analyses of Desulfovibrio vulgaris Hildenborough responses to salt adaptation.” Appl. Environ. Microbiol. 76:1574-1586.
P. P. Peralta-Yahya and J. D. Keasling. 2010. “Advanced biofuel production in microbes.” Biotechnol. J. 5:147-162.
A. S. Shaikh, Y. J. Tang, A. Mukhopadhyay, H. G. Martín, J. Gin, P. Benke, and J. D. Keasling. 2010. “Study of stationary phase metabolism via isotopomer analysis of amino acids from an isolated protein.” Biotechnol. Prog. 26:52-56.
B. J. Rutherford, R. H. Dahl, R. E. Price, H. L. Szmidt, P. L. Benke, A. Mukhopadhyay, and J. D. Keasling. 2010. “Functional genomic study of exogenous n-butanol stress in Escherichia coli.” Appl. Environ. Microbiol. 76:1935-1945.
J. M. Carothers, J. A. Goler, Y. Kapoor, L. Lara, and J. D. Keasling. 2010. “Selecting RNA aptamers for synthetic biology: investigating magnesium dependence and predicting binding affinity.” Nucl. Acids Res. 38:2736-2747.
J. A. Dietrich, A. E. McKee, and J. D. Keasling. 2010. “High-throughput metabolic engineering: advances in small-molecule screening and selection.” Annu. Rev. Biochem. 79:563-590.
M. de la Pena Mattozzi and J. D. Keasling. 2010. “Rationally engineered biotransformation of p-nitrophenol.” Biotechnol. Prog. 26:616-621.
H. V. Scheller, S. Singh, H. Blanch, and J. D. Keasling. 2010. “The Joint BioEnergy Institute (JBEI): Developing new biofuels by overcoming biomass recalcitrance.” Bioenerg. Res. 3:105-107.
J. Kirby, M. Nishimoto, J. G. Park, S. T. Withers, F. Nowroozi, D. Behrendt, E. J. Rutledge, J. L. Fortman, H. E. Johnson, J. V. Anderson, and J. D. Keasling. 2010. “Cloning of casbene and neocembrene synthases from Euphorbiaceae plants and expression in Saccharomyces cerevisiae.” Phytochem. 71:1466-1473.
L. Prach, J. Kirby, J. D. Keasling, T. Alber. 2010. “Diterpene production in Mycobacterium tuberculosis.” FEBS J. 277:3588-3595.
M. J. Dunlop, J. D. Keasling, and A. Mukhopadhyay. 2010. “A model for improving microbial biofuel production using a synthetic feedback loop.” Syst. Synth. Biol. 4:95-104.
C. Wang, S. H. Yoon, A. A. Shah, Y. R. Chung, J. Y. Kim, E. S. Choi, J. D. Keasling, and S. W. Kim. 2010. “Farnesol production from Escherichia coli by harnessing the exogenous mevalonate pathway.” Biotechnol. Bioeng. 107:421-429.
Q. He, Z. He, D. C. Joyner, M. Joachimiak, M. N. Price, Z. K. Yang, H.-C. B. Yen, C. L. Hemme, W. Chen, M. M. Fields, D. A. Stahl, J. D. Keasling, M. Keller, A. P. Arkin, T. C. Hazen, J. D. Wall, and J. Zhou. 2010. “Impact of elevated nitrate on sulfate-reducing bacteria: a comparative study of Desulfovibrio vulgaris.” ISME J. 4:1386-1397.
A. Zhou, Z. He, A. M. Redding-Johanson, A. Mukhopadhyay, C. L. Hemme, M. P. Joachimiak, F. Lou, Y. Deng, K. S. Bender, Q. He, J. D. Keasling, D. A. Stahl, M. W. Fields, T. C. Hazen, A. P. Arkin, J. D. Wall, and J. Zhou. 2010. “Hydrogen peroxide-induced oxidative stress responses in Desulfovibrio vulgaris Hildenborough.” Environ. Microbiol. 12:2645-2657.
J. D. Keasling. 2010. “Manufacturing molecules through metabolic engineering.” Science 330:1355-1358.
C. Rautengarten, E. Baidoo, J. D. Keasling and H. V. Scheller. 2010. “A simple method for enzymatic synthesis of unlabeled and radiolabeled hydroxycinnamate-CoA.” Bioenergy Res. 3:115-122.
A. Eudes, E. E. Baidoo, F. Yang, H. Burd, M. Z. Hadi, F. W. Collins, J. D. Keasling, and D. Loqué. 2010. “Production of tranilast [N-(3',4'-dimethoxycinnamoyl)-anthranilic acid] and its analogs in yeast Saccharomyces cerevisiae.” Appl. Microbiol. Biotechnol. 89:989-1000.

2009

J. R. Anthony, L. C. Anthony, F. Nowroozi, G. Kwon, J. D. Newman, and J. D. Keasling. 2009. “Optimization of the mevalonate-based isoprenoid biosynthetic pathway in E. coli for production of the anti-malarial drug precursor amorpha-4,11-diene.” Met. Eng. 11:13-19.
D. Lubertozzi and J. D. Keasling. 2009. “Developing Aspergillus as a host for heterologous expression.” Biotechnol. Adv. 27:53-75.
W. Shui, S. A. Gilmore, L. Sheu, J. Liu, J. D. Keasling, and C. R. Bertozzi. 2009. Quantitative proteomic profiling of host-pathogen interactions: the macrophage response to Mycobacterium tuberculosis. J. Proteome Res. 8:282-289.
Y. J. Tang, H. G. Martin, P. S. Dehal, A. Deutschbauer, X. Llora, A. Meadows, A. Arkin, and J. D. Keasling. 2009. “Metabolic flux analysis of Shewanella spp. reveals evolutionary robustness in central carbon metabolism.” Biotechnol. Bioeng. 102:1161-1169.
Y. J. Tang, H. Garcia Martin, S. Myers, S. Rodriguez, E. E. K. Baidoo, and J. D. Keasling. 2009. “Advances in analysis of microbial metabolic fluxes via 13C isotopic labeling.” Mass Spec. Rev. 28:362-375.
H. Tsuruta, C. J. Paddon, D. Eng, J. R. Lenihan, T. Horning, L. C. Anthony, R. Regentin, J. D. Keasling, N. S. Renninger, and J. D. Newman. 2009. “High-level production of amorpha-4,11-diene, a precursor of the antimalarial agent artemisinin, in Escherichia coli.” PLOS One 4:e4489 doi:10.1371.
Y. J. Tang, R. Sapra, D. Joyner, T. C. Hazen, S. Myers, D. Reichmuth, H. Blanch, and J. D. Keasling. 2009. “Analysis of metabolic pathways and fluxes in a newly discovered thermophilic and ethanol-tolerant Geobacillus strain.” Biotechnol. Bioeng. 102:1377-1386.
W. D. Marner, A. Shaikh, S. J. Muller, and J. D. Keasling. 2009. “Enzyme immobilization via silaffin-mediated autoencapsulation in a biosilica support.” Biotech. Prog. 25:417-423.
J. Dietrich, Y. Yoshikuni, K. Fisher, F. Woolard, D. Ockey, D. McPhee, N. Renninger, M. Chang, D. Baker, and J. D. Keasling. 2009. “A novel semi-biosynthetic route for artemisinin production using engineered substrate-promiscuous P450BM3.” ACS Chem. Biol. 4:261-267.
J. Kirby and J. D. Keasling. 2009. “Biosynthesis of plant isoprenoids: perspectives for microbial engineering.” Annu. Rev. Plant Biol. 60:335.355.
D. A. Elias, A. Mukhopadhyay, M. P. Joachimiak, E. C. Drury, A. M. Redding, H. C. Yen, M. W. Fields, T. C. Hazen, A. P. Arkin, J. D. Keasling, J. D. Wall. 2009. “Expression profiling of hypothetical genes in Desulfovibrio vulgaris leads to improved functional annotation.” Nucl. Acids Res. 37:2926-2939.
S. H. Yoon, S. H. Lee, A. Das, H. K. Ryu, H. J. Jang, J. Y. Kim, D. K. Oh, J. D. Keasling, and S. W. Kim. 2009. “Combinatorial expression of bacterial whole mevalonate pathway for production of beta-carotene in E. coli.” J. Biotechnol. 140:218-226.
Y. J. Tang, W. Shui, S. Myers, X. Feng, C. Bertozzi, J. D. Keasling. 2009. “Central metabolism in Mycobacterium smegmatis during the transition from O(2)-rich to O (2)-poor conditions as studied by isotopomer-assisted metabolite analysis.” Biotechnol. Prog. 31:1233-1240.
J. E. Dueber, G. C. W, G. R. Malmirchegini, T. S. Moon, C. J. Petzold, A. V. Ullal, K. J. Prather, and J. D. Keasling. 2009. “Synthetic protein scaffolds provide modular control over metabolic flux.” Nat. Biotechnol. 27:753-759.
Y. J. Tang, S. Yi, W.-Q. Zhuang, S. H. Zinder, J. D. Keasling, L. Alvarez-Cohen. 2009. “Investigation of carbon metabolism in Dehalococcoides ethenogenes strain 195 using isotopomer and transcriptomic analyses.” J. Bacteriol. 191:5224-5231.
Z. Li, T. K. Ahn, T. J. Avenson, M. Ballottari, J. A. Cruz, D. M. Kramer, R. Bassi, G. R. Fleming, J. D. Keasling, and K. K. Niyogi. 2009. “Lutein accumulation in the absence of zeaxanthin restores nonphotochemical quenching in the Arabidopsis thaliana npq1 mutant.” Plant Cell 21:1798-1812.
Y. J. Tang, H. G. Martin, A. Deutschbauer, X. Feng, R. Huang, X. Liora, A. Arkin, and J. D. Keasling. 2009. “Invariability of central metabolic flux distribution in Shewanella oneidensis MR-1 under environmental or genetic perturbations.” Biotechnol. Prog. 25:1254-1259.
J. M. Carothers, J. A. Goler, and J. D. Keasling. 2009. “Chemical synthesis using synthetic biology.” Curr. Opin. Biotechnol. 20:498-503.

2008

H. W. Blanch, P. D. Adams, K. M. Andrews-Cramer, W. B. Frommer, B. A. Simmons, and J. D. Keasling. 2008. “Addressing the need for alternative transportation fuels: the Joint BioEnergy Institute.” ACS Chem. Biol. 3:17-20.
W. D. Marner, A. S. Shaikh, S. J. Muller, and J. D. Keasling. 2008. “Morphology of artificial silica matrices formed via autosilification of a silaffin/protein polymer chimera.” Biomacromol. 9:1-5.
J. D. Keasling. 2008. “Synthetic biology for synthetic chemistry.” ACS Chem. Biol. 3:64-76.
A. S. Shaikh, Y, J. Tang, A. Mukhopadhyay, and J. D. Keasling. 2008. “Isotopomer distributions in amino acids from a high expressed protein as a proxy for those from total protein.” Anal. Chem. 80:886-890.
J. D. Keasling and H. Chou. 2008, “Metabolic engineering delivers next-generation biofuels.” Nat. Biotechnol. 26:298-299.
D. M. Wolf, L. Fontaine-Bodin, I. Bischofs, G. Price, J. Keasling, and A. P. Arkin. 2008. “Memory in microbes: quantifying history-dependent behavior in a bacterium.” PLoS ONE. 3:e1700.
J. Kirby, D. W. Romanini, E. M. Paradise, and J. D. Keasling. 2008. “Engineering triterpene production in Saccharomyces cerevisiae – beta-amyrin synthase from Artemisia annua.” FEBS J. 275:1852-1859.
L. Kizer, D. J. Pitera, B. Pfleger, and J. D. Keasling. 2008. “Functional genomics for pathway optimization: application to isoprenoid production.” Appl. Environ. Microbiol. 74:3229-3241.
E. E. K. Baidoo, P. I. Benke, C. Neususs, M. Pelzing, G. Kruppa, J. A. Leary, and J. D. Keasling. 2008. “Capillary electrophoresis-Fourier transform ion cyclotron resonance mass spectrometry for the identification of cationic metabolites via a pH-mediated stack-transient isotrachophoretic method.” Anal. Chem. 80:3112-3122.
E. M. Paradise, J. Kirby, R. Chan, and J. D. Keasling. 2008. “Redirection of flux through the FPP branch-point in Saccharomyces cerevisiae by downregulating squalene synthase.” Biotechnol. Bioeng. 100:371-378.
A. Mukhopadhyay, A. M. Redding, B. J. Rutherford, and J. D. Keasling. 2008. “Importance of systems biology in engineering microbes for biofuel production.” Curr. Opin. Biotechnol. 19:228-234.
D. E. Garcia, E. E. Baidoo, P. I. Benke, F. Pingitore, Y. J. Tang, S. Villa, and J. D. Keasling. 2008. “Separation and mass spectrometry in microbial metabolomics.” Curr. Opin. Microbiol. 11:233-239.
J. L. Fortman, S. Chhabra, A. Mukhopadhyay, H. Chou, T. S. Lee, E. Steen, and J. D. Keasling. 2008. “Biofuel alternatives to ethanol: pumping the microbial well.” Trends in Biotechnology. 26:375-381.
S. P. Gaucher, A. M. Redding, A. Mukhopadhyay, J. D. Keasling, and A. K. Singh. 2008. “Post-translational modifications of Desulfovibrio vulgaris Hildenborough sulfate reduction pathway proteins.” J. Proteome Res. 7:2320-2331.
Y. Yoshikuni, J. A. Dietrich, F. F. Nowroozi, P. C. Babbitt, and J. D. Keasling. 2008. “Redesigning enzymes based on adaptive evolution for optimal function in synthetic metabolic pathways.” Chem. Biol. 15:607-618.
T. S. Ham, S. K. Lee, J. D. Keasling, and A. P. Arkin. 2008. “Design and construction of a double inversion recombination switch for heritable sequential genetic memory.” Plos One 3:e2815.
J. Kirby and J. D. Keasling. 2008. “Metabolic engineering of microorganisms for isoprenoid production.” Nat. Prod. Rep. 25:656-661.
J. D. Keasling. 2008. “From yeast to alkaloids” Nat. Chem. Biol. 4:524-525.
S. K. Lee and J. D. Keasling. 2008. “Heterologous protein production in Escherichia coli using the propionate-inducible pPro system by conventional and auto-induction methods.” Prot. Exp. Purif. 61:197-203.
D. Luberbozzi and J. D. Keasling. 2008. “Expression of a synthetic Artemisia annua amorphadiene synthase in Aspergillus nidulans yields altered product distribution.” J. Ind. Microbiol. Biotechnol. 35:1191-1198.
W. Shui, L. Sheu, J. Liu, B. Smart, C. J. Petzold, T. Y. Hsieh, A. Pitcher, J. D. Keasling, and C. R. Bertozzi. 2008. “Membrane proteomics of phagosomes suggests a connection to autophagy.” Proc. Natl. Acad. Sci. USA 105:16952-16957.
S. K. Lee, H. Chou, T. S. Ham, T. S. Lee and J. D. Keasling. 2008. “Metabolic engineering of microorganisms for biofuels production: from bugs to synthetic biology to fuels.” Curr. Opin. Biotechnol. 19:556-563.
D.-K. Ro, M. Ouellet, E. M. Paradise, H. Burd, D. Eng, C. J. Paddon, J. D. Newman, and J. D. Keasling. 2008. “Induction of multiple pleiotropic drug resistance genes in yeast engineered to produce an increased level of antimalarial drug precursor, artemisinic acid.” BMC Biotechnol. 8:83 (doi:10.1186/1472-6750-8-83).
E. J. Steen, R. Chan, N. Prasad, S. Myers, C. J. Petzold, A. Redding, M. Ouellet, and J. D. Keasling. 2008. “Metabolic engineering of Saccharomyces cerevisiae for the production of n-butanol.” Microb. Cell Fact. 7:36.

2007

Y. J. Tang, A. L. Meadows, and J. D. Keasling. 2007. “A kinetic model describing Shewanella oneidensis MR-1 growth, substrate consumption, and product secretion”. Biotechnol. Bioeng. 96:125-133.
B.F. Pfleger, D. J. Pitera, J. D. Newman, V. J. J. Martin, and J. D. Keasling. 2007. “Microbial sensors for small molecules: development of a mevalonate biosensor.” Metab. Eng. 9:30-38.
S. T. Withers and J. D. Keasling. 2007. “Biosynthesis and engineering of isoprenoid small molecules.” Appl. Microbiol. Biotechnol. 73:980-990.
Y. J. Tang, A. L. Meadows, J. Kirby, and J. D. Keasling. 2007. “Anaerobic central metabolic pathways in Shewanella oneidensis MR-1 reinterpreted in the light of isotopic metabolite labeling.” J. Bacteriol. 189:894-901.
Y. J. Tang, F. Pingitore, A. Mukhopadhyay, R. Phan, T. C. Hazen, and J. D. Keasling. 2007. “Pathway confirmation and flux analysis of central metabolic pathways in Desulfovibrio vulgaris Hildenborough using GC-MS and FT-ICR mass spectrometry. J. Bacteriol. 189:940-949.
Y. J. Tang, J. S. Hwang, D. E. Wemmer, and J. D. Keasling. 2007. “The Shewanella oneidensis MR-1 fluxome under various oxygen conditions.” Appl. Environ. Microbiol. 73:718-729.
S. H. Yoon, J. E. Kim, S. H. Lee, H. M. Park, M. S. Choi, J. Y. Kim, S. H. Lee, Y. C. Shin, J. D. Keasling, and S. W. Kim. 2007. “Engineering the lycopene synthetic pathway in E. coli by comparison of the carotenoid genes of Pantoea agglomerans and Pantoea ananatis.” Appl. Microbiol. Biotechnol. 74:131-139.
Y. Shiba, E. M. Paradise, J. Kirby, D.-K. Ro, and J. D. Keasling. 2007. “Engineering of the pyruvate dehydrogenase bypass in Saccharomyces cerevisiae for high-level production of isoprenoids.” Metab. Eng. 9:160-168.
D. J. Pitera, C. J. Paddon, J. D. Newman, and J. D. Keasling. 2007. “Balancing a heterologous mevalonate pathway for improved isoprenoid production in Escherichia coli.” Metab. Eng. 9:193-207.
Y. J. Tang, J. M. Ashcroft, D. Chen, G. Min, C. Kim, B. Murkhejee, C. Larabell, J. D. Keasling, and F. F. Chen. 2007. “Charge-associated effects of fullerene derivatives on microbial structural integrity and central metabolism.” Nanoletters 7:754-760.
F. Pingitore, Y. Tang, G. H. Kruppa, and J. D. Keasling. 2007. “Analysis of amino acid isotopomers by FT-ICR MS.” Anal. Chem. 79:2483-2490.
Y. Yoshikuni and J. D. Keasling. 2007. “Pathway engineering by designed divergent evolution.” Curr. Opin. Chem. Biol. 11:233-239.
M. C. Y. Chang, R. A. Eachus, W. Trieu, D.-K. Ro, and J. D. Keasling. 2007. “Engineering Escherichia coli for production of functionalized terpenoids using plant P450s.” Nature Chem. Biol. 3:274-277.
Y. J. Tang, R. Chakraborty, H. G. Martın, J. Chu, T, C. Hazen, and J. D. Keasling. 2007. “Flux analysis of central metabolic pathways in Geobacter metallireducens during reduction of soluble Fe(III)-nitrilotriacetic acid.” Appl. Environ. Microbiol. 73:3859-3864.
S. H. Yoon, H. M. Park, J. E. Kim, S. H. Lee, M. S. Choi, J. Y. Kim, D. K. Oh, J. D. Keasling, and S. W. Kim. 2007. “Increased beta-carotene production in recombinant Escherichia coli harboring an engineered isoprenoid precursor Pathway with mevalonate addition.” Biotechnol. Prog. 23:599-605.
A. Mukhopadhyay, A. M. Redding, M. P. Joachimiak, A. P. Arkin, S. E. Borglin, P. S. Dehal, R. Chakraborty, J. T. Geller, T. C. Hazen, Q. He, D. C. Joyner, V. J. J. Martin, J. D. Wall, Z. K. Yang, J. Zhou, and J. D. Keasling. 2007. “Cell wide responses to low oxygen exposure in Desulfovibrio vulgaris Hildenborough.” J. Bacteriol. 189:5996-6010.
S. K. Lee, H. H. Chou, B.F. Pfleger, J. D. Newman, Y. Yoshikuni, and J. D. Keasling. 2007. “Directed evolution of AraC for improved compatibility of arabinose and lactose-inducible promoters.” Appl. Environ. Microbiol. 73:5711-5715.
S. T. Withers, S. S. Gottlieb, B. Lieu, J. D. Newman, and J. D. Keasling. 2007. “Identification of isopentenol biosynthetic genes from Bacillus subtilis using isoprenoid precursor toxicity.” Appl. Environ. Microbiol. 73:6277-6283.
K. D. McMahon, S. Yilmaz, S. He, D. L. Gall, D. Jenkins, and J. D. Keasling. 2007. “Polyphosphate kinase genes from full-scale activated sludge plants.” Appl. Microbiol. Biotechnol. 77:167-173.
B. M. T. da Costa, K. Cornish, and J. D. Keasling. 2007. “Manipulation of intracellular magnesium levels in Saccharomyces cerevisiae with deletion of magnesium transporters.” Appl. Microbiol. Biotechnol. 77:411-425.
R. E. Osterhout, I. A. Figueroa, J. D. Keasling, and A. P. Arkin. 2007. “Global analysis of host response to induction of a latent bacteriophage.” BMC Microbiology. 7:82.
S. Mahendra, C. J. Petzold, E. E. Baidoo, J. D. Keasling, and L. Alvarez-Cohen. 2007. “Identification of the intermediates of in vivo oxidation of 1,4-dioxane by monooxygenase-containing bacteria.” Environ. Sci. Technol. 144:7330-7336.
P. F. Suthers, A. P. Burgard, M. S. Dasika, F. Nowroozi, S. Van Dien, J. D. Keasling, and C. D. Maranas. 2007. “Metabolic flux elucidation for large-scale models using 13C labeled isotopes.” Metab. Eng. 9:387-405.
V. Hale, J. D. Keasling, N. Renninger, and T. T. Diagana. 2007. “Microbially derived artemisinin: a biotechnology solution to the global problem of access to affordable anti-malarial drugs.” Am. J. Trop. Med. Hyg. 77:198-202.

2006

Y. Yoshikuni, V. J. J. Martin, T. E. Ferrin, and J. D. Keasling. 2006. “Engineering cotton (+)-δ-cadinene synthase to an altered function: germacrene D-4-ol synthase.” Chem. Biol. 13:91-98.
D-K. Ro, E. M. Paradise, M. Ouellet, K. J. Fisher, K. L. Newman, J. M. Ndungu, K. A. Ho, R. A. Eachus, R. S. Ham, J. Kirby, M. C. Y. Chang, S. T. Withers, Y. Shiba, R. Sarpong, and J. D. Keasling. 2006. “Production of the antimalarial drug precursor artemisinic acid in engineered yeast.” Nature 440:940-943.
Y. Yoshikuni, T. E. Ferrin, and J. D. Keasling. 2006. “Designed divergent evolution of enzyme function.” Nature 440:1078-1082.
S. K. Lee and J. D. Keasling. 2006. “Propionate-regulated high-yield protein production in Escherichia coli.” Biotechnol. Bioeng. 93:912-918.
S. C. Espy, J. D. Keasling, J. Castillon, and K. Cornish. 2006. “Initiator-independent and initiator-dependent rubber biosynthesis in Ficus elastica.” Arch. Biochem. Biophys. 448:13-22.
T. S. Ham, S. K. Lee, J. D. Keasling, and A. P. Arkin. 2006. “A tightly-regulated inducible expression system utilizing the fim inversion recombination switch.” Biotechnol. Bioeng. 94:1-4.
D. Baker, G. Church, J. Collins, D. Endy, J. Jacobson, J. Keasling, P. Modrich, C. Smolke, and R. Weiss. 2006. “Engineering life: building a FAB for biology.” Scientific American June:44-51.
A. Mukhopadhyay, Z. He, E. J. Alm, A. P. Arkin, E. E. Baidoo, S. C. Borglin, W. Chen, T. C. Hazen, Qiang He, H.-Y. Holman, K. Huang, R. Huang, D. C. Joyner, N. Katz, M. Keller, P. Oeller, A. Redding, J. Sun, J. Wall, J. Wei, Z. Yang , H.-C. Yen, J. Zhou, and J. D. Keasling. 2006. “Salt stress in Desulfovibrio vulgaris Hildenborough: An integrated genomics approach.” J. Bacteriol. 188:4068-4078.
A. M. Redding, A. Mukhopadhyay, D. Joyner, T. C. Hazen, and J. D. Keasling. 2006. “Study of nitrate stress in Desulfovibrio vulgaris Hildenborough using iTRAQ proteomics.” Brief. Funct. Genom. Proteom. 5:133-43.
S. K. Lee and J. D. Keasling. 2006. “A Salmonella-based propionate-inducible expression system for Salmonella enterica.” Gene 37:6-11.
B. M. T. da Costa, J. D. Keasling, C. M. McMahon, and K. Cornish. 2006. “Magnesium regulation of in vitro rubber biosynthesis by Parthenium argentatum Gray.” Phytochemistry 67:1621-1628.
S. H. Yoon, Y. M. Lee, J. E. Kim, S. H. Lee, J. H. Lee, J. Y. Kim, K. H. Jung, Y. C. Shin, J. D. Keasling, and S. W. Kim. 2006. “Enhanced lycopene production in Escherichia coli engineered to synthesize isopentenyl diphosphate and dimethylallyl diphosphate from mevalonate.” Biotechnol. Bioeng. 94:1025-1032.
B. F. Pfleger, D. J. Pitera, C. D. Smolke, and J. D. Keasling. 2006. “Combinatorial engineering of intergenic regions in operons tunes expression of multiple genes.” Nat. Biotechnol. 24:1027-1032.
Y. J. Tang, D. Laidlaw, K. Gani, and J. D. Keasling. 2006. “Evaluation of the effects of various culture conditions on Cr(VI) reduction by Shewanella oneidensis MR-1in a novel high-throughput mini-bioreactor.” Biotechnol. Bioeng. 95:176-184.
H. S. Zahiri, S. H. Yoon, J. D. Keasling, S. H. Lee, K. S. Won, S. C. Yoon, and Y. C. Shin. 2006. “Coenzyme Q(10) production in recombinant Escherichia coli strains engineered with a heterologous decaprenyl diphosphate synthase gene and foreign mevalonate pathway.” Metab. Eng. 8:406-416.
J. D. Newman, J. Marshal, M. Chang, F. Nowroozi, E. Paradise, D. Pitera, K. L. Newman, and J. D. Keasling. 2006. “High-level production of amorpha-4,11-diene in a two-phase partitioning bioreactor of metabolically engineering Escherichia coli.” Biotechnol. Bioeng. 95:684-691.
M. Mattozzi, S. Tehara, and J. D. Keasling. 2006. “Mineralization of paraoxon and use as a sole C and P source by a rationally designed catabolism in Pseudomonas putida.” Appl. Environ. Microbiol. 72:6699-6706.
S. K. Lee and J. D. Keasling. 2006. “Effect of glucose or glycerol as the sole carbon source on gene expression from the Salmonella prpBCDE promoter in Escherichia coli.” Biotechnol. Prog. 22:1547-1551.
M. C. Y. Chang and J. D. Keasling. 2006. “Production of isoprenoid pharmaceuticals by engineered microbes.” Nat. Chem. Biol. 2:674-681.
D. Lubertozzi and J. D. Keasling. 2006. “Marker and promoter effects on heterologous expression in Aspergillus nidulans.” Appl. Microbiol. Biotechnol. 72:1014-1023.

2005

B. M. T. da Costa, J. D. Keasling, and K. Cornish. 2005. “Regulation of rubber biosynthetic rate and molecular weight in Hevea brasiliensis by metal cofactor.” Biomacromolecules 6:279-289.
S. Cooper and J. D. Keasling. 2005. “Experimental and theoretical considerations of P1-plasmid replication and segregation during the E. coli cell cycle.” J. Biol. Sci. 5:222-229.
S. K. Lee, J. D. Newman, and J. D. Keasling. 2005. “Catabolite repression of the propionate catabolic genes in Escherichia coli and Salmonella enterica: Evidence for involvement of the cyclic AMP receptor protein.” J. Bacteriol. 187:2793-2800.
K. Wang, J. D. Keasling, and S. J. Muller. 2005. “Effects of the sequence and size of non-polar residues on self-assembly of amphiphilic peptides. Int. J. Biol. Macromol. 36:232-240.
M. J. Kang, Y. M. Lee, S. H. Yoon, J. H. Kim, S. W. Ock, K. H. Jung, Y. C. Shin, J. D. Keasling, and S. W. Kim. 2005. “Identification of genes affecting lycopene accumulation in Escherichia coli using a shot-gun method.” Biotechnol. Bioeng. 91:636-642.
B. F. Pfleger, N. J. Fawzi, and J. D. Keasling. 2005. “Optimization of DsRed production in Escherichia coli: Effect of ribosome binding site sequestration on translation.” Biotechnol. Bioeng. 92:553-558.
S. K. Lee and J. D. Keasling. 2005. “A propionate-inducible expression system for enteric bacteria.” Appl. Environ. Microbiol. 71:6856-6862.

2004

M. M. Maharbiz, W. J. Holtz, R. T. Howe, and J. D. Keasling. 2004. “Microbioreactor arrays with parametric control for high-throughput experimentation.” Biotechnol. Bioeng. 86:485-90.
E. S. Gilbert and J. D. Keasling. 2004. “Bench Scale Flow Cell for Nondestructive Imaging of Biofilms.” Meth. Microbiol. 16:109-118.
K. K. Reiling, Y. Yoshikuni, V. J. J. Martin, J. Newman, J. Bohlmann, and J. D. Keasling. 2004. “Mono and diterpene production in Escherichia coli.” Biotechnol. Bioeng. 87:200-212.
D. S. Reichmuth, H. W. Blanch, and J. D. Keasling. 2004. “Dibenzothiophene desulfurization pathway improvement using diagnostic GFP fusions.” Biotechnol. Bioeng. 88:94-99.
N. Renninger, R. Knopp, H. Nitsche, D.S. Clark, J. D. Keasling. 2004. “Uranyl precipitation by Pseudomonas aeruginosa via controlled polyphosphate metabolism.” Appl. Environ. Microbiol. 70:7404-7412.

2003

S. K. Tehara and J. D. Keasling. 2003. “Gene cloning, purification, and characterization of a phosphodiesterase from Delftia acidovorans.” Appl. Envir. Microbiol. 69:504-508.
E. S. Gilbert, A. W. Walker and J. D. Keasling. 2003. “A constructed microbial consortium for biodegradation of the organophosphorus insecticide parathion.” Appl Microbiol Biotechnol. 61:77-81.
N. L. Goeden-Wood, J. D. Keasling, and S. J. Muller. 2003. “Self-assembly of a designed protein polymer into b-sheet fibrils and responsive gels.” Macromolecules 36:2932-2938.
R. Knopp, P. J. Panak, L. A. Wray, N. S. Renninger, J. D. Keasling, and H. Nitsche. 2003. “Laser spectroscopic studies of U(VI) with bacterial phosphate species.” Chem. Eur. J. 9:2812-2818.
V. J. J. Martin, D. J. Pitera, S. T. Withers, J. D. Newman, and J. D. Keasling. 2003. “Engineering the mevalonate pathway in Escherichia coli for production of terpenoids.” Nat. Biotechnol. 21:796-802.
I. Chang, E. Gilbert, N. Eliashberg, and J. D. Keasling. 2003. “A three-dimensional, stochastic simulation of biofilm growth and transport-related factors that affect structure.” Microbiology 149:2859-2871.
D. J. Scott, B. M.T. da Costa, S. C. Espy, J. D. Keasling, and Katrina Cornish. 2003. “Activation and inhibition of rubber transferases by metal cofactors and pyrophosphate substrates.” Phytochemistry 64:123-134.
M.M. Maharbiz, W.J. Holtz, S. Sharifzadeh, J. D. Keasling, R. T. Howe. 2003. “A microfabricated electrochemical oxygen generator for high-density cell culture arrays.” IEEE J. Microelectromech. Syst. 12:590-599.
I. S. Aldor and J. D. Keasling. 2003. “Process design for microbial plastic factories: metabolic engineering of polyhydroxyalkanoates.” Curr. Opin. Biotechnol. 14:475-483.
C. Khosla and J. D. Keasling. 2003. “Metabolic engineering for drug discovery and development.” Nature Rev. Drug Disc. 2:1019-1025.

2002

C. D. Smolke and J. D. Keasling. 2002. “Effect of copy number and mRNA processing and stabilization on transcript and protein levels from an engineered dual-gene operon.” Biotechnol. Bioeng. 78:412-424.
N. Renninger, K. D. McMahon, R. Knopp, H. Nitsche, D. S. Clark, and J. D. Keasling. 2002. “Uranyl precipitation by biomass from an enhanced biological phosphorus removal reactor.” Biodegradation 12:401-410.
C. L. Wang, S. C. Ozuna, D. S. Clark, and J. D. Keasling. 2002. “A deep-sea hydrothermal vent isolate, Pseudomonas aeruginosa CW961, requires thiosulfate for Cd2+ tolerance and precipitation.” Biotechnol. Lett. 24:637-641.
A. W. Walker and J. D. Keasling. 2002. “Metabolic engineering of Pseudomonas putida for the utilization of parathion as a carbon and energy source.” Biotechnol. Bioeng. 78:715-721.
V. J. J. Martin, C. D. Smolke, and J. D. Keasling. 2002. “Redesigning cells for production of complex organic molecules.” ASM News 68:336-343.
A. Magyarosy, R. D. Laidlaw, R. Kilaas, C. Echer, D. S. Clark, and J. D. Keasling. 2002. “Nickel accumulation and nickel oxalate precipitation by Aspergillus niger.” Appl. Microbiol. Biotechnol. 59:381-388.
A. Magyarosy, J. Z. Ho, H. Rapoport, S. Dawson, J. Hancock, and J. D. Keasling. 2002. “Chlorxanthomycin, a fluorescent, chlorinated, pentacyclic pyrene from a Bacillus sp.” Appl. Environ. Microbiol. 68:4095-4101.
I. S. Aldor, S.-W. Kim, K. L. Jones, and J. D. Keasling. 2002. “Metabolic engineering of a novel propionate-independent pathway for the production of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) in recombinant Salmonella enterica serovar Typhimurium.” Appl. Environ. Microbiol. 68:3848-3854.
A. Khlebnikov, T. Skaug, and J. D. Keasling. 2002. “Modulation of gene expression from the arabinose-inducible araBAD promoter.” J. Ind. Microbiol. Biotechnol. 29:34-37.
N. L. Goeden-Wood, V. P. Conticello, S. J. Muller, and J. D. Keasling. 2002. “Improved assembly of multimeric genes for the biosynthetic production of protein polymers.” Biomacromolecules 3:874-879.
A. Khlebnikov and J. D. Keasling. 2002. “Effect of lacY expression on homogeneity of induction from the Ptac and Ptrc promoters by natural and synthetic inducers.” Biotechnol. Prog. 18:672-674.
K. D. McMahon, D. Jenkins, and J. D. Keasling. 2002. “Polyphosphate kinase genes from activated sludge carrying out enhanced biological phosphorus removal.” Water Sci. Technol. 46:155-162.
K. D. McMahon, M. A. Dojka, N. R. Pace, D. Jenkins, and J. D. Keasling. 2002. “Polyphosphate kinase from activated sludge performing enhanced biological phosphorus removal.” Appl. Environ. Microbiol. 68:4971-4978.
C. D. Smolke and J. D. Keasling. 2002. “Effect of gene location, mRNA secondary structures, and RNase sites on expression of two genes in an engineered operon.” Biotechnol. Bioeng. 80:762-776.
G.-Y. Wang and J. D. Keasling. 2002. “Amplification of HMG-CoA reductase production enhances carotenoid accumulation in Neurospora crassa.” Met. Eng. 4:193-201.

2001

S.-W. Kim and J. D. Keasling. 2001. “Metabolic engineering of the nonmevalonate isopentenyl diphosphate synthesis pathway in Escherichia coli enhances lycopene production.” Biotechnol. Bioeng. 72:408-415.
C. L. Wang, A. M. Lum, S. C. Ozuna, D. S. Clark, and J. D. Keasling. 2001. “Aerobic sulfide production and cadmium precipitation by Escherichia coli expressing the Treponema denticola cysteine desulfhydrase gene.” Appl. Microbiol. Biotechnol. 56:425-430.
S. E. Cowan, D. Leipmann, and J. D. Keasling. 2001. “Development of engineering biofilms on poly-L-lysine patterned surfaces.” Biotechnol. Lett. 23:1235-1241.
I. Aldor and J. D. Keasling. 2001. “Metabolic engineering of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) composition in recombinant Salmonella enterica serovar Typhimurium.” Biotechnol. Bioeng. 76:108-114.
C. L. Wang, D. S. Clark, and J. D. Keasling. 2001. “Analysis of an engineered sulfate reduction pathway and cadmium precipitation on the cell surface.” Biotechnol. Bioeng. 75:285-291.
C. D. Smolke, V. J. J. Martin, and J. D. Keasling. 2001. “Controlling the metabolic flux through the carotenoid pathway using directed mRNA processing and stabilization.” Met. Eng. 3:313-321.
V. J. J. Martin, Y. Yoshikuni, and J. D. Keasling. 2001. “The in vivo synthesis of plant sesquiterpenes in Escherichia coli.” Biotechnol. Bioeng. 75:497-503.
C. D. Smolke, A. Khlebnikov, and J. D. Keasling. 2001. “Effects of transcription induction homogeneity and transcript stability on expression of two genes in a constructed operon.” Appl. Microbiol. Biotechnol. 57:689-696.
A. Khlebnikov, K. A. Datsenko, T. Skaug, B. L. Wanner, and J. D. Keasling. 2001. “Homogeneous expression of the PBAD promoter in Escherichia coli by constitutive expression of the low-affinity high-capacity AraE transporter.” Microbiology 147:3241-3247.
E. S. Gilbert, A. Khlebnikov, S. E. Cowan, and J. D. Keasling. 2001. “Analysis of biofilm structure and gene expression using fluorescence dual labeling.” Biotechnol. Prog. 17:1180-1182.

2000

D. S. Reichmuth, J. L. Hittle, H. W. Blanch, and J. D. Keasling. 2000. “Biodesulfurization of dibenzothiophene in Escherichia coli is enhanced by expression of a Vibrio harveyi oxidoreductase gene.” Biotechnol. Bioeng. 67:72-79.
J. D. Keasling, S. J. Van Dien, P. Trelstad, N. Renninger, and K. McMahon. 2000. “Application of polyphosphate metabolism to environmental and biotechnological problems.” Biochemistry (Moscow). 65:324-331.
D. G. Bolesch and J. D. Keasling. 2000. “The effect of monovalent ions on polyphosphate binding to Escherichia coli exopolyphosphatase.” Biochem. Biophys. Res. Comm. 274:236-241.
S.-W. Bang, D. S. Clark, and J. D. Keasling. 2000. “Engineering hydrogen sulfide production and cadmium removal by expression of the thiosulfate reductase gene (phsABC) from Salmonella enterica serovar Typhimurium in Escherichia coli.” Appl. Environ. Microbiol. 66:3939-3944.
C. L. Wang, P. D. Maratukulam, A. M. Lum, D. S. Clark, and J. D. Keasling. 2000. “Metabolic engineering of an aerobic sulfate reduction pathway and its application to precipitation of cadmium on the cell surface.” Appl. Environ. Microbiol. 66:4497-4502.
S. E. Cowan, E. Gilbert, D. Liepmann, and J. D. Keasling. 2000. “Commensal interactions in a dual-species biofilm exposed to mixed organic compounds.” Appl. Environ. Microbiol. 66:4481-4485.
S.-W. Bang, D. S. Clark, and J. D. Keasling. 2000. “Cadmium, lead, and zinc removal by expression of the thiosulfate reductase gene from Salmonella typhimurium in Escherichia coli.” Biotechnol. Lett. 22:1331-1335.
D. G. Bolesch and J. D. Keasling. 2000. “Polyphosphate binding and chain length recognition of Escherichia coli exopolyphosphatase.” J. Biol. Chem. 275:33814-33819.
A. Khlebnikov, O. Risa, T. Skaug, T. A. Carrier, and J. D. Keasling. 2000. “Regulatable arabinose-inducible gene expression system with consistent control in all cells of a culture.” J. Bacteriol. 182:7029-7034.
C. D. Smolke, T. A. Carrier, and J. D. Keasling. 2000. “Coordinated, differential expression of two genes through directed mRNA cleavage and stabilization by secondary structures.” Appl. Environ. Microbiol. 66:5399-5405.
K. L. Jones, S.-W. Kim, and J. D. Keasling. 2000. “Low-copy plasmids can perform as well as or better than high-copy plasmids for metabolic engineering of bacteria.” Met. Eng. 2:328-338.
S. E. Cowan, E. Gilbert, A. Khlebnikov, and J. D. Keasling. 2000. “Dual labeling with green fluorescent proteins for confocal microscopy.” Appl. Environ. Microbiol. 66:413-418.

1999

R. Brent Nielsen and J. D. Keasling. 1999. “Reductive dechlorination of chlorinated ethene DNAPLs by a culture enriched from contaminated groundwater.” Biotechnol. Bioeng. 62:160-165.
T. A. Carrier and J. D. Keasling. 1999. “A library of synthetic 5' secondary structures to manipulate mRNA stability in Escherichia coli.” Biotechnol. Prog. 15:58-64.
E. Gilbert, A. Khlebnikov, W. Meyer-Ilse, and J. D. Keasling. 1999. “Use of soft X-ray microscopy for analysis of early-stage biofilm formation.” Wat. Sci. Tech. 39(7):269-272.
S. J. Van Dien and J. D. Keasling. 1999. “Effect of polyphosphate metabolism on the Escherichia coli phosphate-starvation response.” Biotechnol. Prog. 15(4):587-593.
S. E. Cowan, J. Black, J. D. Keasling, and R. M. White. 1999. “Ultrasonic flexural-plate-wave sensor for detecting the concentration of settling E. coli W3110 cells.” Analytical Chemistry. 71(16):3622-3625.
P. L. Trelstad, P. Purdhani, W. Geibdorfer, W. Hillen, and J. D. Keasling. 1999. “Polyphosphate kinase of Acinetobacter sp. Strain ADP1: purification and characterization of the enzyme and its role during changes in extracellular phosphate.” Appl. Environ. Microbiol. 65(9):3780-3786.
J. D. Keasling. 1999. “Gene-expression tools for the metabolic engineering of bacteria.” Trends in Biotechnology 17:452-460.
T. A. Carrier and J. D. Keasling. 1999. “Investigating autocatalytic gene expression systems through mechanistic modeling.” J. Theor. Biol. 201:25-36.

1998

J. D. Keasling, S. J. Van Dien, and J. Pramanik. 1998. “Engineering polyphosphate metabolism in Escherichia coli: implications for bioremediation of inorganic contaminants.” Biotechnol. Bioeng. 58:231-239.
S. J. Van Dien and J. D. Keasling. 1998. “A dynamic model of the Escherichia coli phosphate-starvation response.” J. Theor. Biol. 190:37-49.
J. D. Keasling and S.-W. Bang. 1998. “Recombinant DNA techniques for bioremediation and environmentally-friendly synthesis.” Current Biology 9:135-140.
S. Cooper and J. D. Keasling. 1998. “Cycle-specific replication of chromosomal and F-plasmid origins.” FEMS Microbiol. Lett. 163:217-222.
K. L. Jones and J. D. Keasling. 1998. “Construction and characterization of F plasmid-based expression vectors.” Biotechnol. Bioeng. 59:659-665.
T. A. Carrier, K. L. Jones, and J. D. Keasling. 1998. “mRNA stability and plasmid copy number effects on gene expression from an inducible promoter system.” Biotechnol. Bioeng. 59:666-672.
S. J. Van Dien and J. D. Keasling. 1998. “Optimization of polyphosphate degradation and phosphate secretion using hybrid metabolic pathways and engineered host strains.” Biotechnol. Bioeng. 59:754-761.
J. Pramanik, P. L. Trelstad, and J. D. Keasling. 1998. “A flux-based stoichiometric model of enhanced biological phosphorus removal metabolism.” Wat. Sci. Tech. 37:609-613.
J. Pramanik and J. D. Keasling. 1998. “Effect of carbon source and growth rate on biomass composition and metabolic flux predictions of a stoichiometric model.” Biotechnol. Bioeng. 60:230-238.
S. J. Van Dien and J. D. Keasling. 1998. “Control of polyphosphate metabolism in genetically-engineered Escherichia coli.” Enzyme Microb. Technol. 24:21-25.
J. Pramanik, P. L. Trelstad, A. J. Schuler, D. Jenkins, and J. D. Keasling. 1998. “Development and validation of a flux-based stoichiometric model for enhanced biological phosphorus removal metabolism.” Water Research 33:462-476.

1997

S. J. Van Dien, S. Keyhani, C. Yang, and J. D. Keasling. 1997. “Manipulation of independent synthesis and degradation of polyphosphate in Escherichia coli for investigation of phosphate secretion from the cell.” Appl. Environ. Microbiol. 63:1689-1695.
J. Elmen, W. Pan, S. Y. Leung, A. Magyarosy, and J. D. Keasling. 1997. “Kinetics of toluene degradation by a nitrate-reducing bacterium isolated from a groundwater aquifer.” Biotechnol. Bioeng. 55:82-90.
T. A. Carrier and J. D. Keasling. 1997. “Engineering mRNA stability in E. coli by the addition of synthetic hairpins using a 5’ cassette system.” Biotechnol. Bioeng. 55:577-580.
C. L. Wang, P. C. Michels, S. Dawson, S. Kitisakkul, J. A. Baross, J. D. Keasling, and D. S. Clark. 1997. “Cadmium removal by a new strain of Pseudomonas aeruginosa in aerobic culture.” Appl. Environ. Microbiol. 63:4075-4078.
J. Pramanik and J. D. Keasling. 1997. “A stoichiometric model of Escherichia coli metabolism: incorporation of growth-rate dependent biomass composition and mechanistic energy requirements.” Biotechnol. Bioeng. 56:398-421.
T. A. Carrier and J. D. Keasling. 1997. “Controlling messenger RNA stability in bacteria: strategies for engineering gene expression.” Biotechnol. Prog. 13:699-708.
T. A. Carrier and J. D. Keasling. 1997. “Mechanistic modelling of mRNA decay.” J. Theor. Biol. 189:195-209.

1996

J. D. Keasling and G. A. Hupf. 1996. “Genetic manipulation of polyphosphate metabolism affects cadmium tolerance in Escherichia coli.” Appl. Environ. Microbiol. 62:743-746.
S. T. Sharfstein, S. J. Van Dien, and J. D. Keasling. 1996. “Modulation of the phosphate-starvation response in Escherichia coli by genetic manipulation of the polyphosphate pathways.” Biotechnol. Bioeng. 51:434-438.
N. Shapiro and J. D. Keasling. 1996. “The recA gene and cadmium toxicity in Escherichia coli K-12.” Microbios 86:23-26.
H. Kuo and J. D. Keasling. 1996. “A Monte Carlo simulation of plasmid replication during the bacterial division cycle.” Biotechnol. Bioeng. 52:633-647.
S. Keyhani, J. L. Lopez, D. S. Clark, and J. D. Keasling. 1996. “Intracellular polyphosphate content and cadmium tolerance in Anacystis nidulans R2.” Microbios 88:105-114.
P. Wong, S. Gladney, and J. D. Keasling. 1996. “A mathematical model of the lac operon: inducer exclusion, catabolite repression, and diauxic growth on glucose and lactose.” Biotechnol. Prog. 13:132-143.

1995

J. D. Keasling, H. Kuo, and G. Vahanian. 1995. “A Monte Carlo simulation of the Escherichia coli cell cycle.” J. Theor. Biol. 176:411-430.

1994

J. D. Keasling and S. Cooper. 1994. “Analysis of plasmid replication during the bacterial division cycle.” Methods in Molecular Genetics 3:380-388.
T. R. Hupp, J. D Keasling, S. Cooper, and J. M. Kaguni. 1994. “Synthesis of DnaK protein during the division cycle of Escherichia coli.” Res. Microbiol. 145:99-109.

1993

J. D. Keasling, L. Bertsch, and A. Kornberg. 1993. “Guanosine pentaphosphate phosphohydrolase of Escherichia coli is a long-chain polyphosphatase.” Proc. Natl. Acad. Sci. USA 90:7029-7033.

1992

J. D. Keasling, B. O. Palsson, and S. Cooper. 1992. “Replication of the R6K plasmid during the Escherichia coli cell cycle.” J. Bacteriol. 174:1060-1062.
J. D. Keasling, B. O. Palsson, and S. Cooper. 1992. “Replication of prophage P1 is cell-cycle specific.” J. Bacteriol. 174:4457-4462.
J. D. Keasling, B. O. Palsson, and S. Cooper. 1992. “Replication of mini-F plasmids during the bacterial division cycle.” Res. Microbiol. 143:541-548.

1991

J. D. Keasling, B. O. Palsson, and S. Cooper. 1991. “Cell-cycle-specific F'lac plasmid replication: regulation by cell size control of initiation.” J. Bacteriol. 173:2673-2680.

1990

B. O. Palsson, J. D Keasling, and S. G. Emerson. 1990. “The regulatory mechanisms of human immunodeficiency virus replication predict multiple expression rates.” Proc. Natl. Acad. Sci. USA. 87:772-776.

1989

J. D. Keasling and B. O. Palsson. 1989. “On the kinetics of plasmid replication.” J. Theor. Biol. 136:487-492.
J. D. Keasling and B. O. Palsson. 1989. “ColE1 plasmid replication: a simple kinetic description from a structured model.” J. Theor. Biol. 141:447-461.