Publications: 2008-2011


Dhamankar, H and K. L. J. Prather. 2011. “Microbial chemical factories: recent advances in pathway engineering for synthesis of value added chemicals.” Curr. Opin. Struct. Biol. 21(4):488-494. doi: 10.1016/

Oliveira, P.H., K. L. J. Prather, D. M. F. Prazeres and G. A. Monteiro .  2011. “Mutation detection in plasmid biopharmaceuticals.”  Biotechnol. J. 6(4):378-391. doi: 10.1002/biot.201000372


Lippow, S.M., Moon, T.S., Basu, S., Yoon, S.-H., Li, X., Chapman, B.A., Robison, K., Lipovsek, D. and Prather, K.L.J. “Engineering Enzyme Specificity Using Computational Design of a Defined-Sequence Library.”  Chem. Biol. 17: 1306-1315 (2010). doi: 10.1016/j.chembiol.2010.10.012

Tseng, H-C, Harwell, C.L., Martin, C.H., and Prather, K.L.J. “Biosynthesis of chiral 3-hydroxyvalerate from single propionate-unrelated carbon sources in metabolically engineered E. coli.”  Microb. Cell Fact. 9(96) (2010). doi: 10.1186/1475-2859-9-96

Leonard, E., Ajikumar, P.K., Thayer, K., Xiao, W.-H., Mo, J.D., Tidor, B., Stephanopoulos, and Prather, K.J. “Combining metabolic and protein engineering of a terpenoid biosynthetic pathway for overproduction and selectivity control.”  PNAS 107(31): 13654-13659 (2010). doi:10.1073/pnas.1006138107

Fischer, C.R., Tseng, H-C, Tai, M., Prather, K.L.J., and Stepanopoulos, G. “Assessment of heterologous butyrate and butanol pathway activity by measurement of intracellular pathway intermediates in recombinant Escherichia coli.” Appl. Microbiol. Biotechnol. 88(1):265-275 (2010) . doi: 10.1007/s00253-010-2749-2

Moon, T.S., Dueber, J.E., and Prather, K.L.J. “Use of modular, synthetic scaffolds for improved production of glucaric acid in engineered E. coli.” Metabolic Engineering . 12: 298-305 (2010). doi:10.1016/j.ymben.2010.01.003.

Nielsen, D.R., Yoon, S.-H., Yuan, C.J., Prather, K.J. “Engineering acetoin and meso-2,3 butanediol biosynthesis in E. coli.” Biotechnology Journal. 5: 274-284 (2010). doi:10.1002/biot200900279.

Nielsen, D.R., Amarasiriwardena, G.S., Prather, K.J. “Predicting the adsorption of second generation biofuels by polymeric resins with applications for in situ product recovery (ISPR) .” Bioresource Technology. 101: 2762-2769 (2010). doi:10.1016/j.biortech.2009.12.003

Martin, C.H., Wu, D., Prather, K.J. “Integrated Bioprocessing for the pH-Dependent Production of 4-Valerolactone from Levulinate in Pseudomonas putida KT2440.” App. Environ. Microbiol. 76: 417-424 (2010) doi:10.1128/AEM.01769-09


Dueber, J.E., Wu, G.C., Malmirchegini, G.R., Moon, T.S., Petzold, C.J., Ullal, A.V., Prather, K.J., Keasling, J.D. “Synthetic protein scaffolds provide modular control over metabolic flux.” Nature Biotechnol. 27(8): 753-759 (2009). doi:10.1038/nbt.1557

Oliveira, P.H., Prather, K.J., Prazeres, D.M., and Monteiro, G. in press. “Structural instabilities of plasmid biopharmaceuticals: challenges and implications.”Trends Biotechnol. 27(9):503-511 (2009). doi:10.1016/j.tibtech.2009.06.004

Moon, T.S., Yoon, S.-H., Tsang Mui Ching, M.-J., Lanza, A.M., and Prather, K.L.J. “Enzymatic assay of D-glucoronate using uronate dehydrogenase.” Analytical Biochemistry. 392: 183-185 (2009). doi:10.1016/j.ab.2009.05.032

Nielsen, D.R., Leonard, E., Yoon, S.-H., Tseng, H.-C., Yuan, C. and Prather, K.J. “Engineering alternative butanol production platforms in heterologous bacteria.” Metab. Eng.11: 262-273 (2009). doi:10.1016/j.ymben.2009.05.003

Tseng, H-C, Martin, C, Nielsen, D.R., and Prather, K.L.J. 2009. “Metabolic engineering of Escherichia coli for the enhanced production of (R)- and (S)-3-hydroxybutyrate.”  Appl. Environ. Microbiol. 75(10):3137-3145. doi:10.1128/AEM.02667-08

Leonard, E., Runguphan, W., O’Connor, S., and Prather, K.J. “Opportunities in metabolic engineering to facilitate scalable alkaloid production.”  Nature Chem. Biol 5(5): 292-300 (2009). doi:10.1038/nchembio.160

Martin, C.H., Nielsen, D.R., Solomon, K.V., and Prather, K.L.J. “Synthetic metabolism: Engineering biology at the protein and pathway scales.” Chem. Biol.16(3): 277-286 (2009). doi:10.1016/j.chembiol.2009.01.010

Bower, D.M., and Prather, K.L.J. “Engineering of bacterial strains and vectors for the production of plasmid DNA.” Appl. Microbiol. Biotechnol. 82(5): 805-813 (2009) doi:10.1007/s00253-009-1889-8

Yoon, S.-H., Moon, T.S., Iranpour, P., Lanza, A.M., and Prather, K.J. Cloning and characterization of uronate dehydrogenases from two Pseudomonads and Agrobacterium tumefaciens str. C58 J. Bacteriol. 191(5): 1565-1573 (2009) doi:10.1128/JB.00586-08

Moon, T.S., Yoon, S.-H., Lanza, A.M., Roy-Mayhew, J.D. and Prather, K.L.J. Production of glucaric acid from a synthetic pathway in recombinant Escherichia coli. Appl. Environ. Microbiol. 75: 589-595 (2009) doi:10.1128/AEM.00973-08

Martin, C.H. and Prather, K.L.J. High-titer production of monomeric hydroxyvalerates from levulinic acid in Pseudomonas putida. J. Biotechnol. 139(1): 61-67 (2009) doi:10.1016/j/jbiotec.2008.09.002

Nielsen, D.R. and Prather, K.L.J. In situ product recovery of n-butanol using polymeric resins. Biotechnol. Bioeng. 102: 811-821 (2009) doi:10.1002/bit.2210


Leonard, E., Nielsen, D., Solomon, K., and Prather, K. L. J. Engineering microbes with synthetic biology frameworks. Trends Biotechnol. 26(12): 674-681 (2008) doi:10.1016/j.tibtech.2008.08.003

Rodrigo, G., Carrera, J., Prather, K.L.J., and Jaramillo, A. DESHARKY: Automated design of metabolic pathways for optimal cell growth. Bioinformatics. 24(21): 2554-2556 (2008). doi:10.1093/bioinformatics/btn471

Prather, K.L.J. and Martin, C.H. De novo biosynthetic pathways: rational design of microbial chemical factories. Curr. Opin. Biotechnol. 19(5): 468-474 (2008). doi:10.1016/j.copbio.2008.07.009