• About
• People
  • Fuels Synthesis Leadership
  • Fuels Synthesis Staff
• Groups
  • Biofuels Pathways
  • Metabolic Engineering
  • Biofuels Toxicity & Tolerance
  • Host Engineering
  • Synthetic Biology
• Publications
• Resources
  • Resources
  • Tools

Publications

1. Beller, H. R., E. B. Goh, et al. (2010). "Genes Involved in Long-Chain Alkene Biosynthesis in Micrococcus luteus." Applied and Environmental Microbiology 76(4): 1212-1223.
2. Beller, H. R., E. B. Goh, et al. (2011). "Definitive alkene identification needed for in vitro studies with ole (olefin biosynthesis) proteins." Journal of Biological Chemistry 286(26): le11.
3. Beller, H. R., T. C. Legler, et al. (2011). Genetic manipulation of the obligate chemolithoautotrophic bacterium Thiobacillus denitrificans. Microbial Systems Biology: Methods and Protocols (Methods in Molecular Biology series), Humana Press.*
4. Blanch, H. W. (2011). "Bioprocessing for biofuels." Current Opinion in Biotechnology 23: 1-6.*
5. Blanch, H. W., P. D. Adams, et al. (2008). "Addressing the need for alternative transportation fuels: The Joint BioEnergy Institute." ACS Chemical Biology 3(1): 17-20.
6. Bokinsky, G., P. Peralta-Yahya, et al. (2011). "Synthesis of three advanced biofuels from ionic liquid-pretreated switchgrass using engineered." Proceedings of the National Academy of Sciences.*
7. Carothers, J. M., J. A. Goler, et al. (2011). "Model-driven engineering of RNA devices to quantitatively-program gene expression." Science.*
8. Chertkov, O., A. Copeland, et al. (2011). "Complete genome sequence of Tolumonas auensis type strain (TA 4T)." Standards in Genomic Sciences 5(1).
9. Chhabra, S. R., G. Butland, et al. (2011). "Generalized Schemes for High-Throughput Manipulation of the Desulfovibrio vulgaris Genome." Applied and Environmental Microbiology 77(21): 7595-7604.
10. Chhabra, S. R., M. P. Joachimiak, et al. (2011). "Towards a Rigorous Network of Protein-Protein Interactions of the Model Sulfate Reducer Desulfovibrio vulgaris Hildenborough." PLoS One 6(6): e21470.
11. Chhabra, S. R. and J. Keasling (2011). The Biological Basis | Metabolic Design and Control for Production in Prokaryotes. Comprehensive Biotechnology. M. Moo-Young, Elsevier. 1: 243–255.
12. Christen, B., M. J. Fero, et al. (2010). "High-throughput identification of protein localization dependency networks." Proceedings of the National Academy of Sciences 107(10): 4681-4686.
13. DeAngelis, K. M., C. H. Wu, et al. (2011). "PCR amplification-independent methods for detection of microbial communities by the high-density microarray PhyloChip." Applied and Environmental Microbiology 77(18): 6313-6322.
14. Dietrich, J. A., Y. Yoshikuni, et al. (2009). "A Novel Semi-biosynthetic Route for Artemisinin Production Using Engineered Substrate-Promiscuous P450(BM3)." ACS Chemical Biology 4(4): 261-267.
15. Dueber, J. E., G. C. Wu, et al. (2009). "Synthetic protein scaffolds provide modular control over metabolic flux." Nature Biotechnology 27(8): 753-U107.
16. Dunlop, M. J., Z. Y. Dossani, et al. (2011). "Engineering microbial biofuel tolerance and export using efflux pumps." Molecular Systems Biology 7: 487.
17. Dunlop, M. J., J. D. Keasling, et al. (2010). "A model for improving microbial biofuel production using a synthetic feedback loop." Synthetic and Systems Biology 4(2): 95-104.
18. Eudes, A., E. E. Baidoo, et al. (2011). "Production of tranilast [N-(3',4'-dimethoxycinnamoyl)-anthranilic acid] and its analogs in yeast Saccharomyces cerevisiae." Applied Microbiology and Biotechnology 89(4): 989-1000.
19. Fortman, J. L., S. Chhabra, et al. (2008). "Biofuel alternatives to ethanol: pumping the microbial well." Trends in Biotechnology 26(7): 375-381.
20. Garcia, D. E., E. E. Baidoo, et al. (2008). "Separation and mass spectrometry in microbial metabolomics." Current Opinion in Microbiology 11(3): 233-239.
21. George, A., K. Tran, et al. (2011). "The effect of ionic liquid cation and anion combinations on the macromolecular structure of lignins." Green Chemistry.*
22. Goh, E. B., E. E. Baidoo, et al. (2011). "Engineering of bacterial methyl ketone synthesis for biofuels." Applied and Environmental Microbiology.*
23. Hillson, N. J. (2011). DNA Assembly Method Standardization for Synthetic Biomolecular Circuits and Systems. Design and Analysis of Biomolecular Circuits: Engineering Approaches to Systems and Synthetic Biology. H. Koeppl, D. Densmore, M. di Bernardo and G. Setti. New York, Springer-Verlag: 295-314.
24. Holtz, W. J. and J. D. Keasling (2010). "Engineering Static and Dynamic Control of Synthetic Pathways." Cell 140(1): 19-23.
25. Ito, J., C. J. Petzold, et al. (2010). "The Role of Proteomics in the Development of Cellulosic Biofuels." Current Proteomics 7(2): 121-134.
26. Joshua, C. J., R. Dahl, et al. (2011). "Absence of Diauxie during Simultaneous Utilization of Glucose and Xylose by Sulfolobus acidocaldarius." Journal of Bacteriology 193(6): 1293-1301.
27. Juminaga, D., E. E. Baidoo, et al. (2011). "Modular Engineering of L-Tyrosine Production in Escherichia coli." Applied and Environmental Microbiology.*
28. Keasling, J. (2011). "Joint BioEnergy Institute." Industrial Biotechnology 7(4): 259-260.
29. Keasling, J. D. (2008). "Synthetic biology for synthetic chemistry." ACS Chemical Biology 3(1): 64-76.
30. Keasling, J. D. (2010). "Manufacturing molecules through metabolic engineering." Science 330(6009): 1355-1358.
31. Keasling, J. D. and H. Chou (2008). "Metabolic engineering delivers next-generation biofuels." Nature Biotechnology 26(3): 298-299.
32. Keller, K. L., J. D. Wall, et al. (2011). "Methods for engineering sulfate reducing bacteria of the genus desulfovibrio." Methods in Enzymology 497: 503-517.
33. Kirby, J. and J. D. Keasling (2009). "Biosynthesis of plant isoprenoids: perspectives for microbial engineering." Annual Review of Plant Biology 60: 335-355.
34. Lee, S. K., H. Chou, et al. (2008). "Metabolic engineering of microorganisms for biofuels production: from bugs to synthetic biology to fuels." Current Opinion in Biotechnology 19(6): 556-563.
35. Lee, T. S., R. A. Krupa, et al. (2011). "BglBrick vectors and datasheets; a synthetic biology platform for gene expression." Journal of Biological Engineering 5(1): 12.
36. Ma, S. M., D. E. Garcia, et al. (2011). "Optimization of a heterologous mevalonate pathway through the use of variant HMG-CoA reductases." Metabolic Engineering 13(5): 588-597.
37. Marner, W. D., 2nd, A. S. Shaikh, et al. (2009). "Enzyme immobilization via silaffin-mediated autoencapsulation in a biosilica support." Biotechnology Progress 25(2): 417-423.
38. McAndrew, R. P., P. P. Peralta-Yahya, et al. (2011). "Structure of a Three-Domain Sesquiterpene Synthase: A Prospective Target for Advanced Biofuels Production." Structure 19: 1-9.*
39. Mukhopadhyay, A., N. J. Hillson, et al. (2012). Control of Stress Tolerance in Bacterial Host Organisms for Bioproduction of Fuels. Microbial Stress Tolerance: From Genomics to Biofuels. Z. L. Liu. Berlin / Heidelberg, Springer-Verlag. 22: 209-238.*
40. Mukhopadhyay, A., A. M. Redding, et al. (2008). "Importance of systems biology in engineering microbes for biofuel production." Current Opinion in Biotechnology 19(3): 228-234.
41. Nielsen, J. and J. D. Keasling (2011). "Synergies between synthetic biology and metabolic engineering." Nature Biotechnology 29(8): 693-695.
42. Ouellet, M., P. D. Adams, et al. (2009). "A rapid and inexpensive labeling method for microarray gene expression analysis." BMC Biotechnology 9: 97.
43. Ouellet, M., S. Datta, et al. (2011). "Impact of ionic liquid pretreated plant biomass on Saccharomyces cerevisiae growth and biofuel production." Green Chemistry 13(10): 2743-2749.
44. Peralta-Yahya, P. P. and J. D. Keasling (2010). "Advanced biofuel production in microbes." Biotechnology Journal 5(2): 147-162.
45. Peralta-Yahya, P. P., M. Ouellet, et al. (2011). "Identification and microbial production of a terpene-based advanced biofuel." Nature Communications 2: 483.
46. Pereira, J. H., Z. Chen, et al. (2010). "Biochemical characterization and crystal structure of endoglucanase Cel5A from the hyperthermophilic Thermotoga maritima." Journal of Structural Biology 172(3): 372-379.
47. Petzold, C. J. and J. D. Keasling (2010). Metabolic engineering of E.coli for the production of a precursor to artemisinin, an anti-malarial drug. The Manual of Industrial Microbiology and Biotechnology. R. Balz. Washington, DC, ASM Press: 364-379.
48. Rautengarten, C., E. Baidoo, et al. (2010). "A Simple Method for Enzymatic Synthesis of Unlabeled and Radiolabeled Hydroxycinnamate-CoA." BioEnergy Research 3(2): 115-122.
49. Redding-Johanson, A. M., T. S. Batth, et al. (2011). "Targeted proteomics for metabolic pathway optimization: Application to terpene production." Metabolic Engineering 13(2): 194-203.
50. Rutherford, B. J., R. H. Dahl, et al. (2010). "Functional genomic study of exogenous n-butanol stress in Escherichia coli." Applied and Environmental Microbiology 76(6): 1935-1945.
51. Scheller, H. V., S. Singh, et al. (2010). "The Joint BioEnergy Institute (JBEI): Developing New Biofuels by Overcoming Biomass Recalcitrance." BioEnergy Research 3(2): 105-107.
52. Shaikh, A. S., Y. J. Tang, et al. (2008). "Isotopomer distributions in amino acids from a highly expressed protein as a proxy for those from total protein." Analytical Chemistry 80(3): 886-890.
53. Shaikh, A. S., Y. J. Tang, et al. (2010). "Study of stationary phase metabolism via isotopomer analysis of amino acids from an isolated protein." Biotechnology Progress 26(1): 52-56.
54. Shui, W., L. Sheu, et al. (2008). "Membrane proteomics of phagosomes suggests a connection to autophagy." Proceedings of the National Academy of Sciences 105(44): 16952-16957.
55. Steen, E. J., R. Chan, et al. (2008). "Metabolic engineering of Saccharomyces cerevisiae for the production of n-butanol." Microbial Cell Factories 7: 36.
56. Steen, E. J., Y. Kang, et al. (2010). "Microbial production of fatty-acid-derived fuels and chemicals from plant biomass." Nature 463(7280): 559-562.
57. Tang, Y. J., H. G. Martin, et al. (2009). "Metabolic flux analysis of Shewanella spp. reveals evolutionary robustness in central carbon metabolism." Biotechnology and Bioengineering 102(4): 1161-1169.
58. Tang, Y. J., H. G. Martin, et al. (2009). "Advances in analysis of microbial metabolic fluxes via (13)C isotopic labeling." Mass Spectrometry Reviews 28(2): 362-375.
59. Tang, Y. J., R. Sapra, et al. (2009). "Analysis of metabolic pathways and fluxes in a newly discovered thermophilic and ethanol-tolerant Geobacillus strain." Biotechnology and Bioengineering 102(5): 1377-1386.
60. Tang, Y. J., S. Yi, et al. (2009). "Investigation of carbon metabolism in "Dehalococcoides ethenogenes" strain 195 by use of isotopomer and transcriptomic analyses." Journal of Bacteriology 191(16): 5224-5231.
61. Wipat, A., A. Villalobos, et al. (2011). Synthetic Biology Open Language (SBOL) Version 1.0.0. BioBricks Foundation Request for Comments.
62. Young, M., V. Artsatbanov, et al. (2010). "Genome sequence of the Fleming strain of Micrococcus luteus, a simple free-living actinobacterium." Journal of Bacteriology 192(3): 841-860.
63. Zhang, F. and J. Keasling (2011). "Biosensors and their applications in microbial metabolic engineering." Trends in Microbiology 19(7): 323-329.