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Refereed Publications

  1. Kennedy AB, Liang JC, Smolke CD. 2012. A versatile cis-blocking and trans-activation strategy for ribozyme characterization. Nuc. Acids Res. DOI: 10.1093/nar/gks1036
  2. Michener JK, Nielsen J, Smolke CD. 2012. Identification and treatment of heme depletion attributed to overexpression of a lineage of evolved P450 monooxygenases. Proc. Natl. Acad. Sci. USA. DOI: 10.1073/pnas.1212287109
  3. Liang JC, Chang AL, Kennedy AB, Smolke CD. 2012. A high-throughput, quantitative cell-based screen for efficient tailoring of RNA device activity. Nuc. Acids Res. DOI: 10.1093/nar/gks636. link
  4. Michener JK, Smolke CD. 2012. High-throughput enzyme evolution in Saccharomyces cerevisiae using a synthetic RNA switch. Metab. Eng. 14: 306-16. link
  5. Chen YY, Galloway KE, Smolke CD. 2012. Synthetic biology: advancing biological frontiers by building synthetic systems. Genome Biol. 13: 240. link
  6. Chang AL, Wolf JJ, Smolke CD. 2012. Synthetic RNA switches as a tool for temporal and spatial control over gene expression. Curr. Opin. Biotechnol. 23: 679-88. link
  7. Siddiqui MS, Thodey K, Trenchard I, Smolke CD. 2012. Advancing secondary metabolite biosynthesis in yeast with synthetic biology tools. FEMS Yeast Research. 12: 144-70. link
  8. Chen YY, Smolke CD. 2011. From DNA to targeted therapeutics: bringing synthetic biology to the clinic. Sci. Transl. Med. 3: 106ps42. link
  9. Michener JK, Thodey K, Liang JC, Smolke CD. 2012. Applications of genetically-encoded biosensors for the construction and control of biosynthetic pathways. Metab. Eng. 14: 212-22. link
  10. Liang JC, Bloom RJ, Smolke CD. 2011. Engineering biological systems with engineered RNA molecules. Mol. Cell. 43: 915-26. link
  11. Babiskin AH, Smolke CD. 2011. Synthetic RNA modules for fine-tuning gene expression levels in yeast by modulating RNase III activity. Nuc. Acids Res. 39: 8651-64. link
  12. Smolke CD, Silver PA. 2011. Informing biological design by integration of systems and synthetic biology. Cell. 144: 855-9. link
  13. Babiskin AH, Smolke CD. 2011. Engineering ligand-responsive RNA controllers in yeast through the assembly of RNase III tuning modules. Nuc. Acids Res. 39: 5299-311. link
  14. Babiskin AH, Smolke CD. 2011. A synthetic library of RNA control modules for predictable tuning of gene expression in yeast. Mol. Sys. Biol. 7:471. link
  15. Beisel CL, Chen YY, Culler SJ, Hoff KG, Smolke CD. 2010. Design of small molecule-responsive miRNAs based on structural requirements for Drosha processing. Nuc. Acids Res. 39: 2981-94. link
  16. Culler SJ, Hoff KG, Smolke CD. 2010. Reprogramming cellular behavior with RNA controllers responsive to endogenous proteins. Science. 330: 1251-5. Perspective: Cell biology. The case for RNA. 330: 1185-6. link
  17. Chen YY, Jensen MC, Smolke CD. 2010. Genetic control of mammalian T-cell proliferation with synthetic RNA regulatory systems. Proc. Natl. Acad. Sci. USA. 107: 8531-6. link
  18. Culler SJ, Hoff KG, Voelker RB, Berglund JA, Smolke CD. 2010. Feature Article: Functional selection and systematic analysis of intronic splicing elements identifies active sequence motifs and associated splicing factors. Nuc. Acids Res. 38: 5152-65. link
  19. Hoff KG, Culler SJ, Nguyen PQ, McGuire RM, Silberg JJ, Smolke CD. 2009. In vivo fluorescent detection of Fe-S clusters coordinated by human GRX2. Chem. Biol. 16: 1299-308. Commentary: Lights on iron-sulfur clusters. 16: 1213-4. link
  20. Beisel CL, Smolke CD. 2009. Design principles for riboswitch function. PLoS Comp. Biol. 5: e1000363. link
  21. Win MN, Liang JC, Smolke CD. 2009. Frameworks for programming biological function through RNA parts and devices. Chem. Biol. 16: 298-310. link
  22. Bayer TS, Hoff KG, Beisel CL, Lee JJ, Smolke CD. 2009. Synthetic control of a fitness tradeoff in yeast nitrogen metabolism. J. Biol. Eng. 3: 1. link
  23. Hoff KG, Goodlitt R, Li R, Smolke CD, Silberg JJ. 2009. Fluorescence detection of a protein-bound 2Fe2S cluster. Chembiochem. 10: 667-70. link
  24. Beisel CL, Bayer TS, Hoff KG, Smolke CD. 2008. Model-guided design of ligand-regulated RNAi for programmable control of gene expression. Mol. Sys. Biol. 4: 224. News and Views: Small hairpin RNA as a small molecule sensor. 4: 227. link
  25. Hawkins KM, Smolke CD. 2008. Cover article: Production of benzylisoquinoline alkaloids in Saccharomyces cerevisiae. Nat. Chem. Biol. 4: 564-73. News and Views: From yeast to alkaloids. 4: 524-5. link
  26. Win MN, Smolke CD. 2008. Higher-order cellular information processing with synthetic RNA devices. Science. 322: 456-60. Perspective: Cell biology. RNA computing in a living cell. 322: 387-8. (Additional detail on data processing and raw data is provided here and as an E-letter attached to this article.) link
  27. Win MN, Smolke CD. 2007. From the cover: A modular and extensible RNA-based gene-regulatory platform for engineering cellular function. Proc. Natl. Acad. Sci. USA. 104: 14283-8. Commentary: Targeted cleavage: tuneable cis-cleaving ribozymes. 104: 14881-2. Erratum: Proc. Natl. Acad. Sci. USA. 2009. 106: 15514. (An early online correction was published here.) link
  28. Win MN, Klein JS, Smolke CD. 2006. Codeine-binding RNA aptamers and rapid determination of their binding constants using a direct coupling surface plasmon resonance assay. Nuc. Acids Res. 34: 5670-82. link
  29. Pfleger BF, Pitera DJ, Smolke CD, Keasling JD. 2006. Combinatorial engineering of intergenic regions in operons tunes expression of multiple genes. Nat. Biotech. 24: 1027-32. link
  30. Hawkins KM, Smolke CD. 2006. The regulatory roles of the galactose permease and kinase in the induction response of the GAL network in Saccharomyces cerevisiae. J. Biol. Chem. 281: 13485-92. link
  31. Bayer TS, Smolke CD. 2005. Programmable, ligand-controlled riboregulators of eukaryotic gene expression. Nat. Biotech. 23: 337-43. News and Views: Plug and play with RNA. 23: 306-7. link
  32. Smolke CD, Keasling JD. 2002. Effect of gene location, mRNA secondary structures, and RNase sites on expression of two genes in an engineered operon. Biotech. Bioeng. 80: 762-76. link
  33. Smolke CD, Keasling JD. 2002. Effect of copy number and mRNA processing and stabilization on transcript and protein levels from an engineered dual-gene operon. Biotech. Bioeng. 78: 412-24. link
  34. Smolke CD, Khlebnikov A, Keasling JD. 2001. Effects of transcription induction homogeneity and transcript stability on expression of two genes in a constructed operon. Appl. Micro. Biotech. 57: 689-96. link
  35. Smolke CD, Martin VJJ, Keasling JD. 2001. Controlling the metabolic flux through the carotenoid pathway using directed mRNA processing and stabilization. Met. Eng. 3: 313-21. link
  36. Smolke CD, Carrier TA, Keasling JD. 2000. Coordinated, differential expression of two genes through directed mRNA cleavage and stabilization by secondary structures. Appl. Environ. Microbiol. 66: 5399-405. link

Non-Refereed Publications

  1. Smolke CD, Tyo KE. 2012. Synthetic biology: Emerging methodologies to catalyze the metabolic engineering design cycle. Met. Eng. link
  2. Thodey K, Smolke CD. 2011. Cell Biology. Bringing it together with RNA. Science. 333: 412-3. link
  3. Smolke CD. 2009. Building outside of the box: iGEM and the BioBricks Foundation. Nat. Biotech. 27:1099-102. link
  4. Smolke CD. 2009. Cell Biology. It’s the DNA that counts. Science. 324: 1156-7. link
  5. Win MN, Smolke CD. 2007. RNA as a versatile and powerful platform for engineering genetic regulatory tools. Biotechnology and Genetic Engineering Reviews. 24: 311-46.
  6. Baker D, Church G, Collins J, Endy D, Jacobson J, Keasling J, Modrich P, Smolke C, Weiss R. 2006. Engineering life: building a Fab for biology. Scientific American. 294: 44-51.
  7. Martin VJJ, Smolke CD, Keasling JD. 2002. Redesigning cells for the production of complex organic molecules. ASM News. 68: 336-43. link

Books and Book Chapters

  1. Liang JC, Smolke CD. 2012. Rational design and tuning of ribozyme-based devices. In: Hartig J, editor. Methods in Molecular Biology. 848:439-54. link
  2. Win MN, Liang JC, Smolke CD. 2010. Frameworks for programming RNA devices. In: Mayer G, editor. The Chemical Biology of Nucleic Acids. U.K.: John Wiley & Sons, Ltd. pp. 323-38. link
  3. Win MN, Smolke CD. 2009. Regulating gene expression through engineered RNA technologies. In: Smolke CD, editor. Handbook for Metabolic Pathway Engineering: Tools and Applications. San Diego: CRC Press.
  4. Smolke CD, Martin VJJ, Keasling JD. 2004. Tools for metabolic engineering in Escherichia coli. In: Baneyx F, editor. Protein Expression Technologies: Current Status and Future Trends. U.K.: Horizon Scientific Press.

Edited Works in Print

  1. Smolke CD, editor. 2009. Handbook for Metabolic Pathway Engineering: Fundamentals (volume I). San Diego: CRC Press. Google Books Amazon
  2. Smolke CD, editor. 2009. Handbook for Metabolic Pathway Engineering: Tools and Applications (volume II). San Diego: CRC Press. Google Books Amazon